What do we know about diagnostics and surveillance?

Table of Contents

1 How widespread current exposure is to be able to make immediate policy recommendations on mitigation measures. Denominators for testing and a mechanism for rapidly sharing that information, including demographics, to the extent possible. Sampling methods to determine asymptomatic disease (e.g., use of serosurveys (such as convalescent samples) and early detection of disease (e.g., use of screening of neutralizing antibodies such as ELISAs).

1.0.0.1 Highlights

1.0.0.2 Articles

Date Authors Title LOE(?) & Sample Matches
2020 Pang et al Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review
Journal of Clinical Medicine
I. Systematic Review

Of the total of 570 unique studies on 2019-nCoV, SARS CoV or MERS-CoV vaccines screened, only four were eventually included in the review.
The key limitations of serological testing is the need to collect paired serum samples (in the acute and convalescent phases) from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses.

Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate.

Such neutralizing antibodies can be elicited by active or passive immunization using vaccines or convalescent plasma respectively.
2020 MacIntyre et al Wuhan novel coronavirus 2019nCoV
Global Biosecurity
IV. Other Serological surveys in Wuhan will help determine how much mild or asymptomatic infection there may be.
2020 Hu et al Screening and management of asymptomatic infection of corona virus disease 2019 (COVID-19)
Zhonghua Yu Fang Yi Xue Za Zhi
IV. Other Screening among the high-risk population and improving the sensitivity of measurement may contribute to the detection and management of asymptomatic infection.
2020-02-04 Zhang et al Recent advances in the detection of respiratory virus infection in humans
Journal of Medical Virology
IV. Other Conventional diagnostic tests, such as the assays for rapid detection of antiviral antibodies or viral antigens, are widely used in many clinical laboratories.
2020-02-10 Arabi et al Critical care management of adults with community-acquired severe respiratory viral infection
Intensive Care Med
II. Randomized Controlled Trial

The importance of timing of oseltamivir treatment has been demonstrated in an observational study of 1950 patients admitted to ICUs with influenza A(H1N1) pdm09, which showed a trend toward improved survival for those treated earliest .
Studies varied in the approach for sampling and in the used assays; in some studies, specimen collection and assays were standardized across all patients, while in other studies, sampling and assays were performed selectively.
2020-02-14 Kiselev et al Current Trends in Diagnostics of Viral Infections of Unknown Etiology
Viruses
IV. Prevalence Study

They used 42 virus-positive controls from pediatric patients and 67 unidentified samples .
As of this day, a multitude of clinical tests are available for detection of viruses, e.g., FISH, ELISA (enzyme-linked immunosorbent assay), and PCR-and their numerous modifications.
2020-02-17 Xiao et al Evolving status of the 2019 novel coronavirus Infection: proposal of conventional serologic assays for disease diagnosis and infection monitoring [Commentary/Review]
Journal of Medical Virology
IV. Other Conventional serological assays, such as enzyme-linked immunoassay (ELISA) for specific IgM and IgG antibodies, should offer a high-throughput alternative, which allows for uniform tests for all suspected patients, and can facilitate more complete identification of infected cases and avoidance of unnecessary cross infection among unselected patients.
2020-02-21 Cheng et al Scabies: Application of the Novel Identify-Isolate-Inform Tool for Detection and Management
West J Emerg Med
IV. Prevalence Study

36 Advising patients and parents of young patients to keep fingernails short and clean can assist with preventing secondary infections.
One study showed that real-time PCR and ELISA tests are useful for monitoring treatment efficacy.
2020-02-28 Heymann et al COVID-19: what is next for public health?
The Lancet
IV. Prevalence Study

8 Infected individuals produce a large quantity of virus in the upper respiratory tract during a prodrome period, are mobile, and carry on usual activities, contributing to the spread of infection.
9 The actual case fatality ratio of infection with COVID-19 will eventually be based on all clinical illness and at the time of writing information on subclinical infection is not available and awaits the development of serological tests and serosurveys.
2020-03-01 Xiang et al Evaluation of Enzyme-Linked Immunoassay and Colloidal Gold- Immunochromatographic Assay Kit for Detection of Novel Coronavirus (SARS-Cov-2) Causing an Outbreak of Pneumonia (COVID-19)
medrxiv
IV. Other ELISA and GICA for specific IgM and IgG antibodies is conventional serological assays, they can offer a high-throughput alternative, which allows for uniform tests for all suspected patients, and can facilitate more complete identification of infected cases and avoidance of unnecessary cross infection among unselected All rights reserved.

One group collected 63 samples for Enzyme-linked immunosorbent assay (ELISA) IgG and IgM antibodies.
2020-03-01 Tárnok et al Machine Learning, COVID-19 (2019-nCoV), and multi-OMICS
Cytometry Part A
IV. Other Image cytometry methods 3 and bead‐based flow cytometry methods 4 are at hand to enable for screening and detecting antibody virus interactions and detect viral antigens.
2020-03-03 Yang et al The deadly coronaviruses: The 2003 SARS pandemic and the 2020 novel coronavirus epidemic in China
Journal of Autoimmunity
IV. Prevalence Study

In Wang's study , of the 36 patients in the ICU, four patients received high-flow oxygen therapy, 15 patients received non-invasive ventilation, and 17 patients received invasive ventilation (four patients switched to ECMO).
Sampling techniques, extraction and detection of viral nucleic acids, and diagnostic reagents may affect the test results.
2020-03-04 Flahault et al Has China faced only a herald wave of SARS-CoV-2?
The Lancet
IV. Other Serosurveys can help answer these questions precisely.3 To serosurvey the outbreak would involve testing sera of blood samples from the most representative sample of the population at the epicentre of the epidemic, Wuhan.
2020-03-05 Li et al Molecular immune pathogenesis and diagnosis of COVID-19
Journal of Pharmaceutical Analysis
IV. Prevalence Study

Virus genome sequencing of five patients with pneumonia hospitalized from December 18 to December 29, 2019, revealed the presence of a previously unknown β-CoV strain in all of them .
Clinical diagnosis of COVID-19 is mainly based on epidemiological history, clinical manifestations and some auxiliary examinations, such as nucleic acid detection, CT scan, immune identification technology (Point-of-care Testing (POCT) of IgM/IgG, enzyme-linked immunosorbent assay (ELISA)) and blood culture.
2020-03-05 Spiteri et al First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020
Euro Surveill
IV. Prevalence Study No data on clinical signs e.g.
2020-03-06 Riou et al Adjusted age-specific case fatality ratio during the COVID-19 epidemic in Hubei, China, January and February 2020
medrxiv
IV. Prevalence Study

The model estimates that a total of 82,300 individuals (95%CrI: 73,000-91,800) were infected in Hubei between 1 January and 11 February 2020.
Serological surveys will be needed to better characterize asymptomatic infections .
2020-03-06 Wu et al Nowcasting and forecasting the potential domestic and international spread of the 2019-nCoV outbreak originating in Wuhan, China: a modelling study
The Lancet
IV. Computer Model 41 Additionally, given the extent of spread and level of public concern it has already generated, the clinical spectrum and severity profile of 2019-nCoV infections needs rapid ascertainment by unbiased and reliable methods in unselected samples of cases, especially those with mild or subclinical presentations.
2020-03-08 Liu et al A preliminary study on serological assay for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 238 admitted hospital patients
medrxiv
IV. Other 209 To verify the specificity of the ELISA assays, the serum samples from 70 210 randomly-selected ordinary patients and 50 healthy blood donors were simultaneously 211 .

214 These results confirmed the specificity of the IgG and IgM ELISA assays.
2020-03-08 Woelfel et al Clinical presentation and virological assessment of hospitalized cases of coronavirus disease 2019 in a travel-associated transmission cluster
medrxiv
IV. Other Because IFA is a laborintensive method, ELISA tests should be developed as a screening test.
2020-03-09 Bwire et al Coronavirus disease-2019: is fever an adequate screening for the returning travelers?
Trop Med Health
IV. Other Currently, RT-PCR is a reliable test in detecting both symptomatic and asymptomatic COVID-19.
2020-03-10 Barra et al Analytical sensibility and specificity of two RT-qPCR protocols for SARS-CoV-2 detection performed in an automated workflow
medrxiv
IV. Other RT-qPCR testing of respiratory secretions is routinely used to detect causative viruses in acute respiratory infection and, during a Public Health Emergency of International Concern, the establishment of standardized processes and protocols, as well as sharing of specimens, data, and information is critical.
2020-03-18 Amanat et al A serological assay to detect SARS-CoV-2 seroconversion in humans
medrxiv
IV. Other Conclusion: Serological assays are of critical importance to determine seroprevalence in a given population, define previous exposure and identify highly reactive human donors for the generation of convalescent serum as therapeutic.

Methods: Here we describe serological enzyme-linked immunosorbent assays (ELISA) that we developed using recombinant antigens derived from the spike protein of SARS-CoV-2.
2020-03-19 Haveri et al Serological and molecular findings during SARS-CoV-2 infection: the first case study in Finland, January to February 2020
Euro Surveill
IV. Prevalence Study That IgM and IgG antibodies were present within 2 weeks from the onset of symptoms in our study suggests that early convalescent patients may be suitable sources of therapeutic antibodies .

Monitoring of the binding antibodies is suggested to be a more sensitive method than measuring functional neutralising antibodies for serological detection of human coronavirus (hCoV) infections .
2020-03-20 Liu et al Evaluation of Nucleocapsid and Spike Protein-based ELISAs for detecting antibodies against SARS-CoV-2
medrxiv
IV. Other Serological assays are accurate 87 and efficient methods for the screening for many pathogens, as specific IgM and IgG 88 antibodies can be detected with ELISA, which has relatively high throughput capacity 89 .

rN-and rS-based ELISAs were used to detect IgM and IgG in serum samples 225 of confirmed COVID-19 patients.

16 Therefore, with the current tests it is difficult to achieve a meaningful assessment of 85 the proportion of symptomatic patients that are infected, and a rapid and accurate 86 detection method of COVID-19 is urgently needed.

The positive rates of the rN-based and rS-based ELISAs for antibody (IgM and/or IgG) detection were 80.4% and 82.2%, respectively.
2020-03-20 OKBA et al SARS-CoV-2 specific antibody responses in COVID-19 patients
medrxiv
III-3. Time Series Analysis

All three COVID-19 patients had reactive antibodies by both the IgG (6/10 serum samples) and IgA (7/10 serum samples) ELISAs (Figure 3) .
Additionally, these epidemiological studies can help reveal the extent of virus spread in households, communities and specific settings; which could help guide control measures Serological assays are also needed for evaluation of the results of vaccine trials and development of therapeutic antibodies.

All three COVID-19 patients had reactive antibodies by both the IgG (6/10 serum samples) and IgA (7/10 serum samples) ELISAs (Figure 3) .

Among the 3 inhouse ELISAs tested, the RBD and N ELISAs were more sensitive than S1 ELISA in detecting antibodies in mildly infected patients and showed stronger correlation with PRNT50 titers.

While SARS-CoV patient's sera were reactive as noted earlier, we also detected reactivity of serum samples from the validation cohorts A-D; 10/203 for IgA and 7/203 for IgG ELISAs.

These validated ELISAs for different antigens can be useful for epidemiological studies as well as for evaluation of vaccine-induced immune responses.
2020-03-20 Zhang et al Evaluation of recombinant nucleocapsid and spike proteins for serological diagnosis of novel coronavirus disease 2019 (COVID-19)
medrxiv
IV. Other The serological assays used for early 15 diagnosis are mainly based on detecting specific antibodies against HCoV-19 in a 16 patient's serum and include the enzyme-linked immunosorbent assay (ELISA), the 17 colloidal gold immunochromatography assay (GICA) and the chemiluminescence 18 assay.
2020-03-23 Wan et al Cross-reaction of sera from COVID-19 patients with SARS-CoV assays.
medrxiv
IV. Prevalence Study

7 We retrieved residual samples left over from biochemical tests to obtain serial sera for these 51 patients.
Methods: Tests were carried out using ELISA (total antibodies) and indirect immunofluorescence (IIFA) (IgM & IgG) methods on serial sera from patients confirmed with SARS-CoV-2 infection.
2020-03-23 To et al Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study
The Lancet Infectious Diseases
III-3. Time Series Analysis

12 of 23 patients included in this study have been reported previously, 6 but their clinical information, viral load by single copy RNA-dependent RNA polymerasehelicase gene, antibody response, or viral genome analysis has not been reported before.
Reliable data for profiles of serial viral load and serum antibody responses are needed urgently to guide antiviral treatment, infection control, epidemiological measures, and vaccination.

The antibody profile is vital for timing requests for serological assays and interpretation of antibody test results.
2020-03-23 Hu et al Identification of a super-spreading chain of transmission associated with COVID-19
medrxiv
III-2. Retrospective Cohort

All six fatal cases had comorbidities and five of the seven cancer patients (71%) died within 2-20 days of the disease onset.
The data we retrieved from the electronic medical records included demographic features, comorbidities, clinical presentation, laboratory investigation, RT-PCR testing for SARS-CoV-2, serum specific IgM and IgG antibodies, chest computed tomographic (CT) scan, and the disease outcome.
2020-03-25 Khan et al Analysis of Serologic Cross-Reactivity Between Common Human Coronaviruses and SARS-CoV-2 Using Coronavirus Antigen Microarray
biorxiv
IV. Prevalence Study The assay methodologies used for serologic detection of coronavirus infection include binding and neutralization assays.

Further studies are needed including with SARS-CoV-2 convalescent sera to fully realize the potential of this novel methodology to characterize the seroprevalence of SARS-CoV-2 and the impact of pre-existing cross-reactive antibodies on the disease course.
2020-03-30 Zhou et al Clinical features and outcomes of 197 adult discharged patients with COIVD-19 in Yichang, Hubei
medrxiv
IV. Prevalence Study

For the coagulation tests, Prothrombin time (PT) and activated partial thromboplastin time (APTT) were at the normal range in the majority of patients, while fib was above the normal range in the 78 (39.6%) patients, D-dimmer was above the normal range in the 99 (47.2%) patients.
COVID-19 diagnosis was based on exposures, symptoms, laboratory tests, chest CT and RT-PCR.
2020-03-30 Liu et al Diagnostic Indexes of a Rapid IgG/IgM Combined Antibody Test for SARS-CoV-2
medrxiv
IV. Other The serum samples were used to detect .SARS-CoV-2 IgG/IgM antibodies.
2020-03-30 Liu et al The comparative superiority of IgM-IgG antibody test to real-time reverse transcriptase PCR detection for SARS-CoV-2 infection diagnosis
medrxiv
IV. Other Data were compared between IgM-IgG antibody test and real-time RT-PCR detection for COVID-19 patients.
2020-03-31 Li et al The epidemic of 2019-novel-coronavirus (2019-nCoV) pneumonia and insights for emerging infectious diseases in the future
Microbes and Infection
IV. Prevalence Study

11 January 2020 41 patients have been diagnosed to have infection of the novel coronavirus, with 763 close contacts, 7 severe cases and the first death.
Conventional diagnostic testing methods, such as the assays for detection of antiviral antibodies or viral antigens have been developed and used clinically.
2020-05-31 Ling et al Asymptomatic SARS-CoV-2 infected patients with persistent negative CT findings
European Journal of Radiology
IV. Other Therefore, the detection and isolation of infected cases require more careful strategies and screening practices.

2 Efforts to increase capacity on existing diagnostic platforms and tap into existing surveillance platforms.

2.0.0.1 Highlights

2.0.0.2 Articles

Date Authors Title LOE(?) & Sample Matches
2020 Schwartz et al Potential Maternal and Infant Outcomes from (Wuhan) Coronavirus 2019-nCoV Infecting Pregnant Women: Lessons from SARS, MERS, and Other Human Coronavirus Infections
Viruses
IV. Prevalence Study

A case-control study to determine the effects of SARS on pregnancy compared 10 pregnant and 40 non-pregnant women with the infection at the Princess Margaret Hospital in Hong Kong .
CEPI and partners aim to use existing platforms-that is, the existing "backbone" that can be adapted for use against new pathogens-that are currently in preclinical development for MERS-CoV vaccine candidates.
2020 Pang et al Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review
Journal of Clinical Medicine
I. Systematic Review

Of the total of 570 unique studies on 2019-nCoV, SARS CoV or MERS-CoV vaccines screened, only four were eventually included in the review.
The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations .
2020 Allam et al On the Coronavirus (COVID-19) Outbreak and the Smart City Network: Universal Data Sharing Standards Coupled with Artificial Intelligence (AI) to Benefit Urban Health Monitoring and Management
Healthcare
IV. Prevalence Study The fact that cities are increasingly tuning on the concept of Smart Cities and boasting an increased adoption rate of technological and connected products, existing surveillance networks can be re-calibrated to make use of those new sets of databases.
2020 Shanmugaraj et al Emergence of Novel Coronavirus 2019-nCoV: Need for Rapid Vaccine and Biologics Development
Pathogens
IV. Prevalence Study Currently, plant expression system offers many advantages over other conventional systems that have the potential to tackle the production of vaccine candidates rapidly at affordable cost facilitating the global vaccination programs, especially in resource-poor nations where the vaccines are needed most .
2020 Gorbalenya et al The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2
Nature Microbiology
IV. Other Also, additional diagnostic tools that target the entire species should be developed to complement existing tools optimized to detect individual pathogenic variants (a proactive approach).
2020 Wu et al Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods
Acta Pharmaceutica Sinica B
IV. Other The second strategy is to use existing molecular databases to screen for molecules that may have therapeutic effect on coronavirus 19, 20 .
2020 Shirato et al Development of Genetic Diagnostic Methods for Novel Coronavirus 2019 (nCoV-2019) in Japan
Japanese Journal of Infectious Diseases
IV. Other Diagnostic systems for 2019-nCoV were developed with urgency.
2020-01-23 Note from the editors: novel coronavirus (2019-nCoV)
Euro Surveill
IV. Other on the development of a diagnostic methodology based on RT-PCR of the E and RdRp genes, without the need for virus material; the assays were validated in five international laboratories .
2020-02-04 Zhang et al Recent advances in the detection of respiratory virus infection in humans
Journal of Medical Virology
IV. Other With the development of modern technologies, new diagnostic strategies, including multiplex nucleic acid amplification and microarray-based assays, are emerging.

Conventional diagnostic tests, such as the assays for rapid detection of antiviral antibodies or viral antigens, are widely used in many clinical laboratories.
2020-02-10 Li et al A qualitative study of zoonotic risk factors among rural communities in southern China
Int Health
IV. Prevalence Study

We aimed to obtain a minimum sample size of 20 participants from each of the three provinces, for a total sample size of over 60 participants.
Policies and programmes existing in the communities provide opportunities for zoonotic risk mitigation.
2020-02-16 Bhandari et al Solubility-Weighted Index: fast and accurate prediction of protein solubility
biorxiv
IV. Prevalence Study

AUC, Area Under the ROC Curve; ROC, Receiver Operating Characteristic; , arithmetic W mean of the weights of an amino acid residue optimised from 1,000 bootstrap samples in a cross-validation step.
In addition, SWI outperforms many existing de novo protein solubility prediction tools.
2020-02-22 Nekrutenko et al No more business as usual: agile and effective responses to emerging pathogen threats require open data and open analytics
biorxiv
IV. Prevalence Study

This potentially adaptive change was not observed in the other two samples and lack of raw read data prevented us from identifying it in other geographically and temporally distributed samples.
Here we show that community efforts in developing open analytical software tools over the past ten years, combined with national investments into scientific computational infrastructure, can overcome these deficiencies and provide an accessible platform for tackling global health emergencies in an open and transparent manner.
2020-02-23 Hou et al Development and Evaluation of A CRISPR-based Diagnostic For 2019-novel Coronavirus
medrxiv
IV. Other The diagnostic performance of CRISPR-nCoV was assessed and compared across three technology platforms (mNGS, RT-PCR and CRISPR).
2020-02-23 Adiga et al Evaluating the impact of international airline suspensions on the early global spread of COVID-19
medrxiv
IV. Computer Model Interestingly, most countries with reported cases also have higher IDVI, which may be due to a combination of (a) high connectivity and air traffic to China, (b) better detection and reporting capabilities for imported cases.
2020-02-24 Lamb et al Rapid Detection of Novel Coronavirus (COVID-19) by Reverse Transcription-Loop-Mediated Isothermal Amplification
medrxiv
IV. Other Since this disease is spreading rapidly, centralized labs may have trouble keeping up with testing demands or may need an alternative approach if qRT-PCR kits are not available.
2020-02-26 Gallego et al The COVID-19 outbreak and implications for the Tokyo 2020 Summer Olympic Games
Travel Medicine and Infectious Disease
IV. Other It works to ensure the rapid development of vaccines, diagnostic means, antiviral drugs, and other treatments, and that low and middle-income country have access to them and also seeks a comprehensive risk communication strategy and promotes research and relative scientific advances to this new coronavirus .
2020-02-29 Zhang et al Rapid Molecular Detection of SARS-CoV-2 (COVID-19) Virus RNA Using Colorimetric LAMP
medrxiv
IV. Prevalence Study

In addition to controls, a total of 7 patient RNA samples were tested, 6 of which were determined to be positive by RT-qPCR using ORF1a primers (C q 25-36.5, Table 2 ) and 4 positive with Gene N primers.
The efforts made here will serve as a model for inevitable future outbreaks where the use of next generation portable diagnostics will dramatically expand the reach of our testing capabilities for better healthcare outcomes.

These molecular methods include metagenomics sequencing mNGS and RT-qPCR , both are excellent and sensitive techniques, but approaches not without limitations.
2020-03-04 Memish et al Middle East respiratory syndrome
The Lancet
II. Randomized Controlled Trial

A retrospective study of 136 patients with MERS found that macrolide therapy resulted in no reduction in mortality or faster MERS-CoV RNA clearance compared with those who were not treated with macrolides.
Advances in technology, vaccine platforms, clinical trial designs, and bioinformatics are supporting MERS-CoV vaccine development (appendix .
2020-03-04 Rao et al Cell-Membrane-Mimicking Nanodecoys against Infectious Diseases
ACS Nano
IV. Other 15 Such structural similarity provides the opportunity to develop new therapeutic platforms for broad-spectrum anti-infection applications.
2020-03-04 Chang et al Weaponized Interdependence: China's Economic Statecraft and Social Penetration against Taiwan
Orbis
IV. Prevalence Study However, information and communication technologies have CHANG AND YANG created the opportunities for authoritarian regimes to exploit the openness and interdependence of global networks.
2020-03-05 Manning et al Rapid metagenomic characterization of a case of imported COVID-19 in Cambodia
biorxiv
IV. Other Despite major advances in mNGS technologies and significant decreases in costs associated with sequencing, preparation of sequencing libraries and sufficient bioinformatics capabilities for timely analysis still present a challenge in the developing world.

The example described here serves as a call for continued training and infrastructure to support mNGS capacity in developing countries as bioinformatic tools proliferate and the cost of sequencing decreases.
2020-03-08 Qiu et al Outcome reporting from protocols of clinical trials of Coronavirus Disease 2019 (COVID-19): a review
medrxiv
IV. Prevalence Study Results: 19 registry platforms were searched.
2020-03-09 Anderson et al How will country-based mitigation measures influence the course of the COVID-19 epidemic?
The Lancet
IV. Other Broader-scale social distancing provides time for the health services to treat cases and increase capacity, and, in the longer term, for vaccines and treatments to be developed.
2020-03-10 Chan et al Research Frontiers of Health Emergency and Disaster Risk Management: What Do We Know So Far?
Int J Environ Res Public Health
IV. Prevalence Study Existing surveillance databases, new study tools, and innovation methodologies may help to identify population health risks and support Health-EDRM policy development.

highlighted the development need for relevant research methodologies, risk communication approaches, health data management strategies, practical health emergency study ethical guidelines, bridging global research capacity disparities, and infrastructure constraints, to ensure knowledge advancement in Health-EDRM.

Meanwhile, although new technology platforms (e.g., smartphones and internet) had generated interests and showed promises in efficiency and speed in mass communication in emergencies and crises, community receptivity of communication channels might differ with the nature of the emergency events .
2020-03-12 Ye et al Experience of different upper respiratory tract sampling strategies for detection of COVID-19
Journal of Hospital Infection
IV. Other We believe that these observations should be of value to other centres establishing COVID-19 diagnostic programmes.
2020-03-17 Buckee et al Improving epidemic surveillance and response: big data is dead, long live big data
The Lancet Digital Health
IV. Computer Model Regional or local teams with analytical training and ongoing relationships with government and industry partners should lead to flexible modelling approaches that leverage large curated datasets and international analytical expertise, building on collaborations developed when there are no emerging or ongoing outbreaks.
2020-03-18 Dhama et al COVID-19, an emerging coronavirus infection: advances and prospects in designing and developing vaccines, immunotherapeutics, and therapeutics
Hum Vaccin Immunother
IV. Other 35 The Coalition for Epidemic Preparedness Innovations (CEPI) recently announced the initiation of three programs aimed to develop COVID-19 vaccines by utilizing established vaccine platforms.
2020-03-18 Kandel et al Health security capacities in the context of COVID-19 outbreak: an analysis of International Health Regulations annual report data from 182 countries
The Lancet
IV. Prevalence Study A country's response capacity depends on the strength of its emergency preparedness and the regular testing and updating of national plans and capacities.
2020-03-20 Legido-Quigley et al Are high-performing health systems resilient against the COVID-19 epidemic?
The Lancet
IV. Prevalence Study National laboratory networks developed diagnostic tests once the COVID-19 genetic sequences were published5 and laboratory testing capacity was increased in all three locations, although expansion of the diagnostic capacity to university and large private laboratories in Japan is still ongoing.

National laboratory networks developed diagnostic tests once the COVID-19 genetic sequences were published 5 and laboratory testing capacity was increased in all three locations, although expansion of the diagnostic capacity to university and large private laboratories in Japan is still ongoing.
2020-03-20 Amrane et al Rapid viral diagnosis and ambulatory management of suspected COVID-19 cases presenting at the infectious diseases referral hospital in Marseille, France, - January 31st to March 1st, 2020: A respiratory virus snapshot
Travel Medicine and Infectious Disease
IV. Other This Institute also includes five large NSB3 laboratories with a total area of 1,200 m 2 , on four floors with diagnostic laboratories, research laboratories, and technological platforms .
2020-03-20 Hass et al Integrated Micropillar Polydimethylsiloxane Accurate CRISPR Detection (IMPACT) System for Rapid Viral DNA Sensing
biorxiv
IV. Other 11 Strides have been made to develop POC detection methods which can be deployed in the field, and currently lab-on-chip (LOC) devices or simple test kits which involve real-time polymerase chain reaction (PCR) have emerged as one of the leading choices for meeting the desired criteria.
2020-03-23 Vu et al Financing Vaccines for Global Health Security
medrxiv
IV. Prevalence Study Vaccine developers under this model would most likely sell subscriptions to governments, building upon existing infrastructure, such as the U.S. government's biodefense and pandemic preparedness programs.
2020-03-23 Mao et al Can a Paper-Based Device Trace COVID-19 Sources with Wastewater-Based Epidemiology?
Environ Sci Technol
IV. Other Paper analytical devices enable multiplexed, sensitive assays that rival PCR laboratory assays and provide high-quality, fast precision diagnostics for pathogens.
2020-03-23 Daughton et al The international imperative to rapidly and inexpensively monitor community-wide Covid-19 infection status and trends
Science of The Total Environment
IV. Other National agencies should encourage the development of sewage monitoring capabilities.
2020-03-25 Nunez-Bajo et al Ultra-Low-Cost Integrated Silicon-based Transducer for On-Site, Genetic Detection of Pathogens
biorxiv
IV. Other 1 Ability to produce NA quickly also increases the speed of development and deployment of new test kits to health systems, providing much needed diagnostic capabilities for the detection of novel pathogens (such as SARS-CoV-2).

Despite the advancement of diagnostic technologies targeting nucleic acids (NA), there are still no rapid, handheld, low-cost, easy-to-use and integrated solutions for the testing of infectious diseases at the Point-of-Need (PoN).
2020-03-27 Sousa-Pinto et al Is scaling-up COVID-19 testing cost-saving?
medrxiv
IV. Prevalence Study In fact, the cost COVID-19 tests is expected to vary, as companies are quickly bringing to the market new technologies that promise automated processing and faster response rates.
2020-03-31 FINEGAN et al International Committee of the Red Cross (ICRC): General Guidance for the Management of the Dead Related to COVID-19
Forensic Science International: Synergy
IV. Other All these phases require a thorough understanding of existing capacities, capabilities, and prior acknowledgement of the gaps where solutions are needed.
2020-03-31 Li et al The epidemic of 2019-novel-coronavirus (2019-nCoV) pneumonia and insights for emerging infectious diseases in the future
Microbes and Infection
IV. Prevalence Study

11 January 2020 41 patients have been diagnosed to have infection of the novel coronavirus, with 763 close contacts, 7 severe cases and the first death.
Conventional diagnostic testing methods, such as the assays for detection of antiviral antibodies or viral antigens have been developed and used clinically.
2020-03-31 Yamey et al Ensuring global access to COVID-19 vaccines
The Lancet
IV. Other Use of existing financing systems to support this work offers the benefits of speed and lower transaction costs than for new financing approaches.
2020-04-01 Esposito et al Why is chest CT important for early diagnosis of COVID-19? Prevalence matters
medrxiv
IV. Prevalence Study

23 provide a reliable estimation of CT specificity, since it is the only study assessing performance in distinguishing COVID-19 (219 patients) from other ascertained viral interstitial pneumonia (205 patients).
Moreover, the recent introduction of artificial intelligence (AI) approaches as diagnostic tools for semi-automated COVID-19 CT scan reporting may even shorten this time and improve performances 41 .
2020-04-01 Niehus et al Using observational data to quantify bias of traveller-derived COVID-19 prevalence estimates in Wuhan, China
The Lancet Infectious Diseases
IV. Prevalence Study

We fitted our model using Stan version 2.19.1, 9 and we drew 80 000 samples from the joint posterior distribution of θ high , θ medium , θ low and β using four independent chains (20 000 samples each), and discarded for each chain the first 500 samples (burn-in).
Our findings will support rapid deployment of outbreak surveillance and control capacities in regions at high risk of case importation paired with low surveillance capacity.

Using the second component of the Global Health Security index to stratify likely case-detection capacities, the ability to detect imported cases relative to Singapore was 40% (95% HPDI 22–67) among locations with high surveillance capacity, 37% (18–68) among locations with medium surveillance capacity, and 11% (0–42) among locations with low surveillance capacity.
2020-04-30 Kapata et al Is Africa prepared for tackling the COVID-19 (SARS-CoV-2) epidemic. Lessons from past outbreaks, ongoing pan-African public health efforts, and implications for the future
International Journal of Infectious Diseases
IV. Other Increased governmental and donor investments are required to advance locally led, world-class public health work with surveillance, data and analytics capabilities and further expanding state-of-the-art laboratory capacities with more J o u r n a l P r e -p r o o f trained personnel to sustain capacity to rapidly respond to outbreaks at their source.

3 Recruitment, support, and coordination of local expertise and capacity (public, private—commercial, and non-profit, including academic), including legal, ethical, communications, and operational issues.

3.0.0.1 Highlights

3.0.0.2 Articles

Date Authors Title LOE(?) & Sample Matches
2020 Wang et al Phase-adjusted estimation of the number of Coronavirus Disease 2019 cases in Wuhan, China
Cell Discovery
IV. Computer Model Cooperation has been established with other countries and international organizations.
2020 ZHANG et al Analysis on the layout of China’s emergency research projects during the public health emergency of COVID-19
Chinese Journal of Medical Science Research Management
IV. Other Conclusions In the campaign of science and technology to deal with COVID-19, the leadership of Chinese government and their coordination with local agencies facilitated quick response in both R&D investment and supporting policies.
2020-01-23 Corman et al Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR
Euro Surveill
IV. Prevalence Study

To show that the assays can detect other bat-associated SARS-related viruses, we used the E gene assay to test six batderived faecal samples available from Drexler et al.
CONCLUSION: The present study demonstrates the enormous response capacity achieved through coordination of academic and public laboratories in national and European research networks.

The internal use of samples for diagnostic workflow optimisation was agreed under the medical ethical rules of each of the participating partners.
2020-02-07 Gilbert et al Preparedness and vulnerability of African countries against introductions of 2019-nCoV
medrxiv
IV. Prevalence Study The application of such a vast technical and operational set of interventions depends on countries' public health and laboratory infrastructures and resources.
2020-02-20 Deng et al Characteristics of and Public Health Responses to the Coronavirus Disease 2019 Outbreak in China
J Clin Med
IV. Prevalence Study The responsibilities of the organizations are shown in Table 2 .
2020-02-21 Chang et al Coronavirus Disease 2019: Coronaviruses and Blood Safety
Transfusion Medicine Reviews
IV. Prevalence Study

In a study on the viral load in different samples among 37 MERS patients, investigators found that nearly half of serum samples tested yielded a viral RNA signal during the first week after diagnosis and that the viral load ranged from about 2.1×10 2 to 2.51×10 5 copies/mL.
This research did not receive any specific grant from funding agencies in the public, commercial, or not-for profit sectors.
2020-02-28 Fadel et al Coronavirus outbreak: the role of companies in preparedness and responses
The Lancet Public Health
IV. Other Helped by their occupational practitioners, healthcare advisers, and safety professionals, companies that have a financial capacity and responsibilities (including governmental, federal, or state administrations) will thus have to prepare their business continuity planning for when cases of infected patients occur in the company.
2020-03-02 Brennan et al Responding to health emergencies in the Eastern Mediterranean region in times of conflict
The Lancet
IV. Other WHO's global COVID-19 strategic preparedness and response plan 13 therefore prioritises countries with weak health systems for technical and operational support from international partners.

WHO's global COVID-19 strategic preparedness and response plan13 therefore prioritises countries with weak health systems for technical and operational support from international partners.

15 Humanitarian agencies have adopted various approaches to address these constraints, including investments in local partners, cross-border operations, deconfliction, remote programming, and scaled up advocacy and humanitarian diplomacy.
2020-03-06 Habibi et al Do not violate the International Health Regulations during the COVID-19 outbreak
The Lancet
IV. Prevalence Study Additionally, the IHR does not have robust accountability mechanisms for compliance, enforcement, oversight, and transparency.
2020-03-10 Chan et al Research Frontiers of Health Emergency and Disaster Risk Management: What Do We Know So Far?
Int J Environ Res Public Health
IV. Prevalence Study highlighted the development need for relevant research methodologies, risk communication approaches, health data management strategies, practical health emergency study ethical guidelines, bridging global research capacity disparities, and infrastructure constraints, to ensure knowledge advancement in Health-EDRM.
2020-03-14 Su et al Comparison of clinical characteristics of coronavirus disease (COVID-19) and severe acute respiratory syndrome (SARS) as experienced in Taiwan
Travel Medicine and Infectious Disease
IV. Other This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.
2020-03-16 Liu et al Prevalence and predictors of PTSS during COVID-19 Outbreak in China Hardest-hit Areas: Gender differences matter
Psychiatry Research
IV. Prevalence Study

A total of 285 participants were recruited in the study, among which 124(43.5%) were currently in Wuhan, and 188(66%) were previously in Wuhan.
This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.
2020-03-17 Buckee et al Improving epidemic surveillance and response: big data is dead, long live big data
The Lancet Digital Health
IV. Computer Model For this process to be effective, individuals from different institutions, including academia, industry, nongovernmental organisations (NGOs), and governments, need to be in frequent communication.

Regional or local teams with analytical training and ongoing relationships with government and industry partners should lead to flexible modelling approaches that leverage large curated datasets and international analytical expertise, building on collaborations developed when there are no emerging or ongoing outbreaks.
2020-03-18 Kandel et al Health security capacities in the context of COVID-19 outbreak: an analysis of International Health Regulations annual report data from 182 countries
The Lancet
IV. Prevalence Study The operational readiness index can be used to support WHO, governments, and other international agencies to prioritise their support and implementation of operational readiness capacities for the COVID-19 outbreak.

This coordination and collaboration is reinforced by the introduction of voluntary IHR external evaluation processes, including Joint External Evaluations, which have successfully brought multiple sectors together around common plans for national preparedness capacity building.

Many countries are struggling to sustain or develop their national preparedness capacities, primarily because of a lack of resources, competing national priorities, and a high turnover of health-care workers.
2020-03-19 Zhao et al A systematic approach is needed to contain COVID-19 globally
Science Bulletin
IV. Prevalence Study For example, classification requires collaboration between different government agencies at different administrative levels, which in turn helps to strengthen management coordination.
2020-03-20 Escher et al An Ounce of Prevention: Coronavirus (COVID-19) and Mass Gatherings
PMC
IV. Prevalence Study Governments are tasked with three critical duties in the response to COVID-2019: the coordination of services with access to COVID-19 testing kits, medical supplies and equipment, accurate and timely communication, and maintaining public trust in their government .
2020-03-20 Ramanathan et al Planning and provision of ECMO services for severe ARDS during the COVID-19 pandemic and other outbreaks of emerging infectious diseases
The Lancet Respiratory Medicine
IV. Prevalence Study Use predetermined consensus criteria for rationing of ECMO if indicated; reassess all aspects of a patient's treatment plan regularly, including the need to continue or terminate ECMO; invoke distributive justice only in circumstances where rationing precludes the ability to care for each individual optimally; seek opinions from hospital ethics and medicolegal committees in ethically challenging scenarios Quality assurance and collaborative research Maintain quality assurance and clinical governance frameworks with frequent ECMO quality reviews; ensure collection and sharing of data to inform preparedness and patient care; aim to have ethics approval in place or develop mechanisms for expedient ethics review and approval processes ECMO=extracorporeal membrane oxygenation.
2020-03-20 Kriz et al Teaching-practice as a critical bridge for narrowing the research-practice gap
Industrial Marketing Management
III-3. Time Series Analysis

The wicked problem sessions attract over 40 participants (policy, practitioners, academics), with action research/ learning sessions limited to approximately 12 participants (practitioners and researchers).
Research stakeholders include all activities conducted by tertiary institutions including research and higher education.

Practice stakeholders include all activities undertaken by management practitioners, namely deploying and managing assets and resources on behalf of corporate entities both large and small.

Social stakeholders include the work of governments that fund universities (main providers of research and tertiary education in Australia), regional communities with a stake in general economic prosperity, taxpayers and employees.

The recruitment of companies is undertaken in close collaboration with industry and government stakeholders and the program has been responsible for multiple international export successes.
2020-03-20 Legido-Quigley et al Are high-performing health systems resilient against the COVID-19 epidemic?
The Lancet
IV. Prevalence Study However, their response is vulnerable to shortcomings in the coordination of services; access to adequate medical supplies and equipment; adequacy of risk communication; and public trust in government.
2020-03-20 Gilbert et al Preparedness and vulnerability of African countries against importations of COVID-19: a modelling study
The Lancet
IV. Prevalence Study 1 The application of such a vast technical and operational set of interventions depends on each country's public health and laboratory infrastructures and resources.
2020-03-20 Dewey et al Supporting Clinicians During the COVID-19 Pandemic
Ann Intern Med
IV. Other Other professional organizations, or organizations with access to community discussion boards, could develop similar venues for highlighting best practices in wellness.
2020-03-21 Hsieh et al Putting resiliency of a health system to the test: COVID-19 in Taiwan
Journal of the Formosan Medical Association
IV. Other Our ongoing action to control the spread has been the collaborative work of the private and public sector, key players at the national and local levels, and shared knowledge amongst different expertise ranging from transportation, immigration, economic affairs, labor, education, and healthcare.
2020-03-24 Darlenski et al Covid-19 pandemic and the skin - What should dermatologists know?
Clinics in Dermatology
IV. Other In addition, the scientific communication between dermatologists has been hindered with the cancellation of scientific meetings and academic sessions.
2020-03-25 Uslupehlivan et al Glycoinformatics approach for identifying target positions to inhibit initial binding of SARS-CoV-2 S1 protein to the host cell
biorxiv
IV. Other This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.
2020-03-26 Viswanath et al Working through the COVID-19 outbreak: Rapid review and recommendations for MSK and allied heath personnel
Journal of Clinical Orthopaedics and Trauma
IV. Other This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.
2020-03-26 Miao et al Early chest computed tomography to diagnose COVID-19 from suspected patients: A multicenter retrospective study
medrxiv
IV. Other This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.
2020-03-26 Carico et al Community pharmacists and communication in the time of COVID-19: Applying the health belief model
Research in Social and Administrative Pharmacy
IV. Other Community pharmacists can help address these barriers when they arise by keeping contact information for local governmental and nongovernmental organizations that may provide support for people who are experiencing economic distress.
2020-03-27 Lee et al Epidemic preparedness in urban settings: new challenges and opportunities
The Lancet Infectious Diseases
IV. Prevalence Study 11 Other local authorities have established surge capacity and contingency plans, including strong links with healthcare facilities and national coordination bodies.
2020-03-27 Dudley et al Disparities in Age-Specific Morbidity and Mortality from SARS-CoV-2 in China and the Republic of Korea
medrxiv
III-3. Time Series Analysis No external, corporate or institutional funding support was received for this work.
2020-03-28 Bhat et al COVID 2019 Outbreak: The disappointment in Indian Teachers
Asian Journal of Psychiatry
IV. Other This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.
2020-03-30 Lin et al Which Measures are Effective in Containing COVID-19? Empirical Research Based on Prevention and Control Cases in China
medrxiv
IV. Prevalence Study Implementing a community-wide containment requires close partnerships and cooperation with law enforcement agencies at the local and state levels, and inspection stations are usually established, and legal penalties may be required if there is a violation.

In addition to legal and ethical challenges, All rights reserved.
2020-03-30 Ferstad et al A model to forecast regional demand for COVID-19 related hospital beds
medrxiv
IV. Computer Model When considering the limited healthcare resources anticipated, the need for strengthening collaborative operational planning and research between institutions and across the public and private sectors is paramount.
2020-03-31 FINEGAN et al International Committee of the Red Cross (ICRC): General Guidance for the Management of the Dead Related to COVID-19
Forensic Science International: Synergy
IV. Other On the contrary, the plan describes operational practices, the supporting financial, administrative and logistical systems that allows for the professional and dignified search for, recovery, examination, identification, storage and return of bodies to the families for burial.
2020-03-31 Liu et al Pay attention to situation of SARS-CoV-2 and TCM advantages in treatment of novel coronavirus infection
Chinese Herbal Medicines
IV. Prevalence Study

In clinical study, two mild and two severe COVID-19 pneumonia patients were given combined Chinese and Western medicine treatment, three of whom gained significant improvement in pneumonia associated symptoms.
WHO and governments should adopt a series of countermeasures, including strengthening cooperation and sharing of information between national health agencies and international organizations; humanitarian assistance to countries with insufficient medical resources; to speed up the research and development of vaccines and the approval of antiviral drugs; measures taken by states to reduce or suspend activities that cause public gatherings; and countries issue travel warnings according to the situation.
2020-04-01 Sultan et al AGA Institute Rapid Recommendations for Gastrointestinal Procedures During the COVID-19 Pandemic
Gastroenterology
I. Systematic Review

58, 59 First, the systematic reviews by Offeddu et al included a meta-analysis of 3 observational studies that showed a benefit in using N95 respirators over standard masks in protecting health care workers from SARS (OR = 0.86; 95% CI: 0.
The AGA and a number of other professional medical organizations have been working to lift restrictions on reimbursement for telehealth visits.
2020-04-01 Xie et al Insight into 2019 novel coronavirus — an updated intrim review and lessons from SARS-CoV and MERS-CoV
International Journal of Infectious Diseases
IV. Prevalence Study Funding Source: This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.
2020-04-15 Musazzi et al New regulatory strategies to manage medicines shortages in Europe
International Journal of Pharmaceutics
IV. Prevalence Study Although the proposed definition was relevant only for Marketing Authorization Holders (MAHs) and Regulatory Authorities, it is the first step to promote the communication and the coordination among European pharmaceutical stakeholders, regulators and professionals working in the different National Healthcare Systems for improving their resilience to shortages.
2020-04-30 Zhai et al Mental health care for international Chinese students affected by the COVID-19 outbreak
The Lancet Psychiatry
IV. Other Advice services provided by these departments can help students address academic and financial issues, and other concerns causing distress.
2020-04-30 Djalante et al Building resilience against biological hazards and pandemics: COVID-19 and its implications for the Sendai Framework
Progress in Disaster Science
IV. Prevalence Study International funding organisations, regional government bodies and private entities have proposed major financial measures.
2020-04-30 Georgalakis et al A disconnected policy network: The UK's response to the Sierra Leone Ebola epidemic
Social Science & Medicine
IV. Other Discussions took place on the funding and organisation of the anthropological response.

4 National guidance and guidelines about best practices to states (e.g., how states might leverage universities and private laboratories for testing purposes, communications to public health officials and the public).

4.0.0.1 Highlights

4.0.0.2 Articles

Date Authors Title LOE(?) & Sample Matches
2020 ZHANG et al Analysis on the layout of China’s emergency research projects during the public health emergency of COVID-19
Chinese Journal of Medical Science Research Management
IV. Other Methods Literature investigation method is applied to collect information of scientific research and emergency research projects of COVID-19 funded since January 20th by different entities including national, provincial and municipal administrative departments, public health agencies, research institutes, universities and industries.
2020 Daszak et al A strategy to prevent future pandemics similar to the 2019-nCoV outbreak
Biosafety and Health
IV. Prevalence Study This 'pre-outbreak surveillance' strategy can be coordinated with different sectors of public health, healthcare, agriculture and forestry to implement sample collection and testing of wildlife, domestic animals, and people in collaboration with research institutions.
2020 Jernigan et al Update: Public Health Response to the Coronavirus Disease 2019 Outbreak — United States, February 24, 2020 | MMWR
WHO
IV. Other U.S. government agencies and public health partners are implementing aggressive measures to slow and try to contain transmission of COVID-19 in the United States.
2020 Allam et al On the Coronavirus (COVID-19) Outbreak and the Smart City Network: Universal Data Sharing Standards Coupled with Artificial Intelligence (AI) to Benefit Urban Health Monitoring and Management
Healthcare
IV. Prevalence Study Here, as technological tools and laboratories around the world share data and collectively work to devise tools and cures, similar efforts should be considered between smart city professionals on how collaborative strategies could allow for the maximization of public safety on such and similar scenarios.
2020 @CDCgov et al Initial Public Health Response and Interim Clinical Guidance for the 2019 Novel Coronavirus Outbreak — United States, December 31, 2019–February 4, 2020 | MMWR
WHO
IV. Other CDC, multiple other federal agencies, state and local health departments, and other partners are implementing aggressive measures to slow transmission of 2019-nCoV in the United States, be ready if widespread transmission occurs, and work on medical countermeasures.
2020-02-07 Patel et al Initial Public Health Response and Interim Clinical Guidance for the 2019 Novel Coronavirus Outbreak — United States, December 31, 2019–February 4, 2020
MMWR Morb Mortal Wkly Rep
IV. Other CDC, multiple other federal agencies, state and local health departments, and other partners are implementing aggressive measures to slow transmission of 2019-nCoV in the United States .

CDC is working closely with FDA and public health partners, including the American Public Health Laboratories, to rapidly share these tests domestically and internationally through CDC's International Reagent Resource (https://www.internationalreagentresource.org/).

CDC, multiple other federal agencies, state and local health departments, and other partners are implementing aggressive measures to slow U.S. transmission of 2019-nCoV .
2020-02-12 Hébert-Dufresne et al Beyond R0: the importance of contact tracing when predicting epidemics
medrxiv
IV. Computer Model Despite the potential for genome sequencing to revolutionize outbreak response, the global public health community still struggles to coordinate data sharing across international borders, between academic researchers, and with private companies .
2020-02-13 Reusken et al Laboratory readiness and response for novel coronavirus (2019-nCoV) in expert laboratories in 30 EU/EEA countries, January 2020
Euro Surveill
IV. Other The legal possibilities (General Data Protection Regulation; GDPR) for sharing and the willingness to share positive clinical material among the network laboratories now that the first 37 cases have been confirmed in the EU/EEA will determine the speed with which laboratories can address the clinical sensitivity of their implemented tests while the number of cases in the EU/EEA is still limited.
2020-02-13 Bernard Stoecklin et al First cases of coronavirus disease 2019 (COVID-19) in France: surveillance, investigations and control measures, January 2020
Euro Surveill
IV. Prevalence Study

The was obtained from the three patients confirmed with 2019-nCoV infection.
Rapid and effective collaboration between the clinicians (general practitioners attending the cases, emergency hotline clinicians (SAMU-centre 15) and infectious diseases specialists), the National Reference Centre and the regional and national health authorities has played a crucial role in the system's capacity to quickly detect, isolate and investigate those cases in order to implement adequate control measures.
2020-02-20 Deng et al Characteristics of and Public Health Responses to the Coronavirus Disease 2019 Outbreak in China
J Clin Med
IV. Prevalence Study The health administration departments, public health departments, and medical institutions at all (province, city, county, district, township, and street) levels, and social organizations shall function in epidemic prevention and control and provide guidance for patients and close contact families for disease prevention .
2020-02-23 Zhai et al From Isolation to Coordination: How Can Telemedicine Help Combat the COVID-19 Outbreak?
medrxiv
IV. Other The platform could aggregate COVID-19 patient records across 126 connected hospitals and rapidly expand to enable open collaborations with key stakeholders such as government authorities, research institutions and laboratories.
2020-02-28 Fadel et al Coronavirus outbreak: the role of companies in preparedness and responses
The Lancet Public Health
IV. Other Helped by their occupational practitioners, healthcare advisers, and safety professionals, companies that have a financial capacity and responsibilities (including governmental, federal, or state administrations) will thus have to prepare their business continuity planning for when cases of infected patients occur in the company.
2020-02-28 Shah et al Guide to Understanding the 2019 Novel Coronavirus
Mayo Clinic Proceedings
IV. Other Health care professionals who encounter suspected cases should contact local infection control and public health offices regarding potential cases and appropriate next steps based on regional resources and protocols.
2020-02-28 Jernigan et al Update: Public Health Response to the Coronavirus Disease 2019 Outbreak - United States, February 24, 2020
MMWR. Morbidity and Mortality Weekly Report
IV. Other This report summarizes the aggressive measures that CDC, state and local health departments, multiple other federal agencies, and other partners are implementing to slow and try to contain transmission of COVID-19 in the United States.
2020-02-29 He et al Clinical trials for the treatment of Coronavirus disease 2019 (COVID-19): A rapid response to urgent need
Science China Life Sciences
IV. Other Pharmaceutical companies, government, institutions, physicians and scientists are the main force behind these researches.
2020-03-04 Chang et al Weaponized Interdependence: China's Economic Statecraft and Social Penetration against Taiwan
Orbis
IV. Prevalence Study For example, both approaches include approaching/inviting Taiwan's opinion leaders, 48 China's Economic Statecraft and Social Penetration against Taiwan local politicians, community leaders, 49 and key figures, such as retired ministers, 50 exmilitary generals, religious leaders, school principals, and teachers, as well as young students to take part in cross-Strait forums and various exchange programs organized by China's public and private sectors.
2020-03-06 Henry et al Preliminary epidemiological analysis on children and adolescents with novel coronavirus disease 2019 outside Hubei Province, China: an observational study utilizing crowdsourced data
medrxiv
IV. Prevalence Study

Results: A total of 82 patients were included.
4, 5 Crowdsourcing enables the collection of data from multiple platforms including health-care-oriented social networks, government and public health agencies, and global news sources.
2020-03-07 Baker et al Preparing for a Surge of Coronavirus Cases
The Joint Commission Journal on Quality and Patient Safety
IV. Other As information and recommendations about COVID-19 continue to evolve, we want to emphasize our support of the CDC and other public health partners as the appropriate source of information and guidance for health care organizations and providers.
2020-03-12 Binnicker et al Emergence of a Novel Coronavirus Disease (COVID-19) and the Importance of Diagnostic Testing: Why Partnership between Clinical Laboratories, Public Health Agencies, and Industry Is Essential to Control the Outbreak
Clinical Chemistry
IV. Other Emergence of a Novel Coronavirus Disease (COVID-19) and the Importance of Diagnostic Testing: Why Partnership between Clinical Laboratories, Public Health Agencies, and Industry Is Essential to Control the Outbreak
2020-03-12 Ashrafi-rizi et al Information Typology in Coronavirus (COVID-19) Crisis; a Commentary
Arch Acad Emerg Med
IV. Other In this behavioral pattern, attention must be paid to producers and disseminators of information, including the media, government officials, professionals in various fields (physician, nurses, psychologists, etc.)
2020-03-15 Li et al Progression of Mental Health Services during the COVID-19 Outbreak in China
Int J Biol Sci
IV. Other The guidelines addressed that the hotline services should be set up by psychiatric institutions, students' mental health education and counseling centers at universities, mental health associations and academic societies.
2020-03-17 Buckee et al Improving epidemic surveillance and response: big data is dead, long live big data
The Lancet Digital Health
IV. Computer Model For this process to be effective, individuals from different institutions, including academia, industry, nongovernmental organisations (NGOs), and governments, need to be in frequent communication.

Ministries of health have complex relationships with both the companies that have access to personal data and with the public.
2020-03-17 Geldsetzer et al Using rapid online surveys to assess perceptions during infectious disease outbreaks: a cross-sectional survey on Covid-19 among the general public in the United States and United Kingdom
medrxiv
III-2. Cross Sectional Control The findings from this online survey could guide information campaigns by public health authorities, clinicians, and the media.
2020-03-18 Jiang et al Is a 14-day quarantine period optimal for effectively controlling coronavirus disease 2019 (COVID-19)?
medrxiv
III-3. Time Series Analysis

Methods We compiled and analyzed the patient-level information of 2015 laboratory-confirmed Covid-19 cases including 99 children in 28 Chinese provinces.
To answer these questions, we manually curated the patient-level data from the case reports on official websites of China's provincial public health agencies.
2020-03-20 Khatri et al YouTube as source of information on 2019 novel coronavirus outbreak: A cross sectional study of English and Mandarin content
Travel Medicine and Infectious Disease
III-2. Cross Sectional Control Source of videos was categorized into one of five groups : academic institutions or hospitals, news agencies, government agencies like regional health departments, WHO or independent users.
2020-03-20 Legido-Quigley et al Are high-performing health systems resilient against the COVID-19 epidemic?
The Lancet
IV. Prevalence Study 6 Singapore health authorities provide daily information on mainstream media, the Ministry of Health has Telegram and WhatsApp groups set up with doctors in the public and private sectors where more detailed clinical and logistics information is shared, and authorities use websites to debunk circulating misinformation.
2020-03-20 Kriz et al Teaching-practice as a critical bridge for narrowing the research-practice gap
Industrial Marketing Management
III-3. Time Series Analysis

The wicked problem sessions attract over 40 participants (policy, practitioners, academics), with action research/ learning sessions limited to approximately 12 participants (practitioners and researchers).
Social stakeholders include the work of governments that fund universities (main providers of research and tertiary education in Australia), regional communities with a stake in general economic prosperity, taxpayers and employees.
2020-03-20 Dewey et al Supporting Clinicians During the COVID-19 Pandemic
Ann Intern Med
IV. Other Other professional organizations, or organizations with access to community discussion boards, could develop similar venues for highlighting best practices in wellness.
2020-03-20 Zhao et al Chinese Public Attention to COVID-19 Epidemic: Based on Social Media
medrxiv
IV. Prevalence Study Increasing numbers of public health departments and individuals are using social media platforms to communicate and share information during public health emergencies.
2020-03-23 Ikizler et al COVID-19 and Dialysis Units: What Do We Know Now and What Should We Do?
American Journal of Kidney Diseases
IV. Other Academic centers and large dialysis organizations should rapidly create data collection tools that can complement the basic clinical data collected by CDC and state health departments.
2020-03-24 Xu et al Epidemiological data from the COVID-19 outbreak, real-time case information
Sci Data
IV. Other Government sources include press releases on the official websites of Ministries of Health or Provincial Public Health Commissions, as well as updates provided by the official social media accounts of governmental or public health institutions.
2020-03-24 Haines et al National UK programme of community health workers for COVID-19 response
The Lancet
IV. Other Online courses are available from some academic institutions on COVID-19 and emergency measures to accredit and certificate these courses to agreed standards could be implemented.
2020-03-24 Chavez et al Coronavirus Disease (COVID-19): A primer for emergency physicians
The American Journal of Emergency Medicine
IV. Prevalence Study

60 One study of 204 patients with confirmed COVID-19 suggests 48.5% of patients have gastrointestinal (GI) symptoms.
Collaboration with local and state public health departments is strongly recommended.
2020-03-26 Rios et al Guidelines for preventing respiratory illness in older adults aged 60 years and above living in long-term care: A rapid review of clinical practice guidelines
medrxiv
IV. Prevalence Study

If one or more respiratory samples from ILI cases in a suspected outbreak returns a positive laboratory result for influenza, then an influenza outbreak is confirmed.
Infection control practitioners may be available for advice in local hospitals, state and territory health departments, or as private consultants.

Regional health authorities (RHAs) and provincial health services organizations (PHSOs) are expected to develop regional policies and procedures based on these guidelines.

03 Although not regulatory in scope, these guidelines support infection prevention and control (IP&C) professionals, health care organizations and health care providers in developing, implementing and evaluating IP&C policies, procedures and programs to improve the quality and safety of health care and patient outcomes.
2020-03-26 Zheng et al Recommendations and guidance for providing pharmaceutical care services during COVID-19 pandemic: A China perspective
Research in Social and Administrative Pharmacy
IV. Other Last but not the least, during this pandemic, 112 pharmacists in China used a variety of approaches, such as mobile APPs and collaborating with 113 neighborhood committees and drug companies, to provide consulting services online and ensure 114 patients' drug supply at home.
2020-03-27 Hsiang et al The Effect of Large-Scale Anti-Contagion Policies on the Coronavirus (COVID-19) Pandemic
medrxiv
III-3. Time Series Analysis

We did not collect city level health outcomes recorded prior to January 24, 2020 in provinces that had fewer than ten confirmed cases at that date.
The 10 sources listed for this dataset were the French public health website, the Ministry of Solidarity and 11 Health, French newspapers that reported government information, and regional public health 12 13 websites.

Epidemiological and policy data for each of the six countries in our sample were collected from a variety of in-country data sources, including government public health websites, regional newspaper articles, and Wikipedia crowd-sourced information.
2020-03-31 Liu et al Pay attention to situation of SARS-CoV-2 and TCM advantages in treatment of novel coronavirus infection
Chinese Herbal Medicines
IV. Prevalence Study

In clinical study, two mild and two severe COVID-19 pneumonia patients were given combined Chinese and Western medicine treatment, three of whom gained significant improvement in pneumonia associated symptoms.
WHO and governments should adopt a series of countermeasures, including strengthening cooperation and sharing of information between national health agencies and international organizations; humanitarian assistance to countries with insufficient medical resources; to speed up the research and development of vaccines and the approval of antiviral drugs; measures taken by states to reduce or suspend activities that cause public gatherings; and countries issue travel warnings according to the situation.
2020-03-31 FINEGAN et al International Committee of the Red Cross (ICRC): General Guidance for the Management of the Dead Related to COVID-19
Forensic Science International: Synergy
IV. Other To this effect forensic best practices should always be informed by the advice and latest recommendations from national health authorities and international health organizations, especially the World Health Organization (WHO) , for health personnel handling COVID-19 cases.
2020-03-31 Brown et al Cannabidiol as prophylaxis for SARS-CoV-2 and COVID-19? Unfounded claims versus potential risks of medications during the pandemic
Research in Social and Administrative Pharmacy
IV. Other Pharmacists should instead encourage public health by following federal and state guidance and promoting these practices with our patients.
2020-04-15 Musazzi et al New regulatory strategies to manage medicines shortages in Europe
International Journal of Pharmaceutics
IV. Prevalence Study Such a procedure may be fully integrable with other existing and adopted strategies and, therefore, it may be an added value for both European Regulatory Authorities and other subjects involved in the National pharmaceutical distribution chains and healthcare systems (e.g., manufacturers, wholesalers, hospitals, pharmacies, insurance companies, regional healthcare Authorities).

variable part of algorithm) can be built up according to the features of different settings (e.g., manufacturers, wholesalers, hospitals, pharmacies) or National regulatory frameworks.
2020-04-30 Georgalakis et al A disconnected policy network: The UK's response to the Sierra Leone Ebola epidemic
Social Science & Medicine
IV. Other The British Government assumed responsibility for Sierra Leone and sought guidance from health officials, academics, humanitarian agencies and clinicians.
2020-04-30 Djalante et al Building resilience against biological hazards and pandemics: COVID-19 and its implications for the Sendai Framework
Progress in Disaster Science
IV. Prevalence Study International funding organisations, regional government bodies and private entities have proposed major financial measures.
2020-12-31 Bai et al Chinese experts’ consensus on the Internet of Things-aided diagnosis and treatment of coronavirus disease 2019 (COVID-19)
Clinical eHealth
IV. Prevalence Study This consensus is appropriate for different specialists at all levels of hospitals and even managers at all levels of hospitals, local community development corporations, and public health centers.

5 Development of a point-of-care test (like a rapid influenza test) and rapid bed-side tests, recognizing the tradeoffs between speed, accessibility, and accuracy.

5.0.0.1 Highlights

5.0.0.2 Articles

Date Authors Title LOE(?) & Sample Matches
2020 Pang et al Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review
Journal of Clinical Medicine
I. Systematic Review

Of the total of 570 unique studies on 2019-nCoV, SARS CoV or MERS-CoV vaccines screened, only four were eventually included in the review.
Comparison between the molecular test (i.e RT-PCR) and serological test (i.e., ELISA) showed that the molecular test has better sensitivity and specificity.
2020 GUO et al Comparison and analysis of the detection performance of six new coronavirus nucleic acid detection reagents
Chongqing Medicine
IV. Other Conclusion There are differences in the detection ability of six 2019-nCoV nucleic acid detection reagents for weakly positive samples, and the accuracy, sensitivity and reproducibility of some reagents are not good.
2020 DENG et al Value of chest CT screening in the early COVID-19 outbreak
Chinese Journal of Radiology
IV. Other Take the nucleic acid test results as the gold standard, the sensitivity, specificity and rate of missed diagnosis of CT screening COVID-19 were calculated.

The sensitivity of CT screening COVID-19 was 97.7% (423/433), specificity was 53.9% (83/154) and rate of missed diagnosis was 2.3% (10/433).
2020-01-30 Gostic et al Estimated effectiveness of traveller screening to prevent international spread of 2019 novel coronavirus (2019-nCoV)
medrxiv
IV. Prevalence Study

Using each parameter set, we 162 simulated screening outcomes for a population of 100 infected individuals.
The availability of rapid PCR tests would also be beneficial for case identification at arrival, and 348
2020-02-17 Wang et al A deep learning algorithm using CT images to screen for Corona Virus Disease (COVID-19)
medrxiv
III-3. Time Series Analysis

121 We retrospectively collected CT images from 259 patients, in which the the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.
More importantly, the quality, stability and reproducibility of the 79 detection kits are questionable.

The external testing dataset showed a total accuracy of 79.3% with specificity of 0.83 and sensitivity of 0.67.

Results: The internal validation achieved a total accuracy of 89.5% with specificity of 0.88 and sensitivity of 0.87.
2020-02-21 Kobayashi et al Communicating the Risk of Death from Novel Coronavirus Disease (COVID-19)
J Clin Med
III-3. Time Series Analysis

Out of 218 cases, there are 10 critically ill patients as of 15 February 2020.
where s and T are the sensitivity and the detection window of RT-PCR testing, respectively.
2020-02-27 Li et al Development and Clinical Application of A Rapid IgM-IgG Combined Antibody Test for SARS-CoV-2 Infection Diagnosis
Journal of Medical Virology
IV. Other The overall testing sensitivity was 88.66% and specificity was 90.63%.

The clinical detection sensitivity and specificity of this test were measured using blood samples collected from 397 PCR confirmed COVID-19 patients and 128 negative patients at 8 different clinical sites.
2020-02-27 Peng et al Outbreak of a new coronavirus: what anaesthetists should know
British Journal of Anaesthesia
IV. Prevalence Study

The median age of infected individuals is between 49 and 56 yr. 1 13 Children are rarely diagnosed with 2019-nCoV, a phenomenon that has not yet been explained.
8 This is very significant, as this information allows rapid development of real-time polymerase chain reaction diagnostic tests specific to SARS-CoV-2.
2020-02-27 Jiang et al Application and optimization of RT-PCR in diagnosis of SARS-CoV-2 infection
medrxiv
IV. Other The performances of the first RT-PCR detection in pharyngeal swabs and chest CT were evaluated by sensitivity, specificity, youden's index et al.
2020-02-29 Zhang et al Rapid Molecular Detection of SARS-CoV-2 (COVID-19) Virus RNA Using Colorimetric LAMP
medrxiv
IV. Prevalence Study

In addition to controls, a total of 7 patient RNA samples were tested, 6 of which were determined to be positive by RT-qPCR using ORF1a primers (C q 25-36.5, Table 2 ) and 4 positive with Gene N primers.
The breadth of application highlights the applicability of visual detection methods to provide an advantage in simplicity and portability for enabling new, rapid diagnostics.
2020-03-05 Manning et al Rapid metagenomic characterization of a case of imported COVID-19 in Cambodia
biorxiv
IV. Other This detection directly increased on-the-ground certainty in diagnostic sensitivity and specificity of available assays.
2020-03-06 Chen et al Validity of Wrist and Forehead Temperature in Temperature Screening in the General Population During the Outbreak of 2019 Novel Coronavirus: a prospective real-world study
medrxiv
IV. Other The cut-off value of wrist measurement for detecting tympanic temperature ≥37.3C was 36.2C with a 86.4% sensitivity and a 67.0% specificity, and the best threshold of forehead measurement was also 36.2C with a 93.2% sensitivity and a 60.0% specificity.

NCIT meets the 64 clinical requirements for mass screening in terms of detection efficiency, safety and 65 cost-performance.
2020-03-16 Araujo et al Spread of SARS-CoV-2 Coronavirus likely to be constrained by climate
medrxiv
IV. Computer Model Figure S3 | Metrics of performance on test data obtained by 5--fold cross-validation repeated 4 times: AUC; Sensitivity; and Specificity.
2020-03-19 Haveri et al Serological and molecular findings during SARS-CoV-2 infection: the first case study in Finland, January to February 2020
Euro Surveill
IV. Prevalence Study The assay can be used as confirmatory tool for SARS-CoV-2 specificity in the development of more accessible diagnostic tools such as assays based on detecting binding antibodies.
2020-03-20 Mizumoto et al Transmissibility of 2019 Novel Coronavirus: zoonotic vs. human to human transmission, China, 2019-2020
medrxiv
III-3. Time Series Analysis

From December 8, 2019 to January 21, 2020, we analyzed a total of 425 confirmed cases by date of symptoms onset including information on whether the case was linked to the Huanan Seafood Wholesale Market.
diagnostic tests in order to improve the accuracy and speed of clinical diagnosis and enhance reporting rates.
2020-03-20 Jiang et al Development and validation of a rapid single-step reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) system potentially to be used for reliable and high-throughput screening of COVID-19
medrxiv
IV. Other Rapidity, user-friendliness, and high degree of sensitivity and specificity are desirable features of diagnostic assays for screening purposes.
2020-03-20 Zhang et al Evaluation of recombinant nucleocapsid and spike proteins for serological diagnosis of novel coronavirus disease 2019 (COVID-19)
medrxiv
IV. Other GICA performance was assessed with comparison of viral RNA detection.

The GICA has a sensitivity and specificity of 86.89% (106/122) and 99.39% (656/660), respectively.
2020-03-23 Bai et al Predicting COVID-19 malignant progression with AI techniques
medrxiv
IV. Prevalence Study

Methods: A total of 133 consecutively mild COVID-19 patients at admission who was hospitalized in Wuhan Pulmonary Hospital from January 3 to February 13, 2020, were selected in this retrospective IRB-approved study.
The accuracy of the prediction is 79.2%.
2020-03-23 Villela et al The value of mitigating epidemic peaks of COVID-19 for more effective public health responses
PMC
IV. Prevalence Study

The number of new cases can be assessed by a product between the force of infection, a measure of its transmission intensity, clearly proportional to its prevalence, and the number of susceptible individuals 2 .
Furthermore, diagnostic tests, especially rapid ones, with appropriate levels of sensitivity and specificity will be quite helpful for implementing targeted interventions.
2020-03-23 Rodrigues et al An update on COVID-19 for the radiologist - A British society of Thoracic Imaging statement
Clinical Radiology
IV. Other 15, 16 As such, multiple negative tests may be required to exclude COVID-19 and testing kits may become short in supply.
2020-03-25 Nunez-Bajo et al Ultra-Low-Cost Integrated Silicon-based Transducer for On-Site, Genetic Detection of Pathogens
biorxiv
IV. Other 1 Ability to produce NA quickly also increases the speed of development and deployment of new test kits to health systems, providing much needed diagnostic capabilities for the detection of novel pathogens (such as SARS-CoV-2).
2020-03-27 Huang et al Multiple-Input Deep Convolutional Neural Network Model for COVID-19 Forecasting in China
medrxiv
IV. Computer Model Thus, 67 test methods 103 were designed in the ADAPT system to increase the sensitivity and speed of virus detection.
2020-03-27 Zhou et al A New Predictor of Disease Severity in Patients with COVID-19 in Wuhan, China
medrxiv
III-2. Cross Sectional Control

Between January 1 and February 28, 2020, a total of 393 patients with COVID-19 were enrolled, but only 377 eligible participants were finally included in our analysis.
The sensitivity and specificity were 89.47% and 67.42%.

Statistical performance for the classifier was measured by calculating sensitivity, specificity, and negative and positive predictive values.
2020-03-28 Zhai et al The epidemiology, diagnosis and treatment of COVID-19
International Journal of Antimicrobial Agents
III-2. Matched Case Control

Another study later using the travel history and symptom onset of 88 confirmed cases had a similar mean incubation period, which was 6.4 days (95% CI: 5.6-7.7) .
The good analytical performance of a molecular assay for the detection of SARS-CoV-2 on a high-throughput platform, the cobas 6800, was observed with minimal hands-on time, while offering fast and reliable results .The current laboratory test is time-consuming, and a shortage of commercial kits also intensifies the delayed diagnosis.
2020-03-29 Thompson et al COVID-19 in Endoscopy: Time to do more?
Gastrointestinal Endoscopy
IV. Prevalence Study Hopefully, the development of point-of-care testing with rapid results and increasing testing availability will make this a reality soon.
2020-03-29 Xiong et al Comparative performance of four nucleic acid amplification tests for SARS-CoV-2 virus
biorxiv
IV. Other The results of the consistency test using 46 samples showed that Daan, Sansure, and Hybribio NAATs could detect the samples with a specificity of 100% (30/30) and a sensitivity of 100% (16 /16), whereas Bioperfectus NAAT detected the samples with a specificity of 100% (30/30) and a sensitivity 81.25% (13/16).

The results of the 30 consistency test using 46 samples showed that Daan, Sansure, and Hybribio NAATs 31 could detect the samples with a specificity of 100% (30/30) and a sensitivity of 100% 32 (16 /16), whereas Bioperfectus NAAT detected the samples with a specificity of 100% 33 (30/30) and a sensitivity 81.25% (13/16).
2020-03-30 Liu et al Diagnostic Indexes of a Rapid IgG/IgM Combined Antibody Test for SARS-CoV-2
medrxiv
IV. Other In '8 -15 days' group, the diagnostic indexes of this test kit were 100% for sensitivity, 50% for specificity and 87.5% for accuracy, respectively.

Its diagnostic indexes or so-called test characristics, including sensitivity, specificity, PPV, NPV and accuracy were evaluated to determine its diagnostic usefulness .

Sensitivity, specificity and accuracy in these three groups were 18.8%, 77.8% and 40%; 100%, 50% and 87.5%; 100%, 64.3%, and 93.9, respectively.

Kappa efficiency between IgG/IgM test kit and RT-PCR were 0.75.

The test kit under study performed the worst in '0 -7 days' group, generating a sensitivity of 18.8% and an accuracy of 40%.

The aim of this study was to evaluate the sensitivity, specificity, accuracy, positive predictive value (PPV), negative predictive value (NPV), especially Kappa efficiency with PCR and its anti-interference ability.

This test kit performed the best in '>= 16 days' group, yielding a sensitivity of 100% together with an accuracy of 93.9%, though with a relatively low specificity (64.3%).

The sensitivity and specificity of this ease-of-use IgG/IgM combined test kit were good, plus short turnaround time, no specific requirements for additional equipment or skilled technicians, all of these can collectively contributed to its competence for mass testing.
2020-03-30 Xu et al Analysis and Prediction of False Negative Results for SARS-CoV-2 Detection with Pharyngeal Swab Specimen in COVID-19 Patients: A Retrospective Study
medrxiv
III-2. Retrospective Cohort

In order to implement the out-of-sample prediction, 1,324 patients were randomly divided into training (1,059 cases) and validation samples (265 cases Table 2) .
The predictive AFT model, what we believe to be one of the first statistical models for predicting time window of SARS-CoV-2 detection, could help clinicians improve the accuracy and efficiency of the diagnosis, and hence, optimizes the timing of nucleic acid detection and alleviates the shortage of nucleic acid detection kits around the world.
2020-03-30 Bandyopadhyay et al Machine Learning Approach for Confirmation of COVID-19 Cases: Positive, Negative, Death and Release
medrxiv
IV. Other The performance analysis shows that a high rate of accuracy is obtained by the proposed method.
2020-03-30 Lin et al Evaluations of serological test in the diagnosis of 2019 novel coronavirus (SARS-CoV-2) infections during the COVID-19 outbreak
medrxiv
IV. Prevalence Study

Serums from 29 healthy individuals, 51 tuberculosis patients, and 79 SARS-CoV-2 confirmed patients 25 were employed to evaluate the performance of this approach.
/2020 To explore whether the onset time was significantly linked with the detection sensitivity by this 165 serological chemiluminescence method, comparison and statistical analysis of the sensitivity rates 166 between different onset time patient categories was undertaken.
2020-04-01 Abbas et al Classification of COVID-19 in chest X-ray images using DeTraC deep convolutional neural network
medrxiv
IV. Other A high accuracy of 95.12% (with sensitivity of 97.91%, specificity of 91.87%, and precision of 93.36%) was achieved by DeTraC in the detection of COVID-19 X-ray images from normal, and severe acute respiratory syndrome cases.
2020-05-31 Long et al Diagnosis of the Coronavirus disease (COVID-19): rRT-PCR or CT?
European Journal of Radiology
IV. Prevalence Study

The gold standard for a final diagnosis was positivity of first or repeated rRT-PCR tests.. Amongst the 87 included cases, 36 patients were finally diagnosed with COVID-19 pneumonia.
The sensitivities of both tests were then compared.

Firstly, due to the outbreak of COVID-19 pneumonia in this area, the supply of nucleic acid detection kits was limited, and the rRT-PCR examinations were only performed in patients with fever and positive CT tests.
2020-07-31 Artika et al Pathogenic viruses: Molecular detection and characterization
Infection, Genetics and Evolution
IV. Prevalence Study Other parameters commonly used to measure reliability of a diagnostic assay are specificity, accuracy and precision.

Serology tests lack the sensitivity and specificity required for detection of viruses at a low level.

6 Rapid design and execution of targeted surveillance experiments calling for all potential testers using PCR in a defined area to start testing and report to a specific entity. These experiments could aid in collecting longitudinal samples, which are critical to understanding the impact of ad hoc local interventions (which also need to be recorded).

6.0.0.1 Highlights

6.0.0.2 Articles

Date Authors Title LOE(?) & Sample Matches
2020 Chu et al Molecular Diagnosis of a Novel Coronavirus (2019-nCoV) Causing an Outbreak of Pneumonia
Clin Chem
IV. Other Thus, diagnostic tests specific for this infection are urgently needed for confirming suspected cases, screening patients and conducting virus surveillance.

Molecular tests for rapid detection of this virus are urgently needed for early identification of infected patients.
2020 Vazquez et al Identification of COVID-19 Can be Quicker through Artificial Intelligence framework using a Mobile Phone-Based Survey in the Populations when Cities/Towns Are Under Quarantine
Infection Control & Hospital Epidemiology
IV. Other Such collected data can be used to assist in the preliminary screening and early identification of possible COVID-19 infected individuals.
2020 ZHAO et al Clinical characteristics of 28 patients with novel coronavirus pneumonia
Chinese Journal of Infectious Diseases
IV. Other The clinical manifestations, epidemiological history, laboratory tests, imaging examinations and treatments of patients were analyzed retrospectively.
2020 Diao et al HRCT Imaging Features in Representative Imported Cases of 2019 Novel Coronavirus Pneumonia
Precision Clinical Medicine
IV. Other Our quantitative comparison between the patients in the early and relatively late stage alerts the necessity of prompt screening test and imaging diagnosis when symptoms present, whether the patient has direct epidemiology history or not.
2020 GAO et al How to obtain evidence of vertical transmission in viral infected pregnant women: Reflection on COVID-19 epidemic
Chinese Journal of Perinatal Medicine
IV. Other Well-designed protocols and a disciplined research team are essential for both basic and clinical research, in order to contribute to obtaining more scientific evidence for better understanding of the characteristics of this novel coronavirus.
2020 Khot et al The 2019 Novel Coronavirus Outbreak - A Global Threat
The Journal of the Association of Physicians of India
IV. Other Diagnosis is confirmed with PCR based testing of appropriate respiratory samples.
2020 WEN et al Epidemiological and clinical characteristics of 46 newly-admitted coronavirus disease 2019 cases in Beijing
Chinese Journal of Infectious Diseases
IV. Other Features of clinical symptoms, laboratory inspections and imaging inspections were analyzed.
2020-01-23 Corman et al Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR
Euro Surveill
IV. Prevalence Study

To show that the assays can detect other bat-associated SARS-related viruses, we used the E gene assay to test six batderived faecal samples available from Drexler et al.
These two assays were chosen for further evaluation.
2020-02-03 Wu et al A new coronavirus associated with human respiratory disease in China
Nature
IV. Other The experiments were not randomized and the investigators were not blinded to allocation during experiments and outcome assessment.
2020-02-03 Zhou et al A pneumonia outbreak associated with a new coronavirus of probable bat origin
Nature
IV. Prevalence Study

Of the samples obtained from the seven patients, we found that six BALF and five oral swab samples were positive for 2019-nCoV during the first sampling, as assessed by qPCR and conventional PCR.
The experiments were not randomized and the investigators were not blinded to allocation during experiments and outcome assessment.
2020-02-09 Cao et al Incorporating Human Movement Data to Improve Epidemiological Estimates for 2019-nCoV
medrxiv
IV. Prevalence Study This will allow developing early detection, isolation and quarantine strategies tailored to the very dynamic epidemiological situation, as well as identify potential problems in the implementation of local disease control policies and inform the design of any necessary adjustments.
2020-02-10 Arabi et al Critical care management of adults with community-acquired severe respiratory viral infection
Intensive Care Med
II. Randomized Controlled Trial

The importance of timing of oseltamivir treatment has been demonstrated in an observational study of 1950 patients admitted to ICUs with influenza A(H1N1) pdm09, which showed a trend toward improved survival for those treated earliest .
Studies varied in the approach for sampling and in the used assays; in some studies, specimen collection and assays were standardized across all patients, while in other studies, sampling and assays were performed selectively.
2020-02-17 Wang et al A deep learning algorithm using CT images to screen for Corona Virus Disease (COVID-19)
medrxiv
III-3. Time Series Analysis

121 We retrospectively collected CT images from 259 patients, in which the the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.
Therefore, further 349 optimizing and testing this system is warranted.
2020-02-21 Cheng et al Scabies: Application of the Novel Identify-Isolate-Inform Tool for Detection and Management
West J Emerg Med
IV. Prevalence Study

36 Advising patients and parents of young patients to keep fingernails short and clean can assist with preventing secondary infections.
One study showed that real-time PCR and ELISA tests are useful for monitoring treatment efficacy.
2020-02-21 Chan et al A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster
The Lancet
III-3. Time Series Analysis

Methods In this study, we report the epidemiological, clinical, laboratory, radiological, and microbiological findings of five patients in a family cluster who presented with unexplained pneumonia after returning to Shenzhen, Guangdong province, China, after a visit to Wuhan, and an additional family member who did not travel to Wuhan.
However, improved systematic serial collection and testing of an increased number of such samples is warranted.
2020-02-21 Huang et al Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China
The Lancet
III-2. Cross Sectional Control

14 Of 59 suspected cases, 41 patients were confirmed to be infected with 2019-nCoV.
Testing of respiratory specimens should be done immediately once a diagnosis is suspected.
2020-02-27 Wang et al Increasing Host Cellular Receptor—Angiotensin-Converting Enzyme 2 (ACE2) Expression by Coronavirus may Facilitate 2019-nCoV Infection
biorxiv
IV. Other Three independent experiments are performed in all studies.
2020-03-01 Yan et al A machine learning-based model for survival prediction in patients with severe COVID-19 infection
medrxiv
IV. Other In total, there were 1523 blood samples with complete measurements of these three features for the training and test set of 375 patients plus 228 blood samples for the validation set of 29 .
2020-03-02 Metsky et al CRISPR-based surveillance for COVID-19 using genomically-comprehensive machine learning design
biorxiv
IV. Prevalence Study Ongoing SARS-CoV-2 sequencing is key to developing and monitoring diagnostics and similar surveillance tools.
2020-03-05 Hoffmann et al SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor
Cell
IV. Other The average of three independent experiments performed with triplicate samples is shown.
2020-03-10 Gao et al Prognostic value of NT-proBNP in patients with severe COVID-19
medrxiv
III-3. Time Series Analysis

After screening out the ineligible cases, 54 patients were analyzed in this study.
Data collection of laboratory results were defined using the first-time examination at admission.
2020-03-13 Verity et al Estimates of the severity of COVID-19 disease
medrxiv
IV. Prevalence Study

We used data from 169 recovered individuals with reported recovery dates and reported/imputed onset dates to estimate the onset to recovery distribution.
The only such data providing an assessment of the level of infection in a subset of the population not presenting with symptoms at present is therefore the PCR infection prevalence surveys conducted in international residents of Wuhan that have been repatriated to their home country.
2020-03-14 Li et al High sensitivity detection of coronavirus SARS-CoV-2 using multiplex PCR and a multiplex-PCR-based metagenomic method
biorxiv
IV. Computer Model In addition, optional sequencing can provide further confirmation as well as phylogenetic information of the identified virus(es) for specific strain discrimination, which will be of paramount importance for surveillance purposes that represent a global health imperative.
2020-03-16 Yang et al Rational evaluation of various epidemic models based on the COVID-19 data of China
medrxiv
IV. Computer Model Detailed analyses, comparisons and evaluations among various epidemic models are carried out in Section III.
2020-03-19 Arshad Ali et al The outbreak of Coronavirus Disease 2019 (COVID-19)—An emerging global health threat
Journal of Infection and Public Health
III-3. Time Series Analysis

In 2002, a pandemic of SARS occurred endangering the lives of 8098 individuals with a mortality of 774 patients .
The samples drawn from these individuals were sent for laboratory analyses.
2020-03-20 Gautret et al Hydroxychloroquine and azithromycin as a treatment of COVID-19: results of an open-label non-randomized clinical trial
International Journal of Antimicrobial Agents
IV. Other Each day, patients received a standardized clinical examination and when possible, a nasopharyngeal sample was collected.
2020-03-20 GAUTRET et al Hydroxychloroquine and Azithromycin as a treatment of COVID-19: preliminary results of an open-label non-randomized clinical trial
medrxiv
IV. Other Each day, patients received a standardized clinical examination and when possible, a nasopharyngeal sample was collected.
2020-03-20 OKBA et al SARS-CoV-2 specific antibody responses in COVID-19 patients
medrxiv
III-3. Time Series Analysis

All three COVID-19 patients had reactive antibodies by both the IgG (6/10 serum samples) and IgA (7/10 serum samples) ELISAs (Figure 3) .
Overall, the assays developed and validated in this study could be instrumental for patient contact tracing, serosurveillance studies, as well as vaccine evaluation studies.
2020-03-23 Daughton et al The international imperative to rapidly and inexpensively monitor community-wide Covid-19 infection status and trends
Science of The Total Environment
IV. Other This ability is critical for better informing containment and mitigation strategies as well as for bettertargeting followup diagnostic testing of individuals.
2020-03-23 Rodrigues et al An update on COVID-19 for the radiologist - A British society of Thoracic Imaging statement
Clinical Radiology
IV. Other Guidelines need to be drawn up detailing which patient cohorts have which imaging test.
2020-03-24 Banerjee et al Estimating excess 1- year mortality from COVID-19 according to underlying conditions and age in England: a rapid analysis using NHS health records in 3.8 million adults
medrxiv
IV. Prevalence Study

We included 3,862,012 individuals aged ≥30 years: 1,957, 935 (50.7%) female, 3,331,280 (86.3%) ≤70 years (mean age 43.5 in male and females) and 530732 (13.7%) >70 years (mean age 78.1 in males and 80.2 in females) (Suppl Table 1 ).
Our study had a cohort design with prospective recording of data and follow-up.
2020-03-25 Li et al Clinical observation and management of COVID-19 patients
Emerg Microbes Infect
IV. Other In this case, the current clinical studies are not as rigorous as the traditional clinical trials, but they help draw a quick initial result which can help with the following study design.
2020-03-26 Lourenco et al Fundamental principles of epidemic spread highlight the immediate need for large-scale serological surveys to assess the stage of the SARS-CoV-2 epidemic
medrxiv
IV. Other Urgent development and assessment of such tests should be followed by rapid implementation at scale to provide real-time data.
2020-03-26 Zhang et al COVID-19 infection induces readily detectable morphological and inflammation-related phenotypic changes in peripheral blood monocytes, the severity of which correlate with patient outcome
medrxiv
III-3. Time Series Analysis

Of the 28 COVID-19 patients included in this study, three were admitted to the ICU.
Conclusions: The detection and serial monitoring of this subset of inflammatory monocytes using flow cytometry could be of great help in guiding the prognostication and treatment of patients with COVID-19 and merits further evaluation.
2020-03-26 Santarpia et al Transmission Potential of SARS-CoV-2 in Viral Shedding Observed at the University of Nebraska Medical Center
medrxiv
IV. Other Because sampling 25 personnel were allowed to use judgement and feedback from patients when collecting samples, between 5 and 16 samples were collected from each room, with a mean of 7.35 samples per room and a mode of 6 samples per room.

Further experiments are ongoing to determine viral activity in these samples.
2020-03-26 Rios et al Guidelines for preventing respiratory illness in older adults aged 60 years and above living in long-term care: A rapid review of clinical practice guidelines
medrxiv
IV. Prevalence Study

If one or more respiratory samples from ILI cases in a suspected outbreak returns a positive laboratory result for influenza, then an influenza outbreak is confirmed.
The laboratory where specimens will be sent for testing, if needed.
2020-03-26 Fauver et al Coast-to-coast spread of SARS-CoV-2 in the United States revealed by genomic epidemiology
medrxiv
IV. Prevalence Study

A total of 10 samples from 10 different individuals with cycle-threshold (CT) values less than 35 were selected to move forward with next generation sequencing (NGS).
Our complete workflow included RNA extraction, PCR testing, validation of PCR results, library preparation, sequencing, and live base calling and read mapping.
2020-03-27 Wynants et al Systematic review and critical appraisal of prediction models for diagnosis and prognosis of COVID-19 infection
medrxiv
I. Systematic Review

Based on nine of the 15 studies that reported study dates, data were collected between 8 th December 2019 and 3 rd March 2020.
24 Since the seven imaging studies used either case-control sampling or the method of data collection was unclear, the prevalence in these diagnostic studies may not have been representative of their target population.
2020-03-27 Wei et al How should we implement radiotherapy for cancer patients in China during the endemic period of COVID-19?
Radiotherapy and Oncology
IV. Other Further studies are warranted to determine the optimal isolation period so that clinicians can provide timely and continuous treatment for cancer patients without risking the spread of COVID-19.
2020-03-30 Ebrahimi et al Laboratory findings, signs and symptoms, clinical outcomes of Patients with COVID-19 Infection: an updated systematic review and meta-analysis
medrxiv
I. Systematic Review

The 12 studies obtained from the literature, of which 58.3% of studies were case-control, and 41.7% remaining studies were designed as cross-sectional.
The aim of the current survey is collecting laboratory findings, analysis them and reporting a specific pattern for help to COVID-19 diagnosis.
2020-03-30 An et al Clinical characteristics of the recovered COVID-19 patients with re-detectable positive RNA test
medrxiv
IV. Other Future studies should reduce RP occurrence through using hyper-sensitive detection kit with hyper-specificity, combining detection of multiple samples with more immune markers.
2020-03-30 Xu et al Analysis and Prediction of False Negative Results for SARS-CoV-2 Detection with Pharyngeal Swab Specimen in COVID-19 Patients: A Retrospective Study
medrxiv
III-2. Retrospective Cohort

In order to implement the out-of-sample prediction, 1,324 patients were randomly divided into training (1,059 cases) and validation samples (265 cases Table 2) .
The training and validation were conducted on the same testing and validation samples.
2020-03-30 Xie et al Development and external validation of a prognostic multivariable model on admission for hospitalized patients with COVID-19
medrxiv
III-2. Retrospective Cohort

Second cohort of 151 patients admitted to Jinyintan hospital who were included in a previous study were reused for model validation.
After further external validation in different countries the model will enable better risk stratification and more targeted management of patients with COVID-19.
2020-03-30 Zeng et al Risk assessment of progression to severe conditions for patients with COVID-19 pneumonia: a single-center retrospective study
medrxiv
IV. Other The testing was performed on blood samples collected immediately after hospital admission.
2020-03-30 Dong et al Understand Research Hotspots Surrounding COVID-19 and Other Coronavirus Infections Using Topic Modeling
medrxiv
IV. Computer Model The selected model was used for all subsequent analyses.
2020-03-31 Li et al The epidemic of 2019-novel-coronavirus (2019-nCoV) pneumonia and insights for emerging infectious diseases in the future
Microbes and Infection
IV. Prevalence Study

11 January 2020 41 patients have been diagnosed to have infection of the novel coronavirus, with 763 close contacts, 7 severe cases and the first death.
First of all, Chinese health authorities conducted an immediate investigation to characterize and control the disease, including isolation of suspected patients, monitoring of contact clinical status of patients, and developing diagnostic and treatment procedures .
2020-03-31 Clementi et al Combined prophylactic and therapeutic use maximizes hydroxychloroquine anti-SARS-CoV-2 effects in vitro
biorxiv
IV. Other In this atypical context, in which on-field medicine often anticipates experimental laboratory pre-clinic, there is urgent need of prompt experiments addressing specific clinical questions.
2020-04-01 Vogels et al Analytical sensitivity and efficiency comparisons of SARS-COV-2 qRT-PCR assays
medrxiv
IV. Prevalence Study Analytical comparisons of qRT-PCR primer and probe sets Critical evaluations of the designed primer-probe sets used in the primary SARS-CoV-2 qRT-PCR detection assays are necessary to compare findings across studies, and select appropriate assays for in-house testing.

7 Separation of assay development issues from instruments, and the role of the private sector to help quickly migrate assays onto those devices.

7.0.0.1 Highlights

7.0.0.2 Articles

Date Authors Title LOE(?) & Sample Matches
2020 Allam et al On the Coronavirus (COVID-19) Outbreak and the Smart City Network: Universal Data Sharing Standards Coupled with Artificial Intelligence (AI) to Benefit Urban Health Monitoring and Management
Healthcare
IV. Prevalence Study The fact that cities are increasingly tuning on the concept of Smart Cities and boasting an increased adoption rate of technological and connected products, existing surveillance networks can be re-calibrated to make use of those new sets of databases.
2020-01-23 Corman et al Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR
Euro Surveill
IV. Prevalence Study

To show that the assays can detect other bat-associated SARS-related viruses, we used the E gene assay to test six batderived faecal samples available from Drexler et al.
In all of these situations, virus isolates were available as the primary substrate for establishing and controlling assays and assay performance.
2020-02-04 Zhang et al Recent advances in the detection of respiratory virus infection in humans
Journal of Medical Virology
IV. Other Conventional diagnostic tests, such as the assays for rapid detection of antiviral antibodies or viral antigens, are widely used in many clinical laboratories.
2020-02-11 Khan et al Novel coronavirus: how things are in Wuhan
Clinical Microbiology and Infection
IV. Other In some places, rapid measurement kits are not available.
2020-02-23 Zhai et al From Isolation to Coordination: How Can Telemedicine Help Combat the COVID-19 Outbreak?
medrxiv
IV. Other The platform could aggregate COVID-19 patient records across 126 connected hospitals and rapidly expand to enable open collaborations with key stakeholders such as government authorities, research institutions and laboratories.
2020-02-24 Lamb et al Rapid Detection of Novel Coronavirus (COVID-19) by Reverse Transcription-Loop-Mediated Isothermal Amplification
medrxiv
IV. Other However other groups are working at improving the read outs of RT-LAMP assays including the use of smartphone-integrated sensors to make interpretation of the assay even more user-friendly.
2020-02-28 Fadel et al Coronavirus outbreak: the role of companies in preparedness and responses
The Lancet Public Health
IV. Other Public and private companies must continue to produce or provide their services, but with consideration of the health context.

All health professionals should be involved in the development and implementation of recommendations for companies and their environments
2020-02-29 Zhang et al Rapid Molecular Detection of SARS-CoV-2 (COVID-19) Virus RNA Using Colorimetric LAMP
medrxiv
IV. Prevalence Study

In addition to controls, a total of 7 patient RNA samples were tested, 6 of which were determined to be positive by RT-qPCR using ORF1a primers (C q 25-36.5, Table 2 ) and 4 positive with Gene N primers.
These molecular methods include metagenomics sequencing mNGS and RT-qPCR , both are excellent and sensitive techniques, but approaches not without limitations.
2020-03-01 Shen et al Recent advances and perspectives of nucleic acid detection for coronavirus
Journal of Pharmaceutical Analysis
IV. Prevalence Study The LAMP assay is rapid and does not require expensive reagents or instruments.

Afterwards, the PCR is performed and followed by the detection of PCR product through specific detection methods or instruments.
2020-03-02 Metsky et al CRISPR-based surveillance for COVID-19 using genomically-comprehensive machine learning design
biorxiv
IV. Prevalence Study Assay designs are available at https://adapt.sabetilab.org/.

Sequences for single assays and multiplex panels are available at .
2020-03-04 Chang et al Weaponized Interdependence: China's Economic Statecraft and Social Penetration against Taiwan
Orbis
IV. Prevalence Study The three targets, Silicon Precision Industries Co. (SPIC), Powertech Technology Inc., and ChipMOS Technologies Inc., are all leading chip packing and testing companies in the global arena.
2020-03-05 Li et al Molecular immune pathogenesis and diagnosis of COVID-19
Journal of Pharmaceutical Analysis
IV. Prevalence Study

Virus genome sequencing of five patients with pneumonia hospitalized from December 18 to December 29, 2019, revealed the presence of a previously unknown β-CoV strain in all of them .
After the outbreak of SARS-CoV-2 in China, many companies soon launched RT-qPCR test kits for clinical diagnosis.
2020-03-06 Wang et al Nanopore target sequencing for accurate and comprehensive detection of SARS-CoV-2 and other respiratory viruses
medrxiv
IV. Other The introduction of integration systems or 280 sealed devices such as microfluidics may avoid this situation 26, 27 .
2020-03-10 Chan et al Research Frontiers of Health Emergency and Disaster Risk Management: What Do We Know So Far?
Int J Environ Res Public Health
IV. Prevalence Study Existing surveillance databases, new study tools, and innovation methodologies may help to identify population health risks and support Health-EDRM policy development.
2020-03-12 Park et al Development of Reverse Transcription Loop-mediated Isothermal Amplification (RT-LAMP) Assays Targeting SARS-CoV-2
biorxiv
IV. Other Diagnosis of COVID-19 is currently performed by RT-qPCR methods, but the capacity of RT-qPCR methods is limited by its requirement of high-level facilities and instruments.
2020-03-14 Lagier et al Testing the repatriated for SARS-Cov2: Should laboratory-based quarantine replace traditional quarantine?
Travel Medicine and Infectious Disease
IV. Other Tests were performed on LightCycler 480 instruments (Roche Diagnostics).
2020-03-18 Legido-Quigley et al The resilience of the Spanish health system against the COVID-19 pandemic
The Lancet Public Health
IV. Other These shortages have encouraged profiteering, with private laboratories, for example, charging exorbitant amounts for tests.
2020-03-18 dong et al Highly accurate and sensitive diagnostic detection of SARS-CoV-2 by digital PCR
medrxiv
IV. Other To determine the LoD of N and E assay, 83 measurements of E assay on 5 samples and 71 measurements of N assay on 4 samples were performed in 4 different runs.
2020-03-20 Dewey et al Supporting Clinicians During the COVID-19 Pandemic
Ann Intern Med
IV. Other Leaders should also take initiatives to provide basic provisions during work hours, such as easy access to water, healthy snacks, chargers for phones and other devices, and toiletries.
2020-03-20 Amrane et al Rapid viral diagnosis and ambulatory management of suspected COVID-19 cases presenting at the infectious diseases referral hospital in Marseille, France, - January 31st to March 1st, 2020: A respiratory virus snapshot
Travel Medicine and Infectious Disease
IV. Other This Institute also includes five large NSB3 laboratories with a total area of 1,200 m 2 , on four floors with diagnostic laboratories, research laboratories, and technological platforms .
2020-03-20 Kriz et al Teaching-practice as a critical bridge for narrowing the research-practice gap
Industrial Marketing Management
III-3. Time Series Analysis

The wicked problem sessions attract over 40 participants (policy, practitioners, academics), with action research/ learning sessions limited to approximately 12 participants (practitioners and researchers).
Practitioners have participated in such programs as have government field workers, helping diffuse benefits of these interventions more broadly.

Tools and modules have been developed to assist students in quickly understanding and applying theory to the live businesses, with standout students selected by the SMEs to enter internships.
2020-03-21 Hsieh et al Putting resiliency of a health system to the test: COVID-19 in Taiwan
Journal of the Formosan Medical Association
IV. Other Real-time display of mask availability in local pharmacies across the country was quickly established by the public and private sector.
2020-03-23 Mao et al Can a Paper-Based Device Trace COVID-19 Sources with Wastewater-Based Epidemiology?
Environ Sci Technol
IV. Other Paper analytical devices enable multiplexed, sensitive assays that rival PCR laboratory assays and provide high-quality, fast precision diagnostics for pathogens.

Paper analytical devices have emerged as powerful tools for the rapid diagnosis of pathogens and determination of infection transmission.
2020-03-23 Ikizler et al COVID-19 and Dialysis Units: What Do We Know Now and What Should We Do?
American Journal of Kidney Diseases
IV. Other Regulatory agencies should allow temporary changes in telehealth regulations and patient-care regulations such as allowing patients to swiftly move between health systems.
2020-03-23 Zareie et al A model for COVID-19 prediction in Iran based on China parameters
medrxiv
IV. Other Some hospitals use smart systems.
2020-03-24 Hoe GAN et al Preventing intra-hospital infection and transmission of COVID-19 in healthcare workers
Safety and Health at Work
IV. Other All other system components, namely work tasks, technologies and tools, environmental factors and organizational conditions, serve to enable the healthcare worker to perform his or her role safely and effectively.
2020-03-25 Nunez-Bajo et al Ultra-Low-Cost Integrated Silicon-based Transducer for On-Site, Genetic Detection of Pathogens
biorxiv
IV. Other 1 Ability to produce NA quickly also increases the speed of development and deployment of new test kits to health systems, providing much needed diagnostic capabilities for the detection of novel pathogens (such as SARS-CoV-2).
2020-03-25 Armocida et al The Italian health system and the COVID-19 challenge
The Lancet Public Health
IV. Prevalence Study

2 The Lombardy region has the heaviest burden of the COVID-19 pandemic, with (as of March 19, 2020) 19 884 total cases of the disease, 2168 deaths, and 1006 patients requiring advanced respiratory support.
Third, in response to emergencies, solid partnerships between the private and public sector should be institutionalised.
2020-03-25 Khan et al Analysis of Serologic Cross-Reactivity Between Common Human Coronaviruses and SARS-CoV-2 Using Coronavirus Antigen Microarray
biorxiv
IV. Prevalence Study The protein microarray methodology has been widely used to simultaneously perform binding assays against hundreds of antigens printed onto a nitrocellulose-coated slide for detection of multiple antibody isotypes 5 .
2020-03-26 Rios et al Guidelines for preventing respiratory illness in older adults aged 60 years and above living in long-term care: A rapid review of clinical practice guidelines
medrxiv
IV. Prevalence Study

If one or more respiratory samples from ILI cases in a suspected outbreak returns a positive laboratory result for influenza, then an influenza outbreak is confirmed.
Such surfaces include the following: Breathing circuits (including ventilator accessories and any portions of the breathing circuit inside ventilators), suction devices and systems, or any other devices that are exposed to the patient's oral secretions (including contaminated condensate), urine, feces, and other excretions HEPA filtration systems, which are installed systems or portable systems (i.e., mobile high-efficiency-filter air cleaners [MHEFACs]) used to control room air contamination levels and ensure negative pressure in isolation rooms Any handheld items or other items that can be found in beds, including nurse call buttons, remote controls for televisions, pillow speakers, blood pressure cuffs, and telemetry transmitters Highest infection concern.
2020-03-27 Garrett et al COVID-19: the medium is the message
The Lancet
IV. Other The funds could be dispersed, urgently, to the UN agencies' media operations on the front lines, chiefly WHO and UNICEF, both for their direct operations and for secondary dispersal to lead public health offices in resourcescarce countries.
2020-03-27 Yelin et al Evaluation of COVID-19 RT-qPCR test in multi-sample pools
medrxiv
IV. Other As it uses the standard protocols, reagents and equipment, this pooling method can be applied immediately in current clinical testing laboratories.
2020-03-28 Bradley et al A systems approach to preventing and responding to COVID-19
EClinicalMedicine
IV. Other Systems thinking and methods can help achieve this.
2020-03-29 Srinivasan et al Individualized System for Augmenting Ventilator Efficacy (iSAVE): A Rapidly deployable system to expand ventilator capacity
biorxiv
IV. Other Leveraging offthe-shelf components, the iSAVE can facilitate a rapid expansion of the ventilation capacity of hospitals.
2020-03-30 Li et al Electrophysiology in the time of coronavirus: coping with the great wave.
medrxiv
IV. Prevalence Study Companies which supply equipment have shut offices and distribution networks.
2020-03-30 Sinnott-Armstrong et al Evaluation of Group Testing for SARS-CoV-2 RNA
medrxiv
IV. Prevalence Study Many SARS-CoV-2 testing laboratories are using pipetting robots to rapidly and accurately scale RNA extractions and assays to large numbers of individuals.

Grouped testing, particularly with an iterative test as here, uses more consumables, such as pipette tips, than traditional methods per test.

Hospitals, government offices, corporations, and educational institutions, across which many individuals cannot work from home , require self-isolation following positive results.
2020-03-30 Lin et al Which Measures are Effective in Containing COVID-19? Empirical Research Based on Prevention and Control Cases in China
medrxiv
IV. Prevalence Study The price of this is to force companies and other institutions to stop operations, which is at huge cost.
2020-03-30 Zhou et al Improved deep learning model for differentiating novel coronavirus pneumonia and influenza pneumonia
medrxiv
IV. Prevalence Study

Methods: 35 confirmed NCP cases were consecutively enrolled as training set from 1138 suspected patients in three NCP designated hospitals together with 361 confirmed viral pneumonia patients from center one including 156 IP patients, from May, 2015 to February, 2020.
The error rates of both schemes for the two CT devices (SOMATOM Definition Flash and LightSpeed VCT) from Center 6 were exceptionally high compared to all other CT devices.
2020-03-31 Yamey et al Ensuring global access to COVID-19 vaccines
The Lancet
IV. Other The rudiments of the system would require a global purchasing agent or agents, a substantial but limited-term advanced purchase commitment, and access through the system to financial instruments such as concessional loans or grants and indemnification from liability to offset the risks taken by participating private sector partners.

With sufficient political will and public sector financing, such a system could be established using existing instruments and institutions.
2020-03-31 Singer et al What is ahead for health policy and technology in the 2020s?
Health Policy and Technology
IV. Other Trade and tariff barriers arising from evolving isolationist policies of the USA are also likely to restrict progress on implementation and the health impact of achieving the UN's Sustainable Development Goals, not least through increased international costs of diagnostics, devices and medicines.
2020-04-01 Abhari et al COVID-19 Epidemic in Switzerland: Growth Prediction and Containment Strategy Using Artificial Intelligence and Big Data
medrxiv
IV. Other The economic slowdown and the transition in the use of Switzerland's public and private transportation system are also .
2020-04-30 Lubowitz et al AANA20: The 2020 Annual Meeting of the Arthroscopy Association of North America
Arthroscopy: The Journal of Arthroscopic & Related Surgery
IV. Other Socially, the Welcome Reception in the exhibit hall, morning breakfasts, afternoon "Devices and Desserts," and venerated coffee breaks allow meeting attendeesdfrom members to residents and fellows, to those dipping a toe in the AANA pooldto mix, mingle, reacquaint, and forge new friendships.

8 Efforts to track the evolution of the virus (i.e., genetic drift or mutations) and avoid locking into specific reagents and surveillance/detection schemes.

8.0.0.1 Highlights

8.0.0.2 Articles

Date Authors Title LOE(?) & Sample Matches
2020 Yu et al Genomic analysis of a 2019-nCoV strain in the first COVID-19 patient found in Hangzhou, Zhejiang, China
Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]
IV. Other Fifteen genomes from Wuhan were grouped by mutation sites and others were identified by Wuhan's or specific mutation sites.
2020 GUO et al Comparison and analysis of the detection performance of six new coronavirus nucleic acid detection reagents
Chongqing Medicine
IV. Other The reproducibility of in-batch detections by C reagent was the best, and the CT values of F reagents (N and ORF1ab), E reagents (ORF1ab) and A reagents (ORF1ab) showed changes in trend.
2020 Voice from China: nomenclature of the novel coronavirus and related diseases
Chin Med J (Engl)
IV. Other In more recent times, genetic sequence-based tests have advanced, and such genotyping tests have been able to provide a more rapid and precise typing approach than serological tests.
2020 Cao et al Comparative genetic analysis of the novel coronavirus (2019-nCoV/SARS-CoV-2) receptor ACE2 in different populations
Cell Discovery
IV. Prevalence Study The mutations in these residues were not found in different populations in our study.
2020 Kock et al 2019-nCoV in context: lessons learned?
The Lancet Planetary Health
IV. Prevalence Study These viruses have high mutation and gene recombination rates, making them ideal for pathogen evolution.
2020-01-23 Corman et al Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR
Euro Surveill
IV. Prevalence Study

To show that the assays can detect other bat-associated SARS-related viruses, we used the E gene assay to test six batderived faecal samples available from Drexler et al.
All assays were subjected to replicate testing in order to determine stochastic detection frequencies at each assay's sensitivity end point ( Figure 3A and B).
2020-01-30 Ramaiah et al Insights into Cross-species Evolution of Novel Human Coronavirus 2019-nCoV and Defining Immune Determinants for Vaccine Development
biorxiv
IV. Prevalence Study This nCoV genotype might have been evolved from a bat-CoV by accumulating non-synonymous mutations, indels, and recombination events.
2020-02-11 Gorbalenya et al Severe acute respiratory syndrome-related coronavirus: The species and its viruses – a statement of the Coronavirus Study Group
biorxiv
IV. Other Commonly this evaluation is conducted in silico using phylogenetic analysis that may be complicated by uneven rates of evolution that vary across different virus lineages and genomic sites due to mutation, including exchange of genome regions in closely related viruses (homologous recombination).
2020-02-14 Kiselev et al Current Trends in Diagnostics of Viral Infections of Unknown Etiology
Viruses
IV. Prevalence Study

They used 42 virus-positive controls from pediatric patients and 67 unidentified samples .
The search for viral pathogens is often impeded by their genetic variability, caused by a multitude of factors: gene duplications and exchanges, frequent single-nucleotide mutations, gene-large insertions and rapid adaptation of viruses to new hosts.
2020-02-18 Patino-Galindo et al Recombination and lineage-specific mutations led to the emergence of SARS-CoV-2
biorxiv
IV. Prevalence Study Recombination and lineage-specific mutations led to the emergence of SARS-CoV-2
2020-02-20 Grifoni et al Candidate targets for immune responses to 2019-Novel Coronavirus (nCoV): sequence homology- and bioinformatic-based predictions
biorxiv
IV. Prevalence Study This approach was designed and validated to predict dominant epitopes independently of ethnicity and HLA polymorphism, taking advantage of the extensive cross-reactivity and repertoire overlap between different HLA class II loci and allelic variants.
2020-02-24 Lamb et al Rapid Detection of Novel Coronavirus (COVID-19) by Reverse Transcription-Loop-Mediated Isothermal Amplification
medrxiv
IV. Other Given that viruses are prone to genetic mutation, we likewise examined if RT-LAMP primers had any mismatch with 27 different isolated strains of COVID-19 from various locations.
2020-02-26 Liu et al No credible evidence supporting claims of the laboratory engineering of SARS-CoV-2
Emerg Microbes Infect
IV. Other Evolution is stepwise and accrues mutations gradually over time, whereas synthetic constructs would typically use a known backbone and introduce logical or targeted changes instead of the randomly occurring mutations that are present in naturally isolated viruses such as bat CoV RaTG13.
2020-02-26 Robson et al Computers and viral diseases. Preliminary bioinformatics studies on the design of a synthetic vaccine and a preventative peptidomimetic antagonist against the SARS-CoV-2 (2019-nCoV, COVID-19) coronavirus
Computers in Biology and Medicine
IV. Other Table 1 shows the one letter amino acid code used for peptide and protein primary structure throughout the study and in the following text, and also shows a consensus over conservative substitutions in the course of evolution (as accepted mutations), with common secondary structure propensities, and as alternatives in peptide design, i.e.
2020-02-27 Li et al Epitope-based peptide vaccine design and target site characterization against novel coronavirus disease caused by SARS-CoV-2
biorxiv
IV. Other No mutations were observed in all the selected B- and T-cell epitopes across all isolates from different locations worldwide.
2020-02-27 Okada et al Early transmission patterns of coronavirus disease 2019 (COVID-19) in travellers from Wuhan to Thailand, January 2020
Euro Surveill
IV. Other Within-outbreak sequence divergence is generally low with 0-9 nt differences over the whole genome and mutations unique to individual strains are possibly related to quality differences of the samples and noise of the methods used for sequencing.
2020-03-02 Lv et al Comparative genomic analysis revealed specific mutation pattern between human coronavirus SARS-CoV-2 and Bat-SARSr-CoV RaTG13
biorxiv
IV. Prevalence Study According to random drift hypothesis , these nucleotide mutations among different SARS-CoV-2 strains now available are still determined by neutral evolution.

The adaptive evolution server ( was used to identify eventual sites of positive selection.

Gene mutations such as nucleotide substitutions, deletions and insertions have been frequently reported when comparing SARS-CoV-2 with other viruses .
2020-03-02 Wu et al Mutations, Recombination and Insertion in the Evolution of 2019-nCoV
biorxiv
IV. Other Based on 15 these potentially inheritable mutations and the identifying times and locations, we generated a mutation tree map to track individual shared mutations and show the relationships among different isolates (Fig 2A and S2 ).

Through comprehensive analysis of the available genome sequences of 2019-nCoV strains, we have tracked multiple inheritable SNPs and determined the evolution of 2019-nCoV relative to other coronaviruses.ResultsSystematic analysis of 120 genomic sequences of 2019-nCoV revealed co-circulation of two genetic subgroups with distinct SNPs markers, which can be used to trace the 2019-nCoV spreading pathways to different regions and countries.
2020-03-03 Yang et al The deadly coronaviruses: The 2003 SARS pandemic and the 2020 novel coronavirus epidemic in China
Journal of Autoimmunity
IV. Prevalence Study

In Wang's study , of the 36 patients in the ICU, four patients received high-flow oxygen therapy, 15 patients received non-invasive ventilation, and 17 patients received invasive ventilation (four patients switched to ECMO).
Sampling techniques, extraction and detection of viral nucleic acids, and diagnostic reagents may affect the test results.
2020-03-04 Wu et al Strong evolutionary convergence of receptor-binding protein spike between COVID-19 and SARS-related coronaviruses
biorxiv
IV. Other We used the CONVERG2 31 program to evaluate the probabilities that the observed convergent and parallel substitutions were due to random chance.
2020-03-06 Wang et al Nanopore target sequencing for accurate and comprehensive detection of SARS-CoV-2 and other respiratory viruses
medrxiv
IV. Other Although this was 244 a silent mutation, its presence suggests that the virus may have undergone mutation during the 245 spreading process.
2020-03-07 Tan et al Novel Immunoglobulin Domain Proteins Provide Insights into Evolution and Pathogenesis Mechanisms of SARS-Related Coronaviruses
biorxiv
IV. Prevalence Study These genes often rapidly diversify through recombination and mutations to keep up with 128 the evolution of host resistance.
2020-03-10 Jenkins et al In silico approach to accelerate the development of mass spectrometry-based proteomics methods for detection of viral proteins: Application to COVID-19
biorxiv
IV. Prevalence Study PRM methods monitor multiple transitions simultaneously but at a time cost.
2020-03-11 Grewelle et al Larger viral genome size facilitates emergence of zoonotic diseases
biorxiv
IV. Other Mutations and recombination events have been explored as a source of this variability.

Emergence of new viral diseases is linked to mutation or recombination events.

Viral zoonoses can emerge as a result of large genetic changes associated with recombination or significant mutation-both more likely to occur in large genomes.
2020-03-13 Wang et al The establishment of reference sequence for SARS-CoV-2 and variation analysis
Journal of Medical Virology
IV. Other These findings suggested that there may be selective mutations in SARS-COV-2, and it is necessary to avoid certain regions when designing primers and probes.
2020-03-13 Xi et al Virus strain of a mild COVID-19 patient in Hangzhou representing a new trend in SARS-CoV-2 evolution related to Furin cleavage site
medrxiv
IV. Other Sequence alignment analysis suggested that ZJ01 had 38 mutation sites compared with other SARS-CoV-2 family members (Fig 2A) , in which 35 mutations were unique to ZJ01, including 7 deletions, 4 insertions and 24 substitutions.
2020-03-15 Ye et al Zoonotic origins of human coronaviruses
Int J Biol Sci
IV. Prevalence Study In addition, rapid mutation and genetic recombination also drive HCoV evolution and serve as two important steps in this process .
2020-03-16 Grifoni et al A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2
Cell Host & Microbe
IV. Other This approach was designed and validated to predict dominant epitopes independently of ethnicity and HLA polymorphism, taking advantage of the extensive cross-reactivity and repertoire overlap between different HLA class II loci and allelic variants.
2020-03-17 Ou et al RBD mutations from circulating SARS-CoV-2 strains enhance the structural stability and human ACE2 affinity of the spike protein
biorxiv
IV. Other Here, we analyzed the worldwide RBD mutants and found 18 mutant strains fell into 8 mutation types under high positive selection pressure during the spread.
2020-03-17 Zheng et al Deep Learning-based Detection for COVID-19 from Chest CT using Weak Label
medrxiv
IV. Other During the procedure of testing, data augmentation strategies were not applied.
2020-03-20 Bandoy et al Pandemic dynamics of COVID-19 using epidemic stage, instantaneous reproductive number and pathogen genome identity (GENI) score: modeling molecular epidemiology
medrxiv
IV. Prevalence Study

Probability of further disease spread is evaluated based on the threshold value to 3.9) using serial intervals for 424 patients in Wuhan, China 4 .
Rapidly evolving pathogens undergo genome 142 sequence mutation, selection pressure, random drift and stochastic events between infected 143 individuals 11 .
2020-03-23 Armijos-Jaramillo et al SARS-CoV-2, an evolutionary perspective of interaction with human ACE2 reveals undiscovered amino acids necessary for complex stability
biorxiv
IV. Prevalence Study In order to detect branches and sites under positive/negative selection, two datasets were explored.
2020-03-27 Skums et al Global transmission network of SARS-CoV-2: from outbreak to pandemic
medrxiv
IV. Prevalence Study internal nodes correspond to mutations (columns of the mutation matrix), with the root representing the zero mutation (the absence of mutations);

whenever for each pair of columns in the mutation matrix M , there are no 4 sequences that have all possible combinations of alleles , , , at that positions.

If we remove the SNVs corresponding to vertices of G 4g , then the remaining mutation matrix M can be explained without any repeated mutations.

Next, genomic positions without variation have been removed, leaving m = 274 single nucleotide variants (SNVs) for further analysis.
2020-03-27 Dilucca et al Codon usage and evolutionary rates of the 2019-nCoV genes
biorxiv
IV. Prevalence Study Genes M and E show quite low slopes, indicating that these proteins tend to evolve slowly by 165 accumulating nucleotide mutations on their genes.
2020-03-27 Liebig et al The current state of COVID-19 in Australia: importation and spread
medrxiv
III-3. Time Series Analysis

The outbreak has quickly spread to more than 100 countries reporting over 100,000 confirmed cases.
Such seasonal patterns can help authorities plan for travel policies that consider the varying risk of COVID-19 importations into Australia over time from different countries.
2020-03-28 Karamitros et al SARS-CoV-2 exhibits intra-host genomic plasticity and low-frequency polymorphic quasispecies
biorxiv
IV. Prevalence Study

We analyzed NGS data derived from clinical samples of three Chinese patients infected with SARS-CoV-2, in order to identify small- and large-scale intra-host variations in the viral genome.
This indicates that these variations have been occurred in a rather random fashion and are not subject of selective pressures, which is also supported by the fact that the missense mutations were systematically more, compared to the synonymous mutations.
2020-03-30 Wang et al Genetic Profiles in Pharmacogenes Indicate Personalized Drug Therapy for COVID-19
medrxiv
IV. Prevalence Study

As many as 16 clinical trials related to chloroquine, and two clinical trials for mild and common patients and severe patients will be completed on April 30, 2020 (ChiCTR2000029898, ChiCTR2000029899), each clinical trial includes a total of 100 participants.
Although the mutations distributed in all gene regions, the most common mutation types were intronic, non-synonymous and synonymous mutations ( Figure 3A ).

In addition, these mutations distributed in all gene regions and most of them were rare variations ( Figure 3D ).
2020-04-01 Xie et al Insight into 2019 novel coronavirus — an updated intrim review and lessons from SARS-CoV and MERS-CoV
International Journal of Infectious Diseases
IV. Prevalence Study The 2019-nCoV should be monitored of any possible gene variation of antigenic drift or antigenic conversion, to avoid another round of outbreak.
2020-04-01 Vogels et al Analytical sensitivity and efficiency comparisons of SARS-COV-2 qRT-PCR assays
medrxiv
IV. Prevalence Study As viruses evolve during outbreaks, nucleotide substitutions can emerge in primer or probe binding regions that can alter the sensitivity of PCR assays.
2020-04-01 Sultan et al AGA Institute Rapid Recommendations for Gastrointestinal Procedures During the COVID-19 Pandemic
Gastroenterology
I. Systematic Review

58, 59 First, the systematic reviews by Offeddu et al included a meta-analysis of 3 observational studies that showed a benefit in using N95 respirators over standard masks in protecting health care workers from SARS (OR = 0.86; 95% CI: 0.
Moreover, as innovations in testing (rapid tests, serologic tests of immunity) and treatment or vaccines allow for better risk stratification, one may be able to consider restarting non-time sensitive procedures.
2020-08-31 Li et al Genetic evolution analysis of 2019 novel coronavirus and coronavirus from other species
Infection, Genetics and Evolution
IV. Other Mutations of different SARS-CoV-2 isolates mainly occurs in five genes, including S, N, ORF8, ORF3a, and ORF1ab, with about 42% of the variations are non-synonymous mutation ).

9 Latency issues and when there is sufficient viral load to detect the pathogen, and understanding of what is needed in terms of biological and environmental sampling.

9.0.0.1 Highlights

9.0.0.2 Articles

Date Authors Title LOE(?) & Sample Matches
2020 Wang et al Science in the fight against the novel coronavirus disease
Chin Med J (Engl)
II. Randomized Controlled Trial

They performed a metagenomic analysis of respiratory tract specimens obtained from five patients suffering from the pneumonia in question and identified the virus now known as 2019-nCoV as the causative agent.
Attention should be paid to the spectrum of disease severity and transmission modes to address questions such as how to identify the proportion of asymptomatic infections and whether a patient is contagious during the incubation period.
2020 Kampf et al Potential role of inanimate surfaces for the spread of coronaviruses and their inactivation with disinfectant agents
Infection Prevention in Practice
IV. Other Although the viral load of coronaviruses on inanimate surfaces is not known during an outbreak situation it seems plausible to reduce the viral load on surfaces by disinfection, especially on frequent touch surfaces in the immediate patient surrounding where the highest viral load can be expected.
2020 LING et al Persistence and clearance of viral RNA in 2019 novel coronavirus disease rehabilitation patients
Chinese Medical Journal
IV. Other Conclusions: In brief, as the clearance of viral RNA in patients’ stools was delayed compared to that in oropharyngeal swabs, it is important to identify viral RNA in feces during convalescence.
2020 Chen et al Pathogenicity and Transmissibility of 2019-nCoV—A Quick Overview and Comparison with Other Emerging Viruses
Microbes and Infection
IV. Other Although it remains unclear whether those without symptoms have high enough viral titers for spreading the virus, great attention should be paid to minimize related risks.
2020 Sun et al Potential Factors Influencing Repeated SARS Outbreaks in China
International Journal of Environmental Research and Public Health
IV. Computer Model Therefore, relative to temperature, low humidity seems to be a more critical environmental factor influencing outbreak of human coronavirus disease.
2020-02-11 Hellewell et al Feasibility of controlling 2019-nCoV outbreaks by isolation of cases and contacts
medrxiv
IV. Computer Model When the pathogen has infectiousness before symptom onset, control of outbreaks using contact tracing and isolation is more challenging.
2020-02-13 Cowling et al Epidemiological research priorities for public health control of the ongoing global novel coronavirus (2019-nCoV) outbreak
Euro Surveill
IV. Other Data on viral shedding dynamics could help in assessing duration of infectiousness.
2020-02-14 Kiselev et al Current Trends in Diagnostics of Viral Infections of Unknown Etiology
Viruses
IV. Prevalence Study

They used 42 virus-positive controls from pediatric patients and 67 unidentified samples .
In essence, it offers the means to investigate the taxonomic diversity of a microbial community in an environmental or biological sample as the entirety of present nucleic acids is studied.
2020-02-20 Kim et al Viral Load Kinetics of SARS-CoV-2 Infection in First Two Patients in Korea
J Korean Med Sci
IV. Other Here, we present the viral load kinetics of the first two confirmed patients with mild to moderate illnesses in Korea in whom distinct viral load kinetics are shown.
2020-02-21 Chang et al Coronavirus Disease 2019: Coronaviruses and Blood Safety
Transfusion Medicine Reviews
IV. Prevalence Study

In a study on the viral load in different samples among 37 MERS patients, investigators found that nearly half of serum samples tested yielded a viral RNA signal during the first week after diagnosis and that the viral load ranged from about 2.1×10 2 to 2.51×10 5 copies/mL.
The viral load level rose fast, and the maximal viral load was at around day 4 or day 5 after the onset of fever, after which the viral load quickly decreased.
2020-02-26 Liao et al The landscape of lung bronchoalveolar immune cells in COVID-19 revealed by single-cell RNA sequencing
medrxiv
IV. Prevalence Study

At the individual levels, we also found the higher T cell clonality was consistently remained in the 3 mild patients as compared to the 3 severe patients ( Figure 4D ), supporting that highly expanded CD8 + T cell participated in resolving the SARS-CoV-2 infection.
We assumed that these viral transcripts were likely ambient contaminations of viral loads in the BALF.
2020-02-26 Ji et al TWIRLS, an automated topic-wise inference method based on massive literature, suggests a possible mechanism via ACE2 for the pathological changes in the human host after coronavirus infection
medrxiv
IV. Prevalence Study Therefore, TWIRLS clusters CSSEs according to the rules defined by CSHG distribution, as genetic level research can accurately answer and solve physiological and pathological problems.
2020-03-02 Ji et al TWIRLS, an automated topic-wise inference method based on massive literature, suggests a possible mechanism via ACE2 for the pathological changes in the human host after coronavirus infection
biorxiv
IV. Prevalence Study Therefore, TWIRLS clusters CSSEs according to the rules defined by CSHG distribution, as genetic level research can accurately answer and solve physiological and pathological problems.
2020-03-06 Kraemer et al The effect of human mobility and control measures on the COVID-19 epidemic in China
medrxiv
IV. Computer Model Further, more work will be necessary to understand the differential risk of severe or symptomatic disease to fully understand the age and sex distributions in this outbreak.
2020-03-06 Al-Tawfiq et al Diagnosis of SARS-CoV-2 Infection based on CT scan vs. RT-PCR: Reflecting on Experience from MERS-CoV
Journal of Hospital Infection
IV. Other When considering the viral load in samples, it has shown that upper respiratory tract samples have their peak viral loads 3 days after onset of symptoms, and that nasal, rather than throat samples have the highest viral loads .
2020-03-08 Zhao et al A mathematical model for estimating the age-specific transmissibility of a novel coronavirus
medrxiv
IV. Computer Model Although there was clinical evidence to calculate 259 the parameters related to symptomatic cases such as incubation period, fatality rate, and duration from 260 symptoms onset to diagnosis , more epidemiological data are needed to explore the parameters.
2020-03-09 Tahiri Joutei Hassani et al Le nouveau Coronavirus Covid-19 : quels risques ophtalmiques ?
Journal Français d'Ophtalmologie
IV. Other It would also be useful to take samples from patients in quarantine to determine, in patients who are still asymptomatic but will subsequently develop an infection, at what point in time the virus appears in their tears and in what quantity.
2020-03-11 Zhou et al Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study
The Lancet
III-2. Retrospective Cohort

Before Jan 11, 2020, SARS-CoV-2 RNA detection results were not available in the electronic medical records, from which data for this study were obtained retrospectively; therefore, this study includes 29 of the 41 patients originally reported on.
Third, the estimated duration of viral shedding is limited by the frequency of respiratory specimen collection, lack of quantitative viral RNA detection, and relatively low positive rate of SARS-CoV-2 RNA detection in throatswabs.
2020-03-12 Kujawski et al First 12 patients with coronavirus disease 2019 (COVID-19) in the United States
medrxiv
IV. Prevalence Study

Five patients received only outpatient care and were isolated at home (Patients 1-5), and seven were hospitalized (Patients 6-12) ( Figure 1 ).
More data are needed to better understand how duration of RNA detection, RNA levels, and viable virus are related to symptom progression, illness severity, and transmission.

Serial testing to determine duration of RNA detection and viral shedding is ongoing.

Further investigations are needed to understand clinical course, immunologic response, SARS-CoV-2 RNA detection, virus culture, and transmission, to inform clinical management and public health strategies to prevent disease spread.
2020-03-13 Ghinai et al First known person-to-person transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the USA
The Lancet
IV. Prevalence Study The timing and duration of viral shedding after SARS-CoV-2 infection is unknown.
2020-03-13 Zhang et al Prediction of the COVID-19 outbreak based on a realistic stochastic model
medrxiv
IV. Other our model features the employment of a stochastic dynamic as well as a comprehensive account for the infectious incubation period, the asymptomatic virus carriers, and the medical tracking measure with time latency, which make it probably closer to reality in these aspects.
2020-03-14 Fung et al A tug-of-war between severe acute respiratory syndrome coronavirus 2 and host antiviral defence: lessons from other pathogenic viruses
Emerg Microbes Infect
IV. Prevalence Study

Groups N and P were identified in 13 and 2 individuals, respectively.
The key questions concern how often asymptomatic and presymptomatic virus shedding might occur as well as whether their viral loads could be high.
2020-03-14 Lopez-Rincon et al Accurate Identification of SARS-CoV-2 from Viral Genome Sequences using Deep Learning
biorxiv
IV. Prevalence Study

Next, 115 we removed all the repeated sequences, obtaining a total of 384 unique sequences, with 45 samples belonging to SARS-CoV-2.
This low detection rate can be 15 explained by the variation of viral RNA sequences within virus species, and the viral load in different anatomic sites .
2020-03-15 Yang et al Targeting the Endocytic Pathway and Autophagy Process as a Novel Therapeutic Strategy in COVID-19
Int J Biol Sci
IV. Other More work is thus needed to clarify those important issues.
2020-03-15 Lo et al Evaluation of SARS-CoV-2 RNA shedding in clinical specimens and clinical characteristics of 10 patients with COVID-19 in Macau
Int J Biol Sci
IV. Other Hence, it was impossible to determine whether RNA shedding in specimens correlated to the virus's viability.
2020-03-19 Chen et al Clinical progression of patients with COVID-19 in Shanghai, China
Journal of Infection
IV. Prevalence Study

As of Feb 6, 2020, a total of 249 patients were enrolled in this study.
15 For that reason, studies on the dynamic changes of the viral load are still warranted.
2020-03-21 Munster et al Respiratory disease and virus shedding in rhesus macaques inoculated with SARS-CoV-2
biorxiv
IV. Other Although data on disease in humans are emerging at a steady pace, certain aspects of the pathogenesis of SARS-CoV-2 can only be studied in detail in animal models, where repeated sampling and tissue collection is possible.
2020-03-23 Koo et al Interventions to mitigate early spread of SARS-CoV-2 in Singapore: a modelling study
The Lancet Infectious Diseases
IV. Prevalence Study

20 Asymptomatic individuals were able to infect at a 50% reduced rate compared with their symptomatic counterparts based on estimates from Nishiura and colleagues.
Third, the epidemiological characteristics of COVID-19 remain uncertain in terms of the transmission and infectivity profile of the virus; therefore, estimates of the time between symptom onset and admission to hospital, how infectious an individual is over time, and the asymptomatic rate were based on SARS-CoV.
2020-03-23 Qu et al An Imperative Need for Research on the Role of Environmental Factors in Transmission of Novel Coronavirus (COVID-19)
Environ Sci Technol
IV. Other Taken together, the survival of the COVID-19 virus in different environmental media, including water, PM, dust, and sewage under a variety of environmental parameters warrants systematic investigation immediately.
2020-03-23 Duan et al The feasibility of convalescent plasma therapy in severe COVID-19 patients: a pilot study
medrxiv
II. Randomized Controlled Trial

The neutralizing antibody titers of five patients increased and four patients remained atthe same level after CP transfusion.SARS-CoV-2 RNA, assayed by reverse transcriptase-polymerase chain reaction (RT-PCR), was positive in seven patients and negative in three cases before CP transfusion.
However, the dynamics of the viremia of SARS-CoV-2 was unclear, so the optimal transfusion time point needs to be determined in the future.
2020-03-24 Ma et al Epidemiological parameters of coronavirus disease 2019: a pooled analysis of publicly reported individual data of 1155 cases from seven countries
medrxiv
III-3. Time Series Analysis

For two cases to qualify as an infector-infectee pair and be included in this study, the following two criteria must both be fulfilled.
Specifically, it was aimed to obtain robust estimates of the following epidemiological parameters of COVID-19: 1) incubation period, 2) the upper limit of latent period, as the exact latent period cannot be observed, 3) serial interval, 4) time point of exposure, referring to the day of infectee's exposure to infector relative to the latter's symptom onset date, and 5) R0.

18 Estimation of R0 may require the knowledge of latent period and infectious period, 19, 20 which are both difficult to measure directly.
2020-03-27 Davies et al Age-dependent effects in the transmission and control of COVID-19 epidemics
medrxiv
IV. Computer Model It is critical to determine how infectious subclinical infections are compared to clinical infections in order to properly assess predicted burdens both with and without interventions.
2020-03-27 Lescure et al Clinical and virological data of the first cases of COVID-19 in Europe: a case series
The Lancet Infectious Diseases
III-3. Time Series Analysis

11 The five patients in this case series, at different stages of infection, include two patients with a mild disease at admission and a secondary worsening that resulted in their admission to an intensive care unit (ICU), one initially severely ill patient directly admitted to an ICU for an acute respiratory failure, and two patients with a mild disease diagnosed very early after infection.
Patient 1 had nasopharyngeal samples collected at illness day 6 and patient 2 on day 9, which were positive by rtRT-PCR, with a SARS-CoV-2 viral load of 7·1 log 10 copies per 1000 cells, and detected but not quantifiable viral load, respectively.

It allowed us to describe three patterns: paucisymptomatic patients diagnosed very quickly over their disease course, with an early high nasopharyngeal shedding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within the first 24 h of the illness onset (5·2 and 7·4 log 10 copies per 1000 cells, respectively); patients with a two-step disease progression, with a secondary worsening around 10 days after disease onset despite a decreasing viral load in nasopharyngeal samples; and a patient with a rapid evolution towards multiple organ failure and a persistent high viral load in lower and upper respiratory tract with systemic virus dissemination and virus detection in plasma (ie, an old patient).
2020-03-27 Adekunle et al Delaying the COVID-19 epidemic in Australia: Evaluating the effectiveness of international travel bans
medrxiv
IV. Prevalence Study The infectious classes are late latency 2 and the two stages of symptomatic infectiousness .
2020-03-27 Tan et al A special case of COVID-19 with long duration of viral shedding for 49 days
medrxiv
IV. Prevalence Study

130 patients including the discharged and dead in our hospital between January 14, 2020 and March 19, 2020 were investigated and their clinical indexes were used as references of a hospitalized patient (Case 1), who would be introduced in detail in this study.
The status of lymphocytes and duration of viral shedding are two most common indicators in predicting prognosis of COVID-19 patients.
2020-03-29 Alfano et al Non-invasive surveys of mammalian viruses using environmental DNA
biorxiv
IV. Other Environmental DNA and in particular its subdiscipline invertebrate-derived DNA viral hybridization capture may be a useful and economical tool for identifying and characterizing major viral pathogens particularly in difficult to access sampling environments prior to viral emergence.

Further experiments with field filtration and sample concentration such as methods used with pathogen detection in waste water may improve detection rates .
2020-03-30 Xu et al Analysis and Prediction of False Negative Results for SARS-CoV-2 Detection with Pharyngeal Swab Specimen in COVID-19 Patients: A Retrospective Study
medrxiv
III-2. Retrospective Cohort

In order to implement the out-of-sample prediction, 1,324 patients were randomly divided into training (1,059 cases) and validation samples (265 cases Table 2) .
Hence, it is essential to 5 conduct the test when viral load is high.

Since the time of testing positive was not the exact time the patient reached 8 the threshold of enough viral load for testing positive, the time window was indeed interval censored.
2020-03-30 Lin et al Which Measures are Effective in Containing COVID-19? Empirical Research Based on Prevention and Control Cases in China
medrxiv
IV. Prevalence Study If the symptoms are not contagious before onset, the travel and social distance will not be limited, but necessary disease surveillance should be carried out to determine whether the intervention of public health agencies is needed to ensure the effectiveness of the latent disease surveillance based on the monitoring effect.
2020-03-31 Ejima et al Inferring Timing of Infection Using Within-host SARS-CoV-2 Infection Dynamics Model: Are "Imported Cases" Truly Imported?
medrxiv
IV. Other Conclusions and Relevance: In an early phase of outbreak due to entrance or re-entrance of the virus to countries/communities, collecting viral load data over time from cases from symptom onset is highly recommended, because viral load data are valuable to infer the timing of infection and distinguish between imported cases and ongoing local transmission.
2020-03-31 Boni et al Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic
biorxiv
III-3. Time Series Analysis

Combining regions A′, B, and C, and removing the five mentioned sequences gives us putative nonrecombining region 1, or NRR1, as an alignment of 63 sequences.
Identifying the origins of an emerging pathogen can be critical during the early stages of an outbreak as it may allow for containment measures to be precisely targeted at a stage when the number of daily new infections is still low.
2020-04-01 Shayak et al Transmission Dynamics of COVID-19 and Impact on Public Health Policy
medrxiv
IV. Computer Model This duration, which we call τ2, is the latency period.
2020-04-01 Kalantar-Zadeh et al Impact of Nutrition and Diet on COVID-19 Infection and Implications for Kidney Health and Kidney Disease Management
Journal of Renal Nutrition
IV. Prevalence Study 1 While clinical trials are underway to test these and other agents and related hypotheses, an important question for the nutrition community is whether there are certain nutrients and food patterns that can prevent the viral infection or mitigate its severity.
2020-04-01 Mestres et al The target landscape of N4-hydroxycytidine based on its chemical neighborhood
biorxiv
IV. Other Finally, a statistical analysis is performed to assess how often certain PHRAG descriptors are present in the SoM of each chemical transformation.
2020-12-31 Roda et al Why is it difficult to accurately predict the COVID-19 epidemic?
Infectious Disease Modelling
IV. Computer Model The latency of COVID-19 infection is biologically realistic due to an incubation period as long as 14 days; newly infected individuals may not be infectious while the virus is incubating in the body.

10 Use of diagnostics such as host response markers (e.g., cytokines) to detect early disease or predict severe disease progression, which would be important to understanding best clinical practice and efficacy of therapeutic interventions.

10.0.0.1 Highlights

10.0.0.2 Articles

Date Authors Title LOE(?) & Sample Matches
2020 Pang et al Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review
Journal of Clinical Medicine
I. Systematic Review

Of the total of 570 unique studies on 2019-nCoV, SARS CoV or MERS-CoV vaccines screened, only four were eventually included in the review.
Rapid diagnostics, vaccines and therapeutics are important interventions for the management of the 2019 novel coronavirus (2019-nCoV) outbreak.

Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases.
2020 Liu et al Analysis of factors associated with disease outcomes in hospitalized patients with 2019 novel coronavirus disease
Chin Med J (Engl)
IV. Prevalence Study

In the present study, 78 patients with COVID-19 associated pneumonia included 39 males and 39 females.
Associated results will be used to evaluate the prognosis and to find the optimal treatment regimens for COVID-19 pneumonia.

Clinical data included initial symptoms, clinical presentation, vital signs, therapeutic druguse, respiratory support, and disease outcomes.
2020 Shanmugaraj et al Emergence of Novel Coronavirus 2019-nCoV: Need for Rapid Vaccine and Biologics Development
Pathogens
IV. Prevalence Study Public health officials need to identify the source and virus reservoir, transmission cycle, pathogenesis, inter-human transmission, and clinical manifestations, which might be helpful to develop animal models, diagnostic reagents, anti-viral therapies, and vaccines against this pathogen.
2020 LU et al Clinical analysis of 2019 coronavirus disease (COVID-19) on one case with living-related kidney transplantation
Chinese Journal of Organ Transplantation
IV. Prevalence Study Method The clinical diagnosis and treatment of one relative renal transplant recipient after the occurrence of COVID-19 were analyzed retrospectively, including the course of onset, clinical manifestations, blood routine test, renal function, lung CT scan, nucleic acid detection, outpatient and inpatient therapies and outcomes.
2020-02-01 Li et al The Clinical and Chest CT Features Associated with Severe and Critical COVID-19 Pneumonia
Investigative Radiology
IV. Prevalence Study Many factors are related to the severity of the disease, which can help clinicians to judge the severity of the patient and evaluate the prognosis.
2020-02-05 He et al Integrative Bioinformatics Analysis Provides Insight into the Molecular Mechanisms of 2019-nCoV
medrxiv
IV. Other Our findings could explain the clinical symptoms so far and help clinicians and researchers understand the pathogenesis and design therapeutic strategies for 2019-nCoV.
2020-02-06 Villamil-Gómez et al Fatal human coronavirus 229E (HCoV-229E) and RSV–Related pneumonia in an AIDS patient from Colombia
Travel Medicine and Infectious Disease
IV. Other The identification of coronavirus in high-risk immunocompromised patients may lead to early adoption of a specific therapeutic strategy, but, in the absence of proof of the efficacy of antiviral drugs, the treatment remains only supportive .
2020-02-09 Guan et al Clinical characteristics of 2019 novel coronavirus infection in China
medrxiv
III-2. Retrospective Cohort

The core data sets (including clinical outcomes and symptoms) of 3 patients were lacking due to the incompleteness of original reports, hence this report delineates 1,099 patients with 2019-nCoV ARD from 552 hospitals in 31 provinces/province-level municipalities (Fig.
The disease severity (including oxygen saturation, respiratory rate, blood leukocyte/lymphocyte count and chest X-ray/CT manifestations) predict poor clinical outcomes.
2020-02-19 Kooraki et al Coronavirus (COVID-19) Outbreak: What the Department of Radiology Should Know
Journal of the American College of Radiology
IV. Other Imaging is critical in assessing severity and disease progression in COVID-19 infection.
2020-02-23 Feng et al Early Prediction of Disease Progression in 2019 Novel Coronavirus Pneumonia Patients Outside Wuhan with CT and Clinical Characteristics
medrxiv
III-2. Retrospective Cohort

Results: A total of 141 patients with moderate NCP were included, of which 15 (10.6%) patients developed severe NCP during hospitalization and assigned to the progressive group.
Our results showed that NLR and CT severity score on admission were significant predictors for progression to severe illness.

The CT findings in patients with NCP were associated with inflammatory levels and both them have the potential to predict disease progression.
2020-02-24 El Zowalaty et al From SARS to COVID-19: A previously unknown SARS- related coronavirus (SARS-CoV-2) of pandemic potential infecting humans – Call for a One Health approach
One Health
IV. Prevalence Study

However, it was recently reported that the Chinese Centers for Disease Control and Prevention isolated SARS-CoV-2 from 33 samples out of 585 environmental samples collected from Huanan Seafood Market .
Evaluation of the serologic response of SARS-CoV-2 infected patients according to the disease severity will help determine the potential role of serodiagnostic parameters as prognostic markers.

Evaluation of the serologic response of SARS- CoV-2 infected patients according to the disease severity will help determine the potential role of serodiagnostic parameters as prognostic markers.
2020-03-03 Jia et al Clinical significance of IgM and IgG test for diagnosis of highly suspected COVID-19 infection
medrxiv
IV. Other The detection of CRP is widely used in clinical applications, including the diagnosis and differential diagnosis of acute infectious diseases, the monitoring of postoperative infections, the observation of the efficacy of antibiotics, the detection of disease course and prognosis.
2020-03-03 Tan et al Lymphopenia predicts disease severity of COVID-19: a descriptive and predictive study
medrxiv
IV. Other This study aimed to retrospect and analyze the time-courses of complete blood count of cured and dead patients, in order to obtain key indicators of disease progression and outcome and to provide guidance for subsequent clinical practice.

Identification of a simple and effective indicator to assess disease severity and outcome is urgently needed.

However, efficient indicators for the disease severity, therapeutic response and disease outcome are still incompletely investigated.
2020-03-03 Qi et al Machine learning-based CT radiomics model for predicting hospital stay in patients with pneumonia associated with SARS-CoV-2 infection: A multicenter study
medrxiv
III-2. Cross Sectional Control

Therefore, 31 patients with 72 lesion segments were included in the final analysis.
3 Therefore, the hospital stay in patients with SARS-CoV-2 infection is one of the prognostic indicators, and its non-invasive predicting tool is important for assessing the patients' clinical outcome.

The hospital stay is one of the prognostic indicators, and its non-invasive predicting model based on CT radiomics features is important for assessing the patients' clinical outcome.
2020-03-05 Hoffmann et al SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor
Cell
IV. Other These results have important implications for our understanding of SARS-CoV-2 transmissibility and pathogenesis and reveal a target for therapeutic intervention.
2020-03-06 Yang et al Exuberant elevation of IP-10, MCP-3 and IL-1ra during SARS-CoV-2 infection is associated with disease severity and fatal outcome
medrxiv
IV. Other These results indicated that these 1 2 6 three cytokines could be considered as biomarkers to predict disease progression and 1 2 7 outcome of SARS-CoV-2 infections.
2020-03-06 Zhao et al Clinical and Laboratory Profiles of 75 Hospitalized Patients with Novel Coronavirus Disease 2019 in Hefei, China
medrxiv
IV. Other IL-6 could also be used as 199 an indicator to evaluate infection severity.
2020-03-06 Wang et al Nanopore target sequencing for accurate and comprehensive detection of SARS-CoV-2 and other respiratory viruses
medrxiv
IV. Other In addition, the detection of co-infection may allow the prevention of disease 258 progression from mild to severe or might be useful to inform clinical treatment.
2020-03-08 Qiu et al Outcome reporting from protocols of clinical trials of Coronavirus Disease 2019 (COVID-19): a review
medrxiv
IV. Prevalence Study These outcomes are relevant to the prognosis of disease and safety of therapy.
2020-03-10 Gao et al Prognostic value of NT-proBNP in patients with severe COVID-19
medrxiv
III-3. Time Series Analysis

After screening out the ineligible cases, 54 patients were analyzed in this study.
Investigating prognostic markers for severe patients are required to supply important information for early therapeutic strategy.
2020-03-12 Liu et al Patients of COVID-19 may benefit from sustained lopinavir-combined regimen and the increase of eosinophil may predict the outcome of COVID-19 progression
International Journal of Infectious Diseases
IV. Other Abstract Objectives To explore the epidemiological information, clinical characteristics, therapeutic outcomes and temporal progression of laboratory findings in 2019-coronavirus disease (COVID-19) patients exposed to lopinavir.
2020-03-12 Zhang et al Fecal specimen diagnosis 2019 Novel Coronavirus-Infected Pneumonia
Journal of Medical Virology
IV. Other These results may help to understand the clinical diagnosis and the changes of clinical parameters of COVID-19.
2020-03-12 Kujawski et al First 12 patients with coronavirus disease 2019 (COVID-19) in the United States
medrxiv
IV. Prevalence Study

Five patients received only outpatient care and were isolated at home (Patients 1-5), and seven were hospitalized (Patients 6-12) ( Figure 1 ).
Further investigations are needed to understand clinical course, immunologic response, SARS-CoV-2 RNA detection, virus culture, and transmission, to inform clinical management and public health strategies to prevent disease spread.
2020-03-14 D’Annessa et al Differential Antibody Recognition by Novel SARS-CoV-2 and SARS-CoV Spike Protein Receptor Binding Domains: Mechanistic Insights and Implications for the Design of Diagnostics and Therapeutics
biorxiv
IV. Other In this context, structural knowledge of the proteins of the virus can provide important information to develop strategies against the infection, ranging from diagnosis to therapy.
2020-03-15 Zhou et al Perspectives on therapeutic neutralizing antibodies against the Novel Coronavirus SARS-CoV-2
Int J Biol Sci
IV. Prevalence Study Elucidation of SARS-CoV-2 immunopathogenesis is useful for developing passive antibody therapy, designing vaccines, and understanding of clinical drug interventions.
2020-03-16 Zhang et al Immune phenotyping based on neutrophil-to-lymphocyte ratio and IgG predicts disease severity and outcome for patients with COVID-19
medrxiv
IV. Prevalence Study

Findings: A total of 222 patients were included in this study.
These four immune response phenotypes could be useful to distinguish the severe from the nonsevere cases and predict clinical outcome.
2020-03-18 Sun et al Lower mortality of COVID-19 by early recognition and intervention: experience from Jiangsu Province
Ann Intensive Care
IV. Other Since the severity of disease is closely related to the prognosis, the basic and essential strategies to improve outcomes that we should adhere to remain the early detection of high-risk and critically ill patients .
2020-03-20 Ye et al Clinical characteristics of severe acute respiratory syndrome coronavirus 2 reactivation
Journal of Infection
IV. Other SARS-CoV-2 viral load would also linked to treatment response, disease severity and progression.
2020-03-20 Ahmadi et al Modeling and Forecasting Trend of COVID-19 Epidemic in Iran
medrxiv
IV. Computer Model their relationship to outcomes should be analyzed to evaluate the cost-effectiveness of various diagnostic therapeutic approaches.
2020-03-23 Luo et al Prognostic value of C-reactive protein in patients with COVID-19
medrxiv
IV. Prevalence Study

Hence, 298 patients were finally enrolled in this study, including 141 cases of ordinary illness and 157 cases of severe or critical illness on admission.
Some important biomarkers of infection or critical illness including NLR, SII, procalcitonin, and D-dimer, were found to be associated with clinical outcome and disease severity.
2020-03-23 zhang et al Potential Factors for Prediction of Disease Severity of COVID-19 Patients
medrxiv
III-2. Cross Sectional Control

Results: A total of 43 COVID-19 patients were included in this study, including 29 mild patients and 14 sever patients.
Effective indicators for predicting disease severity in SARS-CoV-2 infected patients are urgently needed.
2020-03-23 To et al Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study
The Lancet Infectious Diseases
III-3. Time Series Analysis

12 of 23 patients included in this study have been reported previously, 6 but their clinical information, viral load by single copy RNA-dependent RNA polymerasehelicase gene, antibody response, or viral genome analysis has not been reported before.
Reliable data for profiles of serial viral load and serum antibody responses are needed urgently to guide antiviral treatment, infection control, epidemiological measures, and vaccination.
2020-03-24 Bian et al Meplazumab treats COVID-19 pneumonia: an open-labelled, concurrent controlled add-on clinical trial
medrxiv
IV. Prevalence Study

11 hospitalized patients who met the inclusion criteria and with no exclusion criteria signs were collected as concurrent control in the same period.
Lymphopenia was common in patients with COVID-19 and SARS patients, and can be used as an indicator of disease severity and prognosis.
2020-03-26 Xu et al Acute kidney injury at early stage as a negative prognostic indicator of patients with COVID-19: a hospital-based retrospective analysis
medrxiv
III-2. Cross Sectional Control

In the present study, 200 patients, who were diagnosed as COVID-19 from January
We provide evidence that the development of AKI at the early stage may be a potential negative prognostic indicator for survival of COVID-19 patients.

We provide evidence that the development of AKI at early stage may be a potential negative prognostic indicator for survival of COVID-19 patients.
2020-03-27 Tan et al A special case of COVID-19 with long duration of viral shedding for 49 days
medrxiv
IV. Prevalence Study

130 patients including the discharged and dead in our hospital between January 14, 2020 and March 19, 2020 were investigated and their clinical indexes were used as references of a hospitalized patient (Case 1), who would be introduced in detail in this study.
The status of lymphocytes and duration of viral shedding are two most common indicators in predicting prognosis of COVID-19 patients.
2020-03-28 Wang et al SARS-CoV-2 proteome microarray for mapping COVID-19 antibody interactions at amino acid resolution
biorxiv
IV. Other Such epitope biomarkers provide insight into the immune response to COVID-19 and are potential targets for COVID-19 diagnosis and vaccine development.
2020-03-30 Dong et al Understand Research Hotspots Surrounding COVID-19 and Other Coronavirus Infections Using Topic Modeling
medrxiv
IV. Computer Model The results also indicate that studies in diagnostics, therapeutics, vaccines, viral genomics, and pathogenesis are urgently needed to minimize the impact of the COVID-19 outbreak.
2020-03-30 Xie et al Development and external validation of a prognostic multivariable model on admission for hospitalized patients with COVID-19
medrxiv
III-2. Retrospective Cohort

Second cohort of 151 patients admitted to Jinyintan hospital who were included in a previous study were reused for model validation.
In conclusion, traditional early warning scores and organ injury markers do not help to predict severity and mortality in patients with COVID-19.
2020-03-31 Ling et al C-reactive protein levels in the early stage of COVID-19
Médecine et Maladies Infectieuses
IV. Other CRP levels could reflect disease severity and should be used as a key indicator for disease monitoring.
2020-05-31 Yang et al New thinking in the treatment of 2019 novel coronavirus pneumonia
Complementary Therapies in Clinical Practice
IV. Prevalence Study Clinicians choose therapeutic principles and methods to comprehensively analyze clinical symptoms and etiology.
2020-07-31 Lippi et al Thrombocytopenia is associated with severe coronavirus disease 2019 (COVID-19) infections: A meta-analysis
Clinica Chimica Acta
I. Systematic Review

The clinical severity was defined as the composite of ICU admission, use of mechanical ventilation or death in two studies , ICU admission in two studies , progression towards ARDS in one study , death in three studies , and need of mechanical ventilation in the remaining study .
In the presence of this rapidly emerging, novel infection uncharacteristic of the era of modern medicine, identification of biomarkers that could predict disease severity and prognosis are essential to guiding clinical care.

As such, biomarkers are needed to identify severe disease among hospitalized patients.

11 Policies and protocols for screening and testing.

11.0.0.1 Highlights

11.0.0.2 Articles

Date Authors Title LOE(?) & Sample Matches
2020 Ralph et al 2019-nCoV (Wuhan virus), a novel Coronavirus: Human-to-human transmission, travel-related cases, and vaccine readiness
Journal of Infection in Developing Countries
IV. Prevalence Study

On 8 January 2020, it was reported that a novel coronavirus had been sequenced from one patient and subsequently identified in some of the other patients with pneumonia , later reported as 15 of the 59 patients .
Diagnostic PCR protocols can be found at https://www.who.int/health-topics/coronavirus/laboratory-diagnostics-for-novel-coronavirus.
2020 HUA et al Strategy of dental clinics to cope with the epidemic period of infectious diseases based on the experience of corona virus disease outbreak
West China Journal of Stomatology
IV. Other Strategies following the National Laws and Standards of China and local standards of several provinces for controlling cross-infection and instituting protective measures for medical staff in dental clinics during an epidemic period are discussed.
2020 Task Force of Pulmonary Function et al Expert consensus on Pulmonary Function Testing during the epidemic of Corona Virus Disease 2019
Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases
IV. Other Indications of pulmonary function testing should be followed strictly.
2020-01-23 Corman et al Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR
Euro Surveill
IV. Prevalence Study

To show that the assays can detect other bat-associated SARS-related viruses, we used the E gene assay to test six batderived faecal samples available from Drexler et al.
reagents, oligonucleotides and positive controls, laboratories working under quality control programmes need to rely on documentation of technical qualification of the assay formulation as well as data from external clinical evaluation tests.
2020-02-10 Arabi et al Critical care management of adults with community-acquired severe respiratory viral infection
Intensive Care Med
II. Randomized Controlled Trial

The importance of timing of oseltamivir treatment has been demonstrated in an observational study of 1950 patients admitted to ICUs with influenza A(H1N1) pdm09, which showed a trend toward improved survival for those treated earliest .
Studies varied in the approach for sampling and in the used assays; in some studies, specimen collection and assays were standardized across all patients, while in other studies, sampling and assays were performed selectively.
2020-02-23 Ge et al Assessing the impact of a symptom-based mass screening and testing intervention during a novel infectious disease outbreak: The case of COVID-19
medrxiv
IV. Other More refined case definitions, screening by experts using telemedicine 103 approaches , or rapid home tests could all be options which reduce the pool of those 104 considered at risk of being infected with the novel pathogen, thus increasing .
2020-02-24 Gostic et al Estimated effectiveness of symptom and risk screening to prevent the spread of COVID-19
eLife
III-3. Time Series Analysis

Depending on the screening strategy (arrival, departure or both) and assumed subclinical fraction (5%, 25%, or 50%), the probability of detecting at least the first two cases ranged from 0.02 to 0.11, and the probability of detecting three or more cases was never better than 0.04 ( Figure 3C ).
Our results have several implications for the design and implementation of traveller screening policies.

Screening programs implemented in other settings will face the same challenges.
2020-02-28 Zhao et al Anesthetic Management of Patients With Suspected or Confirmed 2019 Novel Coronavirus Infection During Emergency Procedures
Journal of Cardiothoracic and Vascular Anesthesia
IV. Other Measurements and Main Results Cross-infection in the operating rooms of the 4 hospitals was effectively reduced by implementing the new measures and procedures.
2020-03-02 Metsky et al CRISPR-based surveillance for COVID-19 using genomically-comprehensive machine learning design
biorxiv
IV. Prevalence Study A protocol for performing this assay is provided in the Methods section and can be used for testing any of the other designs we have provided.
2020-03-06 Shen et al Quantitative computed tomography analysis for stratifying the severity of Coronavirus Disease 2019
Journal of Pharmaceutical Analysis
IV. Other Diagnostic criteria for COVID-19 were based on the diagnosis and treatment protocols from the National Health Commission of the People's Republic of China .
2020-03-08 Qiu et al Outcome reporting from protocols of clinical trials of Coronavirus Disease 2019 (COVID-19): a review
medrxiv
IV. Prevalence Study A total of 97 protocols were included from 160 protocols.
2020-03-10 O’Connell et al The impact of point-of-care testing for influenza A and B on patient flow and management in a medical assessment unit of a general hospital
BMC Res Notes
III-3. Time Series Analysis

RESULTS: The results of the correlation study with a cohort of 54 patients revealed the Abbott ID NOW POCT has 92% sensitivity for the detection of Influenza A, while specificity was 100% for both Influenza A and B.
Turnaround times of Laboratory based screening tests for the diagnosis of influenza may have an impact on the implementation of infection control measures and treatment.
2020-03-12 Meng et al Coronavirus Disease 2019 (COVID-19): Emerging and Future Challenges for Dental and Oral Medicine
Journal of Dental Research
IV. Other For dental practices and hospitals in areas that are (potentially) affected with COVID-19, strict and effective infection control protocols are urgently needed.
2020-03-12 Wang et al Effects of Chinese strategies for controlling the diffusion and deterioration of novel coronavirus-infected pneumonia in China
medrxiv
IV. Computer Model These strategies supply experience and guidelines for other countries to control the COVID-19 epidemic.
2020-03-13 Trilla et al One world, one health: The novel coronavirus COVID-19 epidemic
Medicina Clínica (English Edition)
IV. Other In Spain, the prevention, surveillance and control systems for this new disease are adapted to the guidelines and protocols of the ECDC and the WHO.
2020-03-13 Chen et al COVID-19 control in China during mass population movements at New Year
The Lancet
IV. Other As such, governments should use the closure period for information and education campaigns, community screening, active contact tracing, and isolation and quarantine to maximise impact.
2020-03-13 Zhang et al Prediction of the COVID-19 outbreak based on a realistic stochastic model
medrxiv
IV. Other For the purpose of control and prevention, various containment measures have been implemented by the Chinese authorities, including traffic restrictions, medical tracking, entry or exit screening, isolation, quarantine and awareness campaigns since January 19, 2020.
2020-03-17 Adhikari et al Epidemiology, causes, clinical manifestation and diagnosis, prevention and control of coronavirus disease (COVID-19) during the early outbreak period: a scoping review
Infect Dis Poverty
III-2. Cross Sectional Control

In China, 11 791 cases were confirmed and 17 988 cases were suspected in 34 provinces as of 24:00, 31 January 2020 (Fig.
Under this policy, medical institutes can adopt isolation treatment and observation protocols to prevent and control the spread of the COVID-19.
2020-03-17 Zheng et al Deep Learning-based Detection for COVID-19 from Chest CT using Weak Label
medrxiv
IV. Other During the procedure of testing, data augmentation strategies were not applied.
2020-03-18 Jin et al Core Outcome Set for Clinical Trials on Coronavirus Disease 2019 (COS-COVID)
Engineering
IV. Prevalence Study

The consensus meeting was held on 24 February 2020, and involved 20 participants.
After screening, 78 protocols met the eligibility criteria: 52 with interventions of chemical or biological drugs and 26 with traditional Chinese medicine plus standard treatments.
2020-03-19 Filippi et al COVID-19 OUTBREAK IN NORTHERN ITALY: FIRST PRACTICAL INDICATIONS FOR RADIOTHERAPY DEPARTMENTS
International Journal of Radiation OncologyBiologyPhysics
IV. Other The indications were integrated with the WHO recommendations and with the local health authorities' guidelines.
2020-03-20 Ji et al Analysis of Epidemic Situation of New Coronavirus Infection at Home and Abroad Based on Rescaled Range (R/S) Method
medrxiv
III-3. Time Series Analysis

confirmed abroad, of which 7,755 cases have been confirmed in South Korea and 10,149 cases have been confirmed in Italy.
Strict prevention and screening measures are needed for this.
2020-03-20 Ramanathan et al Planning and provision of ECMO services for severe ARDS during the COVID-19 pandemic and other outbreaks of emerging infectious diseases
The Lancet Respiratory Medicine
IV. Prevalence Study In addition to careful patient selection, strict adherence to standard intensive care management practices and infection control protocols should be among the primary goals of care.
2020-03-20 Massonnaud et al COVID-19: Forecasting short term hospital needs in France
medrxiv
IV. Computer Model Most countries have now implemented control strategies involving contact tracing, quarantine, and isolation measures, which are likely to significantly reduce the R 0 .
2020-03-21 Liu et al Clinical and CT imaging features of the COVID-19 pneumonia: Focus on pregnant women and children
Journal of Infection
IV. Other The protocols were as follows.
2020-03-23 Koo et al Interventions to mitigate early spread of SARS-CoV-2 in Singapore: a modelling study
The Lancet Infectious Diseases
IV. Prevalence Study

20 Asymptomatic individuals were able to infect at a 50% reduced rate compared with their symptomatic counterparts based on estimates from Nishiura and colleagues.
The main control measures at this time are surveillance, standard testing procedures, 36 and quarantine of individuals who are confirmed positive for the virus.
2020-03-23 Wen et al Epidemiological and clinical characteristics of COVID-19 in Shenzhen, the largest migrant city of China
medrxiv
IV. Prevalence Study

In total, there were 29 (7.0%) pediatric patients aged below 15 years, of whom 26 were identified by surveillance and 28 were cases from clusters.
Our results can be used to improve the prediction of transmission risk, design and implementation of intervention measures and strategies, and assessments of intervention effectiveness in similar settings.
2020-03-26 Rios et al Guidelines for preventing respiratory illness in older adults aged 60 years and above living in long-term care: A rapid review of clinical practice guidelines
medrxiv
IV. Prevalence Study

If one or more respiratory samples from ILI cases in a suspected outbreak returns a positive laboratory result for influenza, then an influenza outbreak is confirmed.
03 Although not regulatory in scope, these guidelines support infection prevention and control (IP&C) professionals, health care organizations and health care providers in developing, implementing and evaluating IP&C policies, procedures and programs to improve the quality and safety of health care and patient outcomes.

☐Criteria to assess guideline implementation or adherence to recommendations ☐Criteria for assessing impact of implementing the recommendations ☐Advice on the frequency and interval of measurement ☐Operational definitions of how the criteria should be measured

recommendations ☒Criteria for assessing impact of implementing the recommendations ☒Advice on the frequency and interval of measurement ☐Operational definitions of how the criteria should be measured

recommendations ☐Criteria for assessing impact of implementing the recommendations ☐Advice on the frequency and interval of measurement ☐Operational definitions of how the criteria should be measured

recommendations ☐Criteria for assessing impact of implementing the recommendations ☐Advice on the frequency and interval of measurement ☐Operational definitions of how the criteria should be measured ☐A statement that the guideline will be updated ☐Explicit time interval or explicit criteria to guide decisions about when an update will occur ☐Methodology for the updating procedure ☐Types of facilitators and barriers that were considered ☐Methods by which information regarding the facilitators and barriers to implementing recommendations were sought (e.g., feedback from key stakeholders, pilot testing of guidelines before widespread implementation)
2020-03-27 Lescure et al Clinical and virological data of the first cases of COVID-19 in Europe: a case series
The Lancet Infectious Diseases
III-3. Time Series Analysis

11 The five patients in this case series, at different stages of infection, include two patients with a mild disease at admission and a secondary worsening that resulted in their admission to an intensive care unit (ICU), one initially severely ill patient directly admitted to an ICU for an acute respiratory failure, and two patients with a mild disease diagnosed very early after infection.
Clinical samples for SARS-CoV-2 diagnostic testing were obtained according to WHO guidelines.
2020-03-27 Yelin et al Evaluation of COVID-19 RT-qPCR test in multi-sample pools
medrxiv
IV. Other As it uses the standard protocols, reagents and equipment, this pooling method can be applied immediately in current clinical testing laboratories.
2020-03-27 Soetikno et al Considerations in performing endoscopy during the COVID-19 pandemic
Gastrointestinal Endoscopy
IV. Other All febrile staff should not be allowed to work, and they should be evaluated according to local protocols to screen for potential COVID-19 infections.
2020-03-27 Wu et al Radiotherapy care during a major outbreak of COVID-19 in Wuhan
Advances in Radiation Oncology
IV. Other Health care worker screening: According to the COVID-19 diagnosis guidelines, the staff returning to work must be screened for the disease.
2020-03-28 Tan et al The cardiovascular burden of coronavirus disease 2019 (COVID-19) with a focus on congenital heart disease
International Journal of Cardiology
IV. Other Each institution should develop protocols for appropriate triage, isolation, and treatment of COVID-19 patients who may need such interventions.
2020-03-28 Zhai et al The epidemiology, diagnosis and treatment of COVID-19
International Journal of Antimicrobial Agents
III-2. Matched Case Control

Another study later using the travel history and symptom onset of 88 confirmed cases had a similar mean incubation period, which was 6.4 days (95% CI: 5.6-7.7) .
Notably, a long incubation time means adjustments in screening and control policies .
2020-03-29 Thompson et al COVID-19 in Endoscopy: Time to do more?
Gastrointestinal Endoscopy
IV. Prevalence Study All screening and most surveillance procedures should be delayed.
2020-03-30 Wei et al Radiotherapy Workflow and Protection Procedures During the Coronavirus Disease 2019 (COVID-19) Outbreak: Experience of the Hubei Cancer Hospital in Wuhan, China
Radiotherapy and Oncology
IV. Other The training included learning the latest versions of "COVID-19 Diagnosis and Treatment Plan" and "COVID-19 Protection and Prevention Plan", hand hygiene, proper handling of PPE, disinfection policies and procedures, and quarantine/isolation policies.
2020-03-30 quan et al No SARS-CoV-2 in expressed prostatic secretion of patients with coronavirus disease 2019: a descriptive multicentre study in China
medrxiv
IV. Prevalence Study

All 23 EPS samples of suspected and confirmed patients tested negative for the RNA of SARS-CoV-2 regardless by various grouping methods, such as days of illness, infected symptoms of All rights reserved.
RT-PCR testing was performed according to the recommended protocol.
2020-03-30 Sinnott-Armstrong et al Evaluation of Group Testing for SARS-CoV-2 RNA
medrxiv
IV. Prevalence Study While CDC guidelines caution against using negative test results "as the sole basis for treatment or other patient management decisions," testing criteria currently select for symptomatic individuals.
2020-03-31 Elwood et al SOGC Committee Opinion – COVID-19 in Pregnancy
Journal of Obstetrics and Gynaecology Canada
IV. Other o Testing should be performed as per local guidelines and recommendations.
2020-03-31 Villani et al Patients with advanced basal cell carcinomas in treatment with sonic hedgehog inhibitors during the coronavirus disease 2019 (COVID-19) period: Management and adherence to treatment
Journal of the American Academy of Dermatology
IV. Other Policies in place for infection control (safety measures, protection, screening, and teleconsultations) must be carried out to minimize the risk of infection.
2020-04-01 Xie et al Insight into 2019 novel coronavirus — an updated intrim review and lessons from SARS-CoV and MERS-CoV
International Journal of Infectious Diseases
IV. Prevalence Study An adjustments in screening and control policies may be needed.
2020-04-01 Cesari et al COVID-19 in Italy: Ageism and Decision-Making in a Pandemic
Journal of the American Medical Directors Association
IV. Other No plans or protocols had the time to be tested and verified, at least on a large scale.
2020-04-01 Sultan et al AGA Institute Rapid Recommendations for Gastrointestinal Procedures During the COVID-19 Pandemic
Gastroenterology
I. Systematic Review

58, 59 First, the systematic reviews by Offeddu et al included a meta-analysis of 3 observational studies that showed a benefit in using N95 respirators over standard masks in protecting health care workers from SARS (OR = 0.86; 95% CI: 0.
Moreover, as innovations in testing (rapid tests, serologic tests of immunity) and treatment or vaccines allow for better risk stratification, one may be able to consider restarting non-time sensitive procedures.
2020-04-01 Chen et al Novel Coronavirus International Public Health Emergency: Guidance on Radiation Oncology Facility Operation
Advances in Radiation Oncology
IV. Other There have also been personnel trainings on infection protection that have included information on basic prevention precautions, airborne infection isolation room specifications, epidemiological and clinical characteristics of COVID-19 cases, and simulation exercises on various possible situations with assessments.
2020-07-31 Lv et al Dynamic change process of target genes by RT-PCR testing of SARS-Cov-2 during the course of a Coronavirus Disease 2019 patient
Clinica Chimica Acta
IV. Other Clinical specimens for SARS-CoV-2 diagnostic testing were obtained in accordance with Chinese guidelines .

12 Policies to mitigate the effects on supplies associated with mass testing, including swabs and reagents.

12.0.0.1 Highlights

12.0.0.2 Articles

Date Authors Title LOE(?) & Sample Matches
2020 Chu et al Molecular Diagnosis of a Novel Coronavirus (2019-nCoV) Causing an Outbreak of Pneumonia
Clin Chem
IV. Other Samples from two 2019-nCoV-infected patients were positive in the tests.

Respiratory specimens from two suspected patients were tested by both RT-PCR assays.

To determine the specificity of these assays, negative control samples were tested.

Both patients were positive in the tests (Table 1) .
2020 ZHOU et al Anesthesia management for cesarean section during novel coronavirous epidemic
Chinese Journal of Anesthesiology
IV. Other Narcotic drugs were used for one patient only, and disposable medical supplies were used for anesthetic supplies.
2020 Li et al Extracorporeal membrane oxygenation support in 2019 novel coronavirus disease: indications, timing, and implementation
Chin Med J (Engl)
IV. Other To avoid unnecessary entries and exits, all supplies, including surgical instruments, consumables, medications, and blood products should be carefully inspected, and the number of staff should be restricted in the independent area.
2020-02-21 Chan et al A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster
The Lancet
III-3. Time Series Analysis

Methods In this study, we report the epidemiological, clinical, laboratory, radiological, and microbiological findings of five patients in a family cluster who presented with unexplained pneumonia after returning to Shenzhen, Guangdong province, China, after a visit to Wuhan, and an additional family member who did not travel to Wuhan.
22 Sputum samples were available for testing from patients 5 and 7.
2020-02-24 Lamb et al Rapid Detection of Novel Coronavirus (COVID-19) by Reverse Transcription-Loop-Mediated Isothermal Amplification
medrxiv
IV. Other Personnel trained in collecting blood specimens may also not be available, Furthermore, biological samples may contain chemicals that can inhibit nucleic acid assays if the sample is tested directly without first isolating the RNA.
2020-02-26 Rothan et al The epidemiology and pathogenesis of coronavirus disease (COVID-19) outbreak
Journal of Autoimmunity
IV. Other The public services and facilities should provide decontaminating reagents for cleaning hands on a routine basis.
2020-02-27 Cui et al Clinical features and sexual transmission potential of SARS-CoV-2 infected female patients: a descriptive study in Wuhan, China
medrxiv
IV. Other JL was in charge of the laboratory tasks, including sample processing and detection.
2020-03-05 Konrad et al Rapid establishment of laboratory diagnostics for the novel coronavirus SARS-CoV-2 in Bavaria, Germany, February 2020
Euro Surveill
IV. Other In the following days, health authorities implemented comprehensive measures to prevent further transmission of SARS-CoV-2, including testing of contact persons.
2020-03-05 Johnson et al Potential scenarios for the progression of a COVID-19 epidemic in the European Union and the European Economic Area, March 2020
Euro Surveill
IV. Prevalence Study Public health bodies and research institutions should continue to work together to continuously evaluate the situation, to address knowledge gaps and to assess the effectiveness of targeted interventions with new tests, treatments and vaccines as they are developed.
2020-03-05 Xiao et al Taking the right measures to control COVID-19
The Lancet Infectious Diseases
IV. Prevalence Study The widespread practice of spraying disinfectant and alcohol in the sky, on roads, vehicles, and personnel has no value; moreover, large quantities of alcohol and disinfectant are potentially harmful to humans and should be avoided.3 , 4 Second, in the use of personal protective equipment, we should try to distinguish different risk factors, adopt different epidemic prevention measures, and reduce the waste of personal protective equipment, as these resources are already in short supply.

3, 4 Second, in the use of personal protective equipment, we should try to distinguish different risk factors, adopt different epidemic prevention measures, and reduce the waste of personal protective equipment, as these resources are already in short supply.
2020-03-06 Wu et al Nowcasting and forecasting the potential domestic and international spread of the 2019-nCoV outbreak originating in Wuhan, China: a modelling study
The Lancet
IV. Computer Model Above all, for health protection within China and internationally, especially those locations with the closest travel links with major Chinese ports, preparedness plans should be readied for deployment at short notice, including securing supply chains of pharmaceuticals, personal pro tective equipment, hospital supplies, and the necessary human resources to deal with the consequences of a global outbreak of this magnitude.
2020-03-10 Wu et al Clinical outcomes of 402 patients with COVID-2019 from a single center in Wuhan, China
medrxiv
IV. Prevalence Study

The cohort included 297 patients with confirmed and 105 with suspected diagnosis.
In addition, patients included in these prior studies all had diagnosis confirmed by the nucleic acid tests for pharyngeal swab specimens.
2020-03-11 Chopra et al How Should U.S. Hospitals Prepare for Coronavirus Disease 2019 (COVID-19)?
Ann Intern Med
IV. Other Hospitals should monitor rates of equipment use to ensure an adequate supply of personal protective equipment for those on the front lines and may need to engage hospital security to avoid theft or hoarding of such equipment.
2020-03-13 Rodriguez-Morales et al Clinical, laboratory and imaging features of COVID-19: A systematic review and meta-analysis
Travel Medicine and Infectious Disease
I. Systematic Review

Our review included 19 studies that were published between January 1, 2020, and February 21, 2020, most of them from China and one from Australia (Table 1) , including a total of 2874 patients, ranging from a case series of 9 to a cross-sectional study of 1590 .
Africa, supplies chains, including those for drugs, masks and personal protection equipment, will be challenged.
2020-03-13 Jombart et al Inferring the number of COVID-19 cases from recently reported deaths
medrxiv
III-3. Time Series Analysis In such situations, efforts focusing on social distancing measures such as school closures and self-isolation may be more likely to mitigate epidemic spread.
2020-03-14 Ahmed et al The cancellation of mass gatherings (MGs)? Decision making in the time of COVID-19
Travel Medicine and Infectious Disease
IV. Other As the public starts to purchase supplies, mass purchasing can cause shortages for masks which would be best used by HCWs in the healthcare setting.
2020-03-16 Ye et al Environmental contamination of the SARS-CoV-2 in healthcare premises: An urgent call for protection for healthcare workers
medrxiv
IV. Other Three sets of surface samples were collected using dacron swabs across major hospital function zones, hospital equipment/objects and medical supplies, and HCW's used PPE.

Differences in the positive detection rates of SARS-CoV-2 RNA in the surface swabs between hospital areas, hospital objects and medical supplies, and HCW's used PPE were assessed using Chi-Square tests and/or the Fisher's exact test where appropriate based on cell size.
2020-03-19 Fisher et al The global community needs to swiftly ramp up the response to contain COVID-19
The Lancet
IV. Other The demand on facilities, the number of test kits, personal protective equipment, and medication stockpiles should be forecast to enable scaleup.
2020-03-19 Kinross et al Rapidly increasing cumulative incidence of coronavirus disease (COVID-19) in the European Union/European Economic Area and the United Kingdom, 1 January to 15 March 2020
Euro Surveill
III-3. Time Series Analysis

As at 15 March 2020, COVID-19 cases had been detected in all 30 EU/EEA countries and the United Kingdom (UK) , whereby between 31 December 2019 and that date included, 39,768 cases and 1,727 deaths had been reported, with 17,750 cases and 1,441 deaths from Italy alone .
The rapid risk assessment also lists the public health measures to mitigate the impact of the pandemic.
2020-03-20 Nkengasong et al Looming threat of COVID-19 infection in Africa: act collectively, and fast
The Lancet
IV. Prevalence Study Third, commitment and release of financial resources from partners and donors before a crisis hits Africa will help anticipate demand and address supply chain management, mapping, and stockpiling of COVID-19 response needs, such as large quantities of personal protective equipment, gloves, surgical masks, coveralls, and hoods, and medical countermeasures like antiviral agents.
2020-03-20 Lover et al Sentinel Event Surveillance to Estimate Total SARS-CoV-2 Infections, United States
medrxiv
IV. Computer Model Hospitals and healthcare facilities that do have tests have limited the testing criteria to those with highest potential risk, to optimize the use of scarce resources .
2020-03-21 Poole et al Responding to the COVID-19 pandemic in complex humanitarian crises
Int J Equity Health
IV. Other Resources must be identified to protect healthcare workers, develop and deploy rapid testing, improve surveillance, and enact quarantine and isolation of contacts and cases.
2020-03-23 Coelho et al Assessing the potential impacts of COVID-19 in Brasil: Mobility, Morbidity and Impact to the Health System
medrxiv
IV. Prevalence Study The resulting maps should help authorities in their efforts to prioritize actions and if resource allocation to mitigate the effects of the pandemic.
2020-03-24 Simcock et al COVID-19: Global Radiation Oncology’s Targeted Response for Pandemic Preparedness
Clinical and Translational Radiation Oncology
IV. Prevalence Study

During the weekend over 121 individuals from 17 countries and 6 continents contributed to the online discussion.
These policies will be influenced by national directives and local infection control procedures as well as access and availability of Personal Protection Equipment (PPE).
2020-03-24 Haines et al National UK programme of community health workers for COVID-19 response
The Lancet
IV. Other 5 Additionally, home visits for vulnerable people would allow CHWs to assess whether individuals have adequate supplies of food and medicines for long-term conditions, are aware of basic hygiene precautions, and whether they have mental health problems.
2020-03-24 Miao et al A comparative multi-centre study on the clinical and imaging features of comfirmed and uncomfirmed patients with COVID-19
medrxiv
IV. Prevalence Study

Results This study enrolled 163 patients with 62 confirmed cases and 101 unconfirmed cases.
Nasopharyngeal swabs or sputum specimens were collected for RT-PCR tests.
2020-03-26 Fauver et al Coast-to-coast spread of SARS-CoV-2 in the United States revealed by genomic epidemiology
medrxiv
IV. Prevalence Study

A total of 10 samples from 10 different individuals with cycle-threshold (CT) values less than 35 were selected to move forward with next generation sequencing (NGS).
This effort must ensure that states have sufficient personal protective equipment, sample collection materials, and testing reagents, as these supplies enable effective surveillance.
2020-03-26 Rios et al Guidelines for preventing respiratory illness in older adults aged 60 years and above living in long-term care: A rapid review of clinical practice guidelines
medrxiv
IV. Prevalence Study

If one or more respiratory samples from ILI cases in a suspected outbreak returns a positive laboratory result for influenza, then an influenza outbreak is confirmed.
Preventing respiratory illness in long-term care facilities: Two or more clinical practice guidelines recommended the following: hand hygiene (n=13), wearing personal protective equipment (n=13), social distancing/isolation (n=13), disinfecting surfaces (n=12), droplet precautions (n=12), surveillance and evaluation (n=11), conducting diagnostic testing to confirm suspected respiratory illness (n=10), policies and procedures for visitors (n=9), respiratory hygiene/cough etiquette (n=9), policies and procedures for staff and/or residents (n=9), providing supplies (n=9), education of staff and/or residents (n=8), increasing communication (n=6), consulting or notifying health professionals (n=6), appropriate ventilation practices (n=2), and cohorting equipment (n=2) ( Table 2 , Appendix 6).

Facilities should develop (or review existing) plans to mitigate staffing shortages.

The most commonly recommended prevention strategies across the clinical practice guidelines were hand hygiene, wearing personal protective equipment, social distancing/isolation, disinfecting surfaces, droplet precautions, surveillance and evaluation, conducting diagnostic testing to confirm suspected respiratory illness, policies and procedures for visitors, policies and procedures for staff, and respiratory hygiene/cough etiquette.
2020-03-26 Al-Quteimat et al SARS-CoV-2 outbreak: How can pharmacists help?
Research in Social and Administrative Pharmacy
IV. Prevalence Study Additionally, in light of the lack of a currently approved treatment for COVID-19, pharmacists working in the pharmaceutical supply chain should be prepared to manage any potential medication or pharmacy consumable shortages (such as protective personal equipments, intravenous bags and syringes), to work proactively on having a plan to judiciously use the current resources, and be prepared to face increased case loads or emergency scenarios.
2020-03-26 Pambuccian et al The COVID-19 pandemic: Implications for the cytology laboratory
Journal of the American Society of Cytopathology
IV. Other The recommendations are similar to those given for general and histopathology laboratories , but also include the situations in which cytology laboratory personnel is involved either in the care of patients potentially infected with SARS-CoV-2 during FNA procedures or rapid-onsite evaluation of aspiration or core biopsies or in the preparation of fresh specimens from such patients.
2020-03-26 Miao et al Early chest computed tomography to diagnose COVID-19 from suspected patients: A multicenter retrospective study
medrxiv
IV. Other Nasopharyngeal swabs or sputum specimens were collected for RT-PCR tests.
2020-03-27 Zhao et al A Social Network Model of the COVID-19 Pandemic
medrxiv
IV. Other While the world awaits the development of vaccines and anti-viral medications, traditional public health measures such as isolation of confirmed or suspected cases, quarantine of contacts, and social distancing of the public are effective measures to reduce viral transmission 2, 3 , that have been implemented in many regions and countries 4, 5 .
2020-03-28 Zhong et al Spinal anaesthesia for patients with coronavirus disease 2019 and possible transmission rates in anaesthetists: retrospective, single-centre, observational cohort study
British Journal of Anaesthesia
III-2. Retrospective Cohort

As of March 3, 2020, 80 303 confirmed cases have been documented in China.
False-negative tests may occur using throat swab samples.
2020-03-30 Burns et al Symptom-Based Isolation Policies: Evidence from a Mathematical Model of Outbreaks of Influenza and COVID-19
medrxiv
III-3. Time Series Analysis Furthermore, practical barriers may reduce the strictness with which the policies are enforced, which would reduce the policies' effectiveness.
2020-03-30 Thomas et al Physiotherapy management for COVID-19 in the acute hospital setting: clinical practice recommendations
Journal of Physiotherapy
IV. Prevalence Study

12 In adult patients with COVID-19 and severe ARDS, prone ventilation for 12 to 16 hours per day is recommended.
Unnecessary review of patients with COVID-19 within their isolation room/areas will also have a negative impact on PPE supplies.

1.14 Identify additional physical resources that may be required for physiotherapy interventions and how the risk of cross-infection can be minimised (eg, respiratory equipment; mobilisation, exercise and rehabilitation equipment; and equipment storage).
2020-03-30 Lu et al SARS-CoV-2 detection using digital PCR for COVID-19 diagnosis, treatment monitoring and criteria for discharge
medrxiv
IV. Other A total of 109 samples including 108 clinical specimens and 1 negative control sample were tested in this study.
2020-03-30 Sinnott-Armstrong et al Evaluation of Group Testing for SARS-CoV-2 RNA
medrxiv
IV. Prevalence Study Drawing on the well-studied group testing literature, modeling suggests practical changes to testing protocols which can reduce test costs and stretch a limited test kit supply.
2020-03-31 Papachristofilou et al Contingency plans in a radiation oncology department amid the 2019-nCoV outbreak in Switzerland
Advances in Radiation Oncology
IV. Other a) Supplies of medical instruments, drugs and stockpiles of dispensable materials such as examination gloves, surgical masks, antiseptic fluids were checked and restocked when necessary.
2020-03-31 Kluge et al Refugee and migrant health in the COVID-19 response
The Lancet
IV. Other As governments tighten border controls and implement other measures in response to COVID-19, they need to consider the impacts on refugees and migrants and ensure that such actions do not prevent people from accessing safety, health-care services, and information.
2020-04-01 Fenga et al Forecasting the CoViD19 Diffusion in Italy and the Related Occupancy of Intensive Care Units
medrxiv
IV. Computer Model In fact, the typical lab-workflow is governed by a set of rigid protocols which might be critically affected by factors such as the availability of manpower, swabs, reagents and other laboratory materials.
2020-04-01 Lakkireddy et al Guidance for Cardiac Electrophysiology During the Coronavirus (COVID-19) Pandemic from the Heart Rhythm Society COVID-19 Task Force; Electrophysiology Section of the American College of Cardiology; and the Electrocardiography and Arrhythmias Committee of the Council on Clinical Cardiology, American Heart Association
Heart Rhythm
IV. Prevalence Study Reducing contact between health care personnel and COVID-19 patients is an integral step in limiting its spread and resource utilization, including use of personal protective equipment (PPE).
2020-04-30 Niud et al Deciphering the power of isolation in controlling COVID-19 outbreaks
The Lancet Global Health
IV. Other The identification and testing of potential cases need to be as extensive as is permitted by health care and diagnostic testing capacity-including the identification, testing, and isolation of suspected cases with no or mild disease (eg, influenza-like illness).

13 Technology roadmap for diagnostics.

13.0.0.1 Highlights

13.0.0.2 Articles

Date Authors Title LOE(?) & Sample Matches
2020 Pang et al Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review
Journal of Clinical Medicine
I. Systematic Review

Of the total of 570 unique studies on 2019-nCoV, SARS CoV or MERS-CoV vaccines screened, only four were eventually included in the review.
Rapid diagnostics, vaccines and therapeutics are important interventions for the management of the 2019 novel coronavirus (2019-nCoV) outbreak.

Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases.

The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV.
2020 Cascella et al Features, Evaluation and Treatment Coronavirus (COVID-19)
StatPearls
IV. Other At the same time, scientists around the world work tirelessly, and information about the transmission mechanisms, the clinical spectrum of disease, new diagnostics, and prevention and therapeutic strategies are rapidly developing.
2020 Allam et al On the Coronavirus (COVID-19) Outbreak and the Smart City Network: Universal Data Sharing Standards Coupled with Artificial Intelligence (AI) to Benefit Urban Health Monitoring and Management
Healthcare
IV. Prevalence Study In the current era of technological advancement, such regulations and guidelines are paramount as they have potential to lead to positive or negative outcomes.
2020 Chen et al From SARS-CoV to 2019-nCoV Outbreak: Similarities in the Early Epidemics and Prediction of Future Trends
Chin Med J (Engl)
IV. Prevalence Study

An investigation of family clustering identified 35 clusters involving 105 patients, in families with two or more family members in Guangzhou.
Rapid discovery of the causative agent and development of diagnostic reagents demonstrated that technology has greatly improved in the 17 years since the SARS outbreak.
2020 Shanmugaraj et al Emergence of Novel Coronavirus 2019-nCoV: Need for Rapid Vaccine and Biologics Development
Pathogens
IV. Prevalence Study Major players in the global plant-based biologics market include PlantForm, IBio Inc., Mapp Biopharmaceutical, Inc., Pfizer Inc., Ventria Bioscience, Medicago Inc., Greenovation Biotech GmbH, Kentucky BioProcessing, PhycoBiologics Inc., Synthon, Fraunhofer IME, Healthgen, Planet Biotechnology, and Icon Genetics GmbH.
2020-02-04 Zhang et al Recent advances in the detection of respiratory virus infection in humans
Journal of Medical Virology
IV. Other With the development of modern technologies, new diagnostic strategies, including multiplex nucleic acid amplification and microarray-based assays, are emerging.
2020-02-05 McCloskey et al SARS to novel coronavirus – old lessons and new lessons
Epidemiology and Infection
IV. Prevalence Study Within 4 weeks, by 26 January 2020, the causative organism had been identified as a novel coronavirus, the genome of the virus had been sequenced and published, reverse transcription polymerase chain reaction tests had been developed, the WHO R&D Blueprint had been activated to accelerate diagnostics, therapeutics and vaccine development and a candidate vaccine was ready for initial laboratory testing.
2020-02-06 Jin et al A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)
Mil Med Res
II. Randomized Controlled Trial The next generation sequencing (NGS) and electron microscope technology play a role in the early diagnosis, but their diagnostic values have been weakened by the discovery of specific nucleic acid detection technology.
2020-02-15 Wrapp et al Cryo-EM Structure of the 2019-nCoV Spike in the Prefusion Conformation
biorxiv
IV. Other The CoV spike (S) glycoprotein is a key target for urgently needed vaccines, therapeutic antibodies, and diagnostics.
2020-02-20 新型冠状病毒SARS-CoV-2的实验室检测技术
PMC
IV. Other In this review, the authors gives an overview of the virus laboratory detection technology, including virus isolation and culture, real-time fluorescent PCR, gene sequencing, serological antibody detection, and the gene editing technology based on CRISPR/Cas13 system.
2020-02-23 Hou et al Development and Evaluation of A CRISPR-based Diagnostic For 2019-novel Coronavirus
medrxiv
IV. Other 71 Currently, metagenomics and RT-PCR are two molecular approaches most commonly used 72 diagnostics for this novel virus.
2020-02-25 Mao et al Neurological Manifestations of Hospitalized Patients with COVID-19 in Wuhan, China: a retrospective case series study
medrxiv
III-2. Cross Sectional Control

A total of 214 hospitalized patients with confirmed SARS-CoV-2 infection were included in the present analysis.
SARS-CoV-2 was confirmed by real-time RT-PCR assay using a SARS-CoV-2 nucleic acid detection kit according to the manufacturer's protocol (Shanghai bio-germ Medical Technology Co Ltd).
2020-02-26 Gallego et al The COVID-19 outbreak and implications for the Tokyo 2020 Summer Olympic Games
Travel Medicine and Infectious Disease
IV. Other It works to ensure the rapid development of vaccines, diagnostic means, antiviral drugs, and other treatments, and that low and middle-income country have access to them and also seeks a comprehensive risk communication strategy and promotes research and relative scientific advances to this new coronavirus .
2020-02-29 Wilson et al What goes on board aircraft? Passengers include Aedes, Anopheles, 2019-nCoV, dengue, Salmonella, Zika, et al
Travel Medicine and Infectious Disease
IV. Other Diagnostics have been developed and work on therapeutics and vaccines is underway.
2020-02-29 Zhang et al Rapid Molecular Detection of SARS-CoV-2 (COVID-19) Virus RNA Using Colorimetric LAMP
medrxiv
IV. Prevalence Study

In addition to controls, a total of 7 patient RNA samples were tested, 6 of which were determined to be positive by RT-qPCR using ORF1a primers (C q 25-36.5, Table 2 ) and 4 positive with Gene N primers.
Since the initial description of LAMP, a number of advancements in detection technology have helped establish LAMP as a standard method for simple isothermal diagnostics.
2020-03-01 Shen et al Recent advances and perspectives of nucleic acid detection for coronavirus
Journal of Pharmaceutical Analysis
IV. Prevalence Study Their lately protocol for COVID-19 entitled "A protocol for detection of COVID-19 using CRISPR diagnostics" has been reported on website ( which may provide some reference points for researchers interested in further advancing this diagnostics system, highlighting its potential as a multiplexable, portable, rapid, and quantitative detection platform of nucleic acids.

With the advance in molecular biology technology, nucleic acid detection methods have developed rapidly and become a revolutionary technology for virus detection.
2020-03-03 Yang et al The deadly coronaviruses: The 2003 SARS pandemic and the 2020 novel coronavirus epidemic in China
Journal of Autoimmunity
IV. Prevalence Study

In Wang's study , of the 36 patients in the ICU, four patients received high-flow oxygen therapy, 15 patients received non-invasive ventilation, and 17 patients received invasive ventilation (four patients switched to ECMO).
Since the emergence of SARS-CoV and MERS-CoV, basic research on coronaviruses and advances in vaccine preparation technology can significantly shorten the development time of new coronavirus vaccines.
2020-03-04 Memish et al Middle East respiratory syndrome
The Lancet
II. Randomized Controlled Trial

A retrospective study of 136 patients with MERS found that macrolide therapy resulted in no reduction in mortality or faster MERS-CoV RNA clearance compared with those who were not treated with macrolides.
Advances in technology, vaccine platforms, clinical trial designs, and bioinformatics are supporting MERS-CoV vaccine development (appendix .
2020-03-05 Liu et al Viral Architecture of SARS-CoV-2 with Post-Fusion Spike Revealed by Cryo-EM
biorxiv
IV. Other While the world are jointing efforts to develop diagnostics, therapeutics, and vaccines to fight against COVID-19, information about cultivation, purification and super molecular structure of SARS-CoV-2 in their native state is in need urgently.
2020-03-09 Woo et al Sensitive one-step isothermal detection of pathogen-derived RNAs
medrxiv
IV. Other Therefore, SENSR is more suitable for rapid 328 mass production of diagnostic kits than antibody-based diagnostics.
2020-03-10 Jenkins et al In silico approach to accelerate the development of mass spectrometry-based proteomics methods for detection of viral proteins: Application to COVID-19
biorxiv
IV. Prevalence Study Today, protein array and antibody-based methods are falling out of favor in both research and clinical diagnostics, due in large part to the improvements in LCMS technology.
2020-03-10 O’Connell et al The impact of point-of-care testing for influenza A and B on patient flow and management in a medical assessment unit of a general hospital
BMC Res Notes
III-3. Time Series Analysis

RESULTS: The results of the correlation study with a cohort of 54 patients revealed the Abbott ID NOW POCT has 92% sensitivity for the detection of Influenza A, while specificity was 100% for both Influenza A and B.
*Correspondence: sjpoconnell@bonsecours.ie 2 Shannon Applied Biotechnology Centre, Institute of Technology Tralee, Tralee, Co. Kerry, Ireland Full list of author information is available at the end of the article of studies have been reported outlining the performance of the Alere I POCT (now known as Abbott ID NOW) NAAT versus laboratory based methods such as thermocycler rtPCR and viral culture for Influenza testing .
2020-03-12 Liu et al Research and Development on Therapeutic Agents and Vaccines for COVID-19 and Related Human Coronavirus Diseases
ACS Cent Sci
IV. Other Recently, Generex announced that it is developing a COVID-19 vaccine following a contractual agreement with a Chinese consortium comprised of China Technology Exchange, Beijing Zhonghua Investment Fund Management, Biology Institute of Shandong Academy of Sciences, and Sinotek-Advocates International Industry Development.

Their COVID-19 candidate vaccines targeting the S protein of SARS-CoV-2 were developed using their recombinant nanoparticle vaccine technology along with their proprietary adjuvant Matrix-M.
2020-03-14 Lagier et al Testing the repatriated for SARS-Cov2: Should laboratory-based quarantine replace traditional quarantine?
Travel Medicine and Infectious Disease
IV. Other Tests were performed on LightCycler 480 instruments (Roche Diagnostics).
2020-03-16 Kwon et al Drive-Through Screening Center for COVID-19: a Safe and Efficient Screening System against Massive Community Outbreak
J Korean Med Sci
IV. Other This system may also evolve into a DT respiratory clinic, when rapid diagnostic kit, oral treatment options, and/or vaccines for COVID-19 are available in the future.
2020-03-18 Dhama et al COVID-19, an emerging coronavirus infection: advances and prospects in designing and developing vaccines, immunotherapeutics, and therapeutics
Hum Vaccin Immunother
IV. Other 37 NIAID-VRC scientists are developing a vaccine candidate expressing SARS-CoV-2 S protein in the mRNA vaccine platform technology.
2020-03-18 dong et al Highly accurate and sensitive diagnostic detection of SARS-CoV-2 by digital PCR
medrxiv
IV. Other Currently, real-time qPCR (RT-qPCR) is used as the gold standard for diagnostics of SARS-CoV-2.
2020-03-20 Hass et al Integrated Micropillar Polydimethylsiloxane Accurate CRISPR Detection (IMPACT) System for Rapid Viral DNA Sensing
biorxiv
IV. Other 11 Strides have been made to develop POC detection methods which can be deployed in the field, and currently lab-on-chip (LOC) devices or simple test kits which involve real-time polymerase chain reaction (PCR) have emerged as one of the leading choices for meeting the desired criteria.

This miniaturized and fully packed IMPACT chip demonstrates rapid, sensitive, and simple nucleic acid detection and is an ideal candidate for the next generation molecular diagnostic platform for point-of-care (POC) applications, responding to emerging and deadly pathogen outbreaks.
2020-03-20 Gong et al A Tool to Early Predict Severe 2019-Novel Coronavirus Pneumonia (COVID-19) : A Multicenter Study using the Risk Nomogram in Wuhan and Guangdong, China
medrxiv
III-2. Retrospective Cohort

A total of 372 patients with COVID-19 were enrolled, 9 patients younger than 15 years of age were excluded from the study.
This work is funded by the Science and Technology Program of Guangzhou, China .
2020-03-21 Ding et al All-in-One Dual CRISPR-Cas12a (AIOD-CRISPR) Assay: A Case for Rapid, Ultrasensitive and Visual Detection of Novel Coronavirus SARS-CoV-2 and HIV virus
biorxiv
IV. Other Thus, our method has a great potential for developing next-generation point-of-care molecular diagnostics.

Polymerase chain reaction (PCR) method is the most commonly used technology for pathogen nucleic acid detection and has been considered as a "gold standard" for disease diagnostics due to high sensitivity and specificity.
2020-03-23 Vu et al Financing Vaccines for Global Health Security
medrxiv
IV. Prevalence Study In this study, we examine the economic feasibility of developing and supporting a portfolio of vaccines for the world's most threatening emerging infectious diseases (EIDs) as determined by scientific experts, drawing from the list of targets made by the recently launched global initiative, the Coalition for Epidemic Preparedness Innovations (CEPI) .
2020-03-23 Mao et al Can a Paper-Based Device Trace COVID-19 Sources with Wastewater-Based Epidemiology?
Environ Sci Technol
IV. Other Paper analytical devices enable multiplexed, sensitive assays that rival PCR laboratory assays and provide high-quality, fast precision diagnostics for pathogens.
2020-03-27 Pinto et al ACE2 Expression is Increased in the Lungs of Patients with Comorbidities Associated with Severe COVID-19
medrxiv
IV. Other Pathways from the "ChIP-X Enrichment Analysis" and "Epigenomics Roadmap" databases with Adjusted P-value < 10 -10 were selected.

We then checked in the Roadmap Epigenomics Project database to see whether ACE2 locus contained ChIP-seq information for these histone markers.
2020-03-30 Dong et al Understand Research Hotspots Surrounding COVID-19 and Other Coronavirus Infections Using Topic Modeling
medrxiv
IV. Computer Model We found that topics of clinical characterization, epidemiology, and virus transmission are hotspots for COVID-19 at present, while research on pathogenesis, therapeutics, virus diagnostics, vaccines and viral genomics are urgently needed.

Results: Eight topics emerged overall: clinical characterization, pathogenesis research, therapeutics research, epidemiological study, virus transmission, vaccines research, virus diagnostics, and viral genomics.

The results also indicate that studies in diagnostics, therapeutics, vaccines, viral genomics, and pathogenesis are urgently needed to minimize the impact of the COVID-19 outbreak.

Recently, the WHO has published a Global Research Roadmap with immediate, mid-term and longer-term priorities to enable the implementation of priority research .
2020-03-30 Fan et al Medical treatment of 55 patients with COVID-19 from seven cities in northeast China who fully recovered: a single-center, retrospective, observational study
medrxiv
IV. Other This study was funded by the Shenyang Major Science and Technology Innovation R&D Program (JY2020-9-018 to Y. Chen).
2020-03-30 Huang et al A data-driven tool for tracking and predicting the course of COVID-19 epidemic as it evolves
medrxiv
IV. Other Also 104 since it uses the newest diagnostics, with the testing facilities ramped up, hopefully 105 the numbers are more accurate.
2020-03-31 Yu et al Measures for diagnosing and treating infections by a novel coronavirus responsible for a pneumonia outbreak originating in Wuhan, China
Microbes and Infection
IV. Computer Model At present, many companies engaged in the development of biologicals have marketed nucleic acid detection kits for 2019-nCoV, such as the new coronavirus nucleic acid detection kit (double fluorescence PCR method) from Shuoshi Biotechnology.
2020-03-31 Kames et al Sequence analysis of SARS-CoV-2 genome reveals features important for vaccine design
biorxiv
IV. Other Our analysis identified the spike (S) and nucleocapsid (N) proteins as promising targets for deoptimization and suggests a roadmap for SARS-CoV-2 vaccine development, which can be generalizable to other viruses.
2020-04-01 Vogels et al Analytical sensitivity and efficiency comparisons of SARS-COV-2 qRT-PCR assays
medrxiv
IV. Prevalence Study The first SARS-CoV-2 genome sequence was critical for the development of diagnostics 2 , which led to several molecular assays being developed to detect COVID-19 cases .
2020-04-30 Sohrabi et al World Health Organization declares global emergency: A review of the 2019 novel coronavirus (COVID-19)
International Journal of Surgery
IV. Prevalence Study

To date, 85 individuals have tested positive resulting in the UK public health risk for viral infection being raised from low to moderate .
Regarding diagnostic testing, US-based companies such as Co-Diagnostics and the Novacyt's molecular diagnostics division Primerdesign have launched COVID-2019 testing kits for use in the research setting .

14 Barriers to developing and scaling up new diagnostic tests (e.g., market forces), how future coalition and accelerator models (e.g., Coalition for Epidemic Preparedness Innovations) could provide critical funding for diagnostics, and opportunities for a streamlined regulatory environment.

14.0.0.1 Highlights

14.0.0.2 Articles

Date Authors Title LOE(?) & Sample Matches
2020 Schwartz et al Potential Maternal and Infant Outcomes from (Wuhan) Coronavirus 2019-nCoV Infecting Pregnant Women: Lessons from SARS, MERS, and Other Human Coronavirus Infections
Viruses
IV. Prevalence Study

A case-control study to determine the effects of SARS on pregnancy compared 10 pregnant and 40 non-pregnant women with the infection at the Princess Margaret Hospital in Hong Kong .
On 23 January 2020 the Coalition for Epidemic Preparedness Innovations (CEPI) announced three programs to develop a vaccine against the novel Wuhan coronavirus.
2020 ZHANG et al Analysis on the layout of China’s emergency research projects during the public health emergency of COVID-19
Chinese Journal of Medical Science Research Management
IV. Other Results Along with priorities identified for the emergency response and key research agendas, the national science and technology authorities at all levels and scientific research institutions have deployed a series of new science and technology projects, as well as a number of supporting policies and measures.
2020 Kelvin et al Fear of the novel coronavirus
Journal of Infection in Developing Countries
IV. Other Preparedness and quick responses are necessary, but solidarity and cooperation are also key to fighting emerging infectious diseases all over the world.
2020 DU et al Strategies of strengthening the supporting role of science and technology in public health emergency: A case study on the COVID-19
Chinese Journal of Medical Science Research Management
IV. Other Conclusions Through systematically arrangement for disease controlling and prevention, for the industrial supporting, for the health improvement, for the talent training system and for the cooperation and the communication, we need to fasten the technological innovation for better preparation and responding to public health emergencies.
2020-01-27 Nkengasong et al China’s response to a novel coronavirus stands in stark contrast to the 2002 SARS outbreak response
Nat Med
IV. Prevalence Study This investment in core public-health systems and infrastructure will no doubt be critical in the response to the current 2019-nCoV outbreak.
2020-02-05 McCloskey et al SARS to novel coronavirus – old lessons and new lessons
Epidemiology and Infection
IV. Prevalence Study Organisations such as the Global Outbreak Alert and Response Network (GOARN), the Coalition for Epidemic Preparedness Innovations (CEPI), the Global Research Collaboration For Infectious Disease Preparedness (GloPID-R) and the Global Initiative on Sharing All Influenza Data (GISAID) have been supported by the WHO Research Blueprint and its Global Coordinating Mechanism to provide a forum where those with the expertise and capacity to contribute to managing new threats can come together both between and during outbreaks to develop innovative solutions to emerging problems.
2020-02-19 Heaton et al Frontiers in antiviral therapy and immunotherapy
Clin Transl Immunology
IV. Prevalence Study Plumbing work on research funding and development pipelines through recent changes in the structure of government funding, 2 new public and private joint ventures and specialist undergraduate and postgraduate courses now aim to incorporate pathways to translation at the earliest stages.

Given the reciprocal efforts at accelerating bilateral engagement currently underway, 17 the prospects for new areas of international cooperation and mobility have never been more exciting nor urgent.
2020-02-28 Fadel et al Coronavirus outbreak: the role of companies in preparedness and responses
The Lancet Public Health
IV. Other All health professionals should be involved in the development and implementation of recommendations for companies and their environments
2020-03-02 Brennan et al Responding to health emergencies in the Eastern Mediterranean region in times of conflict
The Lancet
IV. Other WHO's global COVID-19 strategic preparedness and response plan13 therefore prioritises countries with weak health systems for technical and operational support from international partners.

WHO's global COVID-19 strategic preparedness and response plan 13 therefore prioritises countries with weak health systems for technical and operational support from international partners.
2020-03-04 Chang et al Weaponized Interdependence: China's Economic Statecraft and Social Penetration against Taiwan
Orbis
IV. Prevalence Study 10 More important, economic globalization, the development of supply chains, and breakthroughs of network technology have jointly transformed and updated China's coercive capabilities.

The three targets, Silicon Precision Industries Co. (SPIC), Powertech Technology Inc., and ChipMOS Technologies Inc., are all leading chip packing and testing companies in the global arena.
2020-03-04 Shattuck et al The Race to Zero?: China's Poaching of Taiwan's Diplomatic Allies
Orbis
IV. Other 34 The port project would have required a big investment in a project with poor prospects for success, and funding the political campaign of another country's president would have been at odds with Taiwan's democratic norms and its stance against foreign interference in Taiwan's elections.
2020-03-05 Wilder-Smith et al Can we contain the COVID-19 outbreak with the same measures as for SARS?
The Lancet Infectious Diseases
IV. Prevalence Study

On Feb 18, 2020, the Chinese Center for Disease Control and Prevention published their data of the first 72 314 patients including 44 672 patients with confirmed COVID19.
Organisations such as the Global Outbreak Alert and Response Network, the Coalition for Epidemic Preparedness Innovations, and the Global Research Collaboration For Infectious Disease Preparedness, supported by the WHO Research Blueprint and its Global Coordinating Mechanism, were able to accelerate the outbreak response and rapidly initiate technical platforms for the development of vaccines and therapeutics.
2020-03-10 Chan et al Research Frontiers of Health Emergency and Disaster Risk Management: What Do We Know So Far?
Int J Environ Res Public Health
IV. Prevalence Study Existing surveillance databases, new study tools, and innovation methodologies may help to identify population health risks and support Health-EDRM policy development.

highlighted the development need for relevant research methodologies, risk communication approaches, health data management strategies, practical health emergency study ethical guidelines, bridging global research capacity disparities, and infrastructure constraints, to ensure knowledge advancement in Health-EDRM.
2020-03-12 Liu et al Research and Development on Therapeutic Agents and Vaccines for COVID-19 and Related Human Coronavirus Diseases
ACS Cent Sci
IV. Other Manufacture of this batch was funded by the Coalition for Epidemic Preparedness Innovations.
2020-03-13 Rodriguez-Morales et al Clinical, laboratory and imaging features of COVID-19: A systematic review and meta-analysis
Travel Medicine and Infectious Disease
I. Systematic Review

Our review included 19 studies that were published between January 1, 2020, and February 21, 2020, most of them from China and one from Australia (Table 1) , including a total of 2874 patients, ranging from a case series of 9 to a cross-sectional study of 1590 .
Preparedness at different levels, facing a new clinical disease, demands efforts in epidemiological, diagnostic, therapeutic, and preventive fields during a potential pandemic , that threatens to spread to new territories (> 115) and areas with the risk of epidemics.
2020-03-17 Buckee et al Improving epidemic surveillance and response: big data is dead, long live big data
The Lancet Digital Health
IV. Computer Model Much more investment is needed in the validation, implementation, and scaling up of innovations in close intellectual partnership with stakeholders who are responsible for delivering them, 3 rather than continuing to fund the proliferation of solutions divorced from the problems themselves.

Regional or local teams with analytical training and ongoing relationships with government and industry partners should lead to flexible modelling approaches that leverage large curated datasets and international analytical expertise, building on collaborations developed when there are no emerging or ongoing outbreaks.

Urgent investment in surveillance systems and global partnerships are needed to prepare for the pandemics that will continue to emerge in the coming decades.
2020-03-18 Dhama et al COVID-19, an emerging coronavirus infection: advances and prospects in designing and developing vaccines, immunotherapeutics, and therapeutics
Hum Vaccin Immunother
IV. Other 35 The Coalition for Epidemic Preparedness Innovations (CEPI) recently announced the initiation of three programs aimed to develop COVID-19 vaccines by utilizing established vaccine platforms.
2020-03-18 Kandel et al Health security capacities in the context of COVID-19 outbreak: an analysis of International Health Regulations annual report data from 182 countries
The Lancet
IV. Prevalence Study The analyses of the operational readiness index have been used to support the development of a draft WHO strategic preparedness and response plan for COVID-19.
2020-03-20 Kriz et al Teaching-practice as a critical bridge for narrowing the research-practice gap
Industrial Marketing Management
III-3. Time Series Analysis

The wicked problem sessions attract over 40 participants (policy, practitioners, academics), with action research/ learning sessions limited to approximately 12 participants (practitioners and researchers).
Increasingly, the Chinese students/executives in the program are now often creating ventures pitched at service opportunities and social innovations.

The projects have yielded rich research insights into the growth strategies of local companies across multiple industries as well as accelerating their development in practice by embedding novel strategic frameworks into the local business ecosystem.

Nine companies were involved in an endeavour to improve industry outcomes by upskilling participants, building family business leadership skills and helping small businesses unlock growth opportunities.

-Advances leadership quality -Advocacy for lifelong learning -Positive influences on key decision makers -Improved financial returns and leadership skills -Increased ability to manage rapid change -Immersion in EBM -Complex problem solving through "wicked" methods -Access to research in top companies -Alumni networks -On-going research grant opportunities -Increases currency in research and contributions -Immediate feedback mechanism for educators to industry leaders -Keeps educators savvy with higher-order needs of top management teams -Adds executive insights to management and marketing schools

The New Venture Creation course has provided important innovation skills and encouraged student teams to create and kick-start real ventures built around team capabilities, analysis of combined resources and clarification of a feasible opportunity.
2020-03-23 Vu et al Financing Vaccines for Global Health Security
medrxiv
IV. Prevalence Study In this study, we examine the economic feasibility of developing and supporting a portfolio of vaccines for the world's most threatening emerging infectious diseases (EIDs) as determined by scientific experts, drawing from the list of targets made by the recently launched global initiative, the Coalition for Epidemic Preparedness Innovations (CEPI) .

While governments and international agencies have striven to create incentives to attract additional private sector investment in vaccine development, these efforts have so far failed in attracting sufficient capital to enhance preparedness against the world's most deadly emerging pathogens .

While challenges exist (e.g., sustained funding commitments), new initiatives such as CEPI can learn important lessons from these examples .
2020-03-26 Zheng et al Recommendations and guidance for providing pharmaceutical care services during COVID-19 pandemic: A China perspective
Research in Social and Administrative Pharmacy
IV. Other Results Community pharmacy management teams shall support PC services by providing adequate supply of COVID-19 related medications and preventative products, following environment regulations, and providing sufficient staff trainings.
2020-03-27 Yelin et al Evaluation of COVID-19 RT-qPCR test in multi-sample pools
medrxiv
IV. Other We hope that such implementation of a pool test for COVID-19 would allow expanding current screening capacities thereby enabling the expansion of detection in the community, as well as in close integral groups, such as hospital departments, army units, or factory shifts.
2020-03-27 Weissgerber et al Mitigating the impact of conference and travel cancellations on researchers’ futures
PMC
IV. Other Institutions may also consider offering advances to ECRs who are awaiting refunds or reimbursement from conference organizers, travel providers and funding agencies.
2020-03-27 Lee et al Epidemic preparedness in urban settings: new challenges and opportunities
The Lancet Infectious Diseases
IV. Prevalence Study However, urban settings also offer new opportunities (table), such as securing the commitment of local leaders and strengthening public health networks to prevent, detect, and respond to disease threats early.
2020-03-28 Foddai et al Base protocol for real time active random surveillance of coronavirus disease (COVID-19) – Adapting veterinary methodology to public health
One Health
IV. Prevalence Study Collaborations across countries and sectors as a One Health World could be a milestone.
2020-03-30 Erikson et al Will financial innovation transform pandemic response?
The Lancet Infectious Diseases
IV. Other The pandemic bond is an iteration of the trend of turning to the private sector for global health and humanitarian funding solutions.
2020-03-30 Dong et al Understand Research Hotspots Surrounding COVID-19 and Other Coronavirus Infections Using Topic Modeling
medrxiv
IV. Computer Model Data used in this study were obtained from CORD-19, which was prepared by the White House and a coalition of leading research groups in response to the COVID-19 pandemic .
2020-03-30 Truelove et al COVID-19: Projecting the impact in Rohingya refugee camps and beyond
medrxiv
IV. Other The Inter-Agency Standing Committee recently released interim guidance for scaling up the COVID-19 response in camps and camp-like settings that highlights inclusion, protection, and readiness; and has since developed preliminary multisectoral preparedness and response plans.
2020-03-30 Gupta et al Trend Analysis and Forecasting of COVID-19 outbreak in India
medrxiv
IV. Computer Model The Government of India is coming up with quick financial packages for improving the infrastructure and procuring more number of testing kits and developing more number of testing labs.
2020-03-30 Lin et al Which Measures are Effective in Containing COVID-19? Empirical Research Based on Prevention and Control Cases in China
medrxiv
IV. Prevalence Study The price of this is to force companies and other institutions to stop operations, which is at huge cost.
2020-03-31 Yamey et al Ensuring global access to COVID-19 vaccines
The Lancet
IV. Other In February, 2020, the World Bank and the Coalition for Epidemic Preparedness Innovations (CEPI), which funds development of epidemic vaccines, co-hosted a global consultation on these goals.

Investments should proceed in tandem to build national systems for delivery of potential vaccines-eg, using domestic financing and external financing from the World Bank Group's $14 billion COVID-19 Fast Track Facility 13 and reallocations from the Global Fund to Fight AIDS, Tuberculosis and Malaria, Gavi, and Global Financing Facility grants for service delivery.

With advanced market commitments, donors make funding commitments to vaccine manufacturers and, in exchange, companies sign a legally binding commitment to provide the vaccines at a price affordable to low-income and middle-income countries.

8 IFFIm was created to support Gavi, the Vaccine Alliance, but could be used to finance CEPI's COVID-19 vaccine efforts.
2020-03-31 Singer et al What is ahead for health policy and technology in the 2020s?
Health Policy and Technology
IV. Other Trade and tariff barriers arising from evolving isolationist policies of the USA are also likely to restrict progress on implementation and the health impact of achieving the UN's Sustainable Development Goals, not least through increased international costs of diagnostics, devices and medicines.
2020-04-15 Musazzi et al New regulatory strategies to manage medicines shortages in Europe
International Journal of Pharmaceutics
IV. Prevalence Study The unavailability of medicinal products to patients can be due to supply-related factors (e.g., manufacturing issues, regulatory issues, logistics, distribution) and demand-related ones (e.g., fluctuating drug demand, parallel market, tendering, price and reimbursement policies).
2020-04-30 Kapata et al Is Africa prepared for tackling the COVID-19 (SARS-CoV-2) epidemic. Lessons from past outbreaks, ongoing pan-African public health efforts, and implications for the future
International Journal of Infectious Diseases
IV. Other Increased governmental and donor investments are required to advance locally led, world-class public health work with surveillance, data and analytics capabilities and further expanding state-of-the-art laboratory capacities with more J o u r n a l P r e -p r o o f trained personnel to sustain capacity to rapidly respond to outbreaks at their source.
2020-05-31 Friedman et al She Ji: The Next Five Years
She Ji: The Journal of Design, Economics, and Innovation
IV. Other One stream of articles focuses on design innovation in industry, business, non-profit services, and government by promoting a framework of economic and social value creation.

15 New platforms and technology (e.g., CRISPR) to improve response times and employ more holistic approaches to COVID-19 and future diseases.

15.0.0.1 Highlights

15.0.0.2 Articles

Date Authors Title LOE(?) & Sample Matches
2020 Allam et al On the Coronavirus (COVID-19) Outbreak and the Smart City Network: Universal Data Sharing Standards Coupled with Artificial Intelligence (AI) to Benefit Urban Health Monitoring and Management
Healthcare
IV. Prevalence Study Here, as technological tools and laboratories around the world share data and collectively work to devise tools and cures, similar efforts should be considered between smart city professionals on how collaborative strategies could allow for the maximization of public safety on such and similar scenarios.

This is valid as smart cities host a rich array of technological products that can assist in early detection of outbreaks; either through thermal cameras or Internet of Things (IoT) sensors, and early discussions could render efforts towards better management of similar situations in case of future potential outbreaks, and to improve the health fabric of cities generally.
2020 Xinguang Chen et al First two months of the 2019 Coronavirus Disease (COVID-19) epidemic in China: real-time surveillance and evaluation with a second derivative model
Global Health Research and Policy
IV. Prevalence Study Despite the limitations, this study provided new data to encourage those who are infected to better fight against the infections; to inform and encourage the general public, the medical and health professionals and the government to continue their current measures and to think of more measures that are innovative and effective to end the COVID-19 epidemic.
2020-02-04 Zhang et al Recent advances in the detection of respiratory virus infection in humans
Journal of Medical Virology
IV. Other With the development of modern technologies, new diagnostic strategies, including multiplex nucleic acid amplification and microarray-based assays, are emerging.
2020-02-04 Randhawa et al Machine learning using intrinsic genomic signatures for rapid classification of novel pathogens: COVID-19 case study
biorxiv
IV. Other Comparative genomics beyond 65 alignment-based approaches have benefited from the computational power of machine 66 learning.
2020-02-05 Zhou et al Network-based Drug Repurposing for Human Coronavirus
medrxiv
IV. Other Computational approaches offer novel testable hypotheses for systematic drug repositioning [8-10, 12, 13] .
2020-02-19 Heaton et al Frontiers in antiviral therapy and immunotherapy
Clin Transl Immunology
IV. Prevalence Study 4 I anticipate international efforts in these areas over the coming decade will enable the tapping of useful new biological functions and processes, methods for controlling infection, and the deployment of symbiotic or subclinical viruses in new therapies and biotechnologies that are so crucially needed.
2020-02-21 alam et al Functional pangenome analysis suggests inhibition of the protein E as a readily available therapy for COVID-2019
biorxiv
IV. Other This approach, based on using panX 12 , allows us to achieve a higher sensibility in the detection of gene clusters.
2020-02-23 Hou et al Development and Evaluation of A CRISPR-based Diagnostic For 2019-novel Coronavirus
medrxiv
IV. Other The diagnostic performance of CRISPR-nCoV was assessed and compared across three technology platforms (mNGS, RT-PCR and CRISPR).

The copyright holder for this preprint (which was not peer-reviewed) is Here, to address this question and the expanding clinical needs, we developed CRISPR-nCoV, 78 a rapid assay for 2019-nCoV detection, and compared the diagnostic performance among 79 three different technological platforms: metagenomic sequencing, RT-PCR and CRISPR.
2020-02-26 Robson et al Computers and viral diseases. Preliminary bioinformatics studies on the design of a synthetic vaccine and a preventative peptidomimetic antagonist against the SARS-CoV-2 (2019-nCoV, COVID-19) coronavirus
Computers in Biology and Medicine
IV. Other Q-UEL tools, or other similar approaches, can help there.
2020-02-26 Wang et al WeChat, a Chinese social media, may early detect the SARS-CoV-2 outbreak in 2019
medrxiv
IV. Other Technologies using social media, search queries and other Internet resources offer novel and economic approaches for detecting and tracking emerging diseases and have been successfully used in the cases of SARS , influenza , dengue , etc.
2020-02-29 Zhang et al Rapid Molecular Detection of SARS-CoV-2 (COVID-19) Virus RNA Using Colorimetric LAMP
medrxiv
IV. Prevalence Study

In addition to controls, a total of 7 patient RNA samples were tested, 6 of which were determined to be positive by RT-qPCR using ORF1a primers (C q 25-36.5, Table 2 ) and 4 positive with Gene N primers.
These molecular methods include metagenomics sequencing mNGS and RT-qPCR , both are excellent and sensitive techniques, but approaches not without limitations.
2020-03-01 Shen et al Recent advances and perspectives of nucleic acid detection for coronavirus
Journal of Pharmaceutical Analysis
IV. Prevalence Study With the advance in molecular biology technology, nucleic acid detection methods have developed rapidly and become a revolutionary technology for virus detection.
2020-03-02 Wu et al Mutations, Recombination and Insertion in the Evolution of 2019-nCoV
biorxiv
IV. Other will provide insights to rapidly develop novel strategies to treat or prevent diseases associated with the novel emerging infectious viruses.
2020-03-03 Yang et al The deadly coronaviruses: The 2003 SARS pandemic and the 2020 novel coronavirus epidemic in China
Journal of Autoimmunity
IV. Prevalence Study

In Wang's study , of the 36 patients in the ICU, four patients received high-flow oxygen therapy, 15 patients received non-invasive ventilation, and 17 patients received invasive ventilation (four patients switched to ECMO).
Big data and artificial intelligence systems are tools that can be used to fully integrate the information, conduct comprehensive research and analyze public health risks.
2020-03-06 Wang et al Nanopore target sequencing for accurate and comprehensive detection of SARS-CoV-2 and other respiratory viruses
medrxiv
IV. Other Whereas the detection throughput of NTS is not 274 high at present, the NTS method can be integrated into widely used automated or semi-automated 275 platforms to improve the detection throughput in the future 21-23 .
2020-03-09 Woo et al Sensitive one-step isothermal detection of pathogen-derived RNAs
medrxiv
IV. Other In order to rapidly diagnose infectious diseases, a nucleic acid-based 35 diagnosis has emerged as an alternative to the conventional culture-based, or immunoassay-36 based, approaches due to their rapidity or specificity 4-6 .
2020-03-10 Chan et al Research Frontiers of Health Emergency and Disaster Risk Management: What Do We Know So Far?
Int J Environ Res Public Health
IV. Prevalence Study Existing surveillance databases, new study tools, and innovation methodologies may help to identify population health risks and support Health-EDRM policy development.

Not only will such knowledge facilitate a better understanding of new emerging diseases, but also identify treatments, enable a better uptake of community health protection behaviours, examine the usefulness of modern public health measures, and evaluate the effectiveness of technology innovation in health protection; it will also serve to remind researchers, academic, and policy makers that the landscape of Health-EDRM-related research is constantly evolving with global crises and emergencies.
2020-03-10 Barra et al Analytical sensibility and specificity of two RT-qPCR protocols for SARS-CoV-2 detection performed in an automated workflow
medrxiv
IV. Other The use of the synthetic RT-qPCR target to investigate novel assays diagnostic parameters in automated workflows is a quick, simple effective way to be prepared for upcoming threats.
2020-03-10 Broughton et al Rapid Detection of 2019 Novel Coronavirus SARS-CoV-2 Using a CRISPR-based DETECTR Lateral Flow Assay
medrxiv
IV. Other Key advantages of our approach over 127 existing methods such as qRT-PCR include isothermal signal amplification for rapid 128 target detection obviating the need for thermocycling, single nucleotide target 129 specificity (guide RNAs at the N2 site can distinguish SARS-CoV-2 from SARS-CoV 130 and MERS-CoV), integration with portable, low-cost reporting formats such as lateral 131 flow strips, and quick development cycle to address emerging threats from novel 132 zoonotic viruses (<2 weeks for SARS-CoV-2, Supplementary Fig.
2020-03-11 Chopra et al How Should U.S. Hospitals Prepare for Coronavirus Disease 2019 (COVID-19)?
Ann Intern Med
IV. Other Hospitals and health systems must develop agile ways to transmit timely and critical information in times of crises.
2020-03-11 Ayebare et al Adoption of COVID-19 triage strategies for low-income settings
The Lancet Respiratory Medicine
IV. Other This approach is simple and uses readily available technology.
2020-03-12 Ge et al A data-driven drug repositioning framework discovered a potential therapeutic agent targeting COVID-19
biorxiv
IV. Other We developed a data-driven drug repositioning framework, which applies both machine learning and statistical analysis approaches to systematically integrate and mine large-scale knowledge graph, literature and transcriptome data to discover the potential drug candidates against SARS-CoV-2.
2020-03-14 Lopez-Rincon et al Accurate Identification of SARS-CoV-2 from Viral Genome Sequences using Deep Learning
biorxiv
IV. Prevalence Study

Next, 115 we removed all the repeated sequences, obtaining a total of 384 unique sequences, with 45 samples belonging to SARS-CoV-2.
Molecular techniques, such as quantitative real-time RT-PCR and nucleic acid sequencing methods, are widely used to identify pathogens.
2020-03-16 Zhou et al Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2
Cell Discov
IV. Other From a translational perspective, if broadly applied, the network tools developed here could help develop effective treatment strategies for other emerging viral infections and other human complex diseases as well.

Computational approaches offer novel testable hypotheses for systematic drug repositioning 13, 14 .
2020-03-17 Buckee et al Improving epidemic surveillance and response: big data is dead, long live big data
The Lancet Digital Health
IV. Computer Model Despite the challenges above, ongoing advances in computational power, methods, and new data streams offer genuine hope for better surveillance and useful forecasting systems.
2020-03-17 Xiao et al Multiple approaches for massively parallel sequencing of HCoV-19 (SARS-CoV-2) genomes directly from clinical samples
biorxiv
IV. Prevalence Study

Two to five SNVs were identified within each clinical 182 sample, and in all the seven samples, SNVs identified by the three methods were concord-183 ant except that capture missed one SNV at position 16535 in GZMU0014 (Fig.
HCoV-19-RPM for amplicon sequencing data was calculated by the same 384 pipelines we applied for metatranscriptomic and hybrid capture sequencing data.
2020-03-18 Jin et al Core Outcome Set for Clinical Trials on Coronavirus Disease 2019 (COS-COVID)
Engineering
IV. Prevalence Study

The consensus meeting was held on 24 February 2020, and involved 20 participants.
In order to overcome these problems, experts in evidence-based medicine and clinical research methodology have put forward strategies to develop core outcome sets (COSs).
2020-03-20 Kagan et al Scientometric Trends for Coronaviruses and Other Emerging Viral Infections
biorxiv
IV. Prevalence Study One approach is to gather data using different surveillance systems.
2020-03-20 Kriz et al Teaching-practice as a critical bridge for narrowing the research-practice gap
Industrial Marketing Management
III-3. Time Series Analysis

The wicked problem sessions attract over 40 participants (policy, practitioners, academics), with action research/ learning sessions limited to approximately 12 participants (practitioners and researchers).
The experience of business innovation (Von Hippel, 2005) suggests that researchers who expose their emerging theories to early testing in an educational context will generate more novel and robust theories faster than those who try perfecting their work in research silos.
2020-03-21 Ding et al All-in-One Dual CRISPR-Cas12a (AIOD-CRISPR) Assay: A Case for Rapid, Ultrasensitive and Visual Detection of Novel Coronavirus SARS-CoV-2 and HIV virus
biorxiv
IV. Other Therefore, we anticipate that the AIOD-CRISPR assay will facilitate CRISPRbased next-generation molecular diagnostics towards point-of-care applications.
2020-03-23 Mao et al Can a Paper-Based Device Trace COVID-19 Sources with Wastewater-Based Epidemiology?
Environ Sci Technol
IV. Other Paper analytical devices enable multiplexed, sensitive assays that rival PCR laboratory assays and provide high-quality, fast precision diagnostics for pathogens.
2020-03-24 Banerjee et al Estimating excess 1- year mortality from COVID-19 according to underlying conditions and age in England: a rapid analysis using NHS health records in 3.8 million adults
medrxiv
IV. Prevalence Study

We included 3,862,012 individuals aged ≥30 years: 1,957, 935 (50.7%) female, 3,331,280 (86.3%) ≤70 years (mean age 43.5 in male and females) and 530732 (13.7%) >70 years (mean age 78.1 in males and 80.2 in females) (Suppl Table 1 ).
In these times, our science must cross disciplines, disease specialisms and national and jurisdictional borders even more than before and we invite colleagues to improve, develop and validate our models and update estimates and projections using richer, more real time real-world data.
2020-03-24 Hoe GAN et al Preventing intra-hospital infection and transmission of COVID-19 in healthcare workers
Safety and Health at Work
IV. Other All other system components, namely work tasks, technologies and tools, environmental factors and organizational conditions, serve to enable the healthcare worker to perform his or her role safely and effectively.
2020-03-26 Zheng et al Recommendations and guidance for providing pharmaceutical care services during COVID-19 pandemic: A China perspective
Research in Social and Administrative Pharmacy
IV. Other These approaches can also be applied in other countries as new 115 strategies to provide PC and can potentially create new forms of pharmacy service in the future.
2020-03-28 Bradley et al A systems approach to preventing and responding to COVID-19
EClinicalMedicine
IV. Other Systems thinking and methods can help achieve this.
2020-03-29 Thompson et al COVID-19 in Endoscopy: Time to do more?
Gastrointestinal Endoscopy
IV. Prevalence Study It is vital to keep monitoring these metrics throughout the COVID-19 period so that any signals of potential problems can be detected early and more proactive strategies deployed.
2020-03-29 Venkatakrishnan et al Knowledge synthesis from 100 million biomedical documents augments the deep expression profiling of coronavirus receptors
biorxiv
IV. Prevalence Study

This observation was corroborated by complementary gene expression analysis of over 250,000 bulk RNA-seq samples from GTEx 23, 24 and the Gene Expression Omnibus (GEO) along with protein expression analysis from healthy tissue proteomics and immunohistochemistry (IHC) datasets , where lung and other respiratory tissues consistently show lower ACE2 expression compared to the digestive tract and kidney (Figure S3A-D) .
A deep profiling of ACE2 expression in the human body demands a platform that synthesizes biomedical insights encompassing multiple scales, modalities, and pathologies described across the scientific literature and various omics siloes.
2020-03-30 James et al Suppression and Mitigation Strategies for Control of COVID-19 in New Zealand
medrxiv
IV. Prevalence Study Mitigation strategies, which aim to allow the epidemic to go ahead at a controlled rate, keep demand on healthcare systems under capacity, and deliver herd immunity, are a tempting approach for the control of Covid-19.
2020-03-30 Gupta et al Trend Analysis and Forecasting of COVID-19 outbreak in India
medrxiv
IV. Computer Model The study uses exploratory data analysis to report the current situation and uses time-series forecasting methods to predict the future trends.
2020-03-31 Fausto et al Creating a Palliative Care Inpatient Response Plan for COVID19 – The UW Medicine Experience
Journal of Pain and Symptom Management
IV. Other In this context, our regional healthcare systems are challenged to develop strategies to provide high-quality care to patients with COVID-19.
2020-03-31 Lai et al Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): The epidemic and the challenges
International Journal of Antimicrobial Agents
IV. Other All effort s are being made to slow the spread of the illness in order to provide time to better prepare healthcare systems and the general public, to better characterise COVID-19 to guide public-health recommendations, and to develop timely diagnostics, therapeutics and vaccines .
2020-03-31 Li et al The epidemic of 2019-novel-coronavirus (2019-nCoV) pneumonia and insights for emerging infectious diseases in the future
Microbes and Infection
IV. Prevalence Study

11 January 2020 41 patients have been diagnosed to have infection of the novel coronavirus, with 763 close contacts, 7 severe cases and the first death.
New diagnostic strategies including multiplex nucleic acid amplification and microarray-based assays may help in epidemiologic monitoring, along with taking effective prevention steps .
2020-04-01 Amir-Behghadami et al The importance of designing and implementing participatory surveillance system: An approach as early detection and prevention of novel coronavirus (2019-nCov)
American Journal of Infection Control
IV. Other 2 The aforementioned problems have caused the world health systems (especially health systems in the affected countries) to make changes in order to improve and enhance their health systems.
2020-05-31 Friedman et al She Ji: The Next Five Years
She Ji: The Journal of Design, Economics, and Innovation
IV. Other Innovation requires integrating ideas, economics, and technology to create new knowledge at the intersection of different fields.
2020-12-31 Song et al Prospect and application of Internet of Things technology for prevention of SARIs
Clinical eHealth
IV. Prevalence Study The Internet of Things (IoT) technology can be employed to achieve these goals.

In the 21st century, with the combination of wireless sensors and Internet technology, clinicians have been able to apply this convenient and more accurate measurement technology for the observation and prevention of disease.

16 Coupling genomics and diagnostic testing on a large scale.

16.0.0.1 Highlights

16.0.0.2 Articles

Date Authors Title LOE(?) & Sample Matches
2020 Hui et al The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health — The latest 2019 novel coronavirus outbreak in Wuhan, China - International Journal of Infectious Diseases
International Journal of Infectious Diseases
IV. Other The genetic sequence of the 2019-nCoV has become available to the WHO on 12 Jan 2020 and this has facilitated the laboratories in different countries to produce specific diagnostic PCR tests for detecting the novel infection (WHO, 2020b) .
2020 Pang et al Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review
Journal of Clinical Medicine
I. Systematic Review

Of the total of 570 unique studies on 2019-nCoV, SARS CoV or MERS-CoV vaccines screened, only four were eventually included in the review.
These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis.
2020 Kelvin et al Fear of the novel coronavirus
Journal of Infection in Developing Countries
IV. Other The novel coronavirus has a homology with SARS and tools for rapid diagnostic testing have been developed .
2020 Amodio et al Outbreak of Novel Coronavirus (SARS-Cov-2): First Evidences From International Scientific Literature and Pending Questions
Healthcare (Basel)
IV. Prevalence Study The genetic sequence of the SARS-CoV-2 has been shared on 10 January, 2020, in order to allow the production of specific diagnostic PCR tests in different countries for detecting the novel infection .
2020 Voice from China: nomenclature of the novel coronavirus and related diseases
Chin Med J (Engl)
IV. Other In more recent times, genetic sequence-based tests have advanced, and such genotyping tests have been able to provide a more rapid and precise typing approach than serological tests.
2020 Ralph et al 2019-nCoV (Wuhan virus), a novel Coronavirus: Human-to-human transmission, travel-related cases, and vaccine readiness
Journal of Infection in Developing Countries
IV. Prevalence Study

On 8 January 2020, it was reported that a novel coronavirus had been sequenced from one patient and subsequently identified in some of the other patients with pneumonia , later reported as 15 of the 59 patients .
The number of cases in Wuhan continued to increase due to retrospective testing, new cases, and changes in diagnostic evaluation for etiological agents .

At the same website PCR primer sets can be found for diagnostic testing.
2020 Gralinski et al Return of the Coronavirus: 2019-nCoV
Viruses
IV. Prevalence Study

The novel CoV (2019-nCoV) was isolated from a single patient and subsequently verified in 16 additional patients .
The rapid release of 2019-nCoV sequences permitted the research community to quickly become engaged, providing analysis and developing diagnostic tests.
2020-02-04 Randhawa et al Machine learning using intrinsic genomic signatures for rapid classification of novel pathogens: COVID-19 case study
biorxiv
IV. Other Comparative genomics beyond 65 alignment-based approaches have benefited from the computational power of machine 66 learning.
2020-02-04 Zhang et al Recent advances in the detection of respiratory virus infection in humans
Journal of Medical Virology
IV. Other With the development of modern technologies, new diagnostic strategies, including multiplex nucleic acid amplification and microarray-based assays, are emerging.
2020-02-07 Gilbert et al Preparedness and vulnerability of African countries against introductions of 2019-nCoV
medrxiv
IV. Prevalence Study Some lack the diagnostic for rapid testing for the virus, and, if cases are imported, tests will need to be performed abroad.
2020-02-11 Gorbalenya et al Severe acute respiratory syndrome-related coronavirus: The species and its viruses – a statement of the Coronavirus Study Group
biorxiv
IV. Other Comparative genomics forms also the basis for PCR assays that are suitable to detect established viruses and their groups in vitro.
2020-02-11 Khan et al Novel coronavirus: how things are in Wuhan
Clinical Microbiology and Infection
IV. Other Scientists in China are working efficiently, as observed by the early detection of the virus, sequencing of its first genome, designing of rapid detection kits, isolation of the virus in the laboratory and developing a vaccine .
2020-02-13 Reusken et al Laboratory readiness and response for novel coronavirus (2019-nCoV) in expert laboratories in 30 EU/EEA countries, January 2020
Euro Surveill
IV. Other This rapid assessment of the readiness of EU/EEA laboratories for molecular detection of 2019-nCoV demonstrated a fast implementation of molecular diagnostics by the European specialised laboratory networks with a good geographical coverage for testing.
2020-02-18 Peng et al Epidemic analysis of COVID-19 in China by dynamical modeling
medrxiv
IV. Computer Model Meanwhile, this model is validated by data correlation analysis, predicting the recent public data, and back- tracking, as well as sensitivity analysis.
2020-02-21 Cheng et al Scabies: Application of the Novel Identify-Isolate-Inform Tool for Detection and Management
West J Emerg Med
IV. Prevalence Study

36 Advising patients and parents of young patients to keep fingernails short and clean can assist with preventing secondary infections.
30 Serological tests are emerging for both diagnosis and monitoring of treatment efficacy.
2020-02-28 Shah et al Guide to Understanding the 2019 Novel Coronavirus
Mayo Clinic Proceedings
IV. Other 8 Diagnosis is based on polymerase chain reaction testing.
2020-03-03 Yang et al The deadly coronaviruses: The 2003 SARS pandemic and the 2020 novel coronavirus epidemic in China
Journal of Autoimmunity
IV. Prevalence Study

In Wang's study , of the 36 patients in the ICU, four patients received high-flow oxygen therapy, 15 patients received non-invasive ventilation, and 17 patients received invasive ventilation (four patients switched to ECMO).
However, because of a shortage of diagnostic reagents for SARS-CoV-2 detection, different guidelines or programs emphasized comprehensive analysis based on epidemiological history, clinical manifestations and imaging examinations in diagnosis.

Sampling techniques, extraction and detection of viral nucleic acids, and diagnostic reagents may affect the test results.
2020-03-04 Bi et al Epidemiology and Transmission of COVID-19 in Shenzhen China: Analysis of 391 cases and 1,286 of their close contacts
medrxiv
IV. Prevalence Study

Time from symptom onset to death was marked by "+" for the three patients who have died.
Contact-based surveillance is the identification of cases through monitoring and testing of close contacts of confirmed cases.
2020-03-05 Li et al Molecular immune pathogenesis and diagnosis of COVID-19
Journal of Pharmaceutical Analysis
IV. Prevalence Study

Virus genome sequencing of five patients with pneumonia hospitalized from December 18 to December 29, 2019, revealed the presence of a previously unknown β-CoV strain in all of them .
Clinical diagnosis of COVID-19 is mainly based on epidemiological history, clinical manifestations and some auxiliary examinations, such as nucleic acid detection, CT scan, immune identification technology (Point-of-care Testing (POCT) of IgM/IgG, enzyme-linked immunosorbent assay (ELISA)) and blood culture.
2020-03-14 Li et al High sensitivity detection of coronavirus SARS-CoV-2 using multiplex PCR and a multiplex-PCR-based metagenomic method
biorxiv
IV. Computer Model Paragon Genomics' CleanPlex® multiplex PCR reagents and protocol were used.
2020-03-17 Eden et al An emergent clade of SARS-CoV-2 linked to returned travellers from Iran
biorxiv
IV. Other From a public health perspective, the real-time whole genome sequencing (WGS) of emerging viruses enables the informed development and design of molecular diagnostic methods, and tracing patterns of spread across multiple epidemiological scales (i.e.
2020-03-19 Arshad Ali et al The outbreak of Coronavirus Disease 2019 (COVID-19)—An emerging global health threat
Journal of Infection and Public Health
III-3. Time Series Analysis

In 2002, a pandemic of SARS occurred endangering the lives of 8098 individuals with a mortality of 774 patients .
The diagnostic tests available were rapidly updated to identify 2019-nCoV, allowing early recognition and detection of the cases.
2020-03-19 Roussel et al SARS-CoV-2: fear versus data
International Journal of Antimicrobial Agents
IV. Prevalence Study

Among them, 543 samples were positive for coronaviruses, with two deaths (mortality rate 0.36%): 277 samples were HKU1, 146 samples were NL63, 77 samples were OC43 and 43 samples were 229E.
Molecular biology is used for diagnosis.
2020-03-20 Amrane et al Rapid viral diagnosis and ambulatory management of suspected COVID-19 cases presenting at the infectious diseases referral hospital in Marseille, France, - January 31st to March 1st, 2020: A respiratory virus snapshot
Travel Medicine and Infectious Disease
IV. Other The genome sequence of SARS-CoV-2 enabled the rapid design and implementation of dedicated point-of-care real-time RT-PCR diagnostic tests in addition to other respiratory pathogens testing.
2020-03-20 Zhou et al COVID-19: Challenges to GIS with Big Data
Geography and Sustainability
IV. Computer Model In this study, a data-driven multi-scale mapping template was designed.
2020-03-20 Legido-Quigley et al Are high-performing health systems resilient against the COVID-19 epidemic?
The Lancet
IV. Prevalence Study National laboratory networks developed diagnostic tests once the COVID-19 genetic sequences were published 5 and laboratory testing capacity was increased in all three locations, although expansion of the diagnostic capacity to university and large private laboratories in Japan is still ongoing.
2020-03-20 Nkengasong et al Looming threat of COVID-19 infection in Africa: act collectively, and fast
The Lancet
IV. Prevalence Study Because mitigating the potential spread of COVID-19 in Africa will require rapid detection and containment, the laboratory work streams of AFTCOR, Africa CDC, and WHO are working closely to expeditiously scale up diagnostic testing capacity linked to enhanced surveillance and monitoring-eg, at the beginning of February, only two countries in Africa had the diagnostic capacity to test for COVID-19.
2020-03-22 Zhang et al Protein Structure and Sequence Reanalysis of 2019-nCoV Genome Refutes Snakes as Its Intermediate Host and the Unique Similarity between Its Spike Protein Insertions and HIV-1
J Proteome Res
IV. Other However, the reimplementation of the analyses, built on larger scale data sets using state-of-the-art bioinformatics methods and databases, presents clear evidence that rebuts these conclusions.
2020-03-23 Wan et al Cross-reaction of sera from COVID-19 patients with SARS-CoV assays.
medrxiv
IV. Prevalence Study

7 We retrieved residual samples left over from biochemical tests to obtain serial sera for these 51 patients.
These assays maybe be utilized as an interim measure in epidemiological investigations for contact tracing and to determine the extent of community spread of this new emerging virus pending the availability of specific serology tests for SARS-CoV-2.
2020-03-25 Khan et al Analysis of Serologic Cross-Reactivity Between Common Human Coronaviruses and SARS-CoV-2 Using Coronavirus Antigen Microarray
biorxiv
IV. Prevalence Study Widespread testing within the United States is also severely limited by the lack of available testing kits and testing capacity limitations of available public and private laboratories.
2020-03-25 Cheng et al Initial rapid and proactive response for the COVID-19 outbreak — Taiwan's experience
Journal of the Formosan Medical Association
IV. Other The diagnostic capacity was also scaled up to 3000 tests/day by recruiting more laboratories and streamlining the testing algorithm.
2020-03-26 Martin et al An artificial intelligence-based first-line defence against COVID-19: digitally screening citizens for risks via a chatbot
biorxiv
IV. Prevalence Study To track and hopefully curb this pandemic, large-scale laboratory testing for COVID-19 is becoming widespread.
2020-03-27 Lescure et al Clinical and virological data of the first cases of COVID-19 in Europe: a case series
The Lancet Infectious Diseases
III-3. Time Series Analysis

11 The five patients in this case series, at different stages of infection, include two patients with a mild disease at admission and a secondary worsening that resulted in their admission to an intensive care unit (ICU), one initially severely ill patient directly admitted to an ICU for an acute respiratory failure, and two patients with a mild disease diagnosed very early after infection.
For more on SARS-CoV-2 genetic epidemiology see rapid screening and monitoring of the contacts of these patients to detect those with very mild symptoms.
2020-03-27 Rivera et al The Impact of COVID-19 on Radiation Oncology Clinics and Cancer Patients in the U.S.
Advances in Radiation Oncology
IV. Other 23 However, with a surge in demand for testing kits, the ability to do such testing remains unpredictable.
2020-03-28 Zhai et al The epidemiology, diagnosis and treatment of COVID-19
International Journal of Antimicrobial Agents
III-2. Matched Case Control

Another study later using the travel history and symptom onset of 88 confirmed cases had a similar mean incubation period, which was 6.4 days (95% CI: 5.6-7.7) .
As the diagnostic criteria expanded from laboratory examination to chest CT imaging, more than 14,000 patients were diagnosed on February 12, 2020.
2020-03-29 Alfano et al Non-invasive surveys of mammalian viruses using environmental DNA
biorxiv
IV. Other However, identification, surveillance and monitoring of emerging viruses using currently broadly applied approaches based on direct sampling of wildlife requires enormous investment in sampling, particularly for viruses that have low prevalence .
2020-03-30 Sinnott-Armstrong et al Evaluation of Group Testing for SARS-CoV-2 RNA
medrxiv
IV. Prevalence Study Current testing strategies rely on individual tests of cases matching restrictive diagnostic criteria to detect SARS-CoV-2 RNA, limiting testing of asymptomatic and mild cases.

Many SARS-CoV-2 testing laboratories are using pipetting robots to rapidly and accurately scale RNA extractions and assays to large numbers of individuals.

Drawing on the well-studied group testing literature, modeling suggests practical changes to testing protocols which can reduce test costs and stretch a limited test kit supply.
2020-03-30 Liu et al Diagnostic Indexes of a Rapid IgG/IgM Combined Antibody Test for SARS-CoV-2
medrxiv
IV. Other In addition, the number and variety of diagnostic tests should be expanded .
2020-03-30 Xu et al Analysis and Prediction of False Negative Results for SARS-CoV-2 Detection with Pharyngeal Swab Specimen in COVID-19 Patients: A Retrospective Study
medrxiv
III-2. Retrospective Cohort

In order to implement the out-of-sample prediction, 1,324 patients were randomly divided into training (1,059 cases) and validation samples (265 cases Table 2) .
The training and validation were conducted on the same testing and validation samples.
2020-03-31 Singer et al What is ahead for health policy and technology in the 2020s?
Health Policy and Technology
IV. Other Developments in diagnostics are likely to include more advanced imaging, increasing availability of point of care testing (biochemical and genomic), and the further extension of genomics into clinical practice, potentially before and around the time of birth.
2020-03-31 Patil et al Current State and Predicting Future Scenario of Highly Infected Nations for COVID-19 Pandemic
medrxiv
IV. Other This high value can be attributed to large scale testing conducted.
2020-03-31 Singer et al A new pandemic out of China: the Wuhan 2019-nCoV coronavirus syndrome
Health Policy and Technology
IV. Prevalence Study

Complications in the initial 41 patients reported from Wuhan up to 2nd January 2020 included acute respiratory distress syndrome, acute cardiac injury and secondary infection .
Diagnostic tests for 2019-nCoV are already available internationally.
2020-04-01 Vogels et al Analytical sensitivity and efficiency comparisons of SARS-COV-2 qRT-PCR assays
medrxiv
IV. Prevalence Study Accurate diagnostic assays and large-scale testing are critical for mitigating outbreaks of infectious diseases.
2020-04-30 Sohrabi et al World Health Organization declares global emergency: A review of the 2019 novel coronavirus (COVID-19)
International Journal of Surgery
IV. Prevalence Study

To date, 85 individuals have tested positive resulting in the UK public health risk for viral infection being raised from low to moderate .
Regarding diagnostic testing, US-based companies such as Co-Diagnostics and the Novacyt's molecular diagnostics division Primerdesign have launched COVID-2019 testing kits for use in the research setting .
2020-04-30 Phan et al Novel coronavirus: From discovery to clinical diagnostics
Infection, Genetics and Evolution
IV. Other At this time, diagnostic testing for 2019-nCoV can be conducted only at CDC (https://www.cdc.gov/coronavirus/2019-nCoV/guidelines-clinicalspecimens.html).
2020-07-31 Artika et al Pathogenic viruses: Molecular detection and characterization
Infection, Genetics and Evolution
IV. Prevalence Study Advances in molecular biology techniques should be contingent with the development of more effective diagnostic tests for emerging viruses.

17 Enhance capabilities for rapid sequencing and bioinformatics to target regions of the genome that will allow specificity for a particular variant.

17.0.0.1 Highlights

17.0.0.2 Articles

Date Authors Title LOE(?) & Sample Matches
2020 Gralinski et al Return of the Coronavirus: 2019-nCoV
Viruses
IV. Prevalence Study

The novel CoV (2019-nCoV) was isolated from a single patient and subsequently verified in 16 additional patients .
The rapid release of 2019-nCoV sequences permitted the research community to quickly become engaged, providing analysis and developing diagnostic tests.
2020 Cleemput et al Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes
Bioinformatics (Oxford, England)
IV. Other The tool also identifies changes at nucleotides, coding regions and proteins using a novel dynamic aligner to allow tracking new viral mutations (Figure 1 ).
2020 Kelvin et al Fear of the novel coronavirus
Journal of Infection in Developing Countries
IV. Other The novel coronavirus has a homology with SARS and tools for rapid diagnostic testing have been developed .
2020-01-22 Letko et al Functional assessment of cell entry and receptor usage for lineage B β-coronaviruses, including 2019-nCoV
biorxiv
IV. Other Despite significant advances in next generation sequencing technologies, which have facilitated the discovery of thousands of novel animal-derived viruses, tools for downstream functional assessment of these novel sequences are lacking.
2020-02-02 Cleemput et al Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes
biorxiv
IV. Other The tool also identifies changes at nucleotides, coding regions and proteins using a novel dynamic aligner to allow tracking new viral mutations (Figure 1 ).

Our tool also allows detailed analysis of coding regions and proteins for each of the coronavirus species.
2020-02-04 Randhawa et al Machine learning using intrinsic genomic signatures for rapid classification of novel pathogens: COVID-19 case study
biorxiv
IV. Other MLDSP and MLDSP-GUI have demonstrated the ability to identify 79 the genomic signatures (a species-specific pattern known to be pervasive throughout the 80 genome) with species level accuracy that can be used for sequence (dis)similarity 81 analyses.
2020-02-13 Reusken et al Laboratory readiness and response for novel coronavirus (2019-nCoV) in expert laboratories in 30 EU/EEA countries, January 2020
Euro Surveill
IV. Other Nineteen laboratories indicated to have capacity to perform whole genome sequencing on 2019-nCoV in clinical samples, while 15 laboratories could perform partial sequencing.
2020-02-14 Kiselev et al Current Trends in Diagnostics of Viral Infections of Unknown Etiology
Viruses
IV. Prevalence Study

They used 42 virus-positive controls from pediatric patients and 67 unidentified samples .
Until recently, detection of drug-resistant strains required sequencing of only certain parts of viral genome.
2020-02-17 Ai et al Optimizing diagnostic strategy for novel coronavirus pneumonia, a multi-center study in Eastern China
medrxiv
IV. Prevalence Study

Twenty patients were finally laboratoryconfirmed with NCP, among whom 14 patients were positive for the first admission SARS-COV-2 RT-PCR, 3 patients turned to positive in the second test after the first negative result.
Moreover, the nature of unbiased sequencing offers higher tolerance for genetic drift in the target pathogens, whereas certain changes in sequence can result in critical impact on the assay efficiency 21, 22 .
2020-02-18 Lin et al Single-cell Analysis of ACE2 Expression in Human Kidneys and Bladders Reveals a Potential Route of 2019-nCoV Infection
biorxiv
IV. Prevalence Study

We obtained the scRNA-Seq data of healthy bladder tissues of three bladder cancer patients from the Gene Expression Omnibus (GSE108097).
Based on bioinformatics analyses, it has been shown that 2019-nCoV genome is 88% identical with two bat-derived severe acute respiratory syndrome (SARS)-like coronaviruses (bat-SL-CoVZC45 and bat-SL-CoVZXC21), 79% with SARS-CoV, and 50% with MERS- Single-cell RNA sequencing (scRNA-Seq) has been extensively applied in 2019-nCoV research, due to its capability to profile gene expressions for all cell types in multiple tissues unbiasedly at a high resolution.
2020-02-21 Chan et al A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster
The Lancet
III-3. Time Series Analysis

Methods In this study, we report the epidemiological, clinical, laboratory, radiological, and microbiological findings of five patients in a family cluster who presented with unexplained pneumonia after returning to Shenzhen, Guangdong province, China, after a visit to Wuhan, and an additional family member who did not travel to Wuhan.
Unlike the 2003 SARS outbreak, the improved surveillance network and laboratory capability of China was able to recognise this outbreak within a few weeks and announced the virus genome sequences that would allow the development of rapid diagnostic tests and efficient epidemiological control.
2020-02-21 alam et al Functional pangenome analysis suggests inhibition of the protein E as a readily available therapy for COVID-2019
biorxiv
IV. Other The SARS-CoV-2 genome sequence data are a pivotal resource on its own, but can gain greater value when embedded within those of other Betacoronavirus, allowing a comparative pangenomic analysis.
2020-02-25 Zhang et al Characterizing the transmission and identifying the control strategy for COVID-19 through epidemiological modeling
medrxiv
IV. Other High mutation rates have been observed in the genome sequences collected from more than 100 human specimens.
2020-02-29 Zhang et al Rapid Molecular Detection of SARS-CoV-2 (COVID-19) Virus RNA Using Colorimetric LAMP
medrxiv
IV. Prevalence Study

In addition to controls, a total of 7 patient RNA samples were tested, 6 of which were determined to be positive by RT-qPCR using ORF1a primers (C q 25-36.5, Table 2 ) and 4 positive with Gene N primers.
The breadth of application highlights the applicability of visual detection methods to provide an advantage in simplicity and portability for enabling new, rapid diagnostics.
2020-03-01 Shen et al Recent advances and perspectives of nucleic acid detection for coronavirus
Journal of Pharmaceutical Analysis
IV. Prevalence Study The microarray is a detection method with rapid and high throughput.
2020-03-02 Wu et al Mutations, Recombination and Insertion in the Evolution of 2019-nCoV
biorxiv
IV. Other The SNPs of each sequence were defined as the sites variant from the reference sequence.
2020-03-02 Metsky et al CRISPR-based surveillance for COVID-19 using genomically-comprehensive machine learning design
biorxiv
IV. Prevalence Study We hope that the comprehensiveness and high predicted sensitivity and specificity of our designs will enable many groups to proceed rapidly and successfully from assay testing through deployment.
2020-03-03 Yang et al The deadly coronaviruses: The 2003 SARS pandemic and the 2020 novel coronavirus epidemic in China
Journal of Autoimmunity
IV. Prevalence Study

In Wang's study , of the 36 patients in the ICU, four patients received high-flow oxygen therapy, 15 patients received non-invasive ventilation, and 17 patients received invasive ventilation (four patients switched to ECMO).
Rapid identification of the viral genome and the development of rapid diagnostic tests will facilitate the isolation of those who are confirmed as infected .
2020-03-05 Manning et al Rapid metagenomic characterization of a case of imported COVID-19 in Cambodia
biorxiv
IV. Other Despite major advances in mNGS technologies and significant decreases in costs associated with sequencing, preparation of sequencing libraries and sufficient bioinformatics capabilities for timely analysis still present a challenge in the developing world.

Overall, agnostic or unbiased metagenomic sequencing capabilities in-country provide the ability to detect and respond to a variety of pathogens, even those that are unanticipated or unknown.

The example described here serves as a call for continued training and infrastructure to support mNGS capacity in developing countries as bioinformatic tools proliferate and the cost of sequencing decreases.

In resource-limited settings, especially near an outbreak epicenter, conventional deep sequencing or bioinformatics are often challenging.
2020-03-06 Wang et al Nanopore target sequencing for accurate and comprehensive detection of SARS-CoV-2 and other respiratory viruses
medrxiv
IV. Other Moreover, the 97 accurate nucleic acid sequence generated using our pipeline could indicate whether the virulence-98 related genes were mutated during virus spreading, thereby rapidly providing information for 99 subsequent epidemiological analysis.
2020-03-09 Woo et al Sensitive one-step isothermal detection of pathogen-derived RNAs
medrxiv
IV. Other Simultaneous detection of multiple target sites 258 along its genome would enable specific discrimination of this emerging pathogen from 259 others.
2020-03-09 Leng et al Transplantation of ACE2(-) Mesenchymal Stem Cells Improves the Outcome of Patients with COVID-19 Pneumonia
Aging Dis
IV. Other A deep transcriptional state map of MSCs and gene expression at single-cell level was generated after the performance of 10× Genomics high throughput of RNA sequencing.
2020-03-11 Grewelle et al Larger viral genome size facilitates emergence of zoonotic diseases
biorxiv
IV. Other In an age of high-throughput genomics and rapid discovery of new viruses, characterization of recombination and mutation rates is far slower and more laborintensive than genome sequencing, making genome size an appealing first step in zoonotic risk evaluation.

Large genomes are more likely to contain intergenic, non-coding regions that assist in gene regulation but also serve as hotspots for recombination and mutation due to weaker selection to conserve these regions .

More coding regions within the genome could lead to greater plasticity and expanded host range, as reliance on host replication machinery is reduced .
2020-03-14 Li et al High sensitivity detection of coronavirus SARS-CoV-2 using multiplex PCR and a multiplex-PCR-based metagenomic method
biorxiv
IV. Computer Model With 172 pairs of primers, this method enables the detection of low copy numbers, potentially degraded fragments of the viral genome, or even a mutated variant, with high confidence.

The secondary PCR added sample indexes and sequencing adapters, allowing for sequencing of the resulting products by high throughput sequencing.
2020-03-14 Lopez-Rincon et al Accurate Identification of SARS-CoV-2 from Viral Genome Sequences using Deep Learning
biorxiv
IV. Prevalence Study

Next, 115 we removed all the repeated sequences, obtaining a total of 384 unique sequences, with 45 samples belonging to SARS-CoV-2.
In particular, for the case of viruses, Next Generation Sequencing (NGS) genomic samples might not be identified by BLAST, as there are no reference sequences valid for all genomes, as viruses have high mutation frequency .
2020-03-14 Abbott et al Development of CRISPR as a prophylactic strategy to combat novel coronavirus and influenza
biorxiv
IV. Other To characterize the specificity of 22nt crRNAs, we ensured that crRNA do not target any sequences in the human transcriptome.

Our bioinformatics analysis resulted in 6 crRNAs targeting highly conserved genome regions for each of the 8 IAV segments, for a total of 48 crRNAs (Supplemental Table 6 ).

Our bioinformatics analysis also suggested a minimal pool of 6 crRNAs able to target over 90% of sequenced coronaviruses.
2020-03-15 Zheng et al SARS-CoV-2: an Emerging Coronavirus that Causes a Global Threat
Int J Biol Sci
IV. Other The genome sequence of SARS-CoV-2 from clinical samples has been obtained by several laboratories with deep sequencing [8, .
2020-03-17 Xiao et al Multiple approaches for massively parallel sequencing of HCoV-19 (SARS-CoV-2) genomes directly from clinical samples
biorxiv
IV. Prevalence Study

Two to five SNVs were identified within each clinical 182 sample, and in all the seven samples, SNVs identified by the three methods were concord-183 ant except that capture missed one SNV at position 16535 in GZMU0014 (Fig.
Compared with direct metatranscriptomic sequencing, high 240 sensitivity of hybrid capture and amplicon sequencing methods come at a price of low ac-241 curacy, and neither of the two can be used to sequence highly diverse or recombinant vi-242 ruses because the primers and probes are specific to known viral genomes.
2020-03-20 Magar et al Potential Neutralizing Antibodies Discovered for Novel Corona Virus Using Machine Learning
biorxiv
IV. Prevalence Study

In total, 102 sequences of antibody-antigen complexes were mined and added to the 1831 samples, resulting in total number of 1933 training samples.
Recently, the proteomics sequences of 'WH-Human 1' coronavirus became available through Metagenomic RNA sequencing of a patient in Wuhan.
2020-03-23 Mao et al Can a Paper-Based Device Trace COVID-19 Sources with Wastewater-Based Epidemiology?
Environ Sci Technol
IV. Other Paper analytical devices enable multiplexed, sensitive assays that rival PCR laboratory assays and provide high-quality, fast precision diagnostics for pathogens.
2020-03-25 Nunez-Bajo et al Ultra-Low-Cost Integrated Silicon-based Transducer for On-Site, Genetic Detection of Pathogens
biorxiv
IV. Other 1 Ability to produce NA quickly also increases the speed of development and deployment of new test kits to health systems, providing much needed diagnostic capabilities for the detection of novel pathogens (such as SARS-CoV-2).
2020-03-27 Balasubramanian et al Automatic Identification of SARS Coronavirus using Compression-Complexity Measures
biorxiv
IV. Prevalence Study AbstractFinding vaccine or specific antiviral treatment for global pandemic of virus diseases (such as the ongoing COVID-19) requires rapid analysis, annotation and evaluation of metagenomic libraries to enable a quick and efficient screening of nucleotide sequences.
2020-03-27 Shang et al CHEER: hierarCHical taxonomic classification for viral mEtagEnomic data via deep leaRning
biorxiv
IV. Prevalence Study Largescale RNA virus sequencing projects using nextgeneration sequencing technologies have been conducted for different species.
2020-03-27 Sekizuka et al Haplotype networks of SARS-CoV-2 infections in the Diamond Princess cruise ship outbreak
medrxiv
IV. Other Haplotype networks from genomic SNVs (HN-GSNVs) were used to map the genotypes of the SARS-CoV-2 isolates that disseminated in the DP cruise ship after isolation of the passengers on 5 Feb. 5.
2020-03-28 Karamitros et al SARS-CoV-2 exhibits intra-host genomic plasticity and low-frequency polymorphic quasispecies
biorxiv
IV. Prevalence Study

We analyzed NGS data derived from clinical samples of three Chinese patients infected with SARS-CoV-2, in order to identify small- and large-scale intra-host variations in the viral genome.
Our analyses provide insights into the intra-patient pool of viral genomes, identify the frequency levels of rare variants and highlight variable genomic regions and a potential recombination hot-spot within S gene.

The isolated SNVs and genomic rearrangements, reflect the intra-patient capacity of the polymorphic quasispecies, which may arise rapidly during the outbreak, allowing immunological escape of the virus, offering resistance to anti-viral drugs and affecting the sensitivity of the molecular diagnostics assays.

Bioinformatics analysis of NGS data allows the generation of the consensus sequence of a viral genome from the of majority nucleotides at each position but also the identification of non-consensus nucleotides, enabling the exploration of intra-host variability but also its consequences on intra-host viral evolution - .
2020-03-28 Rangan et al RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses
biorxiv
IV. Computer Model Last, we predict regions of the SARS-CoV-2 viral genome have low propensity for RNA secondary structure and are conserved within SARS-CoV-2 strains.
2020-03-29 Alfano et al Non-invasive surveys of mammalian viruses using environmental DNA
biorxiv
IV. Other The ability of oligonucleotides with substantial divergence from the target sequence to capture more distantly related sequences is particularly useful in virology since most viruses are uncharacterized in wildlife and many evolve rapidly.
2020-07-31 Artika et al Pathogenic viruses: Molecular detection and characterization
Infection, Genetics and Evolution
IV. Prevalence Study To accelerate the sequencing process and improve sensitivity, automated sequencing was then developed.

Molecular methods, in particular PCR and DNA sequencing technologies, have become the methods of choice for the detection and characterization of emerging and re-emerging pathogenic viruses.

18 Enhance capacity (people, technology, data) for sequencing with advanced analytics for unknown pathogens, and explore capabilities for distinguishing naturally-occurring pathogens from intentional.

18.0.0.1 Highlights

18.0.0.2 Articles

Date Authors Title LOE(?) & Sample Matches
2020 TAO et al Advantages and challenges of metagenomic next-generation sequencing (mNGS) in the detection of 2019 novel coronavirus
Chinese Journal of Laboratory Medicine
IV. Other Due to its broad coverage of all types of pathogens, mNGS demonstrates incomparable advantage in rapid identification of novel pathogens such as 2019-nCoV.

Currently, metagenomic next-generation sequencing (mNGS) is the most commonly used technology in clinical application.
2020-01-22 Letko et al Functional assessment of cell entry and receptor usage for lineage B β-coronaviruses, including 2019-nCoV
biorxiv
IV. Other Despite significant advances in next generation sequencing technologies, which have facilitated the discovery of thousands of novel animal-derived viruses, tools for downstream functional assessment of these novel sequences are lacking.
2020-02-04 Randhawa et al Machine learning using intrinsic genomic signatures for rapid classification of novel pathogens: COVID-19 case study
biorxiv
IV. Other The main advantage alignment-free methodology offers 316 is the ability to analyze large datasets rapidly.
2020-02-04 Zhang et al Recent advances in the detection of respiratory virus infection in humans
Journal of Medical Virology
IV. Other Conventional diagnostic tests, such as the assays for rapid detection of antiviral antibodies or viral antigens, are widely used in many clinical laboratories.
2020-02-05 Chen et al RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak
Emerg Microbes Infect
IV. Prevalence Study

Obtained BALF samples from two patients with unusual pneumonia.
To identify potential pathogens from the mNGS sequencing results, a pathogen discovery pipeline was carried out on sequenced data.

Thanks to the development of metagenomic next-generation sequencing (mNGS) methodology, the direct investigation of infectious microorganism from original clinical samples is currently achievable .
2020-02-13 Mizumoto et al Early epidemiological assessment of the transmission potential and virulence of coronavirus disease 2019 (COVID-19) in Wuhan City: China, January-February, 2020
medrxiv
IV. Prevalence Study The power of our approach lies in the ability to infer epidemiological parameters with quantified uncertainty from partial observations collected by surveillance systems.
2020-02-14 Xiao et al HIV-1 did not contribute to the 2019-nCoV genome
Emerg Microbes Infect
IV. Other The advances in bioinformatics analysis tools are widely used to easily and rapidly analyse newly obtained sequences.
2020-02-14 Kiselev et al Current Trends in Diagnostics of Viral Infections of Unknown Etiology
Viruses
IV. Prevalence Study

They used 42 virus-positive controls from pediatric patients and 67 unidentified samples .
Metagenomics allows for identification and in-depth studies of unknown viral pathogens by using shotgun sequencing , which has been extensively applied in clinical and environmental research .

Furthermore, available protocols include not only those for metagenomics, but also for studying select organisms, e.g., viruses.

Compared to conventional clinical tests, HTS is universal and more precise at profiling pathogens.

Further applications of this method extend to transcriptomics and proteomics, allowing for a deeper insight into several aspects of pathogens, such as drug resistance, adaptation mechanisms and vast communication networks between species.
2020-02-20 Ziff et al Fractal kinetics of COVID-19 pandemic
medrxiv
III-3. Time Series Analysis

March 3 with a total of 83,000 cases, which so far has been well born out.
This analysis does not aim to quantify any intentional bias in the reported data.
2020-02-20 Liu et al Are pangolins the intermediate host of the 2019 novel coronavirus (2019-nCoV) ?
biorxiv
IV. Prevalence Study

Through metagenomic sequencing and de novo assembling, we recovered 38 contigs ranging from 380 to 3,377 nucleotides, and the nucleotide sequence identities among the contigs from these three samples were 99.54%.
/2020 identify pathogens causing wildlife diseases.
2020-02-23 Hou et al Development and Evaluation of A CRISPR-based Diagnostic For 2019-novel Coronavirus
medrxiv
IV. Other The diagnostic performance of CRISPR-nCoV was assessed and compared across three technology platforms (mNGS, RT-PCR and CRISPR).

The copyright holder for this preprint (which was not peer-reviewed) is Here, to address this question and the expanding clinical needs, we developed CRISPR-nCoV, 78 a rapid assay for 2019-nCoV detection, and compared the diagnostic performance among 79 three different technological platforms: metagenomic sequencing, RT-PCR and CRISPR.
2020-02-26 Liao et al The landscape of lung bronchoalveolar immune cells in COVID-19 revealed by single-cell RNA sequencing
medrxiv
IV. Prevalence Study

At the individual levels, we also found the higher T cell clonality was consistently remained in the 3 mild patients as compared to the 3 severe patients ( Figure 4D ), supporting that highly expanded CD8 + T cell participated in resolving the SARS-CoV-2 infection.
These emerging high dimensional techniques, like scRNA-seq, mass cytometry and multiplex imaging tools , will greatly improve human immunology studies using minimal precious tissue samples.
2020-02-29 Zhang et al Rapid Molecular Detection of SARS-CoV-2 (COVID-19) Virus RNA Using Colorimetric LAMP
medrxiv
IV. Prevalence Study

In addition to controls, a total of 7 patient RNA samples were tested, 6 of which were determined to be positive by RT-qPCR using ORF1a primers (C q 25-36.5, Table 2 ) and 4 positive with Gene N primers.
These molecular methods include metagenomics sequencing mNGS and RT-qPCR , both are excellent and sensitive techniques, but approaches not without limitations.
2020-03-01 Shen et al Recent advances and perspectives of nucleic acid detection for coronavirus
Journal of Pharmaceutical Analysis
IV. Prevalence Study With the advance in molecular biology technology, nucleic acid detection methods have developed rapidly and become a revolutionary technology for virus detection.
2020-03-03 Yang et al The deadly coronaviruses: The 2003 SARS pandemic and the 2020 novel coronavirus epidemic in China
Journal of Autoimmunity
IV. Prevalence Study

In Wang's study , of the 36 patients in the ICU, four patients received high-flow oxygen therapy, 15 patients received non-invasive ventilation, and 17 patients received invasive ventilation (four patients switched to ECMO).
Big data and artificial intelligence systems are tools that can be used to fully integrate the information, conduct comprehensive research and analyze public health risks.
2020-03-04 Rao et al Cell-Membrane-Mimicking Nanodecoys against Infectious Diseases
ACS Nano
IV. Other For example, liposome microarrays can be used for ultrasensitive detection of various types of pathogens including viruses, bacteria, and fungi.
2020-03-05 Manning et al Rapid metagenomic characterization of a case of imported COVID-19 in Cambodia
biorxiv
IV. Other Overall, agnostic or unbiased metagenomic sequencing capabilities in-country provide the ability to detect and respond to a variety of pathogens, even those that are unanticipated or unknown.

Despite major advances in mNGS technologies and significant decreases in costs associated with sequencing, preparation of sequencing libraries and sufficient bioinformatics capabilities for timely analysis still present a challenge in the developing world.

Here we successfully used metagenomic next generation sequencing on an iSeq100 Illumina platform paired with an open-source bioinformatics pipeline to quickly characterize Cambodia’s first case of COVID-2019.
2020-03-09 Woo et al Sensitive one-step isothermal detection of pathogen-derived RNAs
medrxiv
IV. Other Notably, the detection limit was as 160 With the fast and sensitive RNA detection using SENSR, we next attempted to reconfigure 174 this platform for the detection of RNA markers from various pathogens.

Taken together, we demonstrated that SENSR could be easily reconfigured to detect 207 various RNA markers of pathogens by redesigning the probes.

Future efforts on 329 automated probe design will be needed to accelerate the development of SENSR assays for 330 newly emerging pathogens.

Second, SENSR will be a valuable 320 platform for the immediate development of diagnostic tests for emerging pathogens 1,37 321 because of the simple probe design process and broad adaptability of SENSR.
2020-03-12 Park et al Development of Reverse Transcription Loop-mediated Isothermal Amplification (RT-LAMP) Assays Targeting SARS-CoV-2
biorxiv
IV. Other To overcome such cost-restriction of RT-qPCR and still detect pathogens' nucleic acids, isothermal amplification methods have been developed .
2020-03-14 Lopez-Rincon et al Accurate Identification of SARS-CoV-2 from Viral Genome Sequences using Deep Learning
biorxiv
IV. Prevalence Study

Next, 115 we removed all the repeated sequences, obtaining a total of 384 unique sequences, with 45 samples belonging to SARS-CoV-2.
Molecular techniques, such as quantitative real-time RT-PCR and nucleic acid sequencing methods, are widely used to identify pathogens.
2020-03-14 Li et al High sensitivity detection of coronavirus SARS-CoV-2 using multiplex PCR and a multiplex-PCR-based metagenomic method
biorxiv
IV. Computer Model Similar to a recently described metagenomic approach for SARS-CoV-2 identification 43 , we also establish a user-friendly multiplex-PCRbased metagenomic method that is not only able to detect SARS-CoV-2, but could also be applied for the identification of significant sequence mutations within known viruses and to uncover novel pathogens with a limited sequencing depth of approximately 1 million reads.
2020-03-15 Yi et al COVID-19: what has been learned and to be learned about the novel coronavirus disease
Int J Biol Sci
IV. Prevalence Study

On February 11, 2020, a multi-center study on 8,866 patients including 4,021 confirmed COVID-19 patients presented a more updated illustration of the epidemic as follows ( UlBi-HX_rHPXa1qHA2bhdA).
Antibodies are an immunoglobulin (Ig) produced by B lymphocytes to fight pathogens and other foreign objects and they recognize unique molecules in the pathogens and neutralize them directly .
2020-03-21 Ding et al All-in-One Dual CRISPR-Cas12a (AIOD-CRISPR) Assay: A Case for Rapid, Ultrasensitive and Visual Detection of Novel Coronavirus SARS-CoV-2 and HIV virus
biorxiv
IV. Other This straightforward CRISPR-Cas12a nucleic acid sensing system has great potential in enabling CRISPR-based next-generation molecular diagnostics towards point-of-care, quantitation, and digital analysis.
2020-03-23 Mao et al Can a Paper-Based Device Trace COVID-19 Sources with Wastewater-Based Epidemiology?
Environ Sci Technol
IV. Other Paper analytical devices enable multiplexed, sensitive assays that rival PCR laboratory assays and provide high-quality, fast precision diagnostics for pathogens.

Paper analytical devices have emerged as powerful tools for the rapid diagnosis of pathogens and determination of infection transmission.

4 The test could sensitively analyze multiplexed nucleic acid sequences of pathogens within 50 min, which gave a higher-quality and faster precision diagnosis for malaria than PCR.
2020-03-25 Nunez-Bajo et al Ultra-Low-Cost Integrated Silicon-based Transducer for On-Site, Genetic Detection of Pathogens
biorxiv
IV. Other 1 Ability to produce NA quickly also increases the speed of development and deployment of new test kits to health systems, providing much needed diagnostic capabilities for the detection of novel pathogens (such as SARS-CoV-2).

Unlike other biomarkers, such as antibodies or non-genetic molecules originating from pathogens, NA can be chemically amplified, enabling direct detection of low numbers of pathogens (down to single organisms).

This large gap in the diagnostic workflow hampers attempts to contain infectious pathogens from spreading by rapid and early detection.
2020-03-27 Shang et al CHEER: hierarCHical taxonomic classification for viral mEtagEnomic data via deep leaRning
biorxiv
IV. Prevalence Study Largescale RNA virus sequencing projects using nextgeneration sequencing technologies have been conducted for different species.
2020-03-27 Sumner et al Reproducibility and reporting practices in COVID-19 preprint manuscripts
medrxiv
IV. Other When research is truly reproducible, it allows researchers to evaluate and expand upon each other's work.
2020-03-29 Tan et al Response and Operating Room Preparation for the COVID-19 Outbreak: A Perspective from the National Heart Centre Singapore
Journal of Cardiothoracic and Vascular Anesthesia
IV. Other This allowed us to identify potential problems, raise awareness and improve systems workflow.
2020-03-29 Thompson et al COVID-19 in Endoscopy: Time to do more?
Gastrointestinal Endoscopy
IV. Prevalence Study Leveraging information technologies can be helpful in these nonstandard workflows.
2020-03-31 DU et al Traditional Chinese Medicine: an effective treatment for 2019 novel coronavirus pneumonia (NCP)
Chinese Journal of Natural Medicines
IV. Other Although there are many approaches to reduce the pathogen-ic microorganisms in food, detection of pathogenic bacteria remains the key to prevent the outbreaks .
2020-03-31 Yu et al Measures for diagnosing and treating infections by a novel coronavirus responsible for a pneumonia outbreak originating in Wuhan, China
Microbes and Infection
IV. Computer Model MCoV-MS (multiplexed CoV mass spectrometry) uses an array matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) system to accurately identify known human coronaviruses (hCoVs) and to provide phylogenetic evidence for emerging unknown hCoVs .
2020-07-31 Artika et al Pathogenic viruses: Molecular detection and characterization
Infection, Genetics and Evolution
IV. Prevalence Study Currently, molecular methods find wide applications in the diagnosis and research of pathogenic viruses.

Different molecular methods, including metagenomics approaches, have been developed and applied for detection and characterization of viruses in birds (Vibin et al., 2018) .

To accelerate the sequencing process and improve sensitivity, automated sequencing was then developed.
2020-08-05 Rodríguez-González et al An approach to the photocatalytic mechanism in the TiO2-nanomaterials microorganism interface for the control of infectious processes
Applied Catalysis B: Environmental
IV. Other Nowadays, the number of microorganisms has increased due to mutations, resistance to antimicrobial agents and to diverse species that adapt to the new environmental conditions.

19 One Health surveillance of humans and potential sources of future spillover or ongoing exposure for this organism and future pathogens, including both evolutionary hosts (e.g., bats) and transmission hosts (e.g., heavily trafficked and farmed wildlife and domestic food and companion species), inclusive of environmental, demographic, and occupational risk factors.

19.0.0.1 Highlights

19.0.0.2 Articles

Date Authors Title LOE(?) & Sample Matches
2020 Harypursat et al Six weeks into the 2019 coronavirus disease (COVID-19) outbreak- it is time to consider strategies to impede the emergence of new zoonotic infections
Chin Med J (Engl)
IV. Computer Model A significantly large variety of coronavirus species cause a diverse range of diseases in domesticated and wild mammals and birds, and these animals may also be carriers of and reservoirs for coronaviruses .
2020 Ralph et al 2019-nCoV (Wuhan virus), a novel Coronavirus: Human-to-human transmission, travel-related cases, and vaccine readiness
Journal of Infection in Developing Countries
IV. Prevalence Study

On 8 January 2020, it was reported that a novel coronavirus had been sequenced from one patient and subsequently identified in some of the other patients with pneumonia , later reported as 15 of the 59 patients .
While masked palm civets and raccoon dogs were involved in transmission to humans and initially considered potential reservoirs, they are now considered as incidental or spillover hosts .
2020 Kock et al 2019-nCoV in context: lessons learned?
The Lancet Planetary Health
IV. Prevalence Study In some parts of Africa, prevention of Ebola virus and future coronavirus threats require shifts in food habits, a transition from bushmeat being a cultural norm or primary source of protein, and by discouraging agricultural development that brings bats into increased contact with humans or livestock.
2020 Daszak et al A strategy to prevent future pandemics similar to the 2019-nCoV outbreak
Biosafety and Health
IV. Prevalence Study Our recent behavioral risk investigations in China identified low levels of environmental biosecurity and high levels of human-animal contact as key risk factors for zoonotic disease emergence, particularly in local wet and animal markets .
2020 Sun et al Potential Factors Influencing Repeated SARS Outbreaks in China
International Journal of Environmental Research and Public Health
IV. Computer Model Viruses often require intermediate hosts before transmitting from bats to humans.
2020-01-23 Wu et al Real-time tentative assessment of the epidemiological characteristics of novel coronavirus infections in Wuhan, China, as at 22 January 2020
Euro Surveill
IV. Prevalence Study A separate priority is to identify the animal reservoir of this novel pathogen and any intermediary hosts, including potential supply chains of wild or game meat.
2020-01-30 Ramaiah et al Insights into Cross-species Evolution of Novel Human Coronavirus 2019-nCoV and Defining Immune Determinants for Vaccine Development
biorxiv
IV. Prevalence Study CoVs are commonly found in many species of animals, including bats, camels and humans.
2020-02-04 Randhawa et al Machine learning using intrinsic genomic signatures for rapid classification of novel pathogens: COVID-19 case study
biorxiv
IV. Other Bats have been identified 278 as a reservoir of mammalian viruses and cross-species transmission to other mammals, 279 including humans [4, 7, 8, 10, 13, .
2020-02-08 Malik et al Emerging novel coronavirus (2019-nCoV)—current scenario, evolutionary perspective based on genome analysis and recent developments
Vet Q
IV. Prevalence Study The recent nCoV outbreak highlights the hidden wild animal reservoir of the deadly viruses and possible threat of spillover zoonoses.
2020-02-10 Li et al A qualitative study of zoonotic risk factors among rural communities in southern China
Int Health
IV. Prevalence Study

We aimed to obtain a minimum sample size of 20 participants from each of the three provinces, for a total sample size of over 60 participants.
With further urbanization, and subsequent increased interactions between human populations and the changing ecosystems, new risk factors for zoonotic disease transmission will likely emerge.

BACKGROUND: Strategies are urgently needed to mitigate the risk of zoonotic disease emergence in southern China, where pathogens with zoonotic potential are known to circulate in wild animal populations.
2020-02-14 Di Marco et al Opinion: Sustainable development must account for pandemic risk
Proceedings of the National Academy of Sciences
IV. Prevalence Study In fact, intact ecosystems may play an important disease regulation role by maintaining natural disease dynamics in wildlife communities and reducing the probability of contact and pathogen transmission among humans, livestock, and wildlife.

In fact, intact ecosystems may play an important disease regulation role by maintaining natural disease dynamics in wildlife communities and reducing the probability of contact and pathogen transmission among humans, livestock, and wildlife .

Around 70% of EIDs, and almost all recent pandemics, originate in animals (the majority in wildlife), and their emergence stems from complex interactions among wild and/or domestic animals and humans .
2020-02-20 Liu et al Are pangolins the intermediate host of the 2019 novel coronavirus (2019-nCoV) ?
biorxiv
IV. Prevalence Study

Through metagenomic sequencing and de novo assembling, we recovered 38 contigs ranging from 380 to 3,377 nucleotides, and the nucleotide sequence identities among the contigs from these three samples were 99.54%.
Conservation of wildlife and limits of the exposures of humans to wildlife will be important to minimize the spillover risks of coronaviruses from wild animals to humans.

For example, farmed palm civets were suggested to be an intermediate host for SARS to be spilled over to humans although the details on how to link bat and farmed palm civets are unclear In summary, this study suggested pangolins be a natural host of Betacoronavirus, with an unknown potential to infect humans.
2020-02-21 Li et al Analysis of angiotensin-converting enzyme 2 (ACE2) from different species sheds some light on cross-species receptor usage of a novel coronavirus 2019-nCoV
Journal of Infection
IV. Prevalence Study In case cross-species transmission, close contact with sick or asymptomatic companion, domestic and wild animals should be cautious, such as for workers in livestock farming and travellers in the wild.
2020-02-24 El Zowalaty et al From SARS to COVID-19: A previously unknown SARS- related coronavirus (SARS-CoV-2) of pandemic potential infecting humans – Call for a One Health approach
One Health
IV. Prevalence Study

However, it was recently reported that the Chinese Centers for Disease Control and Prevention isolated SARS-CoV-2 from 33 samples out of 585 environmental samples collected from Huanan Seafood Market .
A broad surveillance for SARS-CoV-2 among different animals is warranted within Huanan Seafood Market and the vicinities, and should include potential reservoir hosts such as bats (both in the wild and if found in live animal markets) as well as potential intermediate hosts such as pigs, live poultry, fish, reptiles, and wild animals in close proximity to humans, which not only allow virus transmission among them but also lead to the generation of new viral strains.
2020-02-27 Ahmad et al COVID-19: Zoonotic aspects
Travel Medicine and Infectious Disease
IV. Other The Seafood market located at Wuhan, where different types of wild (snakes and marmots) and domesticated (poultry and bats) animals were sold illegally.
2020-03-04 Zhang et al Insights into the cross-species evolution of 2019 novel coronavirus
Journal of Infection
IV. Other Although humans and bats live in different environments, some wildlife species are susceptible to the novel coronaviruses in nature, highlighting that the need of tracing its origin of 2019 human coronavirus in wild animals.
2020-03-05 Wilder-Smith et al Can we contain the COVID-19 outbreak with the same measures as for SARS?
The Lancet Infectious Diseases
IV. Prevalence Study

On Feb 18, 2020, the Chinese Center for Disease Control and Prevention published their data of the first 72 314 patients including 44 672 patients with confirmed COVID19.
Live animal markets selling multiple species of wild and domestic animals in proximity to large populations of densely housed humans are thought to be the source of both outbreaks.
2020-03-11 Grewelle et al Larger viral genome size facilitates emergence of zoonotic diseases
biorxiv
IV. Other Search key words included "zoonotic", "zoonoses", "emerging disease", "viral spillover", "animal to human transmission", and "animal reservoir virus".
2020-03-14 Fung et al A tug-of-war between severe acute respiratory syndrome coronavirus 2 and host antiviral defence: lessons from other pathogenic viruses
Emerg Microbes Infect
IV. Prevalence Study

Groups N and P were identified in 13 and 2 individuals, respectively.
All seven HCoVs have a zoonotic origin from bats, rodents, or domestic animals.
2020-03-15 Ye et al Zoonotic origins of human coronaviruses
Int J Biol Sci
IV. Prevalence Study The divergence of these host proteins between humans and natural reservoir hosts of HCoVs such as bats, dromedary camels and rodents might constitute a barrier to interspecies transmission.

When HCoV-OC43 crossed species to infect humans from domestic livestock around 1890, a pandemic of respiratory infection was recorded .

To conclude, the most effective way to prevent viral zoonosis is for humans to stay away from the ecological niches of the natural reservoirs of the zoonotic viruses.
2020-03-16 Conway et al Identification of Coronavirus Sequences in Carp cDNA from Wuhan, China
Journal of Medical Virology
IV. Other It is also possible that SARS-like coronaviruses are a common environmental pathogen in the region that may be in aquatic habitats.
2020-03-17 Adhikari et al Epidemiology, causes, clinical manifestation and diagnosis, prevention and control of coronavirus disease (COVID-19) during the early outbreak period: a scoping review
Infect Dis Poverty
III-2. Cross Sectional Control

In China, 11 791 cases were confirmed and 17 988 cases were suspected in 34 provinces as of 24:00, 31 January 2020 (Fig.
Transmission pattern Many domestic and wild animals, including camels, cattle, cats, and bats, may serve as hosts for coronaviruses .
2020-03-19 Arshad Ali et al The outbreak of Coronavirus Disease 2019 (COVID-19)—An emerging global health threat
Journal of Infection and Public Health
III-3. Time Series Analysis

In 2002, a pandemic of SARS occurred endangering the lives of 8098 individuals with a mortality of 774 patients .
Bats were considered to be the natural hosts and the intermediate host was dromedary camels.

It was assumed that bats were the natural hosts.
2020-03-20 Ahmadi et al Modeling and Forecasting Trend of COVID-19 Epidemic in Iran
medrxiv
IV. Computer Model The natural reservoirs of these diseases are mammals and birds, and therefore are considered as zoonotic diseases .
2020-03-21 Sun et al COVID-19: Epidemiology, Evolution, and Cross-Disciplinary Perspectives
Trends in Molecular Medicine
IV. Prevalence Study

Asymptomatic infection was also documented in Germany: two asymptomatic patients' throat samples were tested positive by reverse transcription (RT)-PCR and by virus isolation, while both patients remained well and afebrile for 7 days .
In addition, in light of the fact that there are multiple species of CoVs circulating in wildlife species and that these animals are constantly interacting with each other, host-species expansion or interspecies transmission of new CoV to humans seems to be inevitable.
2020-03-22 Zhang et al Protein Structure and Sequence Reanalysis of 2019-nCoV Genome Refutes Snakes as Its Intermediate Host and the Unique Similarity between Its Spike Protein Insertions and HIV-1
J Proteome Res
IV. Other These data imply that pangolins such as Manis javanica can either be the intermediate hosts of 2019-nCoV for the transmission of bat coronaviruses to humans or serve as alternative natural hosts, together with bats, to provide the genetic material for the origin of 2019-nCoV.
2020-03-25 Qiu et al Clinical and epidemiological features of 36 children with coronavirus disease 2019 (COVID-19) in Zhejiang, China: an observational cohort study
The Lancet Infectious Diseases
IV. Prevalence Study

Clinical and epidemiological features of 36 children with coronavirus disease 2019 (COVID-19) in Zhejiang, China: an observational cohort study
Most coronaviruses cause diseases in their particular host species; 1 those that can infect humans through cross-species transmission have become an important threat to public health.
2020-03-27 Lee et al Epidemic preparedness in urban settings: new challenges and opportunities
The Lancet Infectious Diseases
IV. Prevalence Study Rapid urbanisation might lead to encroachment into natural habitats and closer encounters with wildlife and zoonoses, and increased proximity to animals in backyard farms and food markets also provides opportunities for zoonotic infections.

Areas of poor sanitation with rodents and other animal vectors; live domestic and wild animal markets; animals raised in backyard farms or industrial agricultural facilities in close proximity to humans Improved sanitation and rodent control around humans and animal communities; vaccination of domestic animals for common zoonotic infections; precautions at slaughter to prevent contact with blood; regulating live animal markets to phase out sale of live animals or to ensure that those for sale are raised on commercial farms and have been verified to be disease free the density of people in housing, during commutes using public transportation, and in work environments is high.
2020-03-29 Alfano et al Non-invasive surveys of mammalian viruses using environmental DNA
biorxiv
IV. Other Emerging infectious viruses increasingly threaten human, domestic animal and wildlife health .

Wildlife trade and consumption of bushmeat, especially in Africa and Asia, have increasingly played a role in pathogen spillovers into human populations .

This suggests that eDNA/iDNA-based pathogen surveillance approaches may complement efforts to proactively identify viruses that could potentially spillover to humans or livestock.
2020-03-30 Jagadesh et al In search for the hotspots of Disease X: A biogeographic approach to mapping the predictive risk of WHO s Blueprint Priority Diseases
medrxiv
IV. Other Laboratory outbreaks and outbreak in domestic and wildlife were also excluded.

Lesser species diversity and inter-species interactions makes spillover easier towards the accidental human hosts.
2020-03-30 Ansari et al Deliberate release: Plague – A review
Journal of Biosafety and Biosecurity
IV. Other 3 Plague is primarily a vector-borne illness transmitted by fleas to a variety of wild rodents in many habitats in the world -representing a natural reservoir for the disease.
2020-03-31 Ena et al A novel coronavirus emerges
Revista Clínica Española (English Edition)
IV. Other Many patients were exposed to the seafood market to several potential wildlife animals acting as reservoirs, such as poultry, snakes, bats, and other farm animals.
2020-03-31 Sun et al Atlas of ACE2 gene expression in mammals reveals novel insights in transmission of SARS-Cov-2
biorxiv
IV. Other Besides pets, livestock are another category of mammals that are frequently in direct contact with humans.
2020-04-30 Phan et al Novel coronavirus: From discovery to clinical diagnostics
Infection, Genetics and Evolution
IV. Other The frequent interactions of wild animals with humans make them a common source of zoonotic infections.
2020-07-31 Artika et al Pathogenic viruses: Molecular detection and characterization
Infection, Genetics and Evolution
IV. Prevalence Study Zoonotic viral infections which cause human diseases may come from domestic animals, poultry, livestock and wildlife.

Wildlife, especially mammals and birds, are hosts to a large number of viruses.

Similar to bats, rodents are also natural reservoirs of a number of life-threatening zoonotic viruses.

Bats (order Chiroptera) are important reservoir hosts of emerging viruses.

Comparative quantitative analysis has suggested that bats host more zoonotic viral infections per species than rodents.
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Levels of Evidence in Epidemiology
LevelRating Criteria
IEvidence obtained from a systematic review or meta-analysis of all relevant randomized, controlled trials
IIEvidence obtained from at least one properly designed randomized, controlled trial
III-1Evidence obtained from well-designed pseudorandomized controlled trials (without proper randomization)
III-2Evidence obtained from comparative studies with concurrent controls and allocation not randomized (cohort studies), case-control studies, or interrupted time series with a control group
III-3Evidence obtained from comparative studies with historical control, 2 or more single-arm studies, or interrupted time series without a parallel control group
IVEvidence obtained from descriptive case series, either before testing or before and after testing