What do we know about virus genetics, origin, and evolution?

Table of Contents

1 Real-time tracking of whole genomes and a mechanism for coordinating the rapid dissemination of that information to inform the development of diagnostics and therapeutics and to track variations of the virus over time.

1.0.0.1 Highlights

1.0.0.2 Articles

Date Authors Title LOE(?) & Sample Matches
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 allows tracking of new viral mutations as the outbreak expands globally, which may help to accelerate the development of novel diagnostics, drugs and vaccines to stop the COVID-19 disease.
2020 Voice from China: nomenclature of the novel coronavirus and related diseases
Chin Med J (Engl)
IV. Other Genotyping provides a new clinical diagnostic tool for directing the use of drugs and the development of vaccines.
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 Findings from this study provided useful information in a real time manner to monitor, evaluate and forecast the COVID-19 epidemic in China.
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 allows tracking of new viral mutations as the outbreak expands globally, which may help to accelerate the development of novel diagnostics, drugs and vaccines.AvailabilityAvailable online: and deoliveira@ukzn.ac.zaSupplementary informationSupplementary data is available online.
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 Although these measures might not prevent the eventual establishment of ongoing, widespread transmission of the virus in the United States, they are being implemented to 1) slow the spread of illness; 2) provide time to better prepare health care systems and the general public to be ready if widespread transmission with substantial associated illness occurs; and 3) better characterize 2019-nCoV infection to guide public health recommendations and the development of medical countermeasures including diagnostics, therapeutics, and vaccines.
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 Other effective measures include One health approach, implementation of effective prevention and control strategies, rapid communication and networking, and exploring advances in science and technology for developing rapid and confirmatory diagnostics, enhancing disease surveillance and monitoring, implementation of strict biosecurity measures, and timely efforts toward designing appropriate and effective vaccines and therapeutics (Cheng et al.
2020-02-19 Zhang et al A Novel Coronavirus (COVID-19) Outbreak A Call for Action
Chest
IV. Prevalence Study

12 In the last 2 weeks of January 2020, thirteen children were diagnosed, fortunately with a mild clinical presentation.
The information produced by this research allows the medical and scientific communities to better understand the transmission of COVID-19, to develop rapid diagnostic tests and efficient epidemiologic control, and to facilitate the development of antiviral therapies and vaccines.
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 ABSTRACTEffective countermeasures against the recent emergence and rapid expansion of the 2019-Novel Coronavirus (2019-nCoV) require the development of data and tools to understand and monitor viral spread and immune responses.
2020-02-20 新型冠状病毒SARS-CoV-2的实验室检测技术
PMC
IV. Other The selection of appropriate detection techniques and methods for accurate and rapid identification of pathogens therefore plays a key role in improving the diagnosis and treatment of the patients and containing the outbreak.

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.
2020-02-21 Heymann et al Data sharing and outbreaks: best practice exemplified
The Lancet
IV. Other The genetic sequence of the 2019 novel coronavirus (2019-nCoV) enabled the rapid development of point-of-care real-time RT-PCR diagnostic tests specific for 2019-nCoV (based on full genome sequence data on the Global Initiative on Sharing All Influenza Data [GISAID] platform).
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.
2020-02-29 Bonilla-Aldana et al SARS-CoV, MERS-CoV and now the 2019-novel CoV: Have we investigated enough about coronaviruses? – A bibliometric analysis
Travel Medicine and Infectious Disease
IV. Other The availability of genome sequences, phylogenetic tracing analysis, and development of predictive models to better understand the biology of this virus has been generated almost in real-time, allowing a more rapid monitoring and response when compared to previous coronavirus outbreaks.
2020-02-29 Lee et al Wuhan novel coronavirus (COVID-19): why global control is challenging?
Public Health
IV. Other Surveillance enables the disease to be detected, outbreaks to be tracked, and the efficacy of interventions to be monitored.
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.
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.
2020-03-03 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).
Infection control is based on rapid information dissemination.

Rapid identification of the viral genome and the development of rapid diagnostic tests will facilitate the isolation of those who are confirmed as infected .
2020-03-03 Yang et al Analysis of epidemiological characteristics of coronavirus 2019 infection and preventive measures in Shenzhen China: a heavy population city
medrxiv
IV. Other Big data and artificial intelligence were increasingly important in preventing infectious, which can monitor the population and formulate corresponding measures in time to reduce the spread of the respiratory infectious disease, and easily track patients and close contacts .
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.
Real-time analysis of crowdsourced individual line list data provides a tool for monitoring outbreaks with novel pathogens in early stages, as witnessed with Ebola.
2020-03-07 Taiaroa et al Direct RNA sequencing and early evolution of SARS-CoV-2
biorxiv
IV. Other Following the emergence of SARS-CoV-2, genomic analyses have played a key role in the 41 public health response by informing the design of appropriate molecular diagnostics and 42 corroborating epidemiological efforts to trace contacts .
2020-03-10 Gao et al The epidemiological characteristics of 2019 novel coronavirus diseases (COVID-19) in Jingmen,Hubei,China
medrxiv
IV. Prevalence Study

Findings: Of the 213 cases (108 men and 105 women) , 88 (41%) had exposure to Wuhan.
Cases were analyzed for epidemiological data and were confirmed by real-time PCR.
2020-03-12 Li et al Retrospective analysis of the possibility of predicting the COVID-19 outbreak from Internet searches and social media data, China, 2020
Euro Surveill
IV. Prevalence Study The Internet surveillance data provided an accurate and timely prediction about the outbreak and progression of COVID-19.
2020-03-13 Hsih et al Featuring COVID-19 cases via screening symptomatic patients with epidemiologic link during flu season in a medical center of central Taiwan
Journal of Microbiology, Immunology and Infection
IV. Prevalence Study

Methods Two patients were confirmed positive for SARS-CoV-2 infection by rRT-PCR as COVID-19 patients A and B. Causative pathogens for included patients were detected using FilmArray™ Respiratory Panel.
Rapid detection tools such as FilmArrayTM Respiratory Panel can aid in early diagnosis of causative pathogens.
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 Summary Effective countermeasures against the recent emergence and rapid expansion of the 2019 novel coronavirus (SARS-CoV-2) require the development of data and tools to understand and monitor its spread and immune responses to it.
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.
2020-03-17 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 More broadly, rapid online surveys could be an important tool in tracking the public's knowledge and misperceptions during rapidly moving infectious disease outbreaks.
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 New data sources at our disposal include not only the passively observed big data streams from mobile phones but also detailed environmental data and local sensor information from distributed devices, internet search information, pathogen genomic data that can be generated rapidly during an outbreak to inform the response, 7 and crowd-sourced approaches to monitoring rapidly evolving emergencies.

Taken together, these incentive structures create multiple barriers to rapid data generation and the development of streamlined epidemic forecasting systems that use these new data types.
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) .
The rapid identification of the etiology and the sharing of the genetic sequence of the virus, followed by international collaborative efforts initiated due to the emergence of SARS-CoV-2 have led to the rapid availability of real-time PCR diagnostic assays that support the case ascertainment and tracking of the outbreak .
2020-03-20 Zhou et al COVID-19: Challenges to GIS with Big Data
Geography and Sustainability
IV. Computer Model In the future, with the support of Internet of Things technology, a national classified material transportation monitoring system and national data integration and analysis platform will be gradually established, which will provide more accurate and timely information on the material supply and transportation capacity during emergency policymaking for the whole society.

Here, we discuss ten of these challenges and responses, viz ., 1) rapid construction of a big data information system for the epidemic; 2) rapid problem-oriented big data acquisition and integration; 3) convenient multi-scale dynamic mapping for epidemics; 4) comparison between spatial tracking and the spatiotemporal trajectory of big data; 5) spatiotemporal prediction of the transmission speed and scale of the epidemic; 6) spatial segmentation of the epidemic risk and prevention level; 7) spatial dynamic balancing of supply and demand for medical resources; 8) assessment of the supply of materials and transportation risk; 9) rapid estimation of the population flow and distribution; and 10) monitoring the spatial spread of social sentiment and detection.

In the fight against COVID-19, Geographic Information Systems (GIS) and big data technologies have played an important role in many aspects, including the rapid aggregation of multi-source big data, rapid visualization of epidemic information, spatial tracking of confirmed cases, prediction of regional transmission, spatial segmentation of the epidemic risk and prevention level, balancing and management of the supply and demand of material resources, and social-emotional guidance and panic elimination, which provided solid spatial information support for decision-making, measures formulation, and effectiveness assessment of COVID-19 prevention and control.

The comparison of the spatial track of the patient's activities is a critical technical task for virus tracking and transmission chain reconstruction.
2020-03-20 Krengli et al Running a Radiation Oncology Department at the time of coronavirus: an Italian experience
Advances in Radiation Oncology
IV. Other The Italian government has created a website to keep track of the SARS-CoV-2 spread and its realtime statistics .
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 Moreover, such a diagnostic tool will help with preventing 53 spread of virus by identifying the infected cases and can monitor the health status of infected patients 54 by quantifying the viral load.
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 Concurrently, a multiplex molecular assay that detects respiratory pathogens was performed at the point-of-care laboratory with the Biofire FilmArray Respiratory panel 2 test (Biomérieux, Marcy-l'Etoile, France) or the FTD Respiratory pathogens 21 kit (Fast Track Diagnosis, Luxembourg).
2020-03-20 Zhu et al Reverse transcription loop-mediated isothermal amplification combined with nanoparticles-based biosensor for diagnosis of COVID-19
medrxiv
IV. Other Rapid and precise diagnostic methods are thus immediately needed for diagnosing COVID-19, providing timely treatment and facilitating infection control.
2020-03-24 Jiménez-Pavón et al Physical exercise as therapy to fight against the mental and physical consequences of COVID-19 quarantine: Special focus in older people
Progress in Cardiovascular Diseases
IV. Other The evolution of this pandemic can be followed at different official websites, such as the interactive web-based dashboard to track Covid-19 in real time developed by the Johns Hopkins University Center for Systems Science and Engineering ( or the HealthMap provided by the Boston Children´s Hospital (https://www.healthmap.org/Covid-19/).
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.
2020-03-28 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) .
Rapid and accurate detection of COVID-19 is crucial in controlling outbreaks in the community and in hospitals .
2020-03-30 pawar et al Effects of temperature on COVID-19 transmission
medrxiv
IV. Other The data for countries and regions outside mainland China is collected from an interactive web-based dashboard to track COVID-19 in real time .
2020-03-30 Böttcher et al Why estimating population-based case fatality rates during epidemics may be misleading
medrxiv
III-3. Time Series Analysis

Two out of 19 patients died, on average, 20.5 days after first symptoms occurred and the mean recovery time of the remaining 17 patients is 16.8 days.
The most accurate estimates of M 1 can be obtained if we keep track of the fate of cohorts that were infected within a small time window in the past.
2020-03-30 Caspi et al Climate effect on COVID-19 spread rate: an online surveillance tool
medrxiv
IV. Prevalence Study

Countries with less than 50 diagnosed patients as well as countries not categorized as local transmission according to the WHO situation report as of March 9 were excluded in order to minimize confounding of imported disease transmission.
We hope that the online tool coupling COVID-19 data with climate data will assist in tracking the disease and tailoring the needed measures to contain it.

Online dashboards have proven useful for global COVID-19 tracking.
2020-03-30 Huang et al A data driven time-dependent transmission rate for tracking an epidemic: a case study of 2019-nCoV
Science Bulletin
IV. Computer Model Although the present tool is only for data analysis and event tracking, it also enables us to make an estimate for the future course of the epidemic.
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 Abbas et al Classification of COVID-19 in chest X-ray images using DeTraC deep convolutional neural network
medrxiv
IV. Other Fast detection of the COVID-19 can be contributed to control the spread of 9 the disease.
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 nCapp can conduct the online monitoring, location tracking, alarm linkage, command and dispatch functions, in favor of online and full-time monitoring of changes in symptoms and diseases severity and guiding treatment.

nCapp can also establish an online COVID-19 real-time update database, and it updates the model of diagnosis in real time based on the latest real-world case data to improve diagnostic accuracy.

2 Access to geographic and temporal diverse sample sets to understand geographic distribution and genomic differences, and determine whether there is more than one strain in circulation. Multi-lateral agreements such as the Nagoya Protocol could be leveraged.

2.0.0.1 Highlights

2.0.0.2 Articles

Date Authors Title LOE(?) & Sample Matches
2020 Shanmugaraj et al Emergence of Novel Coronavirus 2019-nCoV: Need for Rapid Vaccine and Biologics Development
Pathogens
IV. Prevalence Study The geographical distribution of the virus has been increasing since the outbreak.
2020 Shrestha et al Nepal’s First Case of COVID-19 and public health response
Journal of Travel Medicine
IV. Prevalence Study SARS, in 2003, spread both within a geographical region and, more significantly, to different cities from a single location, through infected travelers.4 The air-travel frequency from major cities in China to Nepal is lower compared to that of other countries.5 However, there are other factors to consider.
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 Taken together, the differences in AFs of ACE2 coding variants among different populations suggested that the diverse genetic basis might affect ACE2 functions among populations.
2020-01-30 Pullano et al Novel coronavirus (2019-nCoV) early-stage importation risk to Europe, January 2020
Euro Surveill
IV. Prevalence Study The risk pattern of 2019-nCoV importation estimated for Europe varies considerably depending on the geographical extent of the affected areas in China.
2020-02-11 Luczak-Roesch et al Networks of information token recurrences derived from genomic sequences may reveal hidden patterns in epidemic outbreaks: A case study of the 2019-nCoV coronavirus.
medrxiv
IV. Other We aim to devise novel ways to model, visualise and analyse the temporal dynamics of epidemic outbreaks in order to help researchers and other people involved in crisis response to make well-informed and targeted decisions about from which geographical locations and time periods more genetic samples may be required to fully understand the outbreak.
2020-02-14 Li et al Transmission dynamics and evolutionary history of 2019-nCoV
Journal of Medical Virology
IV. Prevalence Study Abstract To investigate the time origin, genetic diversity, and transmission dynamics of the recent 2019-nCoV outbreak in China and beyond, a total of 32 genomes of virus strains sampled from China, Thailand, and USA with sampling dates between 24 December 2019 and 23 January 2020 were analyzed.
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.
Phylogenetic analysis was performed to investigate the genetic relationship between SARS-COV-2 and other pathogenic coronavirus, as well as the diversity among our SARS-COV-2 strains.
2020-02-18 Danchin et al A new transmission route for the propagation of the SARS-CoV-2 coronavirus
medrxiv
IV. Computer Model We explore here how variation in the SARS-CoV-2 virus tropism could influence epidemic spread.
2020-02-23 Hu et al Clinical Characteristics of 24 Asymptomatic Infections with COVID-19 Screened among Close Contacts in Nanjing, China
medrxiv
IV. Prevalence Study

According to the report on "Diamond Princess", among the 1,723 tested travelers, 189 asymptomatic individuals were positive for the COVID-19 virus as of 17 February 2020 10 , which indicated that a large number of asymptomatic carriers and mild patients remain undiscovered in the community.
There were no differences in other characteristics between these 2 groups, possibly due to the limited sample size.
2020-02-26 Yang et al Clinical characteristics and imaging manifestations of the 2019 novel coronavirus disease (COVID-19):A multi-center study in Wenzhou city, Zhejiang, China
Journal of Infection
III-2. Retrospective Cohort

The symptoms of these 12 patients included fever (8 patients), cough (3 patients), expectoration (1 patient), headache (1 patient), sore throat (2 patients), snotty (1 patient), diarrhea (1 patient).
Further comparison studies could be carried out between patients with a long-term time gap of disease onset in the same geographic location.
2020-02-26 Zhang et al Genomic variations of SARS-CoV-2 suggest multiple outbreak sources of transmission
medrxiv
IV. Other Genomic variations of SARS-CoV-2 suggest multiple outbreak sources of transmission
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 As travel becomes more affordable and available, populations with access to air travel have also become more heterogeneous both economically and in geographic origin.
2020-03-02 Basu et al Strategies for vaccine design for corona virus using Immunoinformatics techniques
biorxiv
III-3. Time Series Analysis

From InterPro database, 78 homologous protein sequences are recovered for nonstructural protein NS4 protein for coronavirus as shown in Table 1 .
This distribution varies among the human population according to the population in different geographic regions of the world.
2020-03-05 Manning et al Rapid metagenomic characterization of a case of imported COVID-19 in Cambodia
biorxiv
IV. Other 4, 5 Genetic characterization of the virus from geographically diverse patient samples is key to infer the rate of spread.
2020-03-06 Kissler et al Projecting the transmission dynamics of SARS-CoV-2 through the post-pandemic period
medrxiv
IV. Prevalence Study According to a study of geographic variation in the SARS-CoV-2 basic reproduction number across China, seasonal variations in absolute humidity will be insufficient to prevent the widespread transmission of SARS-CoV-2 .
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.
Data from other countries, in particular the number of cases by date of disease onset and the age and gender distribution of cases and deaths, are necessary to better understand the variability in mortality across settings.
2020-03-06 Wilkinson et al Partial RdRp sequences offer a robust method for Coronavirus subgenus classification
biorxiv
IV. Other When host 179 and geographical origins of isolates falling within unclassified clades was examined, the majority 180 were associated with regional radiations for which little or no genomic or phenotypic data are 181 author/funder.
2020-03-11 Cai et al Sex difference and smoking predisposition in patients with COVID-19
The Lancet Respiratory Medicine
IV. Other With more cases being examined from different ethnic and genetic backgrounds worldwide, ACE2 expression variation can be better analysed and compared to establish whether it contributes to susceptibility to COVID-19 across the different subgroups.
2020-03-11 Li et al Evolutionary history, potential intermediate animal host, and cross-species analyses of SARS-CoV-2
Journal of Medical Virology
IV. Other Abstract To investigate the evolutionary history of the recent outbreak of SARS-CoV-2 in China, a total of 70 genomes of virus strains from China and elsewhere with sampling dates between 24 December 2019 and 3 February 2020 were analyzed.
2020-03-13 Zheng et al The Prediction for Development of COVID-19 in Global Major Epidemic Areas Through Empirical Trends in China by Utilizing State Transition Matrix Model
medrxiv
IV. Computer Model Due to the large outbreaks started at different times all over the world, the effects of seasonal and geographical factors have not been taken into account.
2020-03-16 Araujo et al Spread of SARS-CoV-2 Coronavirus likely to be constrained by climate
medrxiv
IV. Computer Model The uneven colonization of geographic versus climatic space, invites the interpretation that climate is acting as a stronger constraint for the spread of the virus than geographical distances are.
2020-03-17 Huang et al Evidence of the Recombinant Origin and Ongoing Mutations in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)
biorxiv
IV. Other To determine the evolutionary relationship of the SARS-CoV-2, phylogenetic analysis was performed on whole genomic sequences of different CoVs from various hosts.
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.
Finally, seasonality, geographic location, heat and humidity are co-factors, as are age, gender and underlying pathologies.
2020-03-20 Kagan et al Scientometric Trends for Coronaviruses and Other Emerging Viral Infections
biorxiv
IV. Prevalence Study We utilized the WikiData dataset to extract geographic information for academic institutions in order to match a paper with its authors' geographic locations.
2020-03-20 Liu et al Assessing the Global Tendency of COVID-19 Outbreak
medrxiv
IV. Computer Model In this world map, the same set of color coding is used for different actual geographical locations.
2020-03-21 Sardar et al Comparative analyses of SAR-CoV2 genomes from different geographical locations and other coronavirus family genomes reveals unique features potentially consequential to host-virus interaction and pathogenesis
biorxiv
III-3. Time Series Analysis The phylogenetics heterogeneity between different strains is explored by genome variation profiling to find alterations in genetic information during the course of evolution, outbreak, and clinical spectrum caused by the different strains.
2020-03-23 Chin et al Healthcare worker absenteeism, child care costs, and COVID-19 school closures: a simulation analysis
medrxiv
IV. Prevalence Study

We focus our analyses on households with children below age 13 -although children under the age of 5 do not attend school, daycare services would likely also be closed in the event of school closures.
6 The prevalence of these comorbidities also varies geographically in the US, further highlighting the importance of regional analysis.
2020-03-23 Milne et al The Effectiveness of Social Distancing in Mitigating COVID-19 Spread: a modelling analysis
medrxiv
IV. Other The model represents the individual-to-individual contact patterns in as much detail as data sources provide, to accurately describe how the movement of individuals allows virus transmission to spread over a geographic region.
2020-03-24 Xu et al Epidemiological data from the COVID-19 outbreak, real-time case information
Sci Data
IV. Other While administrative units are supplied with shapefiles sources and unique identifiers with these files so that users can understand the corresponding geographic scale which the row represents, with points, different settlements cover different spatial extents.
2020-03-24 Kissler et al Social distancing strategies for curbing the COVID-19 epidemic
medrxiv
IV. Prevalence Study The timing and duration of the interventions will likely need to be tailored geographically due to variation in epidemic timing, seasonal forcing, and critical care capacities.
2020-03-24 Huang et al The Battle Against Coronavirus Disease 2019 (COVID-19): Emergency Management and Infection Control in a Radiology Department
Journal of the American College of Radiology
IV. Other Collaboration with the radiology departments of other hospitals is very important because patients may initially present to different centers, depending on geographic location and travel distance.
2020-03-26 Zhang et al Comparison of the spatiotemporal characteristics of the COVID-19 and SARS outbreaks in mainland China
medrxiv
III-3. Time Series Analysis The different transmission mechanisms of these coronaviruses can also present different spatial and temporal distributions nationally and globally.

Spatiotemporal analyses, which integrate spatial and time-series analyses, can provide additional information on the persistence of patterns over time and illuminate any unusual patterns.
2020-03-26 Menkir et al Estimating the number of undetected COVID-19 cases exported internationally from all of China
medrxiv
IV. Prevalence Study

For each province, we calculate the median number of prevalent cases by day using 1000 posterior samples of new infections per day estimated by Hay et al.
These trends may anticipate differences in the timing and emergence of local transmission in these countries.
2020-03-27 Kang et al Critical Care for Patients with Severe Covid-19 in Sichuan Province, China: Provincial Cohort Study
medrxiv
III-3. Time Series Analysis

Results: Out of 539 confirmed Covid-19 patients, 81 severe cases (15.0%) were identified.
Studies with larger sample size including patients from different cities may further clarify the association between admission timing and patient outcomes.
2020-03-27 Kamikubo et al Epidemiological Tools that Predict Partial Herd Immunity to SARS Coronavirus 2
medrxiv
IV. Prevalence Study A population genetic study of 103 SARS-CoV-2 genomes has identified two viral subtypes designate S and L. 5 The S type is the ancestral version of the virus.
2020-03-27 Skums et al Global transmission network of SARS-CoV-2: from outbreak to pandemic
medrxiv
IV. Prevalence Study Indeed, although the virus genetic diversity is gradually increasing, particular genomic variants continue to be repeatedly sequenced at different time points and geographical locations.
2020-03-28 Miller et al Correlation between universal BCG vaccination policy and reduced morbidity and mortality for COVID-19: an epidemiological study
medrxiv
IV. Other As each country used the same strain for the whole population, difference in strains for different purposes should be gathered in randomized control trials with different subjects from the same population tested with different strains.
2020-03-30 Dong et al Understand Research Hotspots Surrounding COVID-19 and Other Coronavirus Infections Using Topic Modeling
medrxiv
IV. Computer Model Future research could also study the occurrence of topics over time and analyze links to historic events and virus characteristics, in order to better understand possible temporal patterns.
2020-03-30 Kumar et al Comparative Genomic Analysis of Rapidly Evolving SARS CoV-2 Viruses Reveal Mosaic Pattern of Phylogeographical Distribution
biorxiv
IV. Other In near future as more and more genome sequences will become available from different geographical locations, more accurate patterns of their relatedness across the globe will become available
2020-03-30 Hou et al Changing transmission dynamics of COVID-19 in China: a nationwide population-based piecewise mathematical modelling study
medrxiv
IV. Prevalence Study Spatial and temporal heterogeneity would have been larger if these data were included.
2020-03-31 Amariles et al COVID-19 in Colombia endpoints. Are we different, like Europe?
Research in Social and Administrative Pharmacy
IV. Other Therefore, it is possible to establish that the situation in this country will be different from in European Mediterranean and that Colombia could have different endpoints from Spain and Italy.
2020-03-31 Haixu et al Detection of 20 respiratory viruses and bacteria by influenza-like illness surveillance in Beijing, China, 2016–2018
Journal of Infection
IV. Prevalence Study

The series included 47 patients, of whom 15 were taking antibiotic prophylaxis at the time of meningococcal disease onset and 32 were not ( Table 1 ).
However, these geographical differences in the detection rate may have been affected by several other factors, such as different technical approaches, sampling periods, study durations, or target populations (global population, paediatric population, etc.).
2020-03-31 Wang et al Emergence of SARS-like coronavirus poses new challenge in China
Journal of Infection
IV. Prevalence Study

The series included 47 patients, of whom 15 were taking antibiotic prophylaxis at the time of meningococcal disease onset and 32 were not ( Table 1 ).
However, these geographical differences in the detection rate may have been affected by several other factors, such as different technical approaches, sampling periods, study durations, or target populations (global population, paediatric population, etc.).
2020-03-31 Xu et al Genetic diversity and potential recombination between ferret coronaviruses from European and American lineages
Journal of Infection
IV. Prevalence Study

The series included 47 patients, of whom 15 were taking antibiotic prophylaxis at the time of meningococcal disease onset and 32 were not ( Table 1 ).
However, these geographical differences in the detection rate may have been affected by several other factors, such as different technical approaches, sampling periods, study durations, or target populations (global population, paediatric population, etc.).
2020-03-31 Tang et al Emergence of a novel coronavirus causing respiratory illness from Wuhan, China
Journal of Infection
IV. Prevalence Study

The series included 47 patients, of whom 15 were taking antibiotic prophylaxis at the time of meningococcal disease onset and 32 were not ( Table 1 ).
However, these geographical differences in the detection rate may have been affected by several other factors, such as different technical approaches, sampling periods, study durations, or target populations (global population, paediatric population, etc.).
2020-04-01 Zipfel et al Assessing the interactions between COVID-19 and influenza in the United States
medrxiv
IV. Prevalence Study In addition to this strategy, we suggest that the interaction between a novel and circulating pathogen due to shared preventative behaviors or a shared susceptible pool can be leveraged to understand circulation of the former.
2020-04-01 He et al COVID-19, City Lockdown, and Air Pollution: Evidence from China
medrxiv
IV. Prevalence Study Since the risk of disease transmission differed substantially across different locations and different periods, the timing of lockdown also varied.
2020-06-30 Delanghe et al The host’s angiotensin-converting enzyme polymorphism may explain epidemiological findings in COVID-19 infections
Clinica Chimica Acta
IV. Prevalence Study As this D/I polymorphism shows an important geographical variation , we postulated that the variability in D/I genotype distribution might partly explain the variable prevalence of the COVID-19 infection amongst continental European countries.
2020-07-31 Artika et al Pathogenic viruses: Molecular detection and characterization
Infection, Genetics and Evolution
IV. Prevalence Study The mutation pattern of the virus was not geographically related as viruses isolated from same years tended to cluster together, regardless of geographical origin.

3 Evidence that livestock could be infected (e.g., field surveillance, genetic sequencing, receptor binding) and serve as a reservoir after the epidemic appears to be over.

3.0.0.1 Highlights

3.0.0.2 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 .
Bats are believed to be the natural reservoir of MERS-CoV, and dromedary camels can have the virus and have been suggested as possible intermediary hosts as well as a source of infection to humans .
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 .
Surveillance efforts found SARS-CoV viral RNA in both palm civets and raccoon dogs sold in these wet markets ; however, SARS-CoV was not found in the wild, suggesting that those species served as intermediary reservoir as the virus adapted to more efficiently infect humans.
2020 Wu et al Overview of The 2019 Novel Coronavirus (2019-nCoV): The Pathogen of Severe Specific Contagious Pneumonia (SSCP)
J Chin Med Assoc
IV. Prevalence Study

Of the 59 suspected cases, 41 patients were confirmed by nextgeneration sequencing or real-time reverse transcription-polymerase chain reaction (RT-PCR).
5, 13 According to previous studies on the SARS-and MERS-CoV, epidemiologic investigations, their natural reservoir is bat, while palm civet or raccoon dog may be the intermediate (or susceptible) host for SARS-CoV and the dromedary camel for MERS-CoV.
2020 Wu et al The outbreak of COVID-19: An overview
Journal of the Chinese Medical Association : JCMA
IV. Prevalence Study

Of the 59 suspected cases, 41 patients were confirmed by nextgeneration sequencing or real-time reverse transcription-polymerase chain reaction (RT-PCR).
5, 13 According to previous studies on the SARS-and MERS-CoV, epidemiologic investigations, their natural reservoir is bat, while palm civet or raccoon dog may be the intermediate (or susceptible) host for SARS-CoV and the dromedary camel for MERS-CoV.
2020 Daszak et al A strategy to prevent future pandemics similar to the 2019-nCoV outbreak
Biosafety and Health
IV. Prevalence Study The virus itself appears to have a wildlife (bat) origin similar to SARS-CoV, which also emerged in a wildlife market through the interactions of humans and other animals that acted as the intermediate hosts of the virus .
2020 Minjin Wang et al A precision medicine approach to managing Wuhan Coronavirus pneumonia
Precision Clinical Medicine
IV. Prevalence Study

As of January 29, 2020, the virus had been diagnosed in more than 7,000 patients in China and 77 outside this country.
4 Further genetic and amino acid sequencing of the S-protein of 2019-nCoV established that the receptorbinding domain of the S-protein binds to recipient cells and interacts strongly with human angiotensinconverting enzyme 2 (ACE2) receptor molecules.
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 As the human population continues to increase, demand for agricultural land grows, exposing livestock and humans to infections in the wild.
2020-01-28 Chan et al Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan
Emerg Microbes Infect
IV. Other More animal sampling to determine its natural animal reservoir and intermediate animal host in the market is important.
2020-01-30 Bartoszewicz et al Interpretable detection of novel human viruses from genome sequencing data
biorxiv
IV. Prevalence Study Local host adaptation could help switch hosts between the animal reservoir and humans.
2020-02-03 Čivljak et al The third coronavirus epidemic in the third millennium: what’s next?
Croat Med J
IV. Prevalence Study

However, the largest study to date on more than 72 000 patients from China has shown that health care workers make up 3.8% of the patients.
The most likely reservoir was bats, with evidence that the virus was transmitted to a human through an intermediate host, probably a palm civet or raccoon dog .
2020-02-08 Zhang et al Protein structure and sequence re-analysis of 2019-nCoV genome does not indicate snakes as its intermediate host or the unique similarity between its spike protein insertions and HIV-1
biorxiv
IV. Prevalence Study While it is now commonly recognized that bats such as Rhinolophus affinis may serve as the natural reservoir of 2019-nCoV 1 , it is still unclear which animal serves as an intermediate host that brought the bat coronavirus to human hosts.
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.
36 Enforcement of current wildlife protection policy and continued community infrastructure development appears to significantly reduce high-risk contact between humans, wildlife and livestock.
2020-02-11 Sanche et al The Novel Coronavirus, 2019-nCoV, is Highly Contagious and More Infectious Than Initially Estimated
medrxiv
IV. Prevalence Study This suggests that human infections in early December may be due to spillovers from the animal reservoir or limited chains of transmission .
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 .
2020-02-18 Yu et al A familial cluster of infection associated with the 2019 novel coronavirus indicating potential person-to-person transmission during the incubation period
The Journal of Infectious Diseases
IV. Other The epidemiological evidence has shown a potential transmission of the 2019-nCoV during the incubation period.
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.
Although this novel coronavirus might have first originated from animals and now jumped into humans, the possibility of person-to-person transmission could not be excluded, as seen in this family cluster with no known history of exposure to markets or animals, and rapid intercity spread might be possible by air travel.
2020-02-23 Sun et al Clinical characteristics of 50466 patients with 2019-nCoV infection
medrxiv
I. Systematic Review

Results: Ten studies were included in Meta-analysis, including a total number of 50466 patients with 2019-nCoV infection.
Their research suggests that bats may be the reservoir host for 2019-nCoV.
2020-02-23 Hu et al Clinical Characteristics of 24 Asymptomatic Infections with COVID-19 Screened among Close Contacts in Nanjing, China
medrxiv
IV. Prevalence Study

According to the report on "Diamond Princess", among the 1,723 tested travelers, 189 asymptomatic individuals were positive for the COVID-19 virus as of 17 February 2020 10 , which indicated that a large number of asymptomatic carriers and mild patients remain undiscovered in the community.
These findings indicate that asymptomatic carriers can result in person-to-person transmission and should be considered a source of COVID-19 infection.
2020-02-24 Rasmussen et al Coronavirus Disease 2019 (COVID-19) and Pregnancy: What obstetricians need to know
American Journal of Obstetrics and Gynecology
IV. Other The natural reservoir for SARS-CoV is believed to be bats; however, some evidence 138 supported civet cats or raccoon dogs as possible intermediate sources of these illnesses.
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 .
Hypothesizing that bats will be proven as SARS-CoV-2 reservoirs and that adaptation to humans took place in an intermediate host in a live animal market, the following measures would be important: i) Decreasing the risk of transmission from the natural host.
2020-02-26 Rothan et al The epidemiology and pathogenesis of coronavirus disease (COVID-19) outbreak
Journal of Autoimmunity
IV. Other Efforts have been made to search for a reservoir host or intermediate carriers from which the infection may have spread to humans.

Initial reports identified two species of snakes that could be a possible reservoir of the COVID-19.
2020-02-28 Lu et al Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding
The Lancet
IV. Other Fourth, in both SARS-CoV and MERS-CoV, bats acted as the natural reservoir, with another animal (masked palm civet for SARS-CoV 35 and dromedary camels for MERS-CoV) 36 acting as an intermediate host, with humans as terminal hosts.

Although our phylogenetic analysis suggests that bats might be the original host of this virus, an animal sold at the seafood market in Wuhan might represent an intermediate host facilitating the emergence of the virus in humans.

Currently available data suggest that 2019-nCoV infected the human population from a bat reservoir, although it remains unclear if a currently unknown animal species acted as an intermediate host between bats and humans.
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).
It was suggested that civets could serve as an intermediate amplification host.
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.
Intermediate host reservoir: dromedary camels Vaccinating dromedary camels, the source for primary human infection, is a proposed approach to preventing human infection.
2020-03-05 Peters et al Understanding the emerging coronavirus: what it means for health security and infection prevention
Journal of Hospital Infection
IV. Prevalence Study

50 Super spreading individuals were found to have a major impact in the previous MERS, SARS, and Ebola pandemics.
Its likely reservoir is bats, with pangolins identified as the likely intermediate host.
2020-03-13 Berra et al Protocol for a randomized controlled trial testing inhaled nitric oxide therapy in spontaneously breathing patients with COVID-19
medrxiv
II. Randomized Controlled Trial

Based on results reported in Table 2 , the same step could then be repeated increasing sample size from 340 to 500 patients, from 500 patients to 760 and from 760 patients to 1260.
The current outbreak would result from the acquired ability of the virus to undergo human to human transmission , after the jump from the original animal reservoir (most likely a bat).
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.
These camels are the natural reservoir host of MERS-CoV.

However, the direction of this cross-species transmission remains to be determined and the possibility cannot be excluded that both humans and camels might have acquired 229E from an unidentified host including bats .

Although bats are the evolutionary reservoir host and bat CoVs serve as the gene pool of MERS-CoV, humans acquire MERS-CoV from diseased dromedary camels, but not directly from bats.

Their reservoir hosts are selected through evolution.
2020-03-15 Ye et al Zoonotic origins of human coronaviruses
Int J Biol Sci
IV. Prevalence Study However, it has been reported that masked palm civets from the wild or farms without exposure to the live animal markets were largely negative for SARS-CoV , suggesting that masked palm civets might only serve as the intermediate amplifying host but not the natural reservoir of SARS-CoV.
2020-03-15 Zheng et al SARS-CoV-2: an Emerging Coronavirus that Causes a Global Threat
Int J Biol Sci
IV. Other For example, masked palm civet and dromedary camels are the intermediate hosts for SARS-CoV and MERS-CoV respectively .
2020-03-16 Hemida et al The SARS-CoV-2 outbreak from a one health perspective
One Health
IV. Prevalence Study The environment serves as the intermediate vessels between the animals and humans.
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 Bats and pangolins are suspected as the reservoir and the intermediate host.

The receptor binding domain (RBD) of the SARS-CoV-2 S protein plays the key role in the tight binding to human receptor ACE2 for viral entry.
2020-03-17 LIU et al Understanding of guidance for acupuncture and moxibustion interventions on COVID-19 (Second edition) issued by CAAM
World Journal of Acupuncture - Moxibustion
IV. Other The major source of infection is the patients with COVID-19 and asymptomatic SARS-CoV-2 carriers seem also a potential source of infection.
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.
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.
Evidence suggest that the novel coronavirus likely jumped from a primary reservoir (e.g, horseshoe bats) to an intermediary reservoir, possibly generating an outbreak among wild animals in at least one wet market in Wuhan, China .
2020-03-20 Massonnaud et al COVID-19: Forecasting short term hospital needs in France
medrxiv
IV. Computer Model SARS-CoV-2 is a zoonotic virus, and bats are believed to be its reservoir.
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 This novel virus is thought to have originated from an animal reservoir, and acquired the ability to infect human cells using the SARS-CoV cell receptor hACE2.
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 Based on the evidence of a rapidly increasing incidence of infections and the possibility of transmission by asymptomatic carriers , SARS-CoV-2 can be transmitted effectively among humans and exhibits high potential February 20, 2020; 7:4 ] for a pandemic .
2020-03-31 Ena et al A novel coronavirus emerges
Revista Clínica Española (English Edition)
IV. Other Peridomestic animals may serve as intermediate hosts, facilitating the recombination of the virus, and serving as amplification hosts.
2020-04-01 Lodder et al SARS-CoV-2 in wastewater: potential health risk, but also data source
The Lancet Gastroenterology & Hepatology
IV. Other But environmental surveillance of SARS-CoV-2 could serve as a data source, indicating if the virus is circulating in the human population.
2020-04-30 Xu et al Unveiling the Origin and Transmission of 2019-nCoV
Trends in Microbiology
IV. Other It is suspected that palm civets sold in live animal markets were the intermediate host for SARS-CoV .
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.
2020-07-31 Shereen et al COVID-19 infection: Origin, transmission, and characteristics of human coronaviruses
Journal of Advanced Research
IV. Prevalence Study

In 2001 the samples were isolated from the healthy persons of Hongkong and the molecular assessment showed 2.5% frequency rate of antibodies against SARS-coronavirus.
The zoonotic source of SARS-CoV-2 is not confirmed, however, sequence-based analysis suggested bats as the key reservoir.

4 Evidence of whether farmers are infected, and whether farmers could have played a role in the origin.

4.0.0.1 Highlights

4.0.0.2 Articles

Date Authors Title LOE(?) & Sample Matches
2020 LIU et al A survey on awareness of digestive system injury caused by corona virus disease 2019 in gastroenterologists
Chinese Journal of Digestion
IV. Other The percentage of correct answer of digestive system injury caused by COVID-19 in residents, attending physicians, associate chief physicians and chief physicians was 30.9% (134/433), 33.9% (234/691), 32.4% (213/657) and 34.9% (152/435), respectively, however there were no statistically significant differences among physicians of different level (χ 2 =6.60, P > 0.05).
2020 Bodomo et al How African migrants in China cope with barriers to health care
The Lancet Public Health
IV. Other Family elders and religious leaders have a major role as health-care providers for both adult and adolescent members of the African community.
2020 Kavanagh et al Authoritarianism, outbreaks, and information politics
The Lancet Public Health
IV. Other The early history of the 2019-nCoV outbreak raises questions about whether this situation is an example of beneficial autocracy.
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 This rapid advice guideline is suitable for the first frontline doctors and nurses, managers of hospitals and healthcare sections, community residents, public health persons, relevant researchers, and all person who are interested in the 2019-nCoV.

This guideline is suitable for frontline doctors and nurses, managers of hospitals and healthcare sections, healthy community residents, personnel in public healthcare, relevant researchers, and all persons who are interested in the 2019-nCoV management.

During this process, frontline clinicians and nurses have accumulated valuable experience in the diagnosis, treatment and nursing for 2019-nCoV infected patients.
2020-02-11 Khan et al Novel coronavirus: how things are in Wuhan
Clinical Microbiology and Infection
IV. Other Farmers are being directed to maintain hygiene, and seafood markets are being monitored in major cities.
2020-02-14 Wang et al What to do next to control the 2019-nCoV epidemic?
The Lancet
IV. Other First-line medical staff and scientists in China have had a leading role in fighting the outbreak of 2019-nCoVassociated pneumonia.
2020-02-21 Chen et al Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study
The Lancet
IV. Other Among them, there were 47 patients with longterm exposure history, most of whom were salesmen or market managers, and two patients with shortterm exposure history, who were shoppers.
2020-02-24 Rasmussen et al Coronavirus Disease 2019 (COVID-19) and Pregnancy: What obstetricians need to know
American Journal of Obstetrics and Gynecology
IV. Other Women were matched on sex, age, timing of contracting SARS, health care worker status, 173 underlying illness and whether the woman resided in a housing area where there was a large 174 outbreak.
2020-02-26 Rothan et al The epidemiology and pathogenesis of coronavirus disease (COVID-19) outbreak
Journal of Autoimmunity
IV. Other A guideline was published for the medical staff, healthcare providers, and, public health individuals and researchers who are interested in the 2019-nCoV .
2020-03-03 Yang et al Analysis of epidemiological characteristics of coronavirus 2019 infection and preventive measures in Shenzhen China: a heavy population city
medrxiv
IV. Other Hospitals and medical staff played the most important role in the treatment of respiratory infectious diseases.
2020-03-03 Wang et al Clinical Characteristics of Patients with Severe Pneumonia Caused by the 2019 Novel Coronavirus in Wuhan, China
medrxiv
III-2. Cross Sectional Control

Basic characteristics 97 A total of 110 hospitalized patients participated in this study, which included 38 (34.5%) patients with 98 severe pneumonia and 72 (65.5%) patients with non-severe pneumonia.
For patients who were suspected to have the illness, two senior respiratory doctors made 58 the diagnosis together.
2020-03-04 Wang et al Mitigate the effects of home confinement on children during the COVID-19 outbreak
The Lancet
IV. Other 7 Social workers can play an active role in helping parents cope with family issues arising from the situation, when needed.

10, 11 Parents are often important role models in healthy behaviour for children.
2020-03-06 sun et al Study of the mental health status of medical personnel dealing with new coronavirus pneumonia
medrxiv
IV. Prevalence Study

Among 138 patients admitted consecutively from January 1 to 28, 2020, to Zhongnan Hospital of Wuhan University, the proportion of medical personnel was as high as 29% .
The 17 items include: hospital, department, occupation, gender, age, highest education level, work experience, level of expertise, marital status, any children, living status, whether you have participated in training for handling of public health emergencies, whether family members support your working on the front line against coronavirus, whether you have supported in affected areas in Hubei, designated hospitals, department of infectious diseases, fever clinics or emergency department, level of concern whether you and your family have been infected, degree of suspicion that you were infected when coronavirus-related symptoms occurred, and whether you have received medical observation recently.

3.2.1 Degree of suspicion that they were infected when the novel coronavirus-related symptoms occurred, the level of concern whether they and their family members have been infected, whether they have supported in affected areas in Hubei Province, designated hospitals, and other places for the novel coronavirus, and whether family members support them working on the front line COVID-19 patients are the main source of transmission of the disease.

Factors affecting the mental health and status of medical personnel based on their significance from high to low are: the degree of suspicion that they were infected when the novel coronavirus-related symptoms occurred, the level of concern whether they and their family members have been infected, age, whether they have supported in affected areas in Hubei Province, designated hospitals, and other places for the novel coronavirus, and whether family members support them working on the front line (p < 0.05).

or emergency department, level of concern whether you and your family have been infected, degree of suspicion that you were infected when coronavirus-related symptoms occurred, and whether you have received medical observation recently.

of suspicion that they were infected when the novel coronavirus-related symptoms occurred, the level of concern whether they and their family members have been infected, age, whether they have supported in affected areas in Hubei Province, designated hospitals, and other places for the novel coronavirus, and whether their family members support them working on the front line.
2020-03-08 Huang et al Emotional responses and coping strategies of nurses and nursing college students during COVID-19 outbreak
medrxiv
IV. Other During the SARS outbreak, many nurses showed conflicting roles as medical service providers and parents.
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 Whether certain properties such as glycosylation pattern at critical sites of the glycoprotein play a role in the attenuation of neutralizing antibody response needs further clarification.
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.)
2020-03-13 Bhagavathula et al Novel Coronavirus (COVID-19) Knowledge and Perceptions: A Survey of Healthcare Workers
medrxiv
III-2. Cross Sectional Control

A total of 529 HCWs participated, 453 of whom completed the study questionnaire (85.6% response rate), including 234 (51.6%) men and 219 (48.3%) women; most of the participants were below 44 years of age (82.4%).
The majority of participants were doctors (n=137, 30.2%) or medical students (n=134, 29.6%) and were from Asia (68%).
2020-03-15 Zhong et al Knowledge, attitudes, and practices towards COVID-19 among Chinese residents during the rapid rise period of the COVID-19 outbreak: a quick online cross-sectional survey
Int J Biol Sci
III-2. Cross Sectional Control

A total of 6919 participants completed the survey questionnaire.
Residents of other provinces were also eligible for this survey if they were willing to participate.
2020-03-15 Zheng et al SARS-CoV-2: an Emerging Coronavirus that Causes a Global Threat
Int J Biol Sci
IV. Other The association of initially confirmed SARS-CoV-2 cases with Huanan Seafood market suggested that the marketplace has played a role in the early spreading , however, whether it is the origin of the outbreak and what is the native host(s) of SARS-CoV-2 remain uncertain.
2020-03-17 Ying et al Mental health status among family members of health care workers in Ningbo, China during the Coronavirus Disease 2019 (COVID-19) outbreak: a Cross-sectional Study
medrxiv
III-2. Cross Sectional Control

Of the 882 participants who were recruited in this study, 845 completed the questionnaires correctly (response rate of 95.80% ).
In addition, compared with participants who were HCWs, participants who were enterprise workers and were more likely to develop depressive symptoms(OR=1.750, 95%CI:1.104-2.776), while who were government employees or institutions employees were less likely to suffer depressive symptoms (OR=0.529, 95%CI:0.286-0.977).

Compared with participants who were HCWs, those who were enterprise workers were more likely to develop mental health problems, while who were government employees or institutions employees were less likely to report psychological response.
2020-03-19 Wang et al A review of the 2019 Novel Coronavirus (COVID-19) based on current evidence
International Journal of Antimicrobial Agents
II. Randomized Controlled Trial

In a study of 214 COVID-19 patients, 78 (36.4%) patients had neurological manifestations .
The mechanism might be that these components played a therapeutic role by effectively reducing the inflammatory response of the body caused by viruses and bacteria .
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 .
Investigators found that the patients had previously worked in the Huanan Seafood Wholesale Market, a selling hub of animals.
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).
Academics, whether researchers and/or teachers, have always had an important knowledge diffusion and exchange role.

Stakeholders in the commons may be surprised by the size of investment in academics-as-researchers over academics-as-teachers.

In earlier cohorts, most participants came from government or State Owned Enterprises (SOEs).

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 opportunity for Australian academics to immerse themselves in Beijing with executives from an array of China's leading businesses, including consulting, finance and government enterprises, has obvious two-way benefits.
2020-03-20 Cao et al The psychological impact of the COVID-19 epidemic on college students in China
Psychiatry Research
IV. Prevalence Study

Among the sample of 7143 college students, approximately two-third were women 67 (0.94%).
The results of this study indicated college students' anxiety regarding the epidemic was associated with their place of residence, source of parental income, whether living with parents and whether a relative or an acquaintance was infected with COVID-19.

The stability of students' family income (OR = 0.726, 95% CI = .645 -.817) and living with parents (OR = .752, 95% CI = .596 -.950) were also protective factors against anxiety.
2020-03-20 Brooks et al The impact of unplanned school closure on children's social contact: Rapid evidence review
medrxiv
IV. Prevalence Study

The size of the quantitative studies ranged from 35 households (representing 67 children) to 2,229 households (representing 4,171 children).
Students of parents who thought the school closure was not appropriate reported a mean of 4.7 out-of-home activities, compared with a mean of 4.3 activities for students of parents who were unsure and 2.8 for students of parents who thought the closure was appropriate .
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.
Second, we cannot rule out the possibility that some cases with contact history with the Huanan Seafood Wholesale Market got infected by contact with humans.
2020-03-21 Sardar et al Comparative analyses of SAR-CoV2 genomes from different geographical locations and other coronavirus family genomes reveals unique features potentially consequential to host-virus interaction and pathogenesis
biorxiv
III-3. Time Series Analysis Many studies have reported that miRNAs not only act as the signature of tissue expression and function but also as potential biomarkers playing important role in regulating disease pathophysiology .
2020-03-23 Lai et al Factors Associated With Mental Health Outcomes Among Health Care Workers Exposed to Coronavirus Disease 2019
JAMA Netw Open
III-2. Cross Sectional Control CONCLUSIONS AND RELEVANCE: In this survey of heath care workers in hospitals equipped with fever clinics or wards for patients with COVID-19 in Wuhan and other regions in China, participants reported experiencing psychological burden, especially nurses, women, those in Wuhan, and frontline health care workers directly engaged in the diagnosis, treatment, and care for patients with COVID-19.
2020-03-25 Cluver et al Parenting in a time of COVID-19
The Lancet
IV. Other Parents and caregivers are attempting to work remotely or unable to work, while caring for children, with no clarity on how long the situation will last.
2020-03-25 La Marca et al COVID-19: lessons from the Italian reproductive medical experience
Fertility and Sterility
IV. Other The Italian authorities have mandated that even in the absence of evidence of transmission of the virus within reproductive cells, all donors should be interviewed regarding the presence of respiratory symptoms and for recent travel to high-risk areas.
2020-03-26 Al-Quteimat et al SARS-CoV-2 outbreak: How can pharmacists help?
Research in Social and Administrative Pharmacy
IV. Prevalence Study Pharmacists can play a role in this by promoting an empathy culture and helping to prevent the stigmatisation of infected individuals based on ethnicity, population or nationality by broadcasting facts in their communities via various media.
2020-03-26 FANG et al Human Mobility Restrictions and the Spread of the Novel Coronavirus (2019-nCoV) in China
medrxiv
IV. Prevalence Study There is also a possibility that government officials in the epicenter cities had incentives to downplay the severity of the outbreak, at least initially.
2020-03-27 Sumner et al Reproducibility and reporting practices in COVID-19 preprint manuscripts
medrxiv
IV. Other Though not part of the study purpose, we were curious to know if there were differences in transparency practices based on how authors identified themselves.
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.
For patients who were suspected to have the illness, two senior respiratory doctors made the diagnosis together.
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 The fruit-bat migration driven by the deforestation through forest fires in the islands of Sumatra lead to the emergence of Nipah disease in farmers and abattoir workers in Malaysia .
2020-03-31 Shu et al Ark of Life and Hope:Role of Cabin Hospital in Facing COVID-19
Journal of Hospital Infection
IV. Other As clinicians working on the front line of a Cabin hospital, we wish to share our experience of Cabin in the hope that this may play a role in containing the global outbreak.
2020-04-01 He et al Strategic plan for management of COVID-19 in paediatric haematology and oncology departments
The Lancet Haematology
IV. Prevalence Study

7 Children and their parents or guardians should also be informed about the importance of not concealing symptoms associated with COVID-19.
Medical staff, especially those working in hospitals, need to take care of people who have been diagnosed with or are suspected of having COVID-19, as their diagnosis could affect their mental health and they might worry about transmitting the virus to family, friends, or colleagues.

5 Surveillance of mixed wildlife- livestock farms for SARS-CoV-2 and other coronaviruses in Southeast Asia.

5.0.0.1 Highlights

5.0.0.2 Articles

Date Authors Title LOE(?) & Sample Matches
2020 Kock et al 2019-nCoV in context: lessons learned?
The Lancet Planetary Health
IV. Prevalence Study 7, 8 Similarly, early Ebola virus was mostly associated with bushmeat and its consumption in Africa; Nipah virus is associated with date palm sap, fruit, and domestic pig farms; MERS is associated with the camel livestock industry; and H5N1 arose from viral evolution in domestic and wild birds, to ultimately bring all these cases to humans.

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 China is located within a major 'emerging disease hotspot' in Southeast Asia, but there is also a high risk of future diseases originating in sub-Saharan Africa, South Asia and Latin America .

Further, we estimate that there are thousands of other CoVs in bats across Southeast Asia, many of which will have pandemic potential.

Furthermore, the drivers of disease emergence are human activities that are expanding on a global scale, including deforestation, agricultural intensification and the wildlife trade.
2020 Colombia. Ministerio de Salud y Protección et al Acciones en promoción de la salud, prevención y atención de la Infección Respiratoria Aguda - IRA- ante alerta internacional por Nuevo Coronavirus 2019-nCoV
WHO
IV. Other The first cases involved people who were in a fish and wildlife in Wuhan, however, cases have been confirmed in people who were in this and other areas of China and in 20 countries on 4 continents.
2020 Xu et al Systematic Comparison of Two Animal-to-Human Transmitted Human Coronaviruses: SARS-CoV-2 and SARS-CoV
Viruses
IV. Prevalence Study

Among the 8,866 patients who have been confirmed with COVID-19, nearly half of the patients have been aged 50 years or older (47.7%) .
Most cases were in Asia, Europe, and America.
2020-02-02 Zhang et al Transmission and epidemiological characteristics of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infected Pneumonia (COVID-19): preliminary evidence obtained in comparison with 2003-SARS
medrxiv
IV. Other In 2002, a case of SARS appeared in Guangdong Province, China, and then spread to Southeast Asia and all of the world .
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 In addition to China, 24 different countries from Europe, Northern America, Southeast Asia, Eastern Mediterranean, and Western Pacific Asia have reported the confirmed cases of this disease making the total tally of confirmed cases to 20630 worldwide ( Figure 2 ).
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.
5 The mixed landscape has abundant crops, which attracts wild animals into the communities, and livestock rearing is common.

The Yunnan, Guangxi and Guangdong provinces in southern China were selected for this study because of their historical importance in the origin of emerging infectious diseases, 16 diverse wildlife population within protected forests 17 and intensive wildlife farming and trade activities.

36 Enforcement of current wildlife protection policy and continued community infrastructure development appears to significantly reduce high-risk contact between humans, wildlife and livestock.

3 People living in the rural areas of southern China primarily cultivate rice and fruits, raise swine and poultry in households or on small farms, 4 but also traditionally hunt wild animals as an alternative income source.
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 Disease emergence correlates with human population density and wildlife diversity, and is driven by anthropogenic changes such as deforestation and expansion of agricultural land (i.e., land-use change), intensification of livestock production, and increased hunting and trading of wildlife .

Conservation measures that create wildlife corridors to increase habitat connectivity might also increase the risk of disease transmission among disparate wildlife, livestock, and human populations.
2020-02-19 Ji et al Cross‐species transmission of the newly identified coronavirus 2019‐nCoV
Journal of Medical Virology
IV. Other Many patients were potentially exposed to wildlife animals at the Huanan seafood wholesale market, where poultry, snake, bats, and other farm animals were also sold.
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.
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.
2020-02-22 Kwok et al Novel coronavirus (2019-nCoV) cases in Hong Kong and implications for further spread
Journal of Infection
IV. Other Nearly all confirmed cases (14,422, 98.8%) are in the mainland China, with most of the remaining cases in nearby countries or cities in East Asia (Japan, South Korea, Hong Kong, Taiwan, Macau), Southeast Asia (Thailand, Singapore, Malaysia, Vietnam) and Australia accounting for the majority of the remaining cases.
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 .
Such measures include biosurveillance of live animal markets, improved biosecurity in livestock farms, live animal markets and during animal transportation, public education on zoonotic diseases, and the importance of adopting a cooperative approach between agencies.

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.
2020-02-28 Bao et al 2019-nCoV epidemic: address mental health care to empower society
The Lancet
IV. Prevalence Study 2 Nearly 160 cases of 2019-nCoV have been detected and confirmed in southeast Asia (Thailand, Singapore, Malaysia, Vietnam, Philippines, and Cambodia), east Asia (Japan and Korea), south Asia (India, Nepal, and Sri Lanka), western Asia (United Arab Emirates), Europe (Germany, France, Italy, UK, Russia, Finland, Spain, and Sweden), North America (USA and Canada), and Australia.
2020-02-28 Wang et al From Hendra to Wuhan: what has been learned in responding to emerging zoonotic viruses
The Lancet
IV. Other Indeed, this approach has international implications, with risks of exotic zoonotic diseases associated with the huge quantities of illegal bush meat from central and west Africa being imported into Europe and North America.
2020-03-05 Peters et al Understanding the emerging coronavirus: what it means for health security and infection prevention
Journal of Hospital Infection
IV. Prevalence Study

50 Super spreading individuals were found to have a major impact in the previous MERS, SARS, and Ebola pandemics.
In the case of avian influenza, the virus, which circulates naturally in wild bird populations, came into contact with large homogeneous populations of birds in poultry farms.
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.
2020-03-13 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 .
Over the last two months, more than 156,000 cases of a new infectious disease have been confirmed in China and other countries in Asia, Pacific, Europe, Africa, and the Americas [22, 23, .
2020-03-18 Jacobsen et al Will COVID-19 generate global preparedness?
The Lancet
IV. Other The ability to detect viruses in livestock and wildlife is a crucial component of early warning systems for human pandemics.
2020-03-19 Qiu et al Predicting the angiotensin converting enzyme 2 (ACE2) utilizing capability as the receptor of SARS-CoV-2
Microbes and Infection
IV. Other Considering the widespread of stray cats, wildlife markets and stock farms, it was not strange that these animals could serve as potential intermediate hosts of SARS-CoV-2.
2020-03-20 Liu et al Assessing the Global Tendency of COVID-19 Outbreak
medrxiv
IV. Computer Model Western Europe, Southeast Asia to Oceania, the Middle East, and North America will be the four epicenter with the most severe situation.

We predict that there are four regional clusters of the outbreak: Southeast Asia extending southward to Oceania, the Middle East, Western Europe and North America.
2020-03-20 Wenham et al COVID-19: the gendered impacts of the outbreak
The Lancet
IV. Other Travel restrictions cause financial challenges and uncertainty for mostly female foreign domestic workers, many of whom travel in southeast Asia between the Philippines, Indonesia, Hong Kong, and Singapore.
2020-03-27 Lee et al Epidemic preparedness in urban settings: new challenges and opportunities
The Lancet Infectious Diseases
IV. Prevalence Study 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.

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.
2020-03-29 Alfano et al Non-invasive surveys of mammalian viruses using environmental DNA
biorxiv
IV. Other Cervids are regularly sold as bushmeat in wildlife markets and both recent coronavirus epidemics (SARS-CoV and SARS-Cov-2 ) spilled over from wildlife.

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

Emerging infectious viruses increasingly threaten human, domestic animal and wildlife health .

Wildlife markets have recently facilitated the spillover of SARS-CoV-2 to humans resulting in a pandemic .
2020-03-31 Haixu et al Detection of 20 respiratory viruses and bacteria by influenza-like illness surveillance in Beijing, China, 2016–2018
Journal of Infection
IV. Prevalence Study

The series included 47 patients, of whom 15 were taking antibiotic prophylaxis at the time of meningococcal disease onset and 32 were not ( Table 1 ).
It should be noted that backyard and small-scale farms with weak biosecurity systems comprise a very large proportion of pig herds in Asian countries with a developing swine industry, such as in the as of yet ASF-unaffected Asian countries Indonesia, India, and Malaysia.

These viruses emerge from animal trading markets, where veterinary workers need to be vigilant and concerned whether these viruses have the potential to spread between animals and the impact the livestock industry.
2020-03-31 Xu et al Genetic diversity and potential recombination between ferret coronaviruses from European and American lineages
Journal of Infection
IV. Prevalence Study

The series included 47 patients, of whom 15 were taking antibiotic prophylaxis at the time of meningococcal disease onset and 32 were not ( Table 1 ).
It should be noted that backyard and small-scale farms with weak biosecurity systems comprise a very large proportion of pig herds in Asian countries with a developing swine industry, such as in the as of yet ASF-unaffected Asian countries Indonesia, India, and Malaysia.

These viruses emerge from animal trading markets, where veterinary workers need to be vigilant and concerned whether these viruses have the potential to spread between animals and the impact the livestock industry.
2020-03-31 Wang et al Emergence of SARS-like coronavirus poses new challenge in China
Journal of Infection
IV. Prevalence Study

The series included 47 patients, of whom 15 were taking antibiotic prophylaxis at the time of meningococcal disease onset and 32 were not ( Table 1 ).
It should be noted that backyard and small-scale farms with weak biosecurity systems comprise a very large proportion of pig herds in Asian countries with a developing swine industry, such as in the as of yet ASF-unaffected Asian countries Indonesia, India, and Malaysia.

These viruses emerge from animal trading markets, where veterinary workers need to be vigilant and concerned whether these viruses have the potential to spread between animals and the impact the livestock industry.
2020-03-31 Tang et al Emergence of a novel coronavirus causing respiratory illness from Wuhan, China
Journal of Infection
IV. Prevalence Study

The series included 47 patients, of whom 15 were taking antibiotic prophylaxis at the time of meningococcal disease onset and 32 were not ( Table 1 ).
It should be noted that backyard and small-scale farms with weak biosecurity systems comprise a very large proportion of pig herds in Asian countries with a developing swine industry, such as in the as of yet ASF-unaffected Asian countries Indonesia, India, and Malaysia.

These viruses emerge from animal trading markets, where veterinary workers need to be vigilant and concerned whether these viruses have the potential to spread between animals and the impact the livestock industry.
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.
2020-07-31 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.

Indonesia has been diagnosed with the highest number of avian influenza cases in Southeast Asia.

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

6 Experimental infections to test host range for this pathogen.

6.0.0.1 Highlights

6.0.0.2 Articles

Date Authors Title LOE(?) & Sample Matches
2020 Prompetchara et al Immune responses in COVID-19 and potential vaccines: Lessons learned from SARS and MERS epidemic
Asian Pacific Journal of Allergy and Immunology
IV. Other This review aims to provide a comparative view among SARS-CoV, MERS-CoV and the newly epidemic SARS-CoV-2, in the hope to gain a better understanding of the host-pathogen interaction, host immune responses, and the pathogen immune evasion strategies.
2020 YAN et al Functional Cell Receptors for Human Coronavirus
Chinese Journal of Laboratory Medicine
IV. Other Receptor is an important factor affecting host range and interspecific transmission.
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.
2020-01-30 Bartoszewicz et al Interpretable detection of novel human viruses from genome sequencing data
biorxiv
IV. Prevalence Study Local host adaptation could help switch hosts between the animal reservoir and humans.
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 .
Co-infections with bacterial pathogens occur often with RVI.
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 The range of diseases and hosts that specific viruses were confirmed to be associated with have been the .
2020-02-12 Liu et al Neutrophil-to-Lymphocyte Ratio Predicts Severe Illness Patients with 2019 Novel Coronavirus in the Early Stage
medrxiv
III-3. Time Series Analysis

This study was a prospective single-center study, which included 61 patients with 2019-nCoV infection treated at Beijing Ditan Hospital from January 13, 2020 to January 31, 2020.
Age and days were represented by median (range), categorical variables by number (%), and laboratory data by mean (interquartile range).
2020-02-19 Chen et al Clinical and immunologic features in severe and moderate forms of Coronavirus Disease 2019
medrxiv
IV. Prevalence Study

Methods In this single-centre retrospective study, a total of 21 patients with pneumonia who were laboratory-confirmed to be infected with SARS-CoV-2 in Wuhan Tongji hospital were included from Dec 19, 2019 to Jan 27, 2020.
The production of IFN-γ is essential for the resistance against infection of various pathogens 3 8 2 such as virus, bacteria, and parasite 13 .
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%.
The host range of animal origin coronaviruses was promiscuous .
2020-02-21 Qi et al Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses
biorxiv
IV. Other The viruses target host cells via binding host receptors before engaging the infection cycle.
2020-02-23 Wang et al Epidemiological characteristics of 1212 COVID-19 patients in Henan, China
medrxiv
IV. Other Traditionally, incubation period is defined as the period between the infection of an individual by a pathogen and the manifestation of the illness or disease it causes .
2020-02-26 Yang et al Clinical characteristics and imaging manifestations of the 2019 novel coronavirus disease (COVID-19):A multi-center study in Wenzhou city, Zhejiang, China
Journal of Infection
III-2. Retrospective Cohort

The symptoms of these 12 patients included fever (8 patients), cough (3 patients), expectoration (1 patient), headache (1 patient), sore throat (2 patients), snotty (1 patient), diarrhea (1 patient).
Another concern from the point of view of etiology, for a pandemic disease, in general, pathogens tend to reduce their virulence in order to maximize their between-host transmission, 9 and hosts have been selected to reduce the harm caused by their pathogen, otherwise the lack of adaptation in novel hostpathogen associations may suspend the transmission seen in some emerging diseases.

Human coronaviruses are considered as important pathogens that cause respiratory infection.
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.
Host immune responses on some extent determine both protection and pathogenesis to the respiratory viral infections .
2020-02-28 Chen et al A mathematical model for simulating the phase-based transmissibility of a novel coronavirus
Infect Dis Poverty
IV. Computer Model The incubation period of host infection was defined as 1/ω H and the infectious period of host infection was defined as 1/γ H .
2020-02-28 Zhang et al Prediction of receptorome for human-infecting virome
biorxiv
IV. Other AbstractThe virus receptor is key for viral infection of host cells.
2020-02-29 Han et al Estimate the incubation period of coronavirus 2019 (COVID-19)
medrxiv
III-3. Time Series Analysis

We collected a dataset with 59 officially confirmed COVID-19 cases from 10 regions in China except for Hubei province, the assumed origin of the virus.
The incubation period is the time from infection to the onset of the disease.
2020-03-03 Li et al Risk factors related to hepatic injury in patients with corona virus disease 2019
medrxiv
IV. Prevalence Study

Methods: A total of 85 hospitalized patients who were diagnosed with COVID-19 in Beijing Youan Hospital were retrospectively analyzed.
Age and days were represented by median (range), categorical variables by number (%), and laboratory data by mean (interquartile range).
2020-03-04 Rao et al Cell-Membrane-Mimicking Nanodecoys against Infectious Diseases
ACS Nano
IV. Other Another example that utilizes the liposome− pathogen interaction is direct inhibition of the pathogen infection with liposomes.

23 Despite the diversity of pathogens, one similarity they share is how they cause infectious disease: these pathogens usually invade the host by interacting with the host cell membrane first.

In-depth biological research has elucidated different mechanisms of pathogen infection, most of which involve attaching to the cellular membrane biointerface and invading the host cells.
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 .
The binding of the virus with host cell receptors is a significant determinant for the pathogenesis of infection.
2020-03-06 Yu et al Immunodepletion with Hypoxemia: A Potential High Risk Subtype of Coronavirus Disease 2019
medrxiv
III-3. Time Series Analysis

Methods This is a retrospective study from 3 patients with 2019-nCoV infection admitted to Renmin Hospital of Wuhan University, a COVID-2019 designated hospital in Wuhan, from January 31 to February 6, 2020.
Host immune response is essential for the clearance of coronavirus infection, and the balance between coronavirus and host immunity is key to viral pathogenesis and will ultimately determine infection outcome 1 .
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 The production of various cytokines in response to an invading pathogen such as a virus contributes to the host organism's ability to eliminate the pathogen.
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 .
Additional research is needed to elucidate viral and host factors in the pathogenesis of severe and fatal infections.
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.
However, SARS-CoV-2 is also a novel human pathogen that may interact with host antiviral defence in a unique manner.
2020-03-14 Khan et al Modeling the dynamics of novel coronavirus (2019-nCov) with fractional derivative
Alexandria Engineering Journal
IV. Computer Model After getting the infection from the infected bats, the virus has the ability to spread within the host and shown by the route g h S h I h =N h , where g h is the disease transmission coefficient among the host population classes S h and I h .
2020-03-16 Zhang et al Clinical Characteristics of 34 Children with Coronavirus Disease-2019 in the West of China: a Multiple-center Case Series
medrxiv
IV. Prevalence Study

In this case series, data from 34 paediatric patients with COVID-19 were analyzed, including 14 male patients (41.18%) and 20 female patients (58.82%).
Infections of other respiratory pathogens were reported in 16 patients (47.06%).
2020-03-16 Seah et al Can the Coronavirus Disease 2019 (COVID-19) Affect the Eyes? A Review of Coronaviruses and Ocular Implications in Humans and Animals
Ocul Immunol Inflamm
IV. Prevalence Study

In 2004, tear samples collected from 36 suspected SARS-CoV patients were sent for RT-PCR for the SARS-CoV.
30 Hence, understanding the ocular manifestations of animal CoV infections may provide insights into the spectrum of ocular diseases that CoVs can cause.

The ability of CoVs to obtain mutations which facilitate the transmission between animal to humans has made it a zoonotic pathogen of concern.
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.
2, 3 Following SARS-CoV-2 infection, a high viral load and overexuberant host immune response involving innate and acquired immunity, simultaneously contributes to the pathogenesis of COVID-19 and organ injury.
2020-03-17 Xiao et al A Cybernetics-based Dynamic Infection Model for Analyzing SARS-COV-2 Infection Stability and Predicting Uncontrollable Risks
medrxiv
IV. Computer Model Exposed: Individual has been infected with a pathogen, but due to the pathogens incubation period, is not yet infectious.
2020-03-17 Joyce et al A Cryptic Site of Vulnerability on the Receptor Binding Domain of the SARS-CoV-2 Spike Glycoprotein
biorxiv
IV. Other S-a class I fusion protein-is also a critical determinant of viral host range and tissue tropism and the primary target of the host immune response (Li, 2016) .
2020-03-17 Zhao et al Recapitulation of SARS-CoV-2 Infection and Cholangiocyte Damage with Human Liver Organoids
biorxiv
IV. Other 249 We employed Student's t-test or ANOVA test to analyze the parametric 250 experimental results.
2020-03-19 Luan et al Spike protein recognition of mammalian ACE2 predicts the host range and an optimized ACE2 for SARS-CoV-2 infection
Biochemical and Biophysical Research Communications
IV. Other The host tropism of zoonotic coronavirus is hybrid, and it is important to determine the natural host and host range of coronavirus.
2020-03-19 Qiu et al Predicting the angiotensin converting enzyme 2 (ACE2) utilizing capability as the receptor of SARS-CoV-2
Microbes and Infection
IV. Other Receptor recognition is an important factor determining host range and cross-species infection of viruses.
2020-03-19 Qi et al Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses
Biochemical and Biophysical Research Communications
IV. Prevalence Study

GSE136103, 4 samples from cirrhotic patients; Spleen and oesophagus, available from Human Cell Atlas, totally 11 cardiac death donors; Bone marrow, GEO Accession No.
The viruses target host cells via binding host receptors before engaging the infection cycle.
2020-03-21 Sardar et al Comparative analyses of SAR-CoV2 genomes from different geographical locations and other coronavirus family genomes reveals unique features potentially consequential to host-virus interaction and pathogenesis
biorxiv
III-3. Time Series Analysis To gain further insights into host responses to viral infection, we predict that antiviral host-miRNAs may be controlling the viral pathogenesis.

In viral infections, host antiviral miRNAs play a crucial role in the regulation of immune response to virus infection depending upon the viral agent.

As a host defense mechanism, a repertoire of host miRNAs also target invading viruses.
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 It has been reported that infectious viruses, including coronavirus, can survive for long periods outside of its host organism.
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 Wen et al Immune Cell Profiling of COVID-19 Patients in the Recovery Stage by Single-Cell Sequencing
medrxiv
III-3. Time Series Analysis

We analyzed 128,096 scRNA-seq profiles that passed quality control, including 36,442 myeloid cells, 64,247 NKT cells, and 10,177 B cells from five HCs, five ERS, and five LRS patients.
In viral infection, it is generally accepted that host immune responses determine both protection against viral infections and the pathogenesis of respiratory injury .
2020-03-30 Anderson et al Orthogonal genome-wide screenings in bat cells identify MTHFD1 as a target of broad antiviral therapy
biorxiv
IV. Other This is especially true in the field of virus-host interactions, where a 3 plethora of host factors have been identified for a variety of viruses .

The two pathways identified by both CRISPR screen and siRNA screen, endocytosis and 29 protein secretion, have previously been implicated in human host response to a number of viral 30 pathogens 13, 21, 23 To validate the role of these pathways in the bat response to viral infection, we 31 .
2020-03-30 Wu et al Nervous system involvement after infection with COVID-19 and other coronaviruses
Brain, Behavior, and Immunity
IV. Other CoV infections can affect the nervous system, and it is currently believed that CoV in concert with host immune mechanisms may turn these infections into persistent infections that may 17 lead to neurological diseases.
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 .
2020-04-30 Phan et al Novel coronavirus: From discovery to clinical diagnostics
Infection, Genetics and Evolution
IV. Other Although coronavirus is commonly associated with acute respiratory infections in humans, its ability to infect multiple host species and a variety of diseases makes it a complex pathogen .
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 This means that a specific pathogen will be involved according to the infection conditions and the features of the host organism.

The determinants of the pathogenicity and virulence of these microbes depend on microbial and host factors, as is the case with all microbes.

7 Animal host(s) and any evidence of continued spill-over to humans

7.0.0.1 Highlights

7.0.0.2 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 The detection of SARS coronavirus in these species led to a temporary ban of selling of these animals in 2004, thereby preventing additional spill-over events from animals to humans.
2020 Memish et al COVID-19 in the Shadows of MERS-CoV in the Kingdom of Saudi Arabia
Journal of Epidemiology and Global Health
IV. Prevalence Study With the ongoing MERS-CoV circulation in animal reservoir (dromedary camels) in the Arabian Peninsula and the continuing zoonotic spillover with 70% of cases resulting from nosocomial transmission , the risk of emergence of COVID-19 within the same community would be overwhelming to the health-care infrastructure of the countries affected by MERS-CoV.
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 Cascella et al Features, Evaluation and Treatment Coronavirus (COVID-19)
StatPearls
IV. Other Interestingly, these latter viruses have probably originated from bats and then moving into other mammalian hosts — the Himalayan palm civet for SARS-CoV, and the dromedary camel for MERS-CoV — before jumping to humans.
2020 Daszak et al A strategy to prevent future pandemics similar to the 2019-nCoV outbreak
Biosafety and Health
IV. Prevalence Study The virus itself appears to have a wildlife (bat) origin similar to SARS-CoV, which also emerged in a wildlife market through the interactions of humans and other animals that acted as the intermediate hosts of the virus .
2020 Al-Qaness et al Optimization Method for Forecasting Confirmed Cases of COVID-19 in China
J Clin Med
IV. Computer Model The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human .
2020-01-25 Wu et al Complete genome characterisation of a novel coronavirus associated with severe human respiratory disease in Wuhan, China
biorxiv
IV. Other This outbreak highlights the ongoing capacity of viral spill-over from animals to cause severe disease in humans.
2020-01-28 Chan et al Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan
Emerg Microbes Infect
IV. Other More animal sampling to determine its natural animal reservoir and intermediate animal host in the market is important.
2020-01-30 Bartoszewicz et al Interpretable detection of novel human viruses from genome sequencing data
biorxiv
IV. Prevalence Study Local host adaptation could help switch hosts between the animal reservoir and humans.
2020-01-31 Jiang et al An emerging coronavirus causing pneumonia outbreak in Wuhan, China: calling for developing therapeutic and prophylactic strategies
Emerg Microbes Infect
IV. Other These methods are useful for detecting novel coronaviruses not only in humans, but also in animals for identification of animal reservoir or intermediate host of 2019-nCoV.
2020-02-03 Wu et al A new coronavirus associated with human respiratory disease in China
Nature
IV. Other This outbreak highlights the ongoing ability of viral spill-over from animals to cause severe disease in humans.

However, as a variety of animal species were for sale in the market when the disease was first reported, further studies are needed to determine the natural reservoir and any intermediate hosts of WHCV.
2020-02-04 Rahman Qureshi et al Outbreak of novel Corona virus (2019-nCoV); implications for travelers to Pakistan
Travel Medicine and Infectious Disease
IV. Other Transmission of the infection has been reported from animals to 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, .
2020-02-14 Guo et al Long-Term Persistence of IgG Antibodies in SARS-CoV Infected Healthcare Workers
medrxiv
III-3. Time Series Analysis

In addition, serum 112 samples from another 20 subjects, from the 95 SARS cases, were collected in 2015 (Table S3) .
SARS-CoV was initially identified as having occurred through interspecies transmission from small 72 carnivores (e.g., palm civets and raccoon dogs) to humans in 2003.
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%.
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.

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.
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 As a result, non-human primates may be susceptible to 2019-nCoV and serve as animal models for antiviral research or intermediate hosts for cross-species transmission.
2020-02-24 Rasmussen et al Coronavirus Disease 2019 (COVID-19) and Pregnancy: What obstetricians need to know
American Journal of Obstetrics and Gynecology
IV. Other The emergence of these viruses in humans has 251 been attributed to host switching: the virus "jumped" from an intermediary host species (e.g., 252 civet cats for SARS-CoV and dromedary camels for MERS-CoV) to humans.
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 .
SARS-CoV-2 is likely a batorigin coronavirus that was transmitted to humans through a spillover from bats or through yet undetermined intermediate animal host (avian, swine, phocine, bovine, canine, other species) or wild animals.

Hypothesizing that bats will be proven as SARS-CoV-2 reservoirs and that adaptation to humans took place in an intermediate host in a live animal market, the following measures would be important: i) Decreasing the risk of transmission from the natural host.

SARS-CoV-2 is likely a bat-origin coronavirus that was transmitted to humans through a spill over from bats or through an undetermined yet intermediate animal host (avian, swine, phocine, bovine, canine, other species) or wild animals.
2020-02-26 Liu et al No credible evidence supporting claims of the laboratory engineering of SARS-CoV-2
Emerg Microbes Infect
IV. Other A search for an intermediate animal host between bats and humans is needed to identify animal CoVs more closely related to human SARS-CoV-2.
2020-02-26 Rothan et al The epidemiology and pathogenesis of coronavirus disease (COVID-19) outbreak
Journal of Autoimmunity
IV. Other Another piece of evidence that supports the COVID-19 is of bat origin is the existence of a high degree of homology of the ACE2 receptor from a diversity of animal species, thus implicating these animal species as possible intermediate hosts or animal models for COVID-19 infections .
2020-02-27 Ahmad et al COVID-19: Zoonotic aspects
Travel Medicine and Infectious Disease
IV. Other Animal to human transmission can be reduced more quickly as compared to humans .
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.
All three coronaviruses were introduced into humans from wild animals (masked palm civets in SARS, camel in MERS, and unclear intermediary for 2019-nCoV).
2020-02-28 Lu et al Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding
The Lancet
IV. Other Fourth, in both SARS-CoV and MERS-CoV, bats acted as the natural reservoir, with another animal (masked palm civet for SARS-CoV 35 and dromedary camels for MERS-CoV) 36 acting as an intermediate host, with humans as terminal hosts.
2020-02-29 Biscayart et al The next big threat to global health? 2019 novel coronavirus (2019-nCoV): What advice can we give to travellers? – Interim recommendations January 2020, from the Latin-American society for Travel Medicine (SLAMVI)
Travel Medicine and Infectious Disease
IV. Other However, this theory has now been largely discounted and some researchers point towards bats as a reservoir and doubt that the coronavirus could have originated in animals other than birds or mammals ; they are skeptical that the animal host or hosts of 2019-nCoV can be identified without further field and laboratory research.
2020-03-02 Basu et al Strategies for vaccine design for corona virus using Immunoinformatics techniques
biorxiv
III-3. Time Series Analysis

From InterPro database, 78 homologous protein sequences are recovered for nonstructural protein NS4 protein for coronavirus as shown in Table 1 .
Detailed investigations found that SARS-CoV has been transmitted from civet cats to humans and MERS-CoV from camels to humans.
2020-03-03 Xu et al Broad Spectrum Antiviral Agent Niclosamide and Its Therapeutic Potential
ACS Infect Dis
III-3. Time Series Analysis

The outbreak of SARS in southern China between November 2002 and July 2003 eventually resulted in 8098 confirmed cases and 774 deaths reported in 17 countries with a mortality rate of 9%, while MERS, first identified in Saudi Arabia in 2012, has caused a total of 2519 laboratory-confirmed cases including 866 associated deaths with a fatality rate of nearly 34% at the end of January 2020.
EBOV is introduced into humans from wild animals and spreads in the human population through person-to-person transmission.
2020-03-03 Malta et al The coronavirus 2019-nCoV epidemic: Is hindsight 20/20?
EClinicalMedicine
IV. Prevalence Study Ebolavirus outbreaks, like novel coronavirus outbreaks are a result of zoonotic spillover and subsequent human-to-human transmission.
2020-03-04 Wu et al Strong evolutionary convergence of receptor-binding protein spike between COVID-19 and SARS-related coronaviruses
biorxiv
IV. Other Both 2019-nCoV and SARS-CoV have been determined to be of bat origin, with possible intermediate hosts prior to infecting humans 4,5 .
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.
The continued risk of human MERS-CoV outbreaks 7 years after its first discovery, effective human and camel MERS-CoV vaccines appear to be the ideal way to prevent continuing spread of MERS-CoV in dromedary camels in the Middle East and in humans at high risk of acquiring community and nosocomial MERS-CoV infection.
2020-03-09 Walls et al Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein
Cell
IV. Other MERS-CoV was suggested to originate from bats, but the reservoir host fueling spillover to humans is unequivocally dromedary camels (Haagmans et al., 2014; Memish et al., 2013) .
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".
2020-03-13 Singhal et al A Review of Coronavirus Disease-2019 (COVID-19)
Indian J Pediatr
IV. Prevalence Study

The median age was 8 y 11 mo and in 28 children the infection was linked to a family member and 26 children had history of travel/residence to Hubei province in China.
Though the SARS-CoV-2 originated from bats, the intermediary animal through which it crossed over to humans is uncertain.

The first such instance was in 2002-2003 when a new coronavirus of the β genera and with origin in bats crossed over to humans via the intermediary host of palm civet cats in the Guangdong province of China.
2020-03-15 Ye et al Zoonotic origins of human coronaviruses
Int J Biol Sci
IV. Prevalence Study Pervasive evidence has shown that SARS-CoV, MERS-CoV and SARS-CoV-2 have a bat origin and are transmitted to humans via intermediate hosts.

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 .
2020-03-17 Tilocca et al Molecular basis of COVID-19 relationships in different species: a one health perspective
Microbes and Infection
IV. Other A very recent amino acid sequence alignment of ACE2 from different animal species including humans, pets and the major domestic animals highlighted high protein sequence similarity between the tested animal species, suggesting a potential interaction of the viral particles with a wider array of host cells .
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.

Surveillance might prevent the virus establishing itself in another animal species that is in close contact to humans.
2020-03-29 Li et al Coronavirus disease 2019 (COVID-19): current status and future perspective
International Journal of Antimicrobial Agents
III-2. Retrospective Cohort

Analysis of the first 99 confirmed cases of SARS-CoV2 infection revealed that cytokine storm syndromes occurred in patients with severe COVID-19 and 17 (17%) had ARDS and, among them, 11 (11%) patients deteriorated within a short period of time and died of multiple organ failure .
In both of these epidemics, these viruses are likely originated from bats and then infect humans through another intermediate animal hosts [the civet (Paguma larvata) for SARS-CoV and the camel for MERS-CoV] .
2020-03-31 Ena et al A novel coronavirus emerges
Revista Clínica Española (English Edition)
IV. Other Coronaviruses have an animal reservoir, usually wild animals, and can be transmitted to humans.
2020-03-31 Haixu et al Detection of 20 respiratory viruses and bacteria by influenza-like illness surveillance in Beijing, China, 2016–2018
Journal of Infection
IV. Prevalence Study

The series included 47 patients, of whom 15 were taking antibiotic prophylaxis at the time of meningococcal disease onset and 32 were not ( Table 1 ).
4 , 5 GETV infection has been found in multiple vertebrates, including humans, monkeys, birds, pigs, horses, and other mammals, and infection of these species is essential for the maintenance of GETV zoonotic transmission cycles in nature.
2020-03-31 Tang et al Emergence of a novel coronavirus causing respiratory illness from Wuhan, China
Journal of Infection
IV. Prevalence Study

The series included 47 patients, of whom 15 were taking antibiotic prophylaxis at the time of meningococcal disease onset and 32 were not ( Table 1 ).
4 , 5 GETV infection has been found in multiple vertebrates, including humans, monkeys, birds, pigs, horses, and other mammals, and infection of these species is essential for the maintenance of GETV zoonotic transmission cycles in nature.
2020-03-31 Xu et al Genetic diversity and potential recombination between ferret coronaviruses from European and American lineages
Journal of Infection
IV. Prevalence Study

The series included 47 patients, of whom 15 were taking antibiotic prophylaxis at the time of meningococcal disease onset and 32 were not ( Table 1 ).
4 , 5 GETV infection has been found in multiple vertebrates, including humans, monkeys, birds, pigs, horses, and other mammals, and infection of these species is essential for the maintenance of GETV zoonotic transmission cycles in nature.
2020-03-31 Wang et al Emergence of SARS-like coronavirus poses new challenge in China
Journal of Infection
IV. Prevalence Study

The series included 47 patients, of whom 15 were taking antibiotic prophylaxis at the time of meningococcal disease onset and 32 were not ( Table 1 ).
4 , 5 GETV infection has been found in multiple vertebrates, including humans, monkeys, birds, pigs, horses, and other mammals, and infection of these species is essential for the maintenance of GETV zoonotic transmission cycles in nature.
2020-03-31 Pan et al Lessons learned from the 2019-nCoV epidemic on prevention of future infectious diseases
Microbes and Infection
IV. Other According to research results, this coronavirus originated from bats and was transmitted to humans through an intermediate host, the camel .

8 Socioeconomic and behavioral risk factors for this spill-over

8.0.0.1 Highlights

8.0.0.2 Articles

Date Authors Title LOE(?) & Sample Matches
2020 Battegay et al 2019-novel Coronavirus (2019-nCoV): estimating the case fatality rate - a word of caution
Swiss Med Wkly
IV. Other Immunogenetics and socioeconomic factors however, may potentially contribute to differences in susceptibilities to the disease.
2020 Liu et al Critical care response to a hospital outbreak of the 2019-nCoV infection in Shenzhen, China
Critical Care
IV. Other The risk of 2019-nCoV exposure may cause significant psychosocial stress on healthcare workers .
2020-02-05 Ai et al Population movement, city closure and spatial transmission of the 2019-nCoV infection in China
medrxiv
IV. Prevalence Study Secondly, the influence of some 296 important factors, such as socioeconomic and demographic characteristics, were not 297 considered.
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.

The findings provide guidance for future in-depth research on specific risk factors, as well as zoonotic disease control and prevention in southern China and potentially other regions with similar ecological and social contexts.
2020-02-11 Blumberg et al Assessing the plausibility of subcritical transmission of 2019-nCoV in the United States
medrxiv
IV. Other Variation in climate, population density, demographics, social interactions, health care access and public health interventions can all affect transmission.
2020-02-20 Qian et al Psychological responses, behavioral changes and public perceptions during the early phase of the COVID-19 outbreak in China: a population based cross-sectional survey
medrxiv
III-2. Cross Sectional Control

17, 18 Before our survey, Wuhan confirmed 3,215 cases, 19 accounting for 27.3% of all cases across China; 20 Shanghai reported 153 cases, 68 (44.4%) of them from nonlocal residents.
Our results suggested that perceived risk and severity of the disease as well as information reliability were important factors associated with the psychological and behavioral responses.

Perception factors associated with anxiety and behavioral responses Table 1 are controlled for.

We found no evidence that sex, age, educational attainment, working status and marital status were closely associated with psychological and behavioral responses during the novel coronavirus outbreak.

Therefore, the psychological and behavioral responses of the general population play an important role in the control of the outbreak.

14, 15 Behavioral changes are also associated with government involvement level, perceptions of diseases, and the stage of the outbreak, and these factors vary by diseases and settings.
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 Infectious Disease Vulnerability Index (IDVI) is a metric developed by the RAND Corporation to identify countries potentially most vulnerable to poorly controlled infectious disease outbreaks because of confluence of factors including political, economic, public health, healthcare, demographics, and disease dynamics.
2020-02-25 Jin et al Gender differences in patients with COVID-19: Focus on severity and mortality
medrxiv
III-3. Time Series Analysis

In the public data set, the first 37 cases died of COVID-19 in Wuhan city and the 1019 survived patients with COVID-19 from six cities with a high prevalence of the disease were obtained from the Chinese Public Health Science Data Center.
Therefore, Gender is a risk factor for higher severity and mortality in patients with both COVID-19 and SARS independent of age and susceptibility.
2020-02-27 Kwok et al Community responses during the early phase of the COVID-19 epidemic in Hong Kong: risk perception, information exposure and preventive measures
medrxiv
III-2. Cross Sectional Control Respondents were asked about their demographics (including sex, age, living district, education 118 attainment, household income), self-perceived health status, travel history in the past month, occurrence 119 of respiratory symptoms in the past fourteen days and anxiety level using the Hospital, Anxiety and 120 Depression scale -Anxiety (HASD-A) (0-7 = Normal; 8-10 = Borderline abnormal; 11-21 = Abnormal).
2020-03-06 Dai et al Psychological impact of the coronavirus disease 2019 (COVID-19) outbreak on healthcare workers in China
medrxiv
IV. Prevalence Study Risk perception and psychological status were compared by demographic characteristics and COVID-19 exposure experiences.
2020-03-12 Tang et al Coronavirus Disease 2019 (COVID-19) Pneumonia in a Hemodialysis Patient
Kidney Medicine
IV. Other 1 COVID-19 pneumonia has had a significant impact on people's health and social activity behavior and on economic development.
2020-03-16 Araujo et al Spread of SARS-CoV-2 Coronavirus likely to be constrained by climate
medrxiv
IV. Computer Model Although climate is one of many factors likely affecting the spread of the virus, there is no doubt that the host behavior and density with geographical and climate factors .
2020-03-17 Qiu et al Impacts of social and economic factors on the transmission of coronavirus disease (COVID-19) in China
medrxiv
IV. Prevalence Study A main objective of this paper is to quantify the effect of various social and economic factors in mediating the transmission rates of the virus, which may help identify potential behavioral and socioeconomic risk factors for infections.
2020-03-17 Shi et al Temporal relationship between outbound traffic from Wuhan and the 2019 coronavirus disease (COVID-19) incidence in China
medrxiv
III-3. Time Series Analysis

We further estimated that the travel ban may have prevented approximately 19,768 COVID-19 cases (95% CI: 13,589, 25,946) outside of Wuhan by February 29, 2020.
We included demographic, economic, and geographical factors that are potential contributors to the provincial variation in the association between traffic volume and COVID-19 incidence.
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.
Finally, seasonality, geographic location, heat and humidity are co-factors, as are age, gender and underlying pathologies.
2020-03-19 Driggin et al Cardiovascular Considerations for Patients, Health Care Workers, and Health Systems During the Coronavirus Disease 2019 (COVID-19) Pandemic
Journal of the American College of Cardiology
IV. Prevalence Study

A meta-analysis of six studies inclusive of 1,527 patients with COVID-19 examined the prevalence of CVD and reported the prevalence of hypertension, cardiac and cerebrovascular disease, and diabetes to be 17.1%, 16.4%, and 9.7%, respectively .
For instance, age is the strongest risk factor for CVD and the effect of aging on immune function may be equally important for COVID-19 suceptibility and severity.
2020-03-20 Brooks et al The psychological impact of quarantine and how to reduce it: rapid review of the evidence
The Lancet
IV. Prevalence Study

A study 28 of horse owners quarantined because of equine influenza identified several characteristics associated with negative psycho logical impacts: younger age (16-24 years), lower levels of formal educational qualifications, female gender, and having one child as opposed to no children (although having three or more children appeared somewhat protective).
In the reviewed studies, the financial loss as a result of quarantine created serious socioeconomic distress 24 and was found to be a risk factor for symptoms of psychological disorders 22 and both anger and anxiety several months after quarantine.
2020-03-20 Aguilar et al Investigating the Impact of Asymptomatic Carriers on COVID-19 Transmission
medrxiv
IV. Prevalence Study Changes in behavioral patterns in response to an outbreak have an effect on the propagation of a disease.

Particularly, the COVID-19 pandemic has a different characterization in each country in which it has spread due to differences in surveillance capabilities of public health systems, socioeconomic factors, and environmental conditions.
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 Both SPAR and Joint External Evaluation metrics were designed to quantify each country's functional capacity, without accounting for other indirect factors that might compromise the control of emerging epidemics, such as demographic, environmental, socioeconomic, and political conditions.
2020-03-20 Kuwahara et al COVID-19: Active measures to support community-dwelling older adults
Travel Medicine and Infectious Disease
IV. Other ), organizational or community levels, and societal levels to prevent or mitigate the negative impact of social isolation and its related problems (from the preparedness phase) on the already vulnerable among the population during an epidemic such as COVID-19.
2020-03-23 Arenas et al A mathematical model for the spatiotemporal epidemic spreading of COVID19
medrxiv
IV. Computer Model The model captures human behavior features such as: the urban demography, age strata, age-structured contact patterns, and daily recurrent mobility flows.
2020-03-26 Pambuccian et al The COVID-19 pandemic: Implications for the cytology laboratory
Journal of the American Society of Cytopathology
IV. Other Psychologic stress may be experienced differently by different people, and may be modulated by personal factors like age, sex, health status, baseline anxiety level and risk perception.
2020-03-26 Hu et al Risk Factors Associated with Clinical Outcomes in 323 COVID-19 Patients in Wuhan, China
medrxiv
III-2. Retrospective Cohort

At the end of the study, 252 patients had recovered and were discharged, 35 patients had died (overall case fatality rate, 10.8%), and 36 patients were still hospitalized.
Higher BMI (30), hyperglycemia and diabetes, and cardiovascular disease were distinct risk factors for unfavorable clinical outcomes.
2020-03-27 Ghaffarzadegan et al Simulation-based Estimation of the Spread of COVID-19 in Iran
medrxiv
III-3. Time Series Analysis

In the most optimistic scenario for seasonal effects, depending on policy measures, 1.6 million Iranians (90% CI: 0.9M-2.6M) are likely to get infected, and death toll will reach about 58,000 cases (90% CI: 32K-97K), while in the more pessimistic scenarios, death toll may exceed 103,000 cases (90% CI: 56K-172K).
Economic pressures, normalization of death, and behavioral modeling after the more risk seeking (or those already recovered and thus presumably immune) could all weaken the behavioral response when the perceived risks have faded.

Among these three, the first (behavioral response) is endogenous to recent death rate.
2020-03-27 Stier et al COVID-19 attack rate increases with city size
medrxiv
III-3. Time Series Analysis Research on safe types of socioeconomic contact and exchange is therefore paramount so that we can succeed in controlling this outbreak while maintaining livelihoods, socioeconomic capacity, and mental health.
2020-03-27 Ficetola et al Climate affects global patterns of COVID-19 early outbreak dynamics
medrxiv
III-3. Time Series Analysis

We define a local outbreak event when at least 50 positive cases were detected in a given country/region, and calculated the growth rate of confirmed Covid-19 cases between day 1 and day 5, when day 1 was the day at which the 50 cases 10 threshold was reached.
Environmental factors, including seasonal climatic variability, can strongly impact on spatio-temporal patterns of infectious disease outbreaks.

Abstract: Environmental factors, including seasonal climatic variability, can strongly impact on spatio-temporal patterns of infectious disease outbreaks.

Climatic variables were the best drivers of global variation of confirmed Covid-19 cases growth rates.

Climatic variables were the best drivers of global variation of confirmed COVID-19 cases growth rates.

Non-linear relationships between climatic factors and ecological variables are frequent, and have also been proposed for relationships between SARS-CoV-2 occurrence and climate , and in exploratory plots we detected a clear non-linear relationship between r-values and climate.

The huge variation of Covid-19 growth rates among regions with 5 similar climate indeed suggests that diverse and complex social and demographic factors, as well as stochasticity, may strongly contribute to determine the severity of Covid-19 outbreaks.
2020-03-30 Barari et al Evaluating COVID-19 Public Health Messaging in Italy: Self-Reported Compliance and Growing Mental Health Concerns
medrxiv
IV. Prevalence Study Although anxiety might be driving healthy behaviors and pro-health beliefs described above, additional anxiety due to ones' vulnerable status is likely to negatively impact long-term mental health.
2020-03-30 Montemurro et al The emotional impact of COVID-19: from medical staff to common people
Brain, Behavior, and Immunity
IV. Other Infectious disease outbreaks such as COVID-19, as well as other public health events, can cause emotional distress and anxiety.
2020-03-30 Dong et al Prevalence and Factors Associated with Depression and Anxiety of Hospitalized Patients with COVID-19
medrxiv
IV. Prevalence Study

Methods: A total of 144 patients diagnosed with COVID-19 were included in this study.
3) This cross-sectional study is not capable to determine a causal relationship between mental health (anxiety or depression) and the sociodemographic and clinical variables.
2020-03-30 Qi et al COVID-19 transmission in Mainland China is associated with temperature and humidity: a time-series analysis
medrxiv
III-3. Time Series Analysis Environmental factors such as temperature and relative humidity may influence the transmissions of coronavirus

In conclusion, meteorological factors influence COVID-19 transmission and spread, potentially with an interactive effect between daily temperature and relative humidity on COVID-19 incidence.
2020-03-31 Asmundson et al Coronaphobia: Fear and the 2019-nCoV outbreak
Journal of Anxiety Disorders
IV. Other Research on the psychological reactions to previous epidemics and pandemics suggests that various psychological vulnerability factors may play a role in coronaphobia, including individual difference variables such as the intolerance of uncertainty, perceived vulnerability to disease, and anxiety (worry) proneness (Taylor, 2019) .
2020-03-31 Tuech et al Strategy for the practice of digestive and oncological surgery during the Covid-19 epidemic
Journal of Visceral Surgery
IV. Prevalence Study

This prospective trial included 1421 patients, and mortality at 3 months was 6.3%.
Four mortality risk factors, accessible before surgery, were isolated: the urgency of the surgery (relative risk 4.42), neurological antecedents (relative risk 3.85), weight loss above 10% of initial weight (relative risk 3.42) and age above 70 years (relative risk 2.16).
2020-04-01 Messner et al The Institutional and Cultural Context of Cross-National Variation in COVID-19 Outbreaks
medrxiv
IV. Other At the ecological level, regression coefficients are examined to figure out contextual variables influencing the pandemic's exponential growth rate across 96 countries.
2020-04-30 Asmundson et al How health anxiety influences responses to viral outbreaks like COVID-19: What all decision-makers, health authorities, and health care professionals need to know
Journal of Anxiety Disorders
IV. Other These models also suggest that high levels of health anxiety are characterized primarily by catastrophic misinterpretations of bodily sensations and changes, dysfunctional beliefs about health and illness, and maladaptive coping behaviours.

Psychological factors are known to play a vital role in the success of public health strategies used to manage epidemics and pandemics; that is, risk communication, vaccination and antiviral therapy, hygiene practices, and social distancing.
2020-04-30 Banerjee et al The COVID-19 outbreak: Crucial role the psychiatrists can play
Asian Journal of Psychiatry
IV. Prevalence Study Infections can create a range of behavioural and psychological effects.
2020-07-31 Artika et al Pathogenic viruses: Molecular detection and characterization
Infection, Genetics and Evolution
IV. Prevalence Study Biological, social and environmental factors have been linked to the emergence of infectious diseases.

9 Sustainable risk reduction strategies

9.0.0.1 Highlights

9.0.0.2 Articles

Date Authors Title LOE(?) & Sample Matches
2020 Shang et al The outbreak of SARS-CoV-2 pneumonia calls for viral vaccines
WHO
IV. Other This work aims to share strategies and candidate antigens to develop safe and effective vaccines against SARS-CoV-2.
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 .

As plant-made biopharmaceuticals provide efficacious and cost-effective strategies to protect against emerging infectious diseases, plant expression systems can be employed for the development of vaccines against nCoV.
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 Effective prevention and control strategies must be compulsorily implemented to prevent nosocomial infection.
2020-02-07 Gilbert et al Preparedness and vulnerability of African countries against introductions of 2019-nCoV
medrxiv
IV. Prevalence Study Resources and intensified surveillance and capacity capacity should be urgently prioritized towards countries at moderate risk that may be ill-prepared to face the importation and to limit onward transmission.
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 Other effective measures include One health approach, implementation of effective prevention and control strategies, rapid communication and networking, and exploring advances in science and technology for developing rapid and confirmatory diagnostics, enhancing disease surveillance and monitoring, implementation of strict biosecurity measures, and timely efforts toward designing appropriate and effective vaccines and therapeutics (Cheng et al.
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.
31 Existing local preliminary programmes and policies around human and animal health, community development and conservation are considered effective resources to begin or continue developing cost-effective strategies to mitigate zoonotic risks.

Policies and programmes existing in the communities provide opportunities for zoonotic risk mitigation.
2020-02-11 Sanche et al The Novel Coronavirus, 2019-nCoV, is Highly Contagious and More Infectious Than Initially Estimated
medrxiv
IV. Prevalence Study (B) The levels of minimum efforts (lines) of intervention strategies needed to control the virus spread.
2020-02-13 Shen et al Lockdown may partially halt the spread of 2019 novel coronavirus in Hubei province, China
medrxiv
IV. Other The implementation appears to be effective in reducing about 60% of new infections and deaths, and its effect also appears to be sustainable even after its removal.
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 Policies to promote research on these interactions could provide ways to better estimate the likely return on investment of more integrated SDG planning, guide efforts to achieve initiatives such as the GHSA Strategic Plan, and better monitor global progress on EID risk mitigation.

Environmental policies that promote sustainable land-use planning, reduced deforestation, and biodiversity protection, provide ancillary benefits by reducing the types of wildlife contact that can lead to disease emergence .

We therefore urge that EID risk mitigation becomes an integral part of sustainable socioeconomic planning.

Goal 3 of the UN 2030 Agenda for Sustainable Development aims to "ensure healthy lives and promote wellbeing for all at all ages."

Such policies could promote the "land sparing" strategy in production landscapes, which aims to reconcile agricultural activities and biodiversity conservation but also reduces the interaction of humans and livestock with wildlife (and therefore EID risk).

Organizations such as the UN Office For Disaster Risk Reduction (UNDRR) can help ensure that measures directed at risk mitigation and epidemic threat resilience are mainstreamed through coordination in program design and standards, for example via the World Bank-UN Humanitarian-Development-Peace initiative working in conflict-afflicted countries.
2020-02-18 Li et al Risk map of the novel coronavirus (2019-nCoV) in China: proportionate control is needed
medrxiv
IV. Other As such, proportionate control is especially important for sustainable protect human from the infectious diseases.
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.
If the situation changes towards much wider community transmission with multiple international foci, the WHO strategy of containment for elimination could need to be adjusted to include mitigation strategies combined with the following activities currently recommended by STAG-IH on the WHO website.
2020-03-03 Tan et al Lymphopenia predicts disease severity of COVID-19: a descriptive and predictive study
medrxiv
IV. Other The protection, maintenance or promotion of lymphocyte levels might have a good effect on the prevention and treatment of COVID-19.
2020-03-06 Lauro et al The timing of one-shot interventions for epidemic control
medrxiv
IV. Prevalence Study If so, then the intervention is sustainable.

If an intervention is sustainable, it should be kept in place.
2020-03-06 Shang et al On the use of corticosteroids for 2019-nCoV pneumonia
The Lancet
IV. Other This strategy will improve effective control strategies to ultimately contain the virus and protect the health of the public.
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.
2020-03-12 Costantino et al The effectiveness of full and partial travel bans against COVID-19 spread in Australia for travellers from China.
medrxiv
IV. Prevalence Study However, travel bans are not sustainable indefinitely, and a careful risk analysis needs to be done comparing the health and economic consequences of alternative scenarios.
2020-03-14 Lau et al Internationally lost COVID-19 cases
Journal of Microbiology, Immunology and Infection
III-3. Time Series Analysis

Cases with travel history to China peaked on February 1st, Lost COVID-19 cases 3 + MODEL 2020 and seem to reach nearly zero after February 14th, 2020.
This development in countries without sustainable medical surveillance can give further rise to both local and global virus outbreaks.
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.
Prevention and control strategies and methods are reported at three levels: national level, case-related population level, and general population level.
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 country's functional capacity is well advanced and sustainable at all levels of health systems.

24 An effective way of managing airborne infections is applying evidence-based public health prevention strategies.
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 Many nations are diverting their best efforts for the implementation of appropriate preventive and control strategies.
2020-03-18 Jacobsen et al Will COVID-19 generate global preparedness?
The Lancet
IV. Other 8 The Sendai Framework complements the IHR by integrating infrastructure, climate change, and economic considerations into disaster management plans and promoting inclusive policies that protect vulnerable populations during all phases of mitigation, preparedness, response, and recovery.
2020-03-18 Perkins et al Estimating unobserved SARS-CoV-2 infections in the United States
medrxiv
III-3. Time Series Analysis

By March 12, there were a total of 1,514 reported cases and 39 reported deaths that resulted from local transmission of SARS-CoV-2 in the US.
Analyses of the impact of large-scale mitigation efforts in China provide reason for optimism that those measures can be effective.
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 The focus is on building sustainable systems that ensure quality care for patients and their families and staff safety and wellbeing.
2020-03-21 Zhang et al Wuhan and Hubei COVID-19 mortality analysis reveals the critical role of timely supply of medical resources
Journal of Infection
IV. Other Accordingly, the effective implementation of comprehensive control measures and infection-treatment practices is critical for combatting any new pathogens, not only interrupting the transmissions but also saving the patients.
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 combined approach resulted in the largest reduction in cases from baseline (93·0% reduction [IQR 81·5-99·7]).
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 The response, control, and prevention of novel infectious diseases require strong and sustainable international collaborative work and data sharing.
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 ).
These results may inform the need for more stringent suppression measures as well as efforts to target those at highest risk for a range of preventive interventions.
2020-03-25 Giannakeas et al Estimating the maximum daily number of incident COVID-19 cases manageable by a healthcare system
medrxiv
IV. Other Further, the tool can inform the required intensity for non-pharmaceutical societal interventions like physical distancing based on a healthcare system's proximity to the sustainable threshold.
2020-03-26 Tuite et al Mathematical modeling of COVID-19 transmission and mitigation strategies in the population of Ontario, Canada
medrxiv
IV. Prevalence Study Societal disruption measures could include outcomes such as the overall duration of time that the intervention needs to be to achieve the associated reductions in morbidity and mortality.
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.
Facilities should consider implementing the following strategies.
2020-03-27 Alqahtani et al Prevalence, Severity and Mortality associated with COPD and Smoking in patients with COVID-19: A Rapid Systematic Review and Meta-Analysis
medrxiv
I. Systematic Review

A total of 15 studies met the inclusion criteria, which included a total of 2473 confirmed COVID-19 patients.
We strongly advocate public awareness campaigns concentrating on ways to achieve smoking cessation among smokers, and it is possible that an improvement in cessation rates will help to reduce the spread of SARS-CoV-2.
2020-03-30 Ugarov et al Inclusive Costs of NPI Measures for COVID-19 Pandemic: Three Approaches
medrxiv
IV. Other The calculus of total costs would shift more in favor of the herd immunity approach by accounting for increasing capacity of the healthcare system, gradual elimination of suppression measures and for the positive effect of suppression measures on infections from other airborne diseases.
2020-03-30 James et al Suppression and Mitigation Strategies for Control of COVID-19 in New Zealand
medrxiv
IV. Prevalence Study Suppression strategies can succeed in delaying an outbreak, but only for as long as such control measures can be sustained.
2020-03-30 Jenny et al Dynamic Modeling to Identify Mitigation Strategies for Covid-19 Pandemic
medrxiv
IV. Prevalence Study The first mitigation strategy tested with our model is social distancing.
2020-03-31 Singer et al What is ahead for health policy and technology in the 2020s?
Health Policy and Technology
IV. Other A key measurable goal for the success of health policy is assessing Universal Health Coverage, including access to effective and safe medicines and other health targets within the UN's Sustainable Development Goals.
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.
Researchers analyzed the epidemiological benefits of different transmission rates for the establishment of effective strategy in prevention and control strategies for epidemic infectious diseases.
2020-04-15 Musazzi et al New regulatory strategies to manage medicines shortages in Europe
International Journal of Pharmaceutics
IV. Prevalence Study Indeed, especially for old medicinal products, the costs of the upgrade to the required high-quality standards and risk assessment plan may be too high to maintain the MAH economic sustainability.

Moreover, the promising results obtained by some National competent Authorities (e.g., AIFA) suggested that setting up cooperation schemes between administration and other stakeholders, fostering a responsible approach in managing crisis in medicines supply, also allowing, for instance, surveillance/verification programs that may represent rational and effective preventive strategies to monitor the activities of exporting wholesalers and distributors for reducing the risks of product unavailability.
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 The SFDRR's ultimate goal is a substantial reduction of risk and losses, coupled with laying the essential foundations for rapid and sustained recovery and sustainable development.

This year was to be the “super year” for sustainability, a year of strengthening global actions to accelerate the transformations required for achieving the 2030 agenda.

Moreover, SDG 3 is devoted to "good health and well-being", with an emphasis on "early warning, risk reduction and management of national and global health risks" (UN, 2015) .
×
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