What is known about transmission, incubation, and environmental stability?

Table of Contents

1 Range of incubation periods for the disease in humans (and how this varies across age and health status) and how long individuals are contagious, even after recovery.

1.0.0.1 Highlights

1.0.0.2 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 incubation time varies from 2-14 days after infection.
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%) .
During this incubation period, patients are contagious, and it has been reported that each case infected on average 3.77 other people (uncertainty range 2.23-4.82) .
2020 Yang et al Analysis on the epidemic factors for the Corona Virus Disease
Zhonghua Yu Fang Yi Xue Za Zhi
IV. Other Source of infection including the patients, asymptomatic carrier and patients in the incubation period are contagious.
2020 Wang et al Science in the fight against the novel coronavirus disease
Chin Med J (Engl)
II. Randomized Controlled Trial

They performed a metagenomic analysis of respiratory tract specimens obtained from five patients suffering from the pneumonia in question and identified the virus now known as 2019-nCoV as the causative agent.
Attention should be paid to the spectrum of disease severity and transmission modes to address questions such as how to identify the proportion of asymptomatic infections and whether a patient is contagious during the incubation period.
2020 Shang et al The outbreak of SARS-CoV-2 pneumonia calls for viral vaccines
WHO
IV. Other COVID-19 spreads rapidly by human-to-human transmission with a median incubation period of 3.0 days (range, 0 to 24.0), and the time from symptom onset to developing pneumonia is 4.0 days (range, 2.0 to 7.0)3.
2020-01-30 Du et al Risk for Transportation of 2019 Novel Coronavirus (COVID-19) from Wuhan to Cities in China
medrxiv
IV. Prevalence Study We also derived the basic reproduction number by assuming a susceptible-exposed-infectious-recovery (SEIR) model for COVID-19, in which the incubation period is exponentially distributed with mean L in the range of 3 -6 days and the infectious period is also exponentially distributed with mean Z in the range of 2 to 7 days.
2020-02-05 Chowell et al Getting to zero quickly in the 2019-nCov epidemic with vaccines or rapid testing
medrxiv
IV. Prevalence Study Where b is the transmission rate and q is a parameter ranging from 0 to 1 that models the relative infectiousness of individuals during the incubation period of the disease.
2020-02-09 Guan et al Clinical characteristics of 2019 novel coronavirus infection in China
medrxiv
III-2. Retrospective Cohort

The core data sets (including clinical outcomes and symptoms) of 3 patients were lacking due to the incompleteness of original reports, hence this report delineates 1,099 patients with 2019-nCoV ARD from 552 hospitals in 31 provinces/province-level municipalities (Fig.
The median incubation period was 3.0 days (range, 0 to 24.0).
2020-02-11 Hellewell et al Feasibility of controlling 2019-nCoV outbreaks by isolation of cases and contacts
medrxiv
IV. Computer Model A key area of uncertainty is if and for how long individuals are infectious before symptom onset, and if asymptomatic or subclinical infection occurs.
2020-02-11 You et al Estimation of the Time-Varying Reproduction Number of COVID-19 Outbreak in China
medrxiv
IV. Other Infectious period is the duration of which an infected individual can transmit pathogens to a susceptible host.
2020-02-23 Wang et al Epidemiological characteristics of 1212 COVID-19 patients in Henan, China
medrxiv
IV. Other Different infectious diseases have different incubation periods.
2020-02-25 Zhang et al Characterizing the transmission and identifying the control strategy for COVID-19 through epidemiological modeling
medrxiv
IV. Other After incubation, the patient experiences disease onset and becomes infectious (I).
2020-02-27 Zhang et al Clinical characteristics of 82 death cases with COVID-19
medrxiv
III-2. Cross Sectional Control

Methods Clinical data on 82 death cases laboratory-confirmed as SARS-CoV-2 infection were obtained from a Wuhan local hospital′s electronic medical records according to previously designed standardized data collection forms.
Onset survival time was defined as the period between the onset of different symptoms and signs and the time of death.
2020-03-03 Yang et al Epidemiological and clinical features of COVID-19 patients with and without pneumonia in Beijing, China
medrxiv
III-3. Time Series Analysis

A total of 55 consecutive patients with laboratory-confirmed COVID-19 were enrolled in this study.
Furthermore, the disease course of COVID-19, the duration of viral existence, and the transmissibility of SARS-CoV-2 in asymptomatic carriers remain unknown.
2020-03-04 Bi et al Epidemiology and Transmission of COVID-19 in Shenzhen China: Analysis of 391 cases and 1,286 of their close contacts
medrxiv
IV. Prevalence Study

Time from symptom onset to death was marked by "+" for the three patients who have died.
To calculate the potential impact of surveillance and isolation on transmission, we considered a range of possible infectious periods where infectiousness varied over time.
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.
2,10,21,61-63 Immunocompromised patients can present with longer incubation periods of up to 20 days.
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.
These traits include virulence, clinical severity, ease of human-to-human transmission, if the pathogen is transmissible during the disease incubation period (and if yes, then how long that incubation period is).
2020-03-06 Kraemer et al The effect of human mobility and control measures on the COVID-19 epidemic in China
medrxiv
IV. Computer Model Age and sex distributions are important in understanding risk of infection across populations.

Statistical inference of the incubation period: The incubation period is the time interval between infection and symptom onset.
2020-03-06 Zhang et al Clinical features and outcomes of 221 patients with COVID-19 in Wuhan, China
medrxiv
III-2. Cross Sectional Control

The study population included a total of 221 admitted patients with confirmed COVID-19 infection in Zhongnan Hospital of Wuhan University, between January 2, 2019 and and 62 (28.1%), respectively.
6 9 Based on a recent large-scale epidemiological survey, the latency period of the SARS-CoV-2 may extend up to 24 days, even though the proportion of patients with long incubation period is very small, but the medium incubation period remains short at 3 days.
2020-03-11 Klompas et al Coronavirus Disease 2019 (COVID-19): Protecting Hospitals From the Invisible
Ann Intern Med
IV. Other It causes mild but prolonged disease, infected persons are contagious even when minimally symptomatic or asymptomatic, the incubation period can extend beyond 14 days, and some patients seem susceptible to reinfection .
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.
Several properties of this virus make prevention difficult namely, non-specific features of the disease, the infectivity even before onset of symptoms in the incubation period, transmission from asymptomatic people, long incubation period, tropism for mucosal surfaces such as the conjunctiva, prolonged duration of the illness and transmission even after clinical recovery.

The incubation period varies from 2 to 14 d [median 5 d] .

Patients can be infectious for as long as the symptoms last and even on clinical recovery.
2020-03-13 Kretzschmar et al Effectiveness of isolation and contact tracing for containment and slowing down a COVID-19 epidemic: a modelling study
medrxiv
IV. Other We used a stochastic transmission model in which every person generates novel infections according to a probability distribution that is affected by the incubation period distribution (time from infection to symptoms), distribution of the latent period (time from infection to a person becoming infectious), and overall transmissibility.
2020-03-13 Park et al The time scale of asymptomatic transmission affects estimates of epidemic potential in the COVID-19 outbreak
medrxiv
IV. Prevalence Study We model viral spread using a renewal-equation framework , which allows us to model the current incidence of infected individuals (i.e., the rate at which new infections occur in the population) as a function of previous incidence and how infectiousness of an infected individual varies over the course of their infection.

Generation intervals, which are defined as the time between when an individual is infected and when that individual infects another person , depend on the natural history of infection: individuals with subclinical infections may have fast clearance and short generation intervals, or slow viral reproduction and long generation intervals (cf.
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 This disease is characterized as highly contagious and is susceptible to humans of all ages.
2020-03-18 Li et al Propagation analysis and prediction of the COVID-19
medrxiv
IV. Computer Model In the course of disease transmission, the patient from being infected to the morbidity of disease, we call it incubation period.
2020-03-20 Zhang et al Age profile of susceptibility, mixing, and social distancing shape the dynamics of the novel coronavirus disease 2019 outbreak in China
medrxiv
IV. Other As transmission intensifies in other countries, the interplay between age, contact patterns, social distancing, susceptibility to infection and disease, and COVID-19 dynamics remains unclear.
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.
These parameters included how infectious an individual is over time, 20 the proportion of the population assumed to be asymptomatic (7·5%), 21 the cumulative distribution function for the mean incubation period (with SARS-CoV and SARS-CoV-2 having the same mean incubation period of 5·3 days), 3, 22 and the duration of hospital stay after symptom onset (3·5 days).

Third, the epidemiological characteristics of COVID-19 remain uncertain in terms of the transmission and infectivity profile of the virus; therefore, estimates of the time between symptom onset and admission to hospital, how infectious an individual is over time, and the asymptomatic rate were based on SARS-CoV.
2020-03-24 Ma et al Epidemiological parameters of coronavirus disease 2019: a pooled analysis of publicly reported individual data of 1155 cases from seven countries
medrxiv
III-3. Time Series Analysis

For two cases to qualify as an infector-infectee pair and be included in this study, the following two criteria must both be fulfilled.
Incubation period was defined as the time interval between exposure and onset of disease symptoms.

For a disease that is not infectious until onset of symptoms, latent period is equivalent to incubation period, and infectious period can commonly be approximated by the difference of serial interval minus incubation period.
2020-03-24 Wigginton et al Environmental Engineers and Scientists Have Important Roles to Play in Stemming Outbreaks and Pandemics Caused by Enveloped Viruses
Environ Sci Technol
IV. Other 25 Consequently, enveloped viruses likely display a diverse range of environmental behavior, persistence, and fate.
2020-03-24 Lu et al A New, Simple Projection Model for COVID-19 Pandemic
medrxiv
IV. Other For instance, COVID-19's incubation period varies from 1 to 14 days.
2020-03-26 FANG et al Human Mobility Restrictions and the Spread of the Novel Coronavirus (2019-nCoV) in China
medrxiv
IV. Prevalence Study 9 The range of the incubation period for 2019-nCoV is estimated to be 2-14 days, or even as long as 24 days.
2020-03-27 Gross et al Spatio-temporal propagation of COVID-19 pandemics
medrxiv
IV. Other Statistical estimations of the incubating (latency) period of the virus which includes no signs of illness vary between different populations and found to be of about 4-6 days while a long incubation period of 19 days has also been observed .
2020-03-27 Pisano et al Protecting high-risk cardiac patients during the Covid-19 outbreak
Journal of Cardiothoracic and Vascular Anesthesia
IV. Other Moreover, it has been suggested that person-to-person transmission can occur from individuals with an asymptomatic course as well as in the prodromal phase of disease 4,5 , or even after recovery.
2020-03-30 Zhu et al Children are unlikely to have been the primary source of household SARS-CoV-2 infections
medrxiv
IV. Other The mean incubation period across these studies was 7.74 d ± 3.22.
2020-03-30 Lopez et al A modified SEIR model to predict the COVID-19 outbreak in Spain: simulating control scenarios and multi-scale epidemics
medrxiv
IV. Other This way, both the incubation period and the period before recovery, as well as the precise role of asymptomatic population can be better represented at times when these information is highly uncertain.
2020-03-30 Bock et al Mitigation and herd immunity strategy for COVID-19 is likely to fail
medrxiv
IV. Prevalence Study

The time till hospitalisation from the onset of symptoms is assumed to be Gamma distributed with median 1.67 and variance 7.424 [gamma parameters: shape=0.874, loc=0.0, scale=2.915] 10 Patients with non severe progression eventually stay at home and the time from onset of symptoms till staying at home is also assumed to be Gamma distributed with median 2.31. and variance 8.365 [gamma parameters: shape=0.497, loc=0.0, scale=3.923] 11 .
The degree itself depends on how long the individual stays infectious (infectivity time).
2020-03-31 Wittkowski et al The first three months of the COVID-19 epidemic: Epidemiological evidence for two separate strains of SARS-CoV-2 viruses spreading and implications for prevention strategies
medrxiv
IV. Prevalence Study SARS and COVID-19 incubation period plus 2 days (Lauer 2020) ), R0 also determines how long it will take for early cases to become visible after a single import (150-60 days), the peak prevalence of infections (5-22%), and how many people will become immune (55-90%).
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.
At present, one of the characteristics of COVID-19 virus is that the incubation period is very long, and there are many asymptomatic infected persons who do not suffer from the disease for a long time.
2020-04-01 Shlomai et al Global versus focused isolation during the SARS-CoV-2 pandemic-A cost-effectiveness analysis
medrxiv
IV. Other We used R0=2.4 (range 1.4-3.9) , we assumed that the recovery time is 26 days, thus the transmission rate from infected (carrier) patients to susceptible population (β) was 0.09 (range 0.031 to 0.186) .
2020-04-01 Zhu et al Transmission Dynamics and Control Methodology of COVID-19: a Modeling Study
medrxiv
III-3. Time Series Analysis

3) , there are no more than 5 new cases every day from Dec 8 to Dec 28.
Latent period and infectious period follow Weibull distribution , which is a versatile distribution that has the ability to take on the characteristics of other types of distribution.
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.
2020-06-07 Krantz et al True epidemic growth construction through harmonic analysis
Journal of Theoretical Biology
IV. Prevalence Study There are other viruses whose incubation period is short but they are contagious during this period, for example, influenza.
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 The incubation period can be as long as 2 weeks or even longer, and it is highly contagious.
2020-12-31 Li et al Propagation analysis and prediction of the COVID-19
Infectious Disease Modelling
IV. Computer Model In the course of disease transmission, the patient from being infected to the morbidity of disease, we call it incubation period.

2 Prevalence of asymptomatic shedding and transmission (e.g., particularly children).

2.0.0.1 Highlights

2.0.0.2 Articles

Date Authors Title LOE(?) & Sample Matches
2020 Lai et al Asymptomatic carrier state, acute respiratory disease, and pneumonia due to severe acute respiratory syndrome coronavirus 2 (SARSCoV-2): Facts and myths
Journal of Microbiology, Immunology and Infection
IV. Prevalence Study

Regarding children with COVID-19, nine (0.9%) patients aged 0-14 years were found in only one study, 11 while 14 (0.35%) patients were aged ≤ 10 years in another study.
In addition, nosocomial infection of hospitalized patients and healthcare workers, and viral transmission from asymptomatic carriers are possible.
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.
It is reported that both symptomatic and asymptomatic patients with 2019-nCov can play a role in disease transmission via airborne and contact.
2020 Cao et al SARS-CoV-2 infection in children: Transmission dynamics and clinical characteristics
Journal of the Formosan Medical Association
IV. Other With more diagnostic detection done, the proportion of mild infections mainly in children and young adults became higher.
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.
This study aims to present the clinical characteristics of 24 cases with asymptomatic infection screened from close contacts and to show the transmission potential of asymptomatic COVID-19 virus carriers.
2020-02-27 Al-Tawfiq et al Asymptomatic coronavirus infection: MERS-CoV and SARS-CoV-2 (COVID-19)
Travel Medicine and Infectious Disease
IV. Other Asymptomatic carriage of influenza virus was estimated to be 5.2%-35.5% Based on serology, the positivity rate was 13% in asymptomatic SARS 4% in those with mild symptoms, and 82% in those with severe disease .
2020-02-27 Liang et al Prevalence and clinical features of 2019 novel coronavirus disease (COVID-19) in the Fever Clinic of a teaching hospital in Beijing: a single-center, retrospective study
medrxiv
IV. Prevalence Study

In the study period, 2123 patients visited the Fever Clinic because of fever and/or respiratory symptoms, and 342 patients were diagnosed to have pneumonia based on CT scan or in a few cases on Chest X-ray.
The prevalence of COVID-19 in all these pneumonia patients was 6.14% (21/342).
2020-02-28 Cai et al A Case Series of children with 2019 novel coronavirus infection: clinical and epidemiological features
Clinical Infectious Diseases
IV. Other Prolonged virus shedding is observed in respiratory tract and feces at the convalescent stage.
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 We assumed that the relative shedding rate of A P compared to I P was 0.5.
2020-03-03 Yang et al Epidemiological and clinical features of COVID-19 patients with and without pneumonia in Beijing, China
medrxiv
III-3. Time Series Analysis

A total of 55 consecutive patients with laboratory-confirmed COVID-19 were enrolled in this study.
Asymptomatic carriers might transmit SARS-CoV-2.
2020-03-04 Hu et al Clinical characteristics of 24 asymptomatic infections with COVID-19 screened among close contacts in Nanjing, China
Science China Life Sciences
IV. Prevalence Study This study aims to present the clinical characteristics of 24 cases with asymptomatic infection screened from close contacts and to show the transmission potential of asymptomatic COVID-19 virus carriers.
2020-03-09 Anderson et al How will country-based mitigation measures influence the course of the COVID-19 epidemic?
The Lancet
IV. Other Peak demand for health services could still be high and the extent and duration of presymptomatic or asymptomatic transmission-if this turns out to be a feature of COVID-19 infection-will determine the success of this strategy.
2020-03-11 Zhou et al Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study
The Lancet
III-2. Retrospective Cohort

Before Jan 11, 2020, SARS-CoV-2 RNA detection results were not available in the electronic medical records, from which data for this study were obtained retrospectively; therefore, this study includes 29 of the 41 patients originally reported on.
Third, the estimated duration of viral shedding is limited by the frequency of respiratory specimen collection, lack of quantitative viral RNA detection, and relatively low positive rate of SARS-CoV-2 RNA detection in throatswabs.
2020-03-12 Mizumoto et al Estimating the asymptomatic proportion of coronavirus disease 2019 (COVID-19) cases on board the Diamond Princess cruise ship, Yokohama, Japan, 2020
Euro Surveill
III-3. Time Series Analysis

Cases were from a total of 28 countries, with most being nationals of six countries, namely Japan (n = 270 cases), the United States (n = 88 cases), China (n = 58 cases; including 30 from Hong Kong), the Philippines (n = 54 cases), Canada (n = 51 cases) and Australia (n = 49 cases).
Considering the reported similarity in viral loads between asymptomatic and symptomatic patients and that transmission of SARS-CoV-2 by asymptomatic or paucisymptomatic cases may be possible, even though there is no clear evidence as yet of asymptomatic transmission, the relatively high proportion of asymptomatic infections could have public health implications.
2020-03-13 Xing et al Prolonged presence of SARS-CoV-2 in feces of pediatric patients during the convalescent phase
medrxiv
IV. Prevalence Study

Fecal specimens were first collected in two patients (case 1, 1.5-year-old male; and case 2, 5-year-old male) on day 4 after onset of the disease.
Prolonged shedding of SARS-CoV-2 in stools of infected children indicates the potential for the virus to be transmitted through fecal excretion.
2020-03-13 Park et al The time scale of asymptomatic transmission affects estimates of epidemic potential in the COVID-19 outbreak
medrxiv
IV. Prevalence Study Thus, we investigate the relationship between individual-level features of asymptomatic cases (e.g., the probability that an infection is asymptomatic, asymptomatic case duration, transmission by asymptomatic individuals) to dynamics at the population scale.
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.
Studies have shown higher viral loads in the nasal cavity as compared to the throat with no difference in viral burden between symptomatic and asymptomatic people .
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.
Second, the transmission of SARS-CoV-2 from asymptomatic carriers and presymptomatic patients could be even less common, if their viral loads are low and virus shedding is not substantial.

In this regard, epidemiological studies to determine the percentages of asymptomatic carriers and in selected large cohorts of subjects in Wuhan should help clarify the role of asymptomatic virus shedding in SARS-CoV-2 transmission.

Experimental infection of dromedary camels with MERS-CoV results in mild disease, shedding large quantities of the virus from the upper respiratory tract .

The key questions concern how often asymptomatic and presymptomatic virus shedding might occur as well as whether their viral loads could be high.
2020-03-14 Aslam et al COVID-19: Yet Another Coronavirus Challenge in Transplantation
The Journal of Heart and Lung Transplantation
IV. Other Importantly, viral shedding can occur for days for weeks furtively in asymptomatic carrier individuals especially children and fecal shedding has been noted in patients without diarrhea.
2020-03-15 Zheng et al SARS-CoV-2: an Emerging Coronavirus that Causes a Global Threat
Int J Biol Sci
IV. Other Despite the claim of the transmission by asymptomatic contact has been challenged , other asymptomatic carriers were also observed to transmit the viruses of SARS-CoV-2 .
2020-03-18 Lazzerini et al COVID-19 in Italy: momentous decisions and many uncertainties
The Lancet Global Health
IV. Other Data are lacking on the prevalence of the disease among asymptomatic populations, so the real prevalence of COVID-19, its spectrum of presentation, and the real mortality rate all remain unknown.
2020-03-19 Ma et al Do children need a longer time to shed SARS-CoV-2 in stool than adults?
Journal of Microbiology, Immunology and Infection
IV. Other Children show a longer shedding time than adults.

Next, we sought to determine why the shedding time of the virus in feces is longer in children than in adults.

Therefore, we believe that the expression of ACE2 in the intestine of children may differ from that of adults; this difference may explain why children have a longer viral shedding period than adults.
2020-03-20 Aguilar et al Investigating the Impact of Asymptomatic Carriers on COVID-19 Transmission
medrxiv
IV. Prevalence Study The viral loads of asymptomatic carriers are similar to those in symptomatic carriers .
2020-03-20 Nickbakhsh et al Epidemiology of seasonal coronaviruses: Establishing the context for COVID-19 emergence
medrxiv
IV. Prevalence Study

Of 74,241 patient episodes of respiratory illness with sCoV subtyping, 8,912 patients experienced multiple episodes over the study timeframe.
The comparatively lower proportion positive and detection odds for school-aged children compared to younger children may potentially reflect a sustained level of CoV-OC43 immune-mediated protection, whereas waned immunity is expected to leave adults more vulnerable to coronavirus infections .
2020-03-23 Tao et al High incidence of asymptomatic SARS-CoV-2 infection, Chongqing, China
medrxiv
IV. Other Conclusion: The SARS-CoV-2 prevention needs to focus on the screening of asymptomatic patients in the community with a history of contact with the imported population, especially for children and the elderly population.
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.
Even at a low infectivity (R 0 ≤1·5), a high asymptomatic pro portion is problematic, with 58 000 infections (IQR 5400-123 000) occurring at an asymptomatic proportion of 22·7% compared with 1800 infections (200-23 000) at a 7·5% asymptomatic proportion with the combined intervention'.
2020-03-23 Lewnard et al Scientific and ethical basis for social-distancing interventions against COVID-19
The Lancet Infectious Diseases
IV. Prevalence Study The authors estimated that 75% of infections are clinically asymptomatic, although data on the proportion of infections that are asymptomatic are scarce; as shown by Koo and colleagues in sensitivity analyses with higher asymptomatic proportions, this value will influence the effectiveness of social-distancing interventions.
2020-03-24 Ma et al Epidemiological parameters of coronavirus disease 2019: a pooled analysis of publicly reported individual data of 1155 cases from seven countries
medrxiv
III-3. Time Series Analysis

For two cases to qualify as an infector-infectee pair and be included in this study, the following two criteria must both be fulfilled.
Asymptomatic transmission was also observed.

Asymptomatic transmission was also observed in this study (Table 3 ).
2020-03-24 Chavez et al Coronavirus Disease (COVID-19): A primer for emergency physicians
The American Journal of Emergency Medicine
IV. Prevalence Study

60 One study of 204 patients with confirmed COVID-19 suggests 48.5% of patients have gastrointestinal (GI) symptoms.
23, 27 Limited data support viral shedding in asymptomatic patients while increased levels of viral shedding may be more pronounced in those critically ill. Current epidemiologic patterns of COVID- 19 in China indicate that it is highly contagious with sustained spread; the extent of person-to-person transmission within the U.S. was initially limited and continues to evolve daily.
2020-03-25 Khan et al Analysis of Serologic Cross-Reactivity Between Common Human Coronaviruses and SARS-CoV-2 Using Coronavirus Antigen Microarray
biorxiv
IV. Prevalence Study Serology can play an important role in defining both the prevalence of and sensitivity of PCR for SARS-CoV-2 infection, particularly for subclinical infection.
2020-03-26 Pambuccian et al The COVID-19 pandemic: Implications for the cytology laboratory
Journal of the American Society of Cytopathology
IV. Other Although the exact incidence of such asymptomatic infection remains unknown, a meta-analysis of SARS data showed overall seroprevalence rates of 0.1% for the general population and 0.23% for health care workers 23 .
2020-03-26 Koff et al Symptomatology during seasonal coronavirus infections in children is associated with viral and bacterial co-detection
medrxiv
IV. Prevalence Study

The contribution to the spread of the disease by these children 82 currently remains unknown, but is potentially substantial given significant viral shedding also 83 occurs in asymptomatic children , and because they keep mixing with family members and 84 other individuals in the community .
The contribution to the spread of the disease by these children 82 currently remains unknown, but is potentially substantial given significant viral shedding also 83 occurs in asymptomatic children , and because they keep mixing with family members and 84 other individuals in the community .

HCoV carriage and 79 disease seems, as most viral infections, highly seasonal in children.
2020-03-27 Soetikno et al Considerations in performing endoscopy during the COVID-19 pandemic
Gastrointestinal Endoscopy
IV. Other 21 There is a high viral load in the upper respiratory tract, and there is a significant potential for asymptomatic persons to shed and transmit virus.

1, 2 Transmission can occur in both symptomatic and asymptomatic individuals.
2020-03-27 Yadlowsky et al Estimation of SARS-CoV-2 Infection Prevalence in Santa Clara County
medrxiv
IV. Prevalence Study If the prevalence of COVID-19 is between 0.13% and 1.36%, then such a prevalence estimate has implications for the size of the testing necessary to get a reliable estimate of prevalence.
2020-03-28 Hagmann et al COVID-19 in children: More than meets the eye
Travel Medicine and Infectious Disease
IV. Prevalence Study

In the hitherto largest pediatric COVID-19 study that analyzed 2143 children with laboratory-3 confirmed or suspected cases most pediatric patients (94.1%) were diagnosed as asymptomatic, or with mild or moderate disease .
In addition, the evidence of fecal shedding of SARS-CoV-2 in the stool of an asymptomatic child for a prolonged period raises the concern that infants and children who are not toilet-trained could facilitate fecal-oral transmission of the virus .
2020-03-28 Xing et al Prolonged Viral Shedding in Feces of Pediatric Patients with Coronavirus Disease 2019
Journal of Microbiology, Immunology and Infection
IV. Other Persistent shedding of SARS-CoV-2 in stools of infected children raises the possibility that the virus might be transmitted through contaminated fomites.
2020-03-29 Venkatakrishnan et al Knowledge synthesis from 100 million biomedical documents augments the deep expression profiling of coronavirus receptors
biorxiv
IV. Prevalence Study

This observation was corroborated by complementary gene expression analysis of over 250,000 bulk RNA-seq samples from GTEx 23, 24 and the Gene Expression Omnibus (GEO) along with protein expression analysis from healthy tissue proteomics and immunohistochemistry (IHC) datasets , where lung and other respiratory tissues consistently show lower ACE2 expression compared to the digestive tract and kidney (Figure S3A-D) .
The strong intestinal ACE2 expression is particularly interesting given the emerging clinical reports of fecal shedding and persistence post-recovery which may reflect a fecal-oral transmission pattern 10-12 .
2020-03-29 Li et al Anesthesia Management and Perioperative Infection Control in Patients with the Novel Coronavirus
Journal of Cardiothoracic and Vascular Anesthesia
IV. Other Transmission can occur from asymptomatic infected individuals.
2020-03-30 Zhu et al Children are unlikely to have been the primary source of household SARS-CoV-2 infections
medrxiv
IV. Other Asymptomatic infections experienced by children infected with SARS-CoV-2 could have important implications for transmission.

There is a growing body of evidence suggesting that asymptomatic individuals play an important role in the transmission of SARS-CoV-2 in the community 68-70 ; However, such studies do not negate the results of the present study, as both children AND adults can present with an asymptomatic infection.

2 Alternatively, these data may reflect altered viral shedding (either in titre or duration) in children or an alternate, less efficient route of virus transmission from infected children to adults.
2020-04-30 Niud et al Deciphering the power of isolation in controlling COVID-19 outbreaks
The Lancet Global Health
IV. Other 9 However, the efficiency of transmission remains uncertain, and seroprevalence studies among different contacts will be important.
2020-04-30 Yeo et al Enteric involvement of coronaviruses: is faecal–oral transmission of SARS-CoV-2 possible?
The Lancet Gastroenterology & Hepatology
IV. Other Although direct droplet transmission is an important route of transmission, faecal excretion, environmental contamination, and fomites might contribute to viral transmission.

3 Seasonality of transmission.

3.0.0.1 Highlights

3.0.0.2 Articles

Date Authors Title LOE(?) & Sample Matches
2020 Yang et al Analysis on the epidemic factors for the Corona Virus Disease
Zhonghua Yu Fang Yi Xue Za Zhi
IV. Other Routes of SARS-CoV-2 transmission are diversified and the main routes of transmission for COVID-19 are droplet transmission and close contact transmission.
2020 Khot et al The 2019 Novel Coronavirus Outbreak - A Global Threat
The Journal of the Association of Physicians of India
IV. Other The varying transmission patterns, namely, nosocomial transmission and spread through mildly symptomatic cases is an area of concern.
2020 Rocklöv et al COVID-19 outbreak on the Diamond Princess cruise ship: estimating the epidemic potential and effectiveness of public health countermeasures
Journal of Travel Medicine
IV. Other The association of acute respiratory infections (ARI) incidence in passengers is statistically significant with season, destination and duration of travel.
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 Respiratory droplet transmission is the main route of transmission, and it can also be transmitted through contact .
2020-02-11 Chinazzi et al The effect of travel restrictions on the spread of the 2019 novel coronavirus (2019-nCoV) outbreak
medrxiv
IV. Prevalence Study The transmission and mobility model does not account, at this stage, for heterogeneities due to age differences in susceptibility and contact patterns.
2020-02-12 Hébert-Dufresne et al Beyond R0: the importance of contact tracing when predicting epidemics
medrxiv
IV. Computer Model For example, aspects of the social contact network , metapopulation structure , mobility , adaptive behavior , higher-order contact structure , and even other pathogens , all interact to cause complex patterns of disease emergence, spread, and persistence.
2020-02-14 Danon et al A spatial model of CoVID-19 transmission in England and Wales: early spread and peak timing
medrxiv
IV. Other However, seasonality in transmission has a large impact on epidemic timing, peak incidence, and final attack rates.

is the magnitude of the seasonal difference in transmission, ranging from

Our findings suggest that the height of the epidemic and the attack rate is highly dependent on seasonality of transmission and that even small changes in transmission risk can lead to large changes in attack rate due to the spatial disaggregation of the population at risk.
2020-02-17 Neher et al Potential impact of seasonal forcing on a SARS-CoV-2 pandemic
medrxiv
IV. Prevalence Study

The dataset included a total of 52,158 patient samples with 190,257 diagnostic tests, of which 2,084 were positive for any of the coronaviruses (229E = 319; NL63 = 499; OC43 = 604; HKU1 = 355; OC43/HKU1 = 307).
These two scenarios differ slightly in the time of year at which peak transmissibility θ occurs: When transmission is mostly local and seasonality is amplified by .

Variation in transmission and migration rates can result in substantial variation in prevalence between regions.

showing that recent trends in different regions across East-Asia imply that seasonality alone is unlikely to end SARS-CoV-2 spread.
2020-02-26 Benvenuto et al Application of the ARIMA model on the COVID-2019 epidemic dataset
Data Brief
IV. Prevalence Study The correlogram reporting the ACF and PACF showed that both prevalence and incidence of COVID-2019 are not influenced by the seasonality.
2020-02-27 Tian et al Characteristics of COVID-19 infection in Beijing
Journal of Infection
IV. Other Therefore, person-to-person transmission is the main route of transmission.
2020-03-06 Kissler et al Projecting the transmission dynamics of SARS-CoV-2 through the post-pandemic period
medrxiv
IV. Prevalence Study A seasonality factor of 0 indicates no seasonal variation in R0 for SARS-CoV-2.

The seasonality factor represents the amount of seasonal variation in the SARS-CoV-2 R0 relative to the other human betacoronaviruses.

These dynamics will depend on seasonality, the duration of immunity, and the strength of cross-immunity to/from the other human coronaviruses.

A seasonality factor of 1 indicates equivalent seasonal variation in R0, while 0 indicates no seasonal variation (see Table S2 -3).

A seasonality factor of 0.5 indicates that the amplitude of seasonal variation in R0 for SARS-CoV-2 is half the amplitude of the seasonal variation in R0 for the other betacoronaviruses.

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 .
2020-03-09 Anderson et al How will country-based mitigation measures influence the course of the COVID-19 epidemic?
The Lancet
IV. Other Data from the southern hemisphere will assist in evaluating how much seasonality will influence COVID-19 transmission.
2020-03-16 Neher et al Potential impact of seasonal forcing on a SARS-CoV-2 pandemic
Swiss Medical Weekly
IV. Prevalence Study Variation in transmission and migration rates can result in substantial variation in prevalence between regions.
2020-03-18 Dehesh et al Forecasting of COVID-19 Confirmed Cases in Different Countries with ARIMA Models
medrxiv
IV. Computer Model Seasonal differences were used to stabilize the series from seasonality trend.
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 Massonnaud et al COVID-19: Forecasting short term hospital needs in France
medrxiv
IV. Computer Model Several experts suggest that the impact of seasonality on COVID-19 7 .

The critical factor that remains unknown to this date is the potential impact of seasonality on the transmission dynamic of COVID-19.
2020-03-20 Bannister-Tyrrell et al Preliminary evidence that higher temperatures are associated with lower incidence of COVID-19, for cases reported globally up to 29th February 2020
medrxiv
IV. Prevalence Study Seasonal variation in COVID-19 incidence could impact the trajectory of the pandemic.
2020-03-20 Zhang et al Age profile of susceptibility, mixing, and social distancing shape the dynamics of the novel coronavirus disease 2019 outbreak in China
medrxiv
IV. Other As transmission intensifies in other countries, the interplay between age, contact patterns, social distancing, susceptibility to infection and disease, and COVID-19 dynamics remains unclear.
2020-03-20 Nickbakhsh et al Epidemiology of seasonal coronaviruses: Establishing the context for COVID-19 emergence
medrxiv
IV. Prevalence Study

Of 74,241 patient episodes of respiratory illness with sCoV subtyping, 8,912 patients experienced multiple episodes over the study timeframe.
The analyses adjusted for patient age, sex, primary or secondary/tertiary healthcare service, time period with respect to pandemic influenza (as above), and the monthly background prevalence of the sCoV (response variable) to eliminate spurious virus-virus associations owing to unrelated sources of seasonality.
2020-03-24 Kissler et al Social distancing strategies for curbing the COVID-19 epidemic
medrxiv
IV. Prevalence Study Under current critical care capacities, however, the overall duration of the SARS-CoV-2 epidemic could last into 2022, requiring social distancing measures to be in place between 25% (for wintertime R0 = 2 and seasonality, Figure S3A ) and 70% (for wintertime R0 = 2.5 and no seasonality, Figure S2C ) of that time.

However, the necessary duration, frequency, and intensity of this distancing remains unclear in the presence of seasonality.
2020-03-24 Maslov et al Window of Opportunity for Mitigation to Prevent Overflow of ICU capacity in Chicago by COVID-19
medrxiv
IV. Computer Model We found that we could match the emergence of the infection in Illinois with an R0 = 4.0 (annual average), latency = 5 days, infectious period = 3 days, seasonal forcing strength 0.2 and seasonal peak in January.
2020-03-25 Prem et al The effect of control strategies to reduce social mixing on outcomes of the COVID-19 epidemic in Wuhan, China: a modelling study
The Lancet Public Health
IV. Prevalence Study

Each simulation started with 200 or 2000 infectious individuals I 0 , 15 with the rest of the population being in the susceptible state.
Future research should be directed towards understanding the potential seasonality of COVID-19 and the climatic factors that could affect its transmission dynamics.

The effects of seasonality on SARS-CoV-2 are difficult to predict without long time series; supporting evidence for the link between climate and COVID-19 has been largely anecdotal and based on spread in different settings and such analyses are subject to confounding.
2020-03-26 He et al Moving-average based index to timely evaluate the current epidemic situation after COVID-19 outbreak
medrxiv
IV. Other The reliability of the SEIR model can be affected by many factors that are difficult to estimate, including seasonality of coronavirus, inter-city mobility, transmission of travel behavior, and the number of asymptomatic infections.

As mentioned above, the reliability of SEIR model is affected by the seasonality of coronavirus, population mobility, and asymptomatic infection status.
2020-03-26 FANG et al Human Mobility Restrictions and the Spread of the Novel Coronavirus (2019-nCoV) in China
medrxiv
IV. Prevalence Study To the best of our knowledge, this paper is the first to provide a causal interpretation of the impact of city lockdown on human mobility and the spread of 2019-nCoV, and to clearly disentangle the lockdown effects from other potential contributing factors such as panic and virus effect, as well as the seasonal Spring Festival effect (see Section 3).
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.
The strong relationship between local climate and Covid-19 growth rates suggests the possibility of seasonal variation in the spatial pattern of outbreaks, with temperate regions of the Southern Hemisphere becoming at particular risk of severe outbreaks during the next months.

The strong relationship between local climate and COVID-19 growth rates suggests the possibility of seasonal variation in the spatial pattern of outbreaks, with temperate regions of the Southern Hemisphere becoming at particular risk of severe outbreaks during the next months.

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.

The clear relationship between COVID-19 growth rate and climate suggests that seasonal climatic variation may affect the spatial spread and severity of COVID-19 outbreaks , as observed for other virus-caused diseases .
2020-03-27 Davies et al Age-dependent effects in the transmission and control of COVID-19 epidemics
medrxiv
IV. Computer Model If fomite, or faecal-oral routes of transmission are important in transmission, these contact matrices may not be representative of transmission risk.
2020-03-30 Gupta et al Trend Analysis and Forecasting of COVID-19 outbreak in India
medrxiv
IV. Computer Model It is an important method if the data shows trend and not seasonality.
2020-03-30 Carleton et al Causal empirical estimates suggest COVID-19 transmission rates are highly seasonal
medrxiv
III-3. Time Series Analysis

Each line represents a time series of seasonal projections of new cases of COVID-19 per 1 million individuals for each country and every month between April 2020 and January 2021; Northern Hemisphere countries are in orange and Southern hemisphere countries are in blue, with solid lines indicating hemisphere average effects.
It has been hypothesized that if COVID-19 exhibits seasonality, changing temperatures in the coming months will shift transmission patterns around the world.

Causal empirical estimates suggest COVID-19 transmission rates are highly seasonal
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 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.
2020-03-30 Burns et al Symptom-Based Isolation Policies: Evidence from a Mathematical Model of Outbreaks of Influenza and COVID-19
medrxiv
III-3. Time Series Analysis Influenza viral shedding appears to vary by subtype, but the patterns of shedding were similar in both children and adults , and between the seasonal and p(H1N1) outbreaks , although the reproductive number appears different .
2020-03-31 Byass et al Eco-epidemiological assessment of the COVID-19 epidemic in China, January-February 2020
medrxiv
IV. Computer Model Thus other coronaviruses show various seasonal transmission patterns.
2020-04-01 Patterson-Lomba et al Optimal timing for social distancing during an epidemic
medrxiv
IV. Prevalence Study The inclusion of transmission or contact level heterogeneities within the population (e.g., age structure) may play a significant role in the quantitative description of the results in this paper, as would the inclusion of seasonality effects.

4 Physical science of the coronavirus (e.g., charge distribution, adhesion to hydrophilic/phobic surfaces, environmental survival to inform decontamination efforts for affected areas and provide information about viral shedding).

4.0.0.1 Highlights

4.0.0.2 Articles

Date Authors Title LOE(?) & Sample Matches
2020 Kampf et al Potential role of inanimate surfaces for the spread of coronaviruses and their inactivation with disinfectant agents
Infection Prevention in Practice
IV. Other An effective surface disinfection may help to ensure an early containment and prevention of further viral spread.

For the disinfection of small surfaces ethanol (62%e71%; carrier tests) revealed a similar efficacy against coronavirus .
2020 SONG et al Implementation of radiotherapy in a tertiary hospital in Zhejiang province during the epidemic of COVID-19
Chinese Journal of Radiological Medicine and Protection
IV. Other Methods During this epidemic period, available methods including but not limited to: strict disinfection, body temperature monitoring, learning relevant knowledge by all staffs to ensure the safety of radiotherapy treatment.
2020 Seah et al Revisiting the dangers of the coronavirus in the ophthalmology practice
Eye
IV. Other Decontamination and sterilisation protocols of clinical rooms and equipment should also be improved on as coronaviruses have been found to survive in environments outside the body for a long time .
2020-02-11 Hellewell et al Feasibility of controlling 2019-nCoV outbreaks by isolation of cases and contacts
medrxiv
IV. Computer Model This would make effective contact tracing challenging, and good respiratory and hand hygiene would be critical to reduce this route of transmission, coupled with environmental decontamination in healthcare settings.
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.
2020-02-12 Ung et al Community pharmacist in public health emergencies: Quick to action against the coronavirus 2019-nCoV outbreak
Research in Social and Administrative Pharmacy
IV. Prevalence Study 20 Additionally, regular cleaning of surfaces and items will also help to eliminate the potential sources for spread of infection.
2020-02-27 Jiang et al Clinical Data on Hospital Environmental Hygiene Monitoring and Medical Staff Protection during the Coronavirus Disease 2019 Outbreak
medrxiv
IV. Other We found that the virus was present both on surfaces and in the air.

Predetermined environmental surfaces were sampled using swabs at seven o'clock in the morning before disinfection.
2020-02-28 Shah et al Guide to Understanding the 2019 Novel Coronavirus
Mayo Clinic Proceedings
IV. Other Decontamination of work surfaces and equipment with Environmental Protection Agencyeregistered hospital disinfectant is of paramount importance.
2020-02-28 Hellewell et al Feasibility of controlling COVID-19 outbreaks by isolation of cases and contacts
Lancet Glob Health
IV. Computer Model This type of transmission would make effective contact tracing challenging, and good respiratory and hand hygiene would be crucial to reduce this route of transmission, coupled with environmental decontamination in health-care settings.
2020-02-29 Rodríguez-Morales et al Going global – Travel and the 2019 novel coronavirus
Travel Medicine and Infectious Disease
IV. Other Clean and disinfect frequently touched objects and surfaces in the home and work environment.
2020-02-29 Tang et al Stochastic discrete epidemic modeling of COVID-19 transmission in the Province of Shaanxi incorporating public health intervention and case importation
medrxiv
III-3. Time Series Analysis

Given the daily number of newly confirmed imported cases 1 , … , on m consecutive days 1 , … , and the probability = ( − ≤ < − + 1) that an imported case entered Shaanxi province on day j and was confirmed on day i.
As COVID-19 spread has occurred in many regions globally, we believe our study provides an important tool to inform public health decisions regarding travel restriction and social distancing in these regions according to their public health capacity to maintain an effective contact tracing, quarantine and isolation procedure.
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).
a) Environmental hygiene in medical sectors and personal hygiene of health care workers should be maintained .
2020-03-07 Baker et al Preparing for a Surge of Coronavirus Cases
The Joint Commission Journal on Quality and Patient Safety
IV. Other  Implement all elements of standard precautions as outlined in the CDC Core Practices, including o Hand hygiene o Environmental cleaning and disinfection o Risk assessment with use of appropriate personal protective equipment (such as gloves, gowns, face masks) based on activities being performed o Reprocessing of reusable medical equipment between each patient and when soiled  Hand-off communications, both inter-and intrafacility, should include notification of colonization or infection with a potentially transmissible pathogen.
2020-03-16 Araujo et al Spread of SARS-CoV-2 Coronavirus likely to be constrained by climate
medrxiv
IV. Computer Model For example, a recent study examined survival of dried SARS--CoV--1 Coronavirus on smooth surfaces and found that it would be viable for over 5 days at temperatures ranging between 11--25ºC and relative humidity of 40--50%, drastically loosing viability as temperatures and humidity increased .
2020-03-16 Hemida et al The SARS-CoV-2 outbreak from a one health perspective
One Health
IV. Prevalence Study The environmental factors that may contribute to the spread of the virus include air, water, soil, etc.
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.
Several public health measures that may prevent or slow down the transmission of the COVID-19 were introduced; these include case isolation, identification and follow-up of contacts, environmental disinfection, and use of personal protective equipment .
2020-03-17 Kratzel et al Efficient inactivation of SARS-CoV-2 by WHO-recommended hand rub formulations and alcohols
biorxiv
IV. Other Hand Hygiene in Health Care' suggests two alcohol-based formulations for hand 9 sanitization to reduce pathogen infectivity and spreading.
2020-03-20 Chen et al Roles of meteorological conditions in COVID-19 transmission on a worldwide scale
medrxiv
IV. Prevalence Study These meteorological factors such as humidity, visibility, and wind speed can affect droplet stability in the environment, or affect survival of viruses as air temperature does, and thus impact epidemic transmission.
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 Adsorption of the COVID-19 virus on airborne dust and PM could also contribute to long-range transport of the virus Therefore, investigations on adsorption, survival, and behavior of the COVID-19 virus with the surface of PM are needed to help to understand the role of air PM pollution in COVID-19 transmission.
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.
3 On Jan 1, 2020, the market was closed for environmental sanitation and disinfection to prevent further transmission.
2020-03-24 Wigginton et al Environmental Engineers and Scientists Have Important Roles to Play in Stemming Outbreaks and Pandemics Caused by Enveloped Viruses
Environ Sci Technol
IV. Other Relative humidity, fomite material, and air temperature can greatly impact enveloped virus inactivation rates.
2020-03-25 Vahia et al COVID-19, Mental Health and Aging: A Need for New Knowledge to Bridge Science and Service
The American Journal of Geriatric Psychiatry
IV. Other It will be important for the field to assess the range and efficacy of these measures -these may include implementing telepsychiatry for direct care and psychotherapy , using a range of technologies for social engagement and measures to facilitate physical activity and nutrition.
2020-03-25 Nunez-Bajo et al Ultra-Low-Cost Integrated Silicon-based Transducer for On-Site, Genetic Detection of Pathogens
biorxiv
IV. Other The porous surface allows electroplating of high-quality metal films on the surface of the Si substrate by creating an interlocking, high porosity surface to improve adhesion ( Figures 2B & C) .
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.
Influenza viruses are able to survive on environmental surfaces, particularly hard surfaces, for periods of one to two days.

As such, regular cleaning and disinfection of surfaces should be undertaken during a suspected or confirmed outbreak to minimise the spread of influenza and other respiratory viruses.

Virus transfer from porous materials to hands is less efficient due to rapid drying of the virus.23 Increased environmental cleaning can help interrupt virus transmission.

Additionally, enhanced cleaning and disinfection of the ill resident's environment and minimising transfer of residents within and between facilities may help reduce spread.

Environmental cleaning and disinfection: Make sure that EPA-registered, hospital-grade disinfectants are available to allow for frequent cleaning of high-touch surfaces and shared resident care equipment.

In addition, gloves must be worn when it is anticipated that the hands will be in contact with mucous membranes, non-intact skin, tissue, blood, body fluids, secretions, excretions, or equipment and environmental surfaces contaminated with the above.
2020-03-26 Santarpia et al Transmission Potential of SARS-CoV-2 in Viral Shedding Observed at the University of Nebraska Medical Center
medrxiv
IV. Other Health care workers were closely monitored and screened for COVID-19 suggesting the value in implementing IPC protocols that maintain airborne isolation standards including respiratory protection and include routine systematic environmental cleaning and disinfection of patient care areas and surrounding environments.
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.
Given the impact of environmental conditions on the transmission of many pathogens, we tested the hypothesis that the severity of Covid-19 outbreaks across the globe is affected by spatial variation of key environmental factors, such as temperature, air humidity (5, , and pollution [fine particulate matter ; see methods].
2020-03-29 Tan et al Response and Operating Room Preparation for the COVID-19 Outbreak: A Perspective from the National Heart Centre Singapore
Journal of Cardiothoracic and Vascular Anesthesia
IV. Other The anesthetic work environment and its surfaces are at high risk for harboring droplets which can serve as virus reservoirs if proper decontamination processes are not taken.
2020-03-30 pawar et al Effects of temperature on COVID-19 transmission
medrxiv
IV. Other Environmental factors such as atmospheric temperature modulates the survival and spread of virus aerosols.

It was shown that survival of influenza viral aerosols is reduced at higher temperatures .
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
2020-03-30 Zhu et al Association between ambient temperature and COVID-19 infection in 122 cities from China
Science of The Total Environment
IV. Other Both epidemiological and laboratory studies have shown that ambient temperature could affect the transmission and survival of coronaviruses.
2020-03-31 Kampf et al Persistence of coronaviruses on inanimate surfaces and their inactivation with biocidal agents
Journal of Hospital Infection
IV. Other Although the viral load of coronaviruses on inanimate surfaces is not known during an outbreak situation it seem plausible to reduce the viral load on surfaces by disinfection, especially of frequently touched surfaces in the immediate patient surrounding where the highest viral load can be expected.

Surface disinfection with 0.1% sodium hypochlorite or 62e71% ethanol significantly reduces coronavirus infectivity on surfaces within 1 min exposure time.
2020-03-31 Udwadia et al How to protect the protectors: 10 lessons to learn for doctors fighting the COVID-19 Coronavirus
Medical Journal Armed Forces India
II. Randomized Controlled Trial Water and detergent can be used for cleansing environmental surfaces and regularly used hospital disinfectants will suffice.

Environmental controls: Environmental and engineering controls involve adequate ventilation of all health care facilities and proper environmental disinfection.
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 Second, previous studies showed that SARS-CoV and other coronaviruses could survive on environmental surfaces and inanimate objects ; however, the presence of SARS-CoV-2 in the environment has not been reported.
2020-03-31 Lyu et al Expert consensus on the procedure of interventional diagnosis and treatment of cancer patients during the COVID-19 epidemic
Journal of Interventional Medicine
IV. Prevalence Study The infection control department must perform sampling of the surfaces and the air after proper disinfection of the surgical room.

Interventional radiology personnel should strictly follow the standard precautionary principles, with particular importance to personal protection, hand hygiene, ward management, environmental ventilation, disinfection of equipment, and medical waste management, etc.
2020-04-01 Sultan et al AGA Institute Rapid Recommendations for Gastrointestinal Procedures During the COVID-19 Pandemic
Gastroenterology
I. Systematic Review

58, 59 First, the systematic reviews by Offeddu et al included a meta-analysis of 3 observational studies that showed a benefit in using N95 respirators over standard masks in protecting health care workers from SARS (OR = 0.86; 95% CI: 0.
Transfer of organisms from contaminated PPE to hands or clothing may contribute to infection of health care workers and associated contacts.
2020-04-30 Yeo et al Enteric involvement of coronaviruses: is faecal–oral transmission of SARS-CoV-2 possible?
The Lancet Gastroenterology & Hepatology
IV. Other The virus was viable on different surfaces for 48 h at 20°C and 40% relative humidity, although viability decreased to 8 h at 30°C and 80% relative humidity conditions.
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 Since TiO 2 normally has a hemispherical-like morphology, the mechanical damage due to contact will depend on the size of the particles to reach the permeation of the cell wall or to cover it.

The cleaning and disinfection of surfaces is another essential use of the photocatalysis.

The efficiency of disinfection depends on the capacity of the cellular components for the absorption of light from each microbe.

5 Persistence and stability on a multitude of substrates and sources (e.g., nasal discharge, sputum, urine, fecal matter, blood).

5.0.0.1 Highlights

5.0.0.2 Articles

Date Authors Title LOE(?) & Sample Matches
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).
Viral RNAs could be found in nasal discharge, sputum, and sometimes blood or feces.
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).
Viral RNAs could be found in nasal discharge, sputum, and sometimes blood or feces.
2020 WANG et al Analysis of 8 274 cases of new coronavirus nucleic acid detection and co-infection in Wuhan
Chinese Journal of Laboratory Medicine
IV. Other Both respiratory tract samples (nasopharynx, oropharynx, sputum and alveolar lavage fluid) and non-respiratory tract samples (urine, feces, anal swabs, blood and conjunctival sac swabs) were collected.
2020 Cao et al SARS-CoV-2 infection in children: Transmission dynamics and clinical characteristics
Journal of the Formosan Medical Association
IV. Other The infant's urine, stool and sputum were tested negative; however, on February 9, a test on stool was positive.
2020-02-18 Liu et al Longitudinal characteristics of lymphocyte responses and cytokine profiles in the peripheral blood of SARS-CoV-2 infected patients
medrxiv
III-3. Time Series Analysis

Findings: Of the 40 COVID-19 patients enrolled, 13 severe cases showed significant and sustained decreases in lymphocyte counts but increases in neutrophil counts than 27 mild cases.
Specimens, including sputum or alveolar lavatory fluid, blood, urine, and feces, were cultured to identify pathogenic bacteria or fungi that may be associated with the SARS-CoV-2 infection.
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.
5 Briefly, nasopharyngeal and throat swabs and stool and urine samples were taken and put into viral transport media.
2020-02-24 Pan et al Viral load of SARS-CoV-2 in clinical samples
The Lancet Infectious Diseases
IV. Prevalence Study

Here, we report our findings from different types of clinical specimens collected from 82 infected individuals.
Serial samples (throat swabs, sputum, urine, and stool) from two patients in Beijing were collected daily after their hospitalisation (patient 1, days 3-12 post-onset; patient 2, days 4-15 post-onset).

No viral RNA was detected in urine or stool samples from these two patients.
2020-02-24 Lamb et al Rapid Detection of Novel Coronavirus (COVID-19) by Reverse Transcription-Loop-Mediated Isothermal Amplification
medrxiv
IV. Other Simulated patient samples were generated by spiking serum, urine, saliva, oropharyngeal swabs, and nasopharyngeal swabs with a portion of the COVID-19 nucleic sequence.
2020-02-25 Xu et al Clinical and computed tomographic imaging features of novel coronavirus pneumonia caused by SARS-CoV-2
Journal of Infection
IV. Other The virus nucleic acid can be detected in swabs, secretions and sputum from the respiratory tract, blood or excrement.

However, confirmation of infection of this virus requires presence of the virus nucleic acid detected in swabs, secretions and sputum from the respiratory tract, blood or stools.
2020-02-25 Peng et al 2019 Novel Coronavirus can be detected in urine, blood, anal swabs and oropharyngeal swabs samples
medrxiv
IV. Other The virus was found in urine, blood, anal swabs and oropharyngeal swabs.

2019 Novel Coronavirus can be detected in urine, blood, anal swabs and oropharyngeal swabs samples
2020-02-27 Cui et al Clinical features and sexual transmission potential of SARS-CoV-2 infected female patients: a descriptive study in Wuhan, China
medrxiv
IV. Other In addition, SARS-CoV was detected in urine, feces and tears of some SARS-CoV infected patients.
2020-03-03 Young et al Epidemiologic Features and Clinical Course of Patients Infected With SARS-CoV-2 in Singapore
JAMA
IV. Other Virus was detectable in the stool (4/8 [50%]) and blood (1/12 [8%]) by PCR but not in urine.
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).
Coronavirus nucleic acid can be detected in the throat, sputum, lower respiratory tract secretions, blood and tool.
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.
11, 12, 79, 80 MERS-CoV RNA has been detected in blood, urine, and stool-but at much lower viral loads than in the respiratory tract.
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 Methods: We studied viral load courses by RT-PCR in oro- and nasopharyngeal swabs, sputum, stool, blood, and urine in nine hospitalized cases.

Daily measurements of viral load in sputum, pharyngeal swabs, and stool are summarized in Figure 2 .
2020-03-13 Ji et al Analysis clinical features of COVID-19 infection in secondary epidemic area and report potential biomarkers in evaluation
medrxiv
IV. Other In addition, coronavirus nucleic acids were detected in throat swabs, sputum samples, lower respiratory secretions and blood samples .
2020-03-13 Ghinai et al First known person-to-person transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the USA
The Lancet
IV. Prevalence Study For patients with COVID-19, nasopharyngeal, oropharyngeal, serum, sputum, urine, and stool specimens were collected and sent to CDC for testing at initial presentation, and then 10 Criteria were based on published MERS-CoV guidance and additional input from CDC subject matter experts.

For Patient 1, initial nasopharyngeal, oropharyngeal, and sputum specimens collected on DOI 7 were positive, whereas serum and urine were negative.
2020-03-14 Li et al High sensitivity detection of coronavirus SARS-CoV-2 using multiplex PCR and a multiplex-PCR-based metagenomic method
biorxiv
IV. Computer Model RT-PCR has been reported to detect SARS-CoV-2 in saliva 15 , pharyngeal swab, blood, anal swab 16 , urine, stool 17 , and sputum specimens 18 .
2020-03-14 Repici et al Coronavirus (COVID-19) outbreak: what the department of endoscopy should know
Gastrointestinal Endoscopy
IV. Prevalence Study SARS-CoV is known to be stable in feces and urine for at least 1 to 2 days; thus, surfaces might be a possible source of contamination and lead to infection.
2020-03-15 Lo et al Evaluation of SARS-CoV-2 RNA shedding in clinical specimens and clinical characteristics of 10 patients with COVID-19 in Macau
Int J Biol Sci
IV. Other Samples were taken from different specimens, including nasopharyngeal swabs (NPS), sputum, urine, and stool in all patients where available.

Based on our data on SARS-CoV-2 RNA shedding in stool and the possibility of a lag in viral detection in NPS specimens, the assessment of both fecal and respiratory specimen is recommended to enhance diagnostic sensitivity, and also to aid discharge decision before the role of viral RNA shedding in stool is clarified.
2020-03-16 Park et al First Pediatric Case of Coronavirus Disease 2019 in Korea
J Korean Med Sci
IV. Other Serum, saliva, and urine tested negative on hospital days 3 and 8.

Real-time reverse transcription polymerase chain reaction (RT-PCR) for SARS-CoV-2 (Supplementary Data 1) was serially tested for the samples from nasopharynx, throat, saliva, serum, stool, and urine.
2020-03-17 Mackenzie et al COVID-19: a novel zoonotic disease caused by a coronavirus from China: what we know and what we don’t
Microbiol Aust
IV. Other The authors also studied the viral loads in throat swabs, sputum and stool samples in other patients, and found viral loads were as high as 10 11 copies/mL in throat samples, but with a median of 7.99 Â 10 4 , and 7.52 Â 10 5 in sputum.

In a second and more detailed study, the virus load was investigated over Hot Topic consecutive days in two patients from the time of their hospitalisation, with serial samples throat swabs, sputum, urine and stools.
2020-03-18 Diagnosis and treatment plan of Corona Virus Disease 2019 (tentative sixth edition)
Global Health Journal
IV. Other The nucleic acid of 2019-nCoV can be detected in biological specimens such as nasopharyngeal swabs, sputum, other lower respiratory tract secretions, blood and feces.
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 .
In addition, researchers also detected SARS-CoV-2 in the samples of stool, gastrointestinal tract, saliva and urine.
2020-03-19 Nicastri et al Coronavirus disease (COVID-19) in a paucisymptomatic patient: epidemiological and clinical challenge in settings with limited community transmission, Italy, February 2020
Euro Surveill
IV. Other SARS-CoV-2 RNA in stools, nasopharyngeal and oropharyngeal swabs resulted positive at different time points, whereas urine, spermatic fluid, saliva, blood and conjunctival swabs were persistently negative (Table) .
2020-03-21 Fang et al Comparisons of nucleic acid conversion time of SARS-CoV-2 of different samples in ICU and non-ICU patients
Journal of Infection
IV. Prevalence Study

For the enrolled patients, 40.6% (13/32) of them carried underlying diseases, of which the common diseases were hypertension (5 patients) and diabetes (4 patients).
Dynamic clinical samples including nasal swabs, blood, fecal, urine, saliva and tears were collected from each patient for surveillance.
2020-03-21 Hill et al The index case of SARS-CoV-2 in Scotland: a case report
Journal of Infection
IV. Other SARS-CoV-2 PCR on urine, faeces and EDTA blood was negative.
2020-03-23 Chen et al SARS-CoV-2: virus dynamics and host response
The Lancet Infectious Diseases
IV. Other SARS-CoV-2 has been detected in faeces, blood, and urine samples, 9, 10 and it is important to ascertain viral load dynamics in such samples, for prevention and control of the pandemic.
2020-03-24 Wigginton et al Environmental Engineers and Scientists Have Important Roles to Play in Stemming Outbreaks and Pandemics Caused by Enveloped Viruses
Environ Sci Technol
IV. Other Viruses have a direct connection to wastewater and drinking water purification when they are excreted in feces or urine (Table 1) , 9 but there is limited data on the concentration of enveloped viruses in feces and urine.
2020-03-26 Tan et al Viral Kinetics and Antibody Responses in Patients with COVID-19
medrxiv
III-3. Time Series Analysis

A total of 1 260 samples from all 67 patients were collected, including 377 nasopharyngeal swab, 221 sputum, 220 stool, 231 urine and 211 plasma samples ( Table 2) .
Conclusions Nasopharyngeal, sputum and stools rather than blood and urine, were the major shedding routes for SARS-CoV-2, and meanwhile sputum had a prolonged viral shedding.

Clinical specimens including nasopharyngeal swab, sputum, blood, urine and stool were collected periodically (3-6 days interval) after admission.

A total of 1 260 samples from all 67 patients were collected, including 377 nasopharyngeal swab, 221 sputum, 220 stool, 231 urine and 211 plasma samples ( Table 2) .

Results The median duration of SARS-CoV-2 RNA shedding were 12 (3-38), 19 (5-37), and 18 (7-26) days in nasopharyngeal swabs, sputum and stools, respectively.

Clinical specimens including nasopharyngeal swab, sputum, blood, urine and stool were tested periodically according to standardized case report form with final follow-up on February 27.
2020-03-26 Pambuccian et al The COVID-19 pandemic: Implications for the cytology laboratory
Journal of the American Society of Cytopathology
IV. Other From the experience with SARS we can extrapolate that SARS-CoV-2 can be present in fecal and urine samples, in addition to peripheral blood and respiratory samples.
2020-03-27 Lescure et al Clinical and virological data of the first cases of COVID-19 in Europe: a case series
The Lancet Infectious Diseases
III-3. Time Series Analysis

11 The five patients in this case series, at different stages of infection, include two patients with a mild disease at admission and a secondary worsening that resulted in their admission to an intensive care unit (ICU), one initially severely ill patient directly admitted to an ICU for an acute respiratory failure, and two patients with a mild disease diagnosed very early after infection.
Upper and lower (when possible) respiratory tract samples, and also blood, urine, and stool samples (or rectal swabs, if appropriate) were obtained.

During the whole course of the disease of these two patients, SARS-CoV-2 detection by RT-PCR was negative in stools, serum, and urine.
2020-03-30 Zhang et al Virus shedding patterns in nasopharyngeal and fecal specimens of COVID-19 patients
medrxiv
IV. Other A total of 66 upper respiratory swabs, 51 feces, 56 urine and 56 plasma samples were sequentially collected from 23 patients in a designated hospital.
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.
2019-nCoV nucleic acids can be detected in specimens including nasopharyngeal swabs, sputum, lower respiratory tract secretions, blood and stool .
2020-03-31 Yu et al Measures for diagnosing and treating infections by a novel coronavirus responsible for a pneumonia outbreak originating in Wuhan, China
Microbes and Infection
IV. Computer Model A variety of specimens (such as swabs, nasal swabs, nasopharynx or trachea extracts, sputum or lung tissue, blood and feces) should be retained for testing in a timely manner, which gives a higher rate of positive detection of lower respiratory tract specimens.
2020-04-30 Yeo et al Enteric involvement of coronaviruses: is faecal–oral transmission of SARS-CoV-2 possible?
The Lancet Gastroenterology & Hepatology
IV. Other Study of the enteric involvement and viral excretion of SARS-CoV-2 in faeces is required to investigate whether faecal concentrations of SARS-CoV-2 RNA correlate with the severity of the disease and presence or absence of gastrointestinal symptoms, and whether faecal SARS-CoV-2 RNA can also be detected in the incubation or convalescence phases of COVID-19.
2020-07-31 Artika et al Pathogenic viruses: Molecular detection and characterization
Infection, Genetics and Evolution
IV. Prevalence Study Types of specimens commonly collected are those which contain the maximum amount of the target virus (Johnson, 1990) , for example, whole blood and oral swabs are collected and used for detection of Ebola virus (World Health Organization (WHO), 2014); posterior-pharyngeal (throat) swabs or nasal swabs for detection of avian influenza A(H5N1) virus (World Health Organization (WHO), 2006); respiratory, stool, and rectal swab (Chan et al., 2004a) , sputum , urine, serum, plasma and peripheral blood leukocytes specimens (Mahony and Richardson, 2005) for detection of SARS-CoV; serum , plasma, urine (Corman et al., 2016) , whole blood, amniotic fluid, cerebrospinal fluid (CSF), organ tissues such as placenta, fetal brain, eyes (Landry and George, 2017) for detection of Zika virus; saliva, CSF, tears, skin biopsy, urine for detection of rabies virus (Fooks et al., 2009) , serum for detection of Coxsackievirus (Wiyatno et al., 2016) , West Nile virus , Dengue virus (Fahri et al., 2013) , blood for detection of Chikungunya virus , etc.

6 Persistence of virus on surfaces of different materials (e,g., copper, stainless steel, plastic).

6.0.0.1 Highlights

6.0.0.2 Articles

Date Authors Title LOE(?) & Sample Matches
2020-02-03 Zhou et al A pneumonia outbreak associated with a new coronavirus of probable bat origin
Nature
IV. Prevalence Study

Of the samples obtained from the seven patients, we found that six BALF and five oral swab samples were positive for 2019-nCoV during the first sampling, as assessed by qPCR and conventional PCR.
Ultrathin sections (80 nm) of embedded cells were prepared, deposited onto Formvar-coated copper grids (200 mesh), stained with uranyl acetate and lead citrate, and analysed using a 200-kV Tecnai G2 electron microscope.
2020-02-17 Luo et al The role of absolute humidity on transmission rates of the COVID-19 outbreak
medrxiv
IV. Other For example, influenza viruses survive longer on surfaces or in droplets in cold and dry air -increasing the likelihood of subsequent transmission.
2020-02-21 Cheng et al Scabies: Application of the Novel Identify-Isolate-Inform Tool for Detection and Management
West J Emerg Med
IV. Prevalence Study

36 Advising patients and parents of young patients to keep fingernails short and clean can assist with preventing secondary infections.
Additionally, items used by patients and close contacts in the preceding several days such as clothing and linens should be washed and dried at high temperatures (≥60°C), dry-cleaned, or placed in a plastic bag for at least 72 hours if unable to launder.
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 aircraft grow in size and durations of flights lengthen (can exceed 15 hours), exposures and transmission events inside these metal or composite-materials tubes in the sky will increase.
2020-03-10 Doremalen et al Aerosol and surface stability of HCoV-19 (SARS-CoV-2) compared to SARS-CoV-1
medrxiv
IV. Other HCoV-19 was most stable on plastic and stainless steel and viable virus could be detected up to 33 72 hours post application ( Figure 1A ), though the virus titer was greatly reduced (plastic from 10 3.7 to 34 10 0.6 TCID 50 /mL after 72 hours, stainless steel from 10 3.7 to 10 0.6 TCID 50 /mL after 48 hours).
2020-03-10 Liu et al Aerodynamic Characteristics and RNA Concentration of SARS-CoV-2 Aerosol in Wuhan Hospitals during COVID-19 Outbreak
biorxiv
IV. Other Total of 2 aerosol deposition samples were collected using 80 mm diameter filters packed into a holder with an effective deposition area of 43.0 cm 2 and the filters were placed on the floor in two corners of Renmin Hospital ICU room intact for 7 days.
2020-03-13 Zheng et al Infrared assessment of human facial temperature in the presence and absence of common cosmetics
medrxiv
IV. Other Cosmetic #6, a foundation common in facial makeup, showed negligible effect after 5 min, despite the fact that the likely major components of residue are talc, mica, silica, dimethicone, zinc stearate, and titanium oxide.
2020-03-14 Peña-Otero et al Are we ready for the new coronavirus?
Archivos de Bronconeumología (English Edition)
IV. Other Transmission through infected surfaces is likely; human coronaviruses persist on metals, glass, or plastics for more than 9 days.
2020-03-15 Yi et al COVID-19: what has been learned and to be learned about the novel coronavirus disease
Int J Biol Sci
IV. Prevalence Study

On February 11, 2020, a multi-center study on 8,866 patients including 4,021 confirmed COVID-19 patients presented a more updated illustration of the epidemic as follows ( UlBi-HX_rHPXa1qHA2bhdA).
Surgical face masks prevent liquid droplets from a potentially infected individual from traveling through the air or sticking onto surfaces of materials, where they could be passed on to others .
2020-03-16 Araujo et al Spread of SARS-CoV-2 Coronavirus likely to be constrained by climate
medrxiv
IV. Computer Model For example, an experiment examining the stability of MERS--CoV when laying on plastic and steel surfaces, under three environmental treatments (20ºC -40% relative humidity, 30ºC-- 30% RH, 30ºC - 80% RH), revealed that the virus was more stable in 20ºC and 40% RH treatment, decaying gradually in the second and third treatments .
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 For instance, more precipitation increases humidity that may weaken virus transmissions (Lowen and Steel, 2014) .
2020-03-22 Kwatra et al Dermatology practices as vectors for COVID-19 transmission: a call for immediate cessation of non-emergent dermatology visits
Journal of the American Academy of Dermatology
IV. Other 4 Emerging research also suggests that COVID-19 viral particles remain viable in aerosol for several hours and can survive several days on multiple surfaces.
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 2 COVID-19 virus is thought to survive for several hours on surfaces such as aluminum, sterile sponges, or latex surgical gloves, increasing the opportunity for transmission via touch.
2020-03-23 Rodrigues et al An update on COVID-19 for the radiologist - A British society of Thoracic Imaging statement
Clinical Radiology
IV. Other Surfaces should be washed with soap and water or cleaned with a low-or intermediate-level disinfectant.
2020-03-25 Nunez-Bajo et al Ultra-Low-Cost Integrated Silicon-based Transducer for On-Site, Genetic Detection of Pathogens
biorxiv
IV. Other The silicone holder also contained five embedded gold-plated stainless-steel electrodes author/funder.

The porous surface allows electroplating of high-quality metal films on the surface of the Si substrate by creating an interlocking, high porosity surface to improve adhesion ( Figures 2B & C) .

The wafers were dried in air and immersed in a batch containing an aqueous solution of 80 µM KAuCl4 and 0.5% HF for 20 s to deposit Au particles on the surface of the wafer electrolessly.

A sample reservoir (polyethylene; diameter: 5 mm; volume: 40 µl, Figure 1A ) with two holes was thermally bonded across the three-electrode electrochemical cell at 110±10 °C.
2020-03-25 Baig et al The COVID-19 Intubation and Ventilation Pathway (CiVP); a Commentary
Arch Acad Emerg Med
IV. Other A plastic transparent sheet can be placed over the patientâȂŹs head and chest to prevent droplet spread .
2020-03-26 Viswanath et al Working through the COVID-19 outbreak: Rapid review and recommendations for MSK and allied heath personnel
Journal of Clinical Orthopaedics and Trauma
IV. Other SARS-CoV-2 is detectable for up to four hours on copper, up to 24 hours on cardboard and up to two to three days on plastic and stainless steel 6 .
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.
Influenza viruses can persist on hard surfaces and remain viable for up to 24 hours on hard, non-porous surfaces.

Influenza viruses are able to survive on environmental surfaces, particularly hard surfaces, for periods of one to two days.

Virus transfer from porous materials to hands is less efficient due to rapid drying of the virus.23 Increased environmental cleaning can help interrupt virus transmission.

Frequently touched surfaces are those closest to the resident, and should be cleaned more often (for example -bedrails, bedside tables, commodes, doorknobs, sinks, surfaces and equipment close to the resident).

A long-sleeved gown should be worn if it is anticipated that clothing or forearms will be in direct contact with the patient or with environmental surfaces or objects in the patient care environment.
2020-03-27 Sellars et al Interesting times
Br Dent J
IV. Prevalence Study The plastic wrapping could be recycled in appropriate points such as recycling bins for plastic supermarket bags.
2020-03-27 Kenney et al Hydrogen Peroxide Vapor sterilization of N95 respirators for reuse
medrxiv
IV. Other 9 Hydrogen peroxide (HP) vapor is virucidal on hard surfaces, and has been shown not to impair respirator performance.

Although there was complete inactivation of aerosolized Geobacillus stearothermophius, it is unknown if HP vapor would be virucidal since respirators have porous fabric that may harbor virus.
2020-03-27 Cristiano et al Mechanical Ventilator Milano (MVM):A Novel Mechanical Ventilator Designed for Mass Scale Production in response to the COVID-19 Pandemics
medrxiv
IV. Other The construction of both vent traps with transparent plastic containers permits to 2 All rights reserved.
2020-03-30 pawar et al Effects of temperature on COVID-19 transmission
medrxiv
IV. Other The virus can remain viable for up to three days on plastic and stainless steel or in aerosols for upto 3 hours and is relatively more stable than the known human coronaviruses.
2020-03-30 Fletcher et al A novel antiviral formulation inhibits a range of enveloped viruses.
biorxiv
IV. Prevalence Study Virus was placed on formvar coated copper 400 electron microscopy grids for 5 minutes; excess supernatant was removed and the grids were stained with 1% uranyl acetate.
2020-03-31 Kampf et al Persistence of coronaviruses on inanimate surfaces and their inactivation with biocidal agents
Journal of Hospital Infection
IV. Other The analysis of 22 studies reveals that human coronaviruses such as Severe Acute Respiratory Syndrome (SARS) coronavirus, Middle East Respiratory Syndrome (MERS) coronavirus or endemic human coronaviruses (HCoV) can persist on inanimate surfaces like metal, glass or plastic for up to 9 days, but can be efficiently inactivated by surface disinfection procedures with 62–71% ethanol, 0.5% hydrogen peroxide or 0.1% sodium hypochlorite within 1 minute.
2020-03-31 Ensser et al Determination of daily reproduction numbers of SARS-CoV2 based on death cases suggests more rapid initial spread in Italy and the United States
medrxiv
IV. Prevalence Study

Two separate samples of this cell suspension were counted in trypan blue dye; four hemacytometer counts were performed on each sample, and then the eight cell counts were averaged.
The plates were sealed in plastic bags and centrifuged in microplate carriers at 1,200 ϫ g for 2 h at 25°C.
2020-03-31 Lyu et al Expert consensus on the procedure of interventional diagnosis and treatment of cancer patients during the COVID-19 epidemic
Journal of Interventional Medicine
IV. Prevalence Study Disposable plastic films should also cover other items, such as infusion racks, ECG monitors, high-pressure syringes, ventilators, etc.

All item surfaces should be covered with double layers of disposable plastic films, which include surgical instruments, accessories, consumables, surgical beds, instrument tables, etc.
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%.
Surfaces must be disinfected between successive patients.
2020-03-31 Udwadia et al How to protect the protectors: 10 lessons to learn for doctors fighting the COVID-19 Coronavirus
Medical Journal Armed Forces India
II. Randomized Controlled Trial Water and detergent can be used for cleansing environmental surfaces and regularly used hospital disinfectants will suffice.
2020-04-01 Shayak et al Transmission Dynamics of COVID-19 and Impact on Public Health Policy
medrxiv
IV. Computer Model Scientists have found that the pathogen remains on surfaces for a long time ranging from 3 hours in aerosols, 24 hours on cardboard and up to 3 days on plastic and stainless steel.
2020-04-01 Sultan et al AGA Institute Rapid Recommendations for Gastrointestinal Procedures During the COVID-19 Pandemic
Gastroenterology
I. Systematic Review

58, 59 First, the systematic reviews by Offeddu et al included a meta-analysis of 3 observational studies that showed a benefit in using N95 respirators over standard masks in protecting health care workers from SARS (OR = 0.86; 95% CI: 0.
The experimental study by van Doremalen et al further demonstrated that SARS-CoV-2 may stay viable on copper surfaces up to 4 hours, on cardboard surfaces up to 24 hours, and on plastic and stainless steel surfaces up to 72 hours.
2020-04-01 McCuaig et al What We Know So Far (As of March 26, 2020) About COVID-19 – An MRT Point of View
Journal of Medical Imaging and Radiation Sciences
IV. Other Close contact is defined by the United States (US) Centers for Disease Control and Prevention (CDC) as: being within 2 meters of a COVID-19 patient for a prolonged period of time Recent investigation shows that the COVID-19 virus may suspend in the air for two to three hours (depending on heat and humidity, and presumably air flow), and exist on external surfaces for more than three days (more stable on plastic and stainless steel than on copper and carboard) Exercising good hand hygiene is very important to avoid SARS-CoV-2 entering the eyes, nose and mouth after touching an infected surface
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 On the other hand, the deposition of metal nanoparticles on the surface of TiO 2 also represents an efficient strategy in the photocatalytic improvement of this material.

The TiO 2 powder and coated in a plastic film can be used successfully to increase the storage life of some fruits postharvest .

Photocatalytic materials based on TiO 2 remain as an effective alternative for water disinfection air and surfaces, and can be boosted with some chemicals like ozone, hydrogen peroxide, and so on.

For instance, silicone and latex catheters, medical tubes and any medical-grade surface can be coated by TiO 2 and Ag-TiO 2 for the elimination of Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus, which are the pathogenic microorganisms commonly associated with nosocomial infections .

The strip of low density glass material allows it to float in the water and the photocatalytic material works using the solar radiation.

Apart from silver, copper is a metal widely used in conjunction with TiO 2 for antimicrobial purposes.

The base formula of a photocatalytic paint consists of powder TiO 2 as pigment, some extender pigments such as CaCO 3 and silicates, as well as several organic components working as coalescents, dispersing agents, thickeners, additives and a polymeric aqueous suspension, commonly acrylic resins .

These properties are intrinsic to the TiO 2 -based materials and are enhanced by the doping or impregnation of the surface with some metal nanoparticles that exhibit antibacterial properties.

Several textiles such as cotton, polyester and rayon fibers can be coated or grafted with TiO 2 through techniques as sol-gel, reflux, dip-coating, spin-coating and so on .

Other TiO 2 -based nanostructures, such as titanate nanotubes, have also been used in disinfection processes .

7 Natural history of the virus and shedding of it from an infected person

7.0.0.1 Highlights

7.0.0.2 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 transmission of 2019-nCoV is often spread from person to person through the respiratory droplets generated during coughs or sneezes from an infected person.
2020 Chen et al Pathogenicity and Transmissibility of 2019-nCoV—A Quick Overview and Comparison with Other Emerging Viruses
Microbes and Infection
IV. Other Like SARS-CoV, 2019-nCoV can be passed directly from person to person by respiratory droplets, and emerging evidence suggested that it may also be transmitted through contact and fomites.
2020 Fasina et al Novel coronavirus (2019-nCoV) update: What we know and what is unknown
Asian Pacific Journal of Tropical Medicine
IV. Other Person- to-person transmission and familiar association have also been confirmed .
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 .
When evaluating the ability of an animal to be infected by a virus and serve as a model, viral shedding, clinical disease, and seroconversion should be determined.
2020-02-11 Liu et al Assessing the Tendency of 2019-nCoV (COVID-19) Outbreak in China
medrxiv
IV. Prevalence Study It refers to the average value of how many people an infected person can transmit the virus to through natural transmission without external intervention.

During the transmission of virus, the probability of infection in contact with each person is equal.
2020-02-21 Cheng et al Scabies: Application of the Novel Identify-Isolate-Inform Tool for Detection and Management
West J Emerg Med
IV. Prevalence Study

36 Advising patients and parents of young patients to keep fingernails short and clean can assist with preventing secondary infections.
1, 36 Commonly, transmission occurs from person to person via direct skin contact, including by sexual contact.
2020-02-23 Wang et al Epidemiological characteristics of 1212 COVID-19 patients in Henan, China
medrxiv
IV. Other That is, we cannot know who was the intermediate spreader (unknown person B), and when she/he transmitted the virus from person A to person C.
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 value of R 0 was estimated of 2.30 from reservoir to person, and from person to person and 3.58 from person to person which means that the expected number of secondary infections that result from introducing a single infected individual into an otherwise susceptible population was 3.58.

Our results also showed that the R 0 of SARS-CoV-2 was 2.30 from reservoir to person which was lower than that of person to person.

The simulation results showed that the R 0 of SARS-CoV-2 was 3.58 from person to person.

This means that the transmission route was mainly from person to person rather than from reservoir to person in the early stage of the transmission in Wuhan City.

We simulated the natural history of the infection that the proportion of asymptomatic infection was 50%, and the transmissibility of asymptomatic infection was half of that of symptomatic infection, which were different to those of MERS and SARS.
2020-02-29 Hao et al Infection Dynamics of Coronavirus Disease 2019 (Covid-19) Modeled with the Integration of the Eyring Rate Process Theory and Free Volume Concept
medrxiv
IV. Other After an individual is exposed, the transmission of virus particles from one person to another will make an "exposed" person become "infected".
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).
Currently, person to person transmission from patients with pneumonia or even asymptomatic patients during the incubation period are the main conduits for the spread of the infection .

There are three primary ways to transmit the virus, including close person-to-person contact, aerosol transmission, and transmission by touch .
2020-03-03 Peng et al Transmission routes of 2019-nCoV and controls in dental practice
Int J Oral Sci
IV. Other Since 2019-nCoV can be passed directly from person to person by respiratory droplets, emerging evidence suggested that it may also be transmitted through contact and fomites 43, 48 .
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.
Contact tracing of the SARS-CoV-2 suggests that there is a low R 0 and limited person to person transmission.
2020-03-06 Wan et al Risk estimation and prediction by modeling the transmission of the novel coronavirus (COVID-19) in mainland China excluding Hubei province
medrxiv
IV. Computer Model The estimated values of R 0 were 2.30 from reservoir to person and 3.58 from person to person.
2020-03-08 Zhao et al A mathematical model for estimating the age-specific transmissibility of a novel coronavirus
medrxiv
IV. Computer Model f) The incubation period of exposed person is 1/.

Methods: An age-specific susceptible - exposed - symptomatic - asymptomatic - recovered - seafood market (SEIARW) model was developed based on two suspected transmission routes (from market to person and person to person).

The exposed person will become asymptomatic 119 people after a latent period of 1/'.
2020-03-10 Lauer et al The Incubation Period of Coronavirus Disease 2019 (COVID-19) From Publicly Reported Confirmed Cases: Estimation and Application
Ann Intern Med
III-3. Time Series Analysis

We collected data from 181 cases with confirmed SARS-CoV-2 infection detected outside Hubei province before 24 February 2020 ( Table 1) .
For cases without history of travel to Wuhan but with assumed exposure to an infectious person, the interval of possible SARS-CoV-2 exposure was defined as the maximum possible interval of exposure to the infectious person, including time before the infectious person was symptomatic.
2020-03-10 Broughton et al Rapid Detection of 2019 Novel Coronavirus SARS-CoV-2 Using a CRISPR-based DETECTR Lateral Flow Assay
medrxiv
IV. Other Person-to-person transmission from infected individuals 54 with no or mild symptoms has been reported 4,5 .
2020-03-12 Wu et al The SARS-CoV-2 outbreak: what we know
International Journal of Infectious Diseases
IV. Other Health officials have identified evidence of transmission along a chain of 4 "generations" (a person who originally contracted the virus from a nonhuman source infected someone else, who infected another individual, who then infected another individual), suggesting sustained human-to-human transmission .
2020-03-13 Xing et al Prolonged presence of SARS-CoV-2 in feces of pediatric patients during the convalescent phase
medrxiv
IV. Prevalence Study

Fecal specimens were first collected in two patients (case 1, 1.5-year-old male; and case 2, 5-year-old male) on day 4 after onset of the disease.
Prolonged shedding of SARS-CoV-2 in stools of infected children indicates the potential for the virus to be transmitted through fecal excretion.
2020-03-13 Ghinai et al First known person-to-person transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the USA
The Lancet
IV. Prevalence Study These data suggest that personto-person transmission of COVID-19 might be most likely to occur through unprotected, prolonged exposure to a patient with symptomatic COVID-19.

Interpretation Person-to-person transmission of SARS-CoV-2 occurred between two people with prolonged, unprotected exposure while Patient 1 was symptomatic.
2020-03-13 Kretzschmar et al Effectiveness of isolation and contact tracing for containment and slowing down a COVID-19 epidemic: a modelling study
medrxiv
IV. Other We used a stochastic transmission model in which every person generates novel infections according to a probability distribution that is affected by the incubation period distribution (time from infection to symptoms), distribution of the latent period (time from infection to a person becoming infectious), and overall transmissibility.
2020-03-14 Peña-Otero et al Are we ready for the new coronavirus?
Archivos de Bronconeumología (English Edition)
IV. Other The new virus has probably emerged due to coexistence in the intermediate host of a bat coronavirus and a human one, capable of infecting man and being transmitted from person to person.
2020-03-16 Hemida et al The SARS-CoV-2 outbreak from a one health perspective
One Health
IV. Prevalence Study In the light of the One Health concept, control of this emerging virus requires the reduction of the viral shedding to the environment from the main reservoirs, for animal-person transmission and from humans for person-person transmission .

This approach will reduce the virus load in the contaminated hands from virus droplets, which might touch the nose or mouse of persons.
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 Similar to SARS-CoV and MERS-CoV, the COVID-19 can be transmitted from person to person.
2020-03-19 Zeri et al Contact lens practice in the time of COVID-19
Contact Lens and Anterior Eye
IV. Other The last source is an indirect contact transmission where an infected person touches a surface that is then touched by the second person.
2020-03-24 Wang et al Tracking and forecasting milepost moments of the epidemic in the early-outbreak: framework and applications to the COVID-19
medrxiv
IV. Computer Model found that the virus can be transmitted from person to person and that it has a high interpersonal transmission rate.
2020-03-26 FANG et al Human Mobility Restrictions and the Spread of the Novel Coronavirus (2019-nCoV) in China
medrxiv
IV. Prevalence Study The incubation period of 2019-nCoV is long in comparison with SARS; moreover, the virus can transmit while the person is still asymptomatic, which increases the probability a person with the Novel Coronavirus will travel and unknowingly spread the virus to others.
2020-03-26 Santarpia et al Transmission Potential of SARS-CoV-2 in Viral Shedding Observed at the University of Nebraska Medical Center
medrxiv
IV. Other Surface samples taken in patient care areas for 10 MERS and SARS have shown positive PCR results ; however, experts question the possibility of transmission through contact with surfaces that have been contaminated by an infected person, either by the direct contact of the infected person or the settling of virus-laden particles onto the surface .
2020-03-27 Sanchez-Taltavull et al Modelling strategies to organize healthcare workforce during pandemics: application to COVID-19
medrxiv
IV. Other In the classical Susceptible Infectious Recovered (SIR) model, a susceptible patient (S) can be infected (I), and the infected person can recover (R), without the risk of reinfection.

is the infection rate when the person is infected by a co-worker, is the activation rate of the sickness, in which a patient in a latent state starts presenting symptoms.
2020-03-28 Xing et al Prolonged Viral Shedding in Feces of Pediatric Patients with Coronavirus Disease 2019
Journal of Microbiology, Immunology and Infection
IV. Other Persistent shedding of SARS-CoV-2 in stools of infected children raises the possibility that the virus might be transmitted through contaminated fomites.
2020-03-29 Li et al Anesthesia Management and Perioperative Infection Control in Patients with the Novel Coronavirus
Journal of Cardiothoracic and Vascular Anesthesia
IV. Other Transmission can occur from asymptomatic infected individuals.
2020-03-30 Thomas et al Physiotherapy management for COVID-19 in the acute hospital setting: clinical practice recommendations
Journal of Physiotherapy
IV. Prevalence Study

12 In adult patients with COVID-19 and severe ARDS, prone ventilation for 12 to 16 hours per day is recommended.
The virus is transmitted from person to person through respiratory secretions.
2020-03-30 Zhou et al Forecasting the Worldwide Spread of COVID-19 based on Logistic Model and SEIR Model
medrxiv
IV. Computer Model The SARS-CoV-2 virus spreads mainly from person-to-person through between people who are in close contact with one another, and through respiratory droplets produced when an infected person coughs or sneezes 2 .
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 in which s is the transmissibility (i.e., probability of infection given contact between a susceptible and infected individual), c À is the average rate of contact between susceptible and infected individuals, and d is the duration of infectiousness.
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.
The virus can be transmitted continuously from person to person; and there is evidence that the disease is prevalent worldwide.
2020-03-31 Bukhari et al The diagnostic evaluation of Convolutional Neural Network (CNN) for the assessment of chest X-ray of patients infected with COVID-19
medrxiv
IV. Other The mode of transmission is person to person via respiratory droplets and median incubation period is four days .
2020-04-01 Zhu et al Transmission Dynamics and Control Methodology of COVID-19: a Modeling Study
medrxiv
III-3. Time Series Analysis

3) , there are no more than 5 new cases every day from Dec 8 to Dec 28.
Infectious period: period during which an infected person can transmit a pathogen to a susceptible ;
2020-04-01 Shayak et al Transmission Dynamics of COVID-19 and Impact on Public Health Policy
medrxiv
IV. Computer Model From our viewpoint, a dead person is as capable of transmitting disease as a person recovered in quarantine, so w can take care of both of them.
2020-05-31 Yang et al Patients with respiratory symptoms are at greater risk of COVID-19 transmission
Respiratory Medicine
IV. Other Second, the duration of virus shedding from nasopharynx was longer.
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 The virus is transmitted mainly through infected respiratory droplets and on close contact with the infected person.

8 Implementation of diagnostics and products to improve clinical processes

8.0.0.1 Highlights

8.0.0.2 Articles

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

Of the total of 570 unique studies on 2019-nCoV, SARS CoV or MERS-CoV vaccines screened, only four were eventually included in the review.
Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases.

Rapid diagnostics, vaccines and therapeutics are important interventions for the management of the 2019 novel coronavirus (2019-nCoV) outbreak.
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 ZHAO et al Clinical characteristics of 28 patients with novel coronavirus pneumonia
Chinese Journal of Infectious Diseases
IV. Other The clinical manifestations, epidemiological history, laboratory tests, imaging examinations and treatments of patients were analyzed retrospectively.
2020-01-30 Gostic et al Estimated effectiveness of traveller screening to prevent international spread of 2019 novel coronavirus (2019-nCoV)
medrxiv
IV. Prevalence Study

Using each parameter set, we 162 simulated screening outcomes for a population of 100 infected individuals.
Our results have several implications for the design and implementation of control measures.
2020-02-02 Lei et al Potent neutralization of 2019 novel coronavirus by recombinant ACE2-Ig
biorxiv
IV. Other These ACE2 fusion proteins could be also used for diagnosis and as research reagents in the development of vaccines and inhibitors.
2020-02-03 Pharma mobilizes to combat the coronavirus
C&EN Global Enterprise
IV. Other With infections steadily rising, major drug companies are mobilizing to develop diagnostics, vaccines, and possible treatments for the virus, 2019-nCoV.
2020-02-05 Zhou et al Network-based Drug Repurposing for Human Coronavirus
medrxiv
IV. Other Our approach can minimize the translational gap between preclinical testing results and clinical outcomes, which is a significant problem in the rapid development of efficient treatment strategies for the emerging 2019-nCoV outbreak.
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.
2020-02-14 Di Marco et al Opinion: Sustainable development must account for pandemic risk
Proceedings of the National Academy of Sciences
IV. Prevalence Study Although technologies to monitor EID risk are advancing rapidly, policies to deal with such risk are largely reactive, focusing on outbreak investigation and control and on development of vaccines and therapeutic drugs targeting known pathogens.
2020-02-19 Heaton et al Frontiers in antiviral therapy and immunotherapy
Clin Transl Immunology
IV. Prevalence Study 4 I anticipate international efforts in these areas over the coming decade will enable the tapping of useful new biological functions and processes, methods for controlling infection, and the deployment of symbiotic or subclinical viruses in new therapies and biotechnologies that are so crucially needed.
2020-02-19 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.
2020-02-19 Kooraki et al Coronavirus (COVID-19) Outbreak: What the Department of Radiology Should Know
Journal of the American College of Radiology
IV. Other Although further investigations on the clinical and radiologic aspects of the COVID-19 are ongoing, imaging will continue to be a crucial component in patient management.
2020-02-22 Zhang et al Inactivating porcine coronavirus before nuclei acid isolation with the temperature higher than 56 °C damages its genome integrity seriously
biorxiv
IV. Other Nucleic acid detection of 2019-nCoV is one of the key indicators for clinical diagnosis.
2020-02-24 Shi et al Radiological findings from 81 patients with COVID-19 pneumonia in Wuhan, China: a descriptive study
The Lancet Infectious Diseases
IV. Prevalence Study

Four patterns of evolution throughout the series of CT scans were observed among these 57 patients: initial progression to peak level, followed by radiographic improvement (type 1), seen in 26 (46%) patients (figure 6), of whom 24 (92%) patients were discharged from hospital (median stay 25 days [IQR 20-27]); radiographic deterioration (type 2), seen in 18 (32%) patients (figure 5), of whom two (11%) died (patients 2 and 3); radiographic improvement (type 3), seen in eight (14%) patients, of whom five (63%) were discharged from hospital (median stay 19 days ; and unchanged radiographic appearance (type 4), seen in five (9%) patients, all of whom were still in hospital at the cutoff date (Feb 8).
Combining assessment of imaging features with clinical and laboratory findings could facilitate early diagnosis of COVID-19 pneumonia.
2020-02-25 Han et al Coronavirus 2019-nCoV: A brief perspective from the front line
Journal of Infection
II. Randomized Controlled Trial

24 The most common symptoms are fever (87.9%), fatigue (69.6%), dry cough (67.7%) and myalgia (34.8%), and these are accompanied with rhinobyon, rhinorrhoea, pharyngalgia and diarrhea in few patients 24 ( Table 1 ) of these patients were characterized by dyspnea and hypoxemia, which can rapidly progress to acute respiratory distress syndrome (ARDS), septic shock, metabolic acidosis, coagulation dysfunction, and even multiple organ dysfunction syndrome (MODS) in one week.
18, 19 The diagnosis is based on the epidemiological risks, clinical features and laboratory tests.
2020-02-27 Fan et al Clinical Features of COVID-19 Related Liver Damage
medrxiv
IV. Other A total of 148 cases were analyzed for clinical features, laboratory parameters (including liver function tests), medications and the length of stay.
2020-02-28 Jernigan et al Update: Public Health Response to the Coronavirus Disease 2019 Outbreak - United States, February 24, 2020
MMWR. Morbidity and Mortality Weekly Report
IV. Other Although these measures might not prevent 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 state and local health departments, health care systems, businesses, educational organizations, and the general public in the event that widespread transmission occurs; and 3) better characterize COVID-19 to guide public health recommendations and the development and deployment of medical countermeasures, including diagnostics, therapeutics, and vaccines.
2020-02-29 Wilson et al What goes on board aircraft? Passengers include Aedes, Anopheles, 2019-nCoV, dengue, Salmonella, Zika, et al
Travel Medicine and Infectious Disease
IV. Other Diagnostics have been developed and work on therapeutics and vaccines is underway.
2020-03-02 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).
However, because of a shortage of diagnostic reagents for SARS-CoV-2 detection, different guidelines or programs emphasized comprehensive analysis based on epidemiological history, clinical manifestations and imaging examinations in diagnosis.
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.
59 The development of nanobased formulations is another useful strategy for improving the pharmacological and pharmacokinetic properties of niclosamide and maximizing its therapeutic potential for clinical applications.
2020-03-03 Qi et al Machine learning-based CT radiomics model for predicting hospital stay in patients with pneumonia associated with SARS-CoV-2 infection: A multicenter study
medrxiv
III-2. Cross Sectional Control

Therefore, 31 patients with 72 lesion segments were included in the final analysis.
All imaging processes were blinded to clinical data.
2020-03-04 Memish et al Middle East respiratory syndrome
The Lancet
II. Randomized Controlled Trial

A retrospective study of 136 patients with MERS found that macrolide therapy resulted in no reduction in mortality or faster MERS-CoV RNA clearance compared with those who were not treated with macrolides.
Advances in technology, vaccine platforms, clinical trial designs, and bioinformatics are supporting MERS-CoV vaccine development (appendix .
2020-03-10 O’Connell et al The impact of point-of-care testing for influenza A and B on patient flow and management in a medical assessment unit of a general hospital
BMC Res Notes
III-3. Time Series Analysis

RESULTS: The results of the correlation study with a cohort of 54 patients revealed the Abbott ID NOW POCT has 92% sensitivity for the detection of Influenza A, while specificity was 100% for both Influenza A and B.
Turnaround times of Laboratory based screening tests for the diagnosis of influenza may have an impact on the implementation of infection control measures and treatment.
2020-03-12 Liu et al Research and Development on Therapeutic Agents and Vaccines for COVID-19 and Related Human Coronavirus Diseases
ACS Cent Sci
IV. Other 55 Additional collaboration in the areas of antiviral discovery processes and clinical trial performance will enhance patients' access to drug candidates with improved therapeutic potential and ideally reduce the amount of time required to bring these drugs to market.

Thus, for both diseases, more patents have been devoted to the development of therapeutic agents as opposed to diagnostic methods and vaccines.
2020-03-12 Zhang et al Fecal specimen diagnosis 2019 Novel Coronavirus-Infected Pneumonia
Journal of Medical Virology
IV. Other These results may help to understand the clinical diagnosis and the changes of clinical parameters of COVID-19.
2020-03-13 Qiao et al What are the risks of COVID-19 infection in pregnant women?
The Lancet
IV. Other 4 The meeting covered the topics of diagnostics, vaccines, and therapeutics for COVID19, alongside questions of how to best integrate social science into the response and protection of healthcare workers from infection.
2020-03-16 Zhou et al Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2
Cell Discov
IV. Other Our approach can minimize the translational gap between preclinical testing results and clinical outcomes, which is a significant problem in the rapid development of efficient treatment strategies for the emerging 2019-nCoV/SARS-CoV-2 outbreak.
2020-03-17 Bedford et al COVID-19: towards controlling of a pandemic
The Lancet
IV. Other Comparative analysis of different quarantine strategies and contexts for their effectiveness and social acceptability Enhance and develop an ethical framework for outbreak response that includes better equity for access to interventions for all countries Promote the development of point-of-care diagnostic tests Determine the best ways to apply knowledge about infection prevention and control in health-care settings in resource-constrained countries (including identification of optimal personal protective equipment) and in the broader community, specifically to understand behaviour among different vulnerable groups Support standardised, best evidence-based approach for clinical management and better outcomes and implement randomised, controlled trials for therapeutics and vaccines as promising agents emerge Validation of existing serological tests, including those that have been developed by commercial entities, and establishment of biobanks and serum panels of well characterised COVID-19 sera to support such efforts Complete work on animal models for vaccine and therapeutic research and development include some identified by the global community and by the Research and Development Blueprint Scientific Advisory Group.
2020-03-18 Jin et al Core Outcome Set for Clinical Trials on Coronavirus Disease 2019 (COS-COVID)
Engineering
IV. Prevalence Study

The consensus meeting was held on 24 February 2020, and involved 20 participants.
The outcomes obtained after data cleaning were assigned to seven different categories: clinical symptoms, physical and chemical detection, viral nucleic acid detection, quality of life, significant events, disease process, and safety indexes.

Researchers are encouraged to apply the COS-COVID for the evaluation of different interventions (either pharmaceutical or non-pharmaceutical therapies) in clinical trials on COVID-19.
2020-03-20 Zhao et al Chinese Public Attention to COVID-19 Epidemic: Based on Social Media
medrxiv
IV. Prevalence Study To fight against COVID-19 and promote the prevention and control of the epidemic, researchers have recently made efforts in various aspects; their research involves epidemiological research 5, 6, 7 , diagnostic methods of the novel coronavirus 8, 9, 10, 11 , clinical characteristics of the disease 12, 13, 14, 15, 16 , characteristics of disease transmission 17, 18, 19 , development of candidate therapies 20, 21, 22 , the identification of animal hosts 23, 24, 25, 26 , etc.
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.
Findings suggest that the development of rapid diagnostic tests could help bring the epidemic more rapidly under control.
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 Moreover, an improved understanding of ARDS, including rapid identification of ARDS phenotypes, could enable more precise use of therapeutics such as ECMO during outbreaks.
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.
Clinical signs, disease onset, laboratory tests (including rRT-PCR and CT), treatments, co-morbidities, complications, and outcome data were collected from EMR.
2020-03-26 Lourenco et al Fundamental principles of epidemic spread highlight the immediate need for large-scale serological surveys to assess the stage of the SARS-CoV-2 epidemic
medrxiv
IV. Other Urgent development and assessment of such tests should be followed by rapid implementation at scale to provide real-time data.
2020-03-26 Zheng et al Recommendations and guidance for providing pharmaceutical care services during COVID-19 pandemic: A China perspective
Research in Social and Administrative Pharmacy
IV. Other Medications and COVID-19 131 preventative products are essential for community patients' chronic disease management and 132 control of the pandemic.
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) .
Combining assessment of imaging features with clinical and laboratory findings could facilitate early diagnosis of COVID-19 pneumonia .
2020-03-30 Fan et al Medical treatment of 55 patients with COVID-19 from seven cities in northeast China who fully recovered: a single-center, retrospective, observational study
medrxiv
IV. Other Demographic information, symptoms, laboratory indicators, treatment processes, and clinical outcomes were collected.
2020-03-30 Dong et al Understand Research Hotspots Surrounding COVID-19 and Other Coronavirus Infections Using Topic Modeling
medrxiv
IV. Computer Model The results also indicate that studies in diagnostics, therapeutics, vaccines, viral genomics, and pathogenesis are urgently needed to minimize the impact of the COVID-19 outbreak.

We found that topics of clinical characterization, epidemiology, and virus transmission are hotspots for COVID-19 at present, while research on pathogenesis, therapeutics, virus diagnostics, vaccines and viral genomics are urgently needed.
2020-03-30 Xu et al Analysis and Prediction of False Negative Results for SARS-CoV-2 Detection with Pharyngeal Swab Specimen in COVID-19 Patients: A Retrospective Study
medrxiv
III-2. Retrospective Cohort

In order to implement the out-of-sample prediction, 1,324 patients were randomly divided into training (1,059 cases) and validation samples (265 cases Table 2) .
Conclusion: Testing outcome and positive window of SARS-CoV-2 detection for COVID-19 patients were associated with CT imaging results, blood routine tests, and clinical symptoms.
2020-03-31 Singer et al What is ahead for health policy and technology in the 2020s?
Health Policy and Technology
IV. Other Developments in diagnostics are likely to include more advanced imaging, increasing availability of point of care testing (biochemical and genomic), and the further extension of genomics into clinical practice, potentially before and around the time of birth.
2020-03-31 Bukhari et al The diagnostic evaluation of Convolutional Neural Network (CNN) for the assessment of chest X-ray of patients infected with COVID-19
medrxiv
IV. Other The organization and collection of the data of patient of COVID -19 from different countries of world may be planned and subjected to research for further improvement in the diagnostic modalities.
2020-03-31 Lai et al Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): The epidemic and the challenges
International Journal of Antimicrobial Agents
IV. Other All effort s are being made to slow the spread of the illness in order to provide time to better prepare healthcare systems and the general public, to better characterise COVID-19 to guide public-health recommendations, and to develop timely diagnostics, therapeutics and vaccines .
2020-04-15 Musazzi et al New regulatory strategies to manage medicines shortages in Europe
International Journal of Pharmaceutics
IV. Prevalence Study The application of a modern pharmaceutical quality system promotes a systematic and continuous evaluation, understanding and refining of the formulation and the manufacturing process by the identification of the critical material attributes and process parameters and by the determination of the existing functional relationship between such factors and the responses (i.e.
2020-07-31 Artika et al Pathogenic viruses: Molecular detection and characterization
Infection, Genetics and Evolution
IV. Prevalence Study Further molecular characterization to better understand these viruses is required for the development of diagnostic tests and countermeasures.

9 Disease models, including animal models for infection, disease and transmission

9.0.0.1 Highlights

9.0.0.2 Articles

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

The novel CoV (2019-nCoV) was isolated from a single patient and subsequently verified in 16 additional patients .
For the MERS-CoV outbreak, smoking, hypertension, diabetes, cardiovascular disease, and/or other chronic illnesses have been present in the majority of deaths and correspond to findings in animal models .
2020 Wang et al Phase-adjusted estimation of the number of Coronavirus Disease 2019 cases in Wuhan, China
Cell Discovery
IV. Computer Model SEIR model is a prediction model forecasting the number of infections in the future.
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 Rocklöv et al COVID-19 outbreak on the Diamond Princess cruise ship: estimating the epidemic potential and effectiveness of public health countermeasures
Journal of Travel Medicine
IV. Other Models with interventions were calibrated to reports of total infection occurrence, while models simulating the counterfactual scenarios where left with the naïve parameter settings (no countermeasures).
2020-01-28 Shao et al Beware of asymptomatic transmission: Study on 2019-nCoV prevention and control measures based on extended SEIR model
biorxiv
IV. Other The SI model is a basic model, and other warehouse models are derived models built according .
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.
2020-02-07 Tang et al Estimation of the Transmission Risk of the 2019-nCoV and Its Implication for Public Health Interventions
J Clin Med
III-3. Time Series Analysis

To obtain the relatively reliable data, we used the exponential growth law to deduce the number of reported cases per day from 31 December 2019 to 10 January 2020 (called dataRev2) or from 10 to 15 January 2020 (called dataRev1) based on the 41 cases on that date, as shown in Figure 1A .
A deterministic compartmental model was devised based on the clinical progression of the disease, epidemiological status of the individuals, and intervention measures.
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 Further research is warranted on establishing animal models for the current 2019-nCoV unrevealing viral events of replication, transmission, and pathogenesis in humans.
2020-02-12 Xiong et al Simulating the infected population and spread trend of 2019-nCov under different policy by EIR model
medrxiv
IV. Computer Model SEIR model has been widely used for modeling infectious diseases.

Furthermore, the asymptomatic infection and transmission characters should be considered in the transmission model.
2020-02-18 Zhou et al Evaluating new evidence in the early dynamics of the novel coronavirus COVID-19 outbreak in Wuhan, China with real time domestic traffic and potential asymptomatic transmissions
medrxiv
IV. Prevalence Study

The infection status of a total of 2,666 individuals that successfully evacuated from Wuhan between Jan. 29 and Feb. 2, 2020 were used in this study.
Both the SEIR and SEAIR models were fitted to the infection data, and SEIR model has better performance than the SEAIR model based on WAIC (Table 1) .
2020-02-18 Peng et al Epidemic analysis of COVID-19 in China by dynamical modeling
medrxiv
IV. Computer Model As the dynamical model can reach interpretable conclusions on the outbreak, a cascade of SEIR models are developed to simulate the processes of transmission from infection source, hosts, reservoir to human 30 .
2020-02-19 Klepac et al Contacts in context: large-scale setting-specific social mixing matrices from the BBC Pandemic project
medrxiv
IV. Prevalence Study

The main dataset used in this study consisted of 36,155 participants reporting 378,559 contacts.
The matrices we present can be directly incorporated into mathematical models of transmission to predict the dynamics of infection with and between key demographic groups and settings .
2020-02-20 Shao et al The reproductive number R0 of COVID-19 based on estimate of a statistical time delay dynamical system
medrxiv
III-3. Time Series Analysis Our group has developed some models for the growth rate of COVID-19 (TDD-NCP models and Fudan-CCDC models ) after Jin suggested to use the time delay model to fit the real data .
2020-02-20 Ziff et al Fractal kinetics of COVID-19 pandemic
medrxiv
III-3. Time Series Analysis

March 3 with a total of 83,000 cases, which so far has been well born out.
Other approaches use rate equations such as the SEIR and logistical models.

The classic epidemiological approach in studying this growth is to quantify a reproduction number and infection time, and this is the approach followed by many studies on the epidemiology of this disease.
2020-02-23 Li et al A Note on COVID-19 Diagnosis Number Prediction Model in China
medrxiv
IV. Computer Model Common models of infectious disease included meta-population models, individual-based network models, and simple SIR-type models that incorporate the effects of reactive behavior changes or inhomogeneous mixing 16 .
2020-02-23 Tang et al Novel Coronavirus 2019 (Covid-19) epidemic scale estimation: topological network-based infection dynamic model
medrxiv
IV. Other Conclusions: Using dynamic network models and dynamic parameters for different time periods is an effective way of infection scale modeling.
2020-02-26 Rothan et al The epidemiology and pathogenesis of coronavirus disease (COVID-19) outbreak
Journal of Autoimmunity
IV. Other Epidemiological changes in COVID-19 infection should be monitored taking into account potential routes of transmission and subclinical infections, in addition to the adaptation, evolution, and virus spread among humans and possible intermediate animals and reservoirs.
2020-03-06 Aleta et al Evaluation of the potential incidence of COVID-19 and effectiveness of contention measures in Spain: a data-driven approach
medrxiv
IV. Other Furthermore, metapopulation models are composed by two types of dynamics: the disease dynamics governed by the chosen compartmental model, SEIR in our case, and the mobility of the individuals across the subpopulations that make up the whole metapopulation system.

Stochastic SEIR-metapopulation models are routinely used to study the temporal and spatial transmission of diseases like the COVID-19.

The dynamics of the disease is governed by an SEIR compartmental model.
2020-03-15 Lo et al Evaluation of SARS-CoV-2 RNA shedding in clinical specimens and clinical characteristics of 10 patients with COVID-19 in Macau
Int J Biol Sci
IV. Other The MuLBSTA score , which is a model proposed in 2019 for predicting mortality in viral pneumonia and consists of six indices including multi-lobular infiltration, lymphopenia, bacterial co-infection, smoking history, hypertension and age, was calculated.
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 As the models are strongly featured by cities, we name the two types of models as Shanghai model and Wuhan model.
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 Animal model is an important tool in the study of infectious diseases.
2020-03-20 Russo et al Tracing DAY-ZERO and Forecasting the Fade out of the COVID-19 Outbreak in Lombardy, Italy: A Compartmental Modelling and Numerical Optimization Approach.
medrxiv
IV. Computer Model ., with the The parameters of the model are:

The first models mainly focused on the estimation of the basic reproduction number R 0 using dynamic mechanistic 35 mathematical models ( ), but also simple exponential growth models (see e.g.
2020-03-24 Roques et al Mechanistic-statistical SIR modelling for early estimation of the actual number of cases and mortality rate from COVID-19
medrxiv
IV. Other SIR models are the most standard ODE-based epidemiological models.
2020-03-25 Ren et al EPIDEMIOLOGICAL AND CLINICAL CHARACTERISTICS OF HEART TRANSPLANT RECIPIENTS DURING THE 2019 CORONAVIRUS OUTBREAK IN WUHAN, CHINA: A DESCRIPTIVE SURVEY REPORT
The Journal of Heart and Lung Transplantation
IV. Prevalence Study

There are 63 men and 24 women, average age is 51±12 years, 80 (92.0%) of them lived together with relatives, the number of relatives ranged from 1 to 8.
For the MERS-CoV outbreak, smoking, hypertension, diabetes, cardiovascular disease, and/or other chronic illnesses were present in the majority of deaths and correspond to findings in animal models.
2020-03-25 Qiang et al Using the spike protein feature to predict infection risk and monitor the evolutionary dynamic of coronavirus
Infect Dis Poverty
IV. Prevalence Study

The features of the 507 human samples in our dataset were used to show the patterns with the multidimensional scaling method.
In this study, the RF algorithm is used to construct models and make predictions for the crossspecies transmission of coronavirus.
2020-03-27 Sanchez-Taltavull et al Modelling strategies to organize healthcare workforce during pandemics: application to COVID-19
medrxiv
IV. Other Different types of mathematical models have been used to study epidemiology.

Furthermore, SEIR models have applied in this context by including persons in quarantine (QSEIR model) .
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) .
Different models based on the clinical progression of the disease were devised to estimate the basic reproductive number.
2020-03-30 Liu et al Government Responses Matter: Predicting Covid-19 cases in US under an empirical Bayesian time series framework
medrxiv
III-3. Time Series Analysis

These countries have more days from time zero than US, where time zero is defined as first day with 100 or more (100+) cases as a heuristic but widely used choice 1 .
Models used in these forecasting are mainly the susceptible-infected-removed (SIR) models and its variants .
2020-03-30 Burns et al Symptom-Based Isolation Policies: Evidence from a Mathematical Model of Outbreaks of Influenza and COVID-19
medrxiv
III-3. Time Series Analysis This class of SEIR models has been used extensively to model influenza and COVID-19 (e.g.

The cohort structure and other parameters are adjustable to model outbreaks in different settings and by different pathogens.
2020-03-30 Zhou et al Forecasting the Worldwide Spread of COVID-19 based on Logistic Model and SEIR Model
medrxiv
IV. Computer Model On the other hand, SEIR model introduces more variables and factors by considering the interaction and association of multiple groups of people, it is more reasonable than the logistic model as it follows the rules of infectious disease development, but the predict results vary greatly when considering different interventions and settings.

Logistic growth model, basic SEIR model and adjusted SEIR model were adopted for predicting.
2020-03-30 Buhat et al A mathematical model of COVID-19 transmission between frontliners and the general public
medrxiv
IV. Computer Model The model cannot be immediately utilized to make predictions on the spread of COVID-19 but it provides us insights on the transmission of a disease between two populations with different characteristics in terms of factors affecting the spread of a disease, such as the basic reproduction number and susceptibility rate.
2020-03-31 Pais et al Predicting the evolution and control of COVID-19 pandemic in Portugal.
medrxiv
IV. Computer Model Compartmental models such as SIR models (Susceptible, Infected and Resistant) are deterministic approaches that have been successful in describing the dynamics of virus infection in populations, including COVID-19 .
2020-03-31 Wittkowski et al The first three months of the COVID-19 epidemic: Epidemiological evidence for two separate strains of SARS-CoV-2 viruses spreading and implications for prevention strategies
medrxiv
IV. Prevalence Study This data is consistent with the results from the SIR model (see Epidemiological Models).
2020-03-31 Sun et al Atlas of ACE2 gene expression in mammals reveals novel insights in transmission of SARS-Cov-2
biorxiv
IV. Other Thus, both observations argue against using mice as the optimal animal model for studying coronavirus related diseases.
2020-03-31 Patil et al Current State and Predicting Future Scenario of Highly Infected Nations for COVID-19 Pandemic
medrxiv
IV. Other Many prediction models are being proposed for the current pandemic namely SIRD model , GLEaM , Mechanistic-statistical SIR , SEIRUS model .
2020-03-31 Zahiri et al Prediction of Peak and Termination of Novel Coronavirus Covid-19 Epidemic in Iran
medrxiv
IV. Computer Model More complicated mathematical models were obtained as the susceptible-exposedinfectious-recovered (SEIR) model.
2020-04-01 Shayak et al Transmission Dynamics of COVID-19 and Impact on Public Health Policy
medrxiv
IV. Computer Model The models in this paper are based on individual-based stochastic influenza models .
2020-04-01 Garcia-Iglesias et al Early behavior of Madrid Covid-19 disease outbreak: A mathematical model
medrxiv
IV. Computer Model Material and Methods: A simulated mathematical model was built, based on a SIR epidemiological model and the reported characteristics of Wuhan Covid-19 disease outbreak.
2020-04-01 Zhu et al Transmission Dynamics and Control Methodology of COVID-19: a Modeling Study
medrxiv
III-3. Time Series Analysis

3) , there are no more than 5 new cases every day from Dec 8 to Dec 28.
Such an epidemic model is known as the SEIR model.
2020-04-01 Jia et al Modelling COVID-19 transmission: from data to intervention
The Lancet Infectious Diseases
IV. Prevalence Study Mathematical models have been used to simulate scenarios and predict evolution of infectious diseases since the early 20th century.
2020-12-31 Roda et al Why is it difficult to accurately predict the COVID-19 epidemic?
Infectious Disease Modelling
IV. Computer Model When a large number of models are under consideration or the models are not nested, the model selection rules are different.

In modeling terms, given the confirmed-case data, there is a linkage between the model parameter r and the transmission rate b, and potentially also with other model parameters.

10 Tools and studies to monitor phenotypic change and potential adaptation of the virus

10.0.0.1 Highlights

10.0.0.2 Articles

Date Authors Title LOE(?) & Sample Matches
2020 Chen et al Pathogenicity and Transmissibility of 2019-nCoV—A Quick Overview and Comparison with Other Emerging Viruses
Microbes and Infection
IV. Other Related information can help to reveal how the virus is evolving and adapting to new conditions and whether the outbreak has the potential to persist.
2020-01-30 Ramaiah et al Insights into Cross-species Evolution of Novel Human Coronavirus 2019-nCoV and Defining Immune Determinants for Vaccine Development
biorxiv
IV. Prevalence Study Our findings emphasize the requirement for continuous surveillance of CoV strains in live animal markets to better understand the viral adaptation to human host and to develop practical solutions to prevent the emergence of novel pathogenic CoV strains.

Occasionally, the animal CoVs can acquire genetic mutations by errors during genome replication or recombination mechanism, which can further expand their tropism to humans.
2020-01-31 Koenig et al 2019-nCoV: The Identify-Isolate-Inform (3I) Tool Applied to a Novel Emerging Coronavirus
West J Emerg Med
IV. Prevalence Study

One preliminary, small-scale study of 41 patients in Wuhan China, reported 6 deaths (15% mortality) with a median age of 49.0 years.
Investigators adapted the "Identify, Isolate, Inform" (3I) Tool for use in suspected cases of 2019-nCoV.

This adaptation of the Identify-Isolate-Inform Tool serves as a resource for healthcare workers who need to make clear, rapid assessments when confronted with potential patients.
2020-02-05 Boldog et al Risk assessment of novel coronavirus COVID-19 outbreaks outside China
medrxiv
IV. Other As new measures are implemented, or there is a change in travel patterns, these parameters may change in time as well.
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 It is necessary to obtain much more clinically isolated viruses with time and geographical variety to assess the extent of the virus mutations, and also whether these mutations indicate adaptability to human hosts .
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 These studies analyze diverse environmental specimens and assemble genomic sequence of viruses, which circulate in nature and have never been characterized on the phenotypic level.

To connect this development to health care, diagnostic tools that target the entire species should complement existing tools that detect individual pathogenic variants.
2020-02-11 Sarkar et al The Essential Facts of Wuhan Novel Coronavirus Outbreak in China and Epitope-based Vaccine Designing against COVID-19
biorxiv
IV. Other These tools are used to dissect the genome and genetic makeup of a pathogen for developing a potential vaccine.
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.
6 In the study, the data of 61 patients with 2019-nCoV pneumonia were analyzed, the baseline characteristics of patients in the mild and severe groups were described and compared, and the dynamic changes of laboratory indexes and imaging were demonstrated.
2020-02-14 Kiselev et al Current Trends in Diagnostics of Viral Infections of Unknown Etiology
Viruses
IV. Prevalence Study

They used 42 virus-positive controls from pediatric patients and 67 unidentified samples .
Further applications of this method extend to transcriptomics and proteomics, allowing for a deeper insight into several aspects of pathogens, such as drug resistance, adaptation mechanisms and vast communication networks between species.
2020-02-20 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.
2020-02-21 Heymann et al Data sharing and outbreaks: best practice exemplified
The Lancet
IV. Other This information includes routes of transmission and transmissibility, the natural history of infection in humans, the populations at risk, the successful clinical practices that are being used to manage patients, the laboratory information needed to diagnose patients, and the genetic sequence information used to assess viral stability.
2020-02-24 Shi et al Radiological findings from 81 patients with COVID-19 pneumonia in Wuhan, China: a descriptive study
The Lancet Infectious Diseases
IV. Prevalence Study

Four patterns of evolution throughout the series of CT scans were observed among these 57 patients: initial progression to peak level, followed by radiographic improvement (type 1), seen in 26 (46%) patients (figure 6), of whom 24 (92%) patients were discharged from hospital (median stay 25 days [IQR 20-27]); radiographic deterioration (type 2), seen in 18 (32%) patients (figure 5), of whom two (11%) died (patients 2 and 3); radiographic improvement (type 3), seen in eight (14%) patients, of whom five (63%) were discharged from hospital (median stay 19 days ; and unchanged radiographic appearance (type 4), seen in five (9%) patients, all of whom were still in hospital at the cutoff date (Feb 8).
Serial CT imaging of patients could help to con tinuously monitor disease changes.
2020-02-25 Li et al Clinical characteristics of 25 death cases infected with COVID-19 pneumonia: a retrospective review of medical records in a single medical center, Wuhan, China
medrxiv
III-2. Cross Sectional Control

In the patients' last examination before death, white blood cell and neutrophil counts were elevated in 17 patients (17/25, 68%) and 18 patients (18/25, 72%), lymphocyte counts were decreased in 22 patients (22/25, 88%).
In order to screen out biochemical indicators that are meaningful for the diagnosis of disease progression, we consulted the laboratory test results of all the dead patients, among which 16 patients had repeated measurements.
2020-03-01 Han et al A Diabetic Patient With 2019-nCoV Infection Who Recovered and Was Discharged From Hospital
Journal of Thoracic Imaging
IV. Other Computed tomography scans of patients helped monitor the changes continuously, which could timely provide the information of the evolution of the disease or therapeutic effect to clinicians.
2020-03-02 Li et al The within-host viral kinetics of SARS-CoV-2
biorxiv
IV. Other The PRCC method is used to analyze the sensitivities of model parameters and the drug effects on virus growth are also implemented to analyze the model.
2020-03-03 Rello et al Coronavirus Disease 2019 (COVID-19): A critical care perspective beyond China
Anaesthesia Critical Care & Pain Medicine
III-3. Time Series Analysis

Among 37 ventilated patients in the Wuhan cohort , only 4 (10.8%) were alive and free of mechanical ventilation 28-days after ICU admission.
Serial CT scans have been used to monitor evolution.
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).
Such changes thus have the potential to lead to variants that have high pathogenic potential when transmitted to humans .
2020-03-05 Johnson et al Potential scenarios for the progression of a COVID-19 epidemic in the European Union and the European Economic Area, March 2020
Euro Surveill
IV. Prevalence Study The potential adaptation of influenza surveillance systems should be evaluated.
2020-03-06 Cao et al Clinical Features of Patients Infected with the 2019 Novel Coronavirus (COVID-19) in Shanghai, China
medrxiv
IV. Prevalence Study

Results: Of 198 patients, the median duration from disease onset to hospital admission was 4 days.
To determine the major clinical features that appeared during COVID-19 progression, the dynamic changes in 11 clinical laboratory parameters, including haematological and biochemical parameters, were tracked from day 1 to day 15 after the onset of the disease at 2-day intervals (Fig.
2020-03-11 Grewelle et al Larger viral genome size facilitates emergence of zoonotic diseases
biorxiv
IV. Other The capacity to produce genetic variability is a defining feature among viruses that are able to jump to new host species.

Even in the absence of phenotypic plasticity conferred by large genomes, viruses with large genomes have high potential to generate variability that promotes cross-species transmission events.

These two characteristics provide ample opportunity for Coronaviruses to evolve new traits and establish themselves in new host species.
2020-03-12 Zhang et al Fecal specimen diagnosis 2019 Novel Coronavirus-Infected Pneumonia
Journal of Medical Virology
IV. Other These results may help to understand the clinical diagnosis and the changes of clinical parameters of COVID-19.
2020-03-12 Liu et al Patients of COVID-19 may benefit from sustained lopinavir-combined regimen and the increase of eosinophil may predict the outcome of COVID-19 progression
International Journal of Infectious Diseases
IV. Other Abstract Objectives To explore the epidemiological information, clinical characteristics, therapeutic outcomes and temporal progression of laboratory findings in 2019-coronavirus disease (COVID-19) patients exposed to lopinavir.
2020-03-13 Xi et al Virus strain of a mild COVID-19 patient in Hangzhou representing a new trend in SARS-CoV-2 evolution related to Furin cleavage site
medrxiv
IV. Other Viruses frequently undergo mutation and adjust its RSCU under evolutionary selection pressure to adapt to the host, facilitating better replication and dissemination 41 .
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.
More pathogenic CoV strains may be generated by recombination, leading to the acquirement of novel proteins or protein features for host adaptation.
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.
2020-03-16 Fu et al Influence factors of death risk among COVID-19 patients in Wuhan, China: a hospital-based case-cohort study
medrxiv
III-2. Cross Sectional Control

The aim of this study was to analyze the influence factors of death risk among 200 COVID-19 patients.
The association of demographic data, clinical characteristics and biochemical indexes with death risk was analyzed.
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.
2020-03-20 Li et al Coronavirus Disease (COVID-19): Spectrum of CT Findings and Temporal Progression of the Disease
Academic Radiology
IV. Other Due to the need for prevention and control of infection, chest radiography was adopted for ICU patients, whereas serial CT examinations were used for all other patients to monitor the dynamic changes of the disease.
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.
2020-03-22 Li et al Emergence of SARS-CoV-2 through Recombination and Strong Purifying Selection
biorxiv
IV. Other Extensive recombination among bat coronaviruses and strong purifying selection pressure among viruses from humans, bats and pangolin may allow such closely related viruses ready jump between species and adapt to the new hosts.
2020-03-26 Tang et al Comparison of Hospitalized Patients with Acute Respiratory Distress Syndrome Caused by COVID-19 and H1N1
Chest
III-2. Retrospective Cohort

In terms of prognoses, 26 patients (17.6%) with COVID-19 were not discharged by the time that the present study was published.
Therefore, these differential pathological changes may present as distinguishing imaging characteristics during clinical assessments.
2020-03-27 Skums et al Global transmission network of SARS-CoV-2: from outbreak to pandemic
medrxiv
IV. Prevalence Study The question whether this pattern is due to founder effects, epidemiological settings or differences in phenotypic features across SARS-CoV-2 genomic variants remains open and will require further investigation.
2020-03-27 Sekizuka et al Haplotype networks of SARS-CoV-2 infections in the Diamond Princess cruise ship outbreak
medrxiv
IV. Other 1D ), suggesting that early generations of SARS-CoV-2 variants may acquire possible pivotal mutations to adapt to humans.
2020-03-27 Hsiang et al The Effect of Large-Scale Anti-Contagion Policies on the Coronavirus (COVID-19) Pandemic
medrxiv
III-3. Time Series Analysis

We did not collect city level health outcomes recorded prior to January 24, 2020 in provinces that had fewer than ten confirmed cases at that date.
7, 14, 22 The rate of this exponential growth may change daily and is determined by epidemiological factors, such as disease infectivity and contact networks, as well as policies that induce behavior changes.
2020-03-28 Karamitros et al SARS-CoV-2 exhibits intra-host genomic plasticity and low-frequency polymorphic quasispecies
biorxiv
IV. Prevalence Study

We analyzed NGS data derived from clinical samples of three Chinese patients infected with SARS-CoV-2, in order to identify small- and large-scale intra-host variations in the viral genome.
These variants, in combination with the genetic profile of the host, can potentially influence the natural history of the infection, the viral phenotype, but also the sensitivity of molecular and serological diagnostics assays , .

As it is well documented, recombination events lead to substantial changes in genetic diversity of RNA viruses , .
2020-03-28 Bal et al Molecular characterization of SARS-CoV-2 in the first COVID-19 cluster in France reveals an amino-acid deletion in nsp2 (Asp268Del)
Clinical Microbiology and Infection
IV. Other Specific studies using high depth of coverage to assess 75 quasispecies are needed to characterize potential intra-host adaptation.
2020-03-30 Ferstad et al A model to forecast regional demand for COVID-19 related hospital beds
medrxiv
IV. Computer Model Users are referred to online tools to estimate changes in doubling time associated with the impact of socialdistancing interventions.
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 In contrast, siRNA screening relies on temporary knockdown 12 of genes in an individual well format, a methodology suited for examining short-term phenotypic 13 changes.
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 Our study was the first to map the predictive risk of the disease emergence using species distribution models and to establish the impact of environmental factors on their emergence.
2020-03-31 Mousavizadeh et al Genotype and phenotype of COVID-19: Their roles in pathogenesis
Journal of Microbiology, Immunology and Infection
IV. Other The genetic and phenotypic structure of COVID-19 in pathogenesis is important.
2020-03-31 Gong et al Sequence variation among SARS-CoV-2 isolates in Taiwan
biorxiv
IV. Other The genome 1 9 1 variation of these viruses is thought to facilitate successful adaption to the environment of 1 9 2 various hosts.
2020-03-31 Boni et al Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic
biorxiv
III-3. Time Series Analysis

Combining regions A′, B, and C, and removing the five mentioned sequences gives us putative nonrecombining region 1, or NRR1, as an alignment of 63 sequences.
The existing diversity and dynamic process of recombination amongst lineages in the bat reservoir demonstrate how difficult it will be to identify viruses with potential to cause significant human outbreaks before they emerge.
2020-04-01 Garcia-Iglesias et al Early behavior of Madrid Covid-19 disease outbreak: A mathematical model
medrxiv
IV. Computer Model /2020 evaluate the evolution of Covid-19 disease outbreak and to monitor the results of PHM undertaken by the governments.
2020-07-31 Artika et al Pathogenic viruses: Molecular detection and characterization
Infection, Genetics and Evolution
IV. Prevalence Study The ability of pathogenic viruses to adapt to new environments, cross species barriers, develop resistance to antiviral drugs, and to evade existing vaccines is associated with the accumulation of mutations throughout their genomes.

11 Immune response and immunity

11.0.0.1 Highlights

11.0.0.2 Articles

Date Authors Title LOE(?) & Sample Matches
2020 Du et al Subunit Vaccines Against Emerging Pathogenic Human Coronaviruses
Frontiers in Microbiology
III-3. Time Series Analysis Similarly, some viral-vectored vaccines can elicit specific antibody and cellular immune responses with neutralizing activity and protection, but they might also induce anti-vector immunity or present preexisting immunity, causing some harmful immune responses.

Vaccination pathways are important in inducing efficient immune responses, and different immunization routes may elicit different immune responses to the same protein antigens.
2020 Cao et al SARS-CoV-2 infection in children: Transmission dynamics and clinical characteristics
Journal of the Formosan Medical Association
IV. Other Trained immunity, as a new immune model, refers to the use of certain vaccines such as Bacille Calmette-Guérin (BCG) to train innate immunity to generate immune memory.
2020 Lee et al Are children less susceptible to COVID-19?
Journal of Microbiology, Immunology and Infection
IV. Other A more vigorous immune response in adults may also explain a detrimental immune response that is associated with acute respiratory distress syndrome.
2020 Wu et al Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods
Acta Pharmaceutica Sinica B
IV. Other In terms of the human immune system, the innate immune system response plays an important role in controlling the replication and infection of coronavirus, and interferon is expected to enhance the immune response 11 .
2020-02-05 He et al Integrative Bioinformatics Analysis Provides Insight into the Molecular Mechanisms of 2019-nCoV
medrxiv
IV. Other ACE2 is also related to adaptive immune responses .

In this current study, the GSEA analysis showed that the high expression of ACE2 was related to innate immune response, acquired immune response, B cell regulatory immunity and cytokine secretion, and enhanced the inflammatory response induced by IL-1, IL-10, IL-6, IL-8 cytokines.
2020-02-07 Wang et al ACE2 expression by colonic epithelial cells is associated with viral infection, immunity and energy metabolism
medrxiv
IV. Other By contrast, humoral immunity, phagocytosis All rights reserved.
2020-02-11 Abdelmageed et al Design of multi epitope-based peptide vaccine against E protein of human COVID-19: An immunoinformatics approach
biorxiv
IV. Other The immune response of T cell is considered as a long lasting response compared to B cell, where the antigen can easily escape the antibody memory response .
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) .
This study provides valuable information regarding humoral immune responses against SARS-CoV and the 2019-nCoV.
2020-02-23 Zheng et al Comparative study of the lymphocyte change between COVID-19 and non-COVID-19 pneumonia cases suggesting uncontrolled inflammation might not be the main reason of tissue injury
medrxiv
IV. Other Because CD4+ Th cells are critical for the regulation of both cellular immunity and humoral immunity, 17 it is reasonable that these cells are most sensitive to the total anti-virus immune responses.
2020-02-25 Ma et al 2019 novel coronavirus disease in hemodialysis (HD) patients: Report from one HD center in Wuhan, China
medrxiv
IV. Prevalence Study

230 patients and 33 staff in our HD center were included in this study.
In the antiviral immune response, cellular immunity (including T cells and NK cells) plays a central role, while humoral immunity plays a coordinating role.
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.
A well co-ordinated innate and adaptive immune response may rapidly control of the virus, while a failed immune response leads to viral spreading, cytokine storm, and high mortality .

Host immune responses on some extent determine both protection and pathogenesis to the respiratory viral infections .
2020-03-03 Zhao et al Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019
medrxiv
III-3. Time Series Analysis

Among totally 368 cases of COVID-19 patients admitted in the hospital (before Feb 9, 2020), 173 patients of them (47%) were enrolled in the study ( Table 1) (Table 1) .
The total antibody and IgG antibody could be used to understand the epidemiology of SARS-CoV-2 infection and to assist in determining the level of humoral immune response in patients.
2020-03-06 Zhang et al Serological detection of 2019-nCoV respond to the epidemic: A useful complement to nucleic acid testing
medrxiv
IV. Other Antibodies are the products of humoral immune response after infection with viruses.
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 42 In viral infection, the S protein, but not the other structural proteins, M, E, and N in SARS-CoV, elicits an immune response.
2020-03-15 Zhou et al Perspectives on therapeutic neutralizing antibodies against the Novel Coronavirus SARS-CoV-2
Int J Biol Sci
IV. Prevalence Study On the other hand, patients with SARS-CoV infection had the strong humoral immune response to SARS-CoV .

Resistance to SARS-CoV infections is associated with both innate and adaptive immune responses .

The adaptive immune response mainly consists of cellular (T cell) and humoral (B cell) responses.

The innate immune response to SARS-CoV has not been completely defined .

These NAbs can provide passive immune responses to viral infection.

NAbs provide important specific immune defense against viral infections in patients .
2020-03-15 Ye et al Zoonotic origins of human coronaviruses
Int J Biol Sci
IV. Prevalence Study The severe symptoms are mainly due to the hyperactivation of immune response and the cytokine storm wherein the stronger the immune response, the more severe the lung damage.
2020-03-15 Yi et al COVID-19: what has been learned and to be learned about the novel coronavirus disease
Int J Biol Sci
IV. Prevalence Study

On February 11, 2020, a multi-center study on 8,866 patients including 4,021 confirmed COVID-19 patients presented a more updated illustration of the epidemic as follows ( UlBi-HX_rHPXa1qHA2bhdA).
However, the N protein of SARS-CoV can help the virus escape from the immune responses .
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.
The activated host immunity is characterized as lymphopenia, cytokine release storm (CRS), and dysfunctional immune responses to virus-specific antigen.
2020-03-16 Shi et al Immunopathological characteristics of coronavirus disease 2019 cases in Guangzhou, China
medrxiv
IV. Prevalence Study

Increased serum IL-6, IP-10, MCP-1, MIP-1A, and TNFα were observed in COVID-19 patients 8 .
However, the comprehensive status of either innate immunity or adaptive immunity in COVID-19 patients remains largely unknown.
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 The present study identifies likely targets of the human immune response to SARS-CoV-2, encompassing both the B and T cell arms of the adaptive immune response.

The immune response to SARS-CoV-2 in humans awaits characterization, but human immune responses against other coronaviruses have been investigated.
2020-03-17 Huang et al Blood single cell immune profiling reveals the interferon-MAPK pathway mediated adaptive immune response for COVID-19
medrxiv
IV. Prevalence Study

Data from 134,620 PBMCs and 83,387 TCR and 12,601 BCR clones was obtained, and 56 blood cell subtypes and 23 new cell marker genes were identified from 16 participants.
These results suggested that immune deficiency or immune over-reacts may make patients with COVID-19 go to worse condition because of their imbalance adaptive immune response .
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 The immune responses to these vaccine candidates were evaluated in BALB/c mice for cellular and humoral immune responses, which showed that RVbased vaccine stimulates significantly higher levels of cellular immunity and earlier antibody responses in comparison to the GEM particle vector.

22 The S protein has a major role in the induction of protective immunity during infection with SARS-CoV by eliciting neutralizing-antibodies and T-cell responses.
2020-03-20 Dong et al Characterization of anti-viral immunity in recovered individuals infected by SARS-CoV-2
medrxiv
IV. Prevalence Study

Clinical and pathological characteristics of the 12 COVID-19 patients in this study were shown in Table 1 .
had protective humoral immunity to SARS-CoV-2.

There was no significant antibody response to main protease in sera from several patients (data not shown), suggesting that it may not serve as an antigen for humoral immunity.
2020-03-21 Ong et al COVID-19 coronavirus vaccine design using reverse vaccinology and machine learning
biorxiv
IV. Prevalence Study Moreover, it has become increasingly clear that multiple 80 immune responses, including those induced by humoral or cell-mediated immunity, are 81 responsible for correlates of protection than antibody titers alone 9 .
2020-03-23 Wu et al Clinical Characteristics of 74 Children with Coronavirus Disease 2019
medrxiv
IV. Other Innate immunity is able to react more rapidly in response to pathogen invasion than adaptive immunity.

Their adaptive immunity is less developed to mount an inflammatory response during immune dysregulation phase induced by viral infection.
2020-03-23 Dashraath et al Coronavirus Disease 2019 (COVID-19) Pandemic and Pregnancy
American Journal of Obstetrics and Gynecology
IV. Other Immune system 233 Cytokines produced by T-helper (Th) lymphocytes regulate immunity and inflammation.
2020-03-27 Wang et al Elevated serum IgM levels indicate poor outcome in patients with coronavirus disease 2019 pneumonia: A retrospective case-control study
medrxiv
IV. Prevalence Study

Further, a paired case-control study was conducted where each deceased case was matched to three mild-moderate patients of similar age.
Antibodies are key components in the immune responses to viral infections 5, 6 .
2020-03-27 Yang et al Analysis of adaptive immune cell populations and phenotypes in the patients infected by SARS-CoV-2
medrxiv
IV. Other These data provide a clue that the adaptive immunity in most people could be primed to induce a significant immune response against SARS-CoV-2 infection upon receiving standard medical care.
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 .
2020-03-28 Tan et al The cardiovascular burden of coronavirus disease 2019 (COVID-19) with a focus on congenital heart disease
International Journal of Cardiology
IV. Other The second stage is the adaptive immunity stage, when the body develops an antibody response to the virus.
2020-03-31 Shah et al Use of Systemic Immunomodulatory Therapies During the Coronavirus Disease 2019 (COVID-19) Pandemic
Journal of the American Academy of Dermatology
IV. Other CD4+ T-cell immunity is critical to host defense against viral pathogens.
2020-03-31 Rahman et al Epitope-based chimeric peptide vaccine design against S, M and E proteins of SARS-CoV-2 etiologic agent of global pandemic COVID-19: an in silico approach
biorxiv
IV. Other Immune simulation predicted significant primary immune response with increased IgM and secondary immune response with high levels of both IgG1 and IgG2.
2020-04-01 Jain et al Scrutinizing the SARS-CoV-2 protein information for the designing an effective vaccine encompassing both the T-cell and B-cell epitopes
biorxiv
IV. Other The constructed vaccine product has high population coverage and along with adaptive immunity, can as well lead to initiation of innate immune response further enhancing the generation of memory immunity.

In SARS-CoV infection, TLR3 signaling contributes to the innate immune response against the viral infection .
2020-05-31 Farag et al Viroporins and inflammasomes: A key to understand virus-induced inflammation
The International Journal of Biochemistry & Cell Biology
IV. Prevalence Study Innate immunity is the first arm of immune response to viral infections.

Production of these cytokines is essential for activation of the whole immune response against the viral infection.
2020-06-30 Liu et al Why are pregnant women susceptible to COVID-19? An immunological viewpoint
Journal of Reproductive Immunology
IV. Prevalence Study

A total of eighteen pregnant women infected with NCP (mean age: 30 years) had one or two common clinical symptoms, such as fever, cough, cholecystitis, sore throat, and diarrhea.
Innate immune cells, such as NK cells and monocytes, respond more strongly to viral challenges, while some adaptive immune responses are down-regulated during pregnancy, e.g.

12 Effectiveness of movement control strategies to prevent secondary transmission in health care and community settings

12.0.0.1 Highlights

12.0.0.2 Articles

Date Authors Title LOE(?) & Sample Matches
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.
The in-hospital preventive control measures should vary among patients, close contacts, and health care workers in precision medicine approach.
2020 Lai et al Asymptomatic carrier state, acute respiratory disease, and pneumonia due to severe acute respiratory syndrome coronavirus 2 (SARSCoV-2): Facts and myths
Journal of Microbiology, Immunology and Infection
IV. Prevalence Study

Regarding children with COVID-19, nine (0.9%) patients aged 0-14 years were found in only one study, 11 while 14 (0.35%) patients were aged ≤ 10 years in another study.
In this stage of lack of effective drugs, the implementation of infection control interventions and traffic control bundle to effectively limit droplet, contact, and fomite transmission is the only way to slow the spread of the SARS-CoV-2.

These infection control interventions include early identification of cases and their contacts, avoiding close contact with people with airway symptoms, appropriate hand washing, and enhanced standard infection prevention, and control practices in the healthcare setting.
2020 ZHOU et al Epidemiological survey on a family aggregation COVID-19 in Y County, Chenzhou City, Hunan
Shanghai Journal of Preventive Medicine
IV. Other The awareness of family members' protection, the education of new coronavirus pneumonia prevention and control in key groups should be strengthened to avoid the occurrence and spread of family aggregation epidemic.
2020-01-28 Ming et al Breaking down of the healthcare system: Mathematical modelling for controlling the novel coronavirus (2019-nCoV) outbreak in Wuhan, China
biorxiv
IV. Computer Model Earlier studies on the effectiveness of spread control measures during infectious disease pandemic showed large-scale strategies, such as closure of school closure, case isolation, household quarantine, internal travel restrictions and border control, were able to delay the spread and/or reduce incidence rate at certain periods through the outbreak season.
2020-01-31 Koenig et al 2019-nCoV: The Identify-Isolate-Inform (3I) Tool Applied to a Novel Emerging Coronavirus
West J Emerg Med
IV. Prevalence Study

One preliminary, small-scale study of 41 patients in Wuhan China, reported 6 deaths (15% mortality) with a median age of 49.0 years.
The mode of transmission has implications for the types of personal protective equipment (PPE) needed to protect healthcare providers in the prehospital, clinic, and hospital settings.
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.
Overall, 19.1% of all MERS cases have been among health care workers, and more than half of all laboratory-confirmed secondary cases were transmitted from human to human in health care settings, at least in part due to shortcomings in infection prevention and control .

The spread of the epidemic can only be contained and SARS-CoV-2 transmission in hospitals by strict compliance with infection prevention and control measures (contact, droplet, and airborne precautions) .
2020-02-05 Ai et al Population movement, city closure and spatial transmission of the 2019-nCoV infection in China
medrxiv
IV. Prevalence Study On the one hand, the result could help assess 254 effectiveness of the prevention and control efforts.
2020-02-10 Li et al A qualitative study of zoonotic risk factors among rural communities in southern China
Int Health
IV. Prevalence Study

We aimed to obtain a minimum sample size of 20 participants from each of the three provinces, for a total sample size of over 60 participants.
Policies and programmes existing in the communities provide opportunities for zoonotic risk mitigation.
2020-02-12 Xiong et al Simulating the infected population and spread trend of 2019-nCov under different policy by EIR model
medrxiv
IV. Computer Model And the transmission rate without prevention measures is β =k*b= 0.1934.
2020-02-13 Bernard Stoecklin et al First cases of coronavirus disease 2019 (COVID-19) in France: surveillance, investigations and control measures, January 2020
Euro Surveill
IV. Prevalence Study

The was obtained from the three patients confirmed with 2019-nCoV infection.
The objective of the surveillance is to identify imported cases early and to prevent secondary transmission whether in the community or among healthcare workers (HCW).
2020-02-19 Klepac et al Contacts in context: large-scale setting-specific social mixing matrices from the BBC Pandemic project
medrxiv
IV. Prevalence Study

The main dataset used in this study consisted of 36,155 participants reporting 378,559 contacts.
For directly transmitted respiratory pathogens such as influenza, measles and coronaviruses, social mixing patterns shape the risk of individual-level infection and population-level transmission dynamics , as well as the effectiveness of control measures targeted at specific age groups .
2020-02-21 Heymann et al Data sharing and outbreaks: best practice exemplified
The Lancet
IV. Other Front-line health workers can be initially at risk and infected when they examine and treat patients who present with a respiratory infection; if handwashing or other infection prevention and control measures are not in place, these health workers are at great risk of infection and become the inadvertent carriers to patients who are in hospital for other diseases and treatments, family members, and the community.
2020-02-21 Wang et al A novel coronavirus outbreak of global health concern
The Lancet
IV. Prevalence Study

3 In The Lancet, Chaolin Huang and colleagues 7 report clinical features of the first 41 patients admitted to the designated hospital in Wuhan who were confirmed to be infected with 2019-nCoV by Jan 2, 2020.
Front-line health workers can be initially at risk and infected when they examine and treat patients who present with a respiratory infection; if handwashing or other infection prevention and control measures are not in place, these health workers are at great risk of infection and become the inadvertent carriers to patients who are in hospital for other diseases and treatments, family members, and the community.
2020-02-24 Gostic et al Estimated effectiveness of symptom and risk screening to prevent the spread of COVID-19
eLife
III-3. Time Series Analysis

Depending on the screening strategy (arrival, departure or both) and assumed subclinical fraction (5%, 25%, or 50%), the probability of detecting at least the first two cases ranged from 0.02 to 0.11, and the probability of detecting three or more cases was never better than 0.04 ( Figure 3C ).
Alongside increased general surveillance/alertness in healthcare settings, such measures could help reduce the risk of local transmission and superspreading, but their quantitative effectiveness is unknown.
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.
Hospital infection prevention and control programmes aid with case identification through screening and testing, and they execute isolation infection prevention measures to ensure healthcare settings are safe from infection transmission.
2020-02-28 Bao et al 2019-nCoV epidemic: address mental health care to empower society
The Lancet
IV. Prevalence Study Health-care workers are also at risk of getting infected, and they carry a large burden in the clinical treatment and public prevention efforts in Chinese hospitals and community settings.
2020-03-03 Peng et al Transmission routes of 2019-nCoV and controls in dental practice
Int J Oral Sci
IV. Other Effective infection control strategies are needed to prevent the spread of 2019-nCoV through these contact routines.
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).
The NHC also formulated a community prevention and control program for SARS-CoV-2 pneumonia to strengthen community-level epidemic prevention measures to control the spread of the outbreak .
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 prevention of transmission of MERS-CoV in the community and in health-care settings is crucial to preventing outbreaks and further spread.

To prevent community transmission, contact tracing, quarantine or isolation of close contacts, and public education are important measures.
2020-03-05 Spiteri et al First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020
Euro Surveill
IV. Prevalence Study Additional research is needed to complement surveillance data to build knowledge on the infectious period, modes of transmission, basic and effective reproduction numbers, and effectiveness of prevention and case management options also in settings outside of China.
2020-03-12 Wang et al Effects of Chinese strategies for controlling the diffusion and deterioration of novel coronavirus-infected pneumonia in China
medrxiv
IV. Computer Model These strategies therefore provide experience and effective guidelines for other countries to control the diffusion of COVID-19.
2020-03-16 Huang et al Triaging patients in the outbreak of the 2019 novel coronavirus
medrxiv
IV. Other To control the transmission of the coronavirus and avoid nosocomial infection, triage procedures based on epidemiology were implemented in a local hospital of the city.
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.
Preventive measures such as masks, hand hygiene practices, avoidance of public contact, case detection, contact tracing, and quarantines have been discussed as ways to reduce transmission.
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 Infection prevention and control at the community and healthcare facility level is key for prevention, control and containment of the infection.

Reporting from communities, health-care facilities, and points of entry are crucial for prevention and detection of infectious disease outbreaks.
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 .
Optimal infection control and treatment strategies for COVID-19 should be shared with the entire healthcare community.
2020-03-20 Wenham et al COVID-19: the gendered impacts of the outbreak
The Lancet
IV. Other Experience from past outbreaks shows the importance of incorporating a gender analysis into preparedness and response efforts to improve the effectiveness of health interventions and promote gender and health equity goals.
2020-03-20 Ahmadi et al Modeling and Forecasting Trend of COVID-19 Epidemic in Iran
medrxiv
IV. Computer Model The top priorities in Iran are now circular and comprehensive efforts to conduct epidemiological studies and identification of all aspects of the disease (source of disease, reservoir, pathways, infectivity, incubation period, incidence and prevalence, pathogenicity, immunogenicity, herd immunity, causes, epidemic and pandemic pattern, primary and secondary attack rates, response time, time needed for isolation and quarantine, treatment regimens, vaccines and other prevention methods, disease surveillance and statistical reporting) and evidence-based interventions and epidemic control.
2020-03-23 Wen et al Epidemiological and clinical characteristics of COVID-19 in Shenzhen, the largest migrant city of China
medrxiv
IV. Prevalence Study

In total, there were 29 (7.0%) pediatric patients aged below 15 years, of whom 26 were identified by surveillance and 28 were cases from clusters.
Our results can be used to improve the prediction of transmission risk, design and implementation of intervention measures and strategies, and assessments of intervention effectiveness in similar settings.
2020-03-23 Milne et al The Effectiveness of Social Distancing in Mitigating COVID-19 Spread: a modelling analysis
medrxiv
IV. Other 5, 6 Methods A community-based simulation model capturing the demographics and movement patterns of individuals in an Australian city, with the virus transmission characteristics of COVID-19, was used to evaluate the potential effectiveness of a range of social distancing strategies.
2020-03-23 Coelho et al Assessing the potential impacts of COVID-19 in Brasil: Mobility, Morbidity and Impact to the Health System
medrxiv
IV. Prevalence Study Social vulnerability is expected to affect the effectiveness of mitigation strategies to reduce morbidity and mortality.
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.
9 The implementation of school closure and workplace distancing can therefore be considered as a potential secondary control response in the event of infection quarantine failure and the establishment of community transmission.
2020-03-23 Wang et al Effectiveness and cost-effectiveness of public health measures to control COVID-19: a modelling study
medrxiv
IV. Prevalence Study The enforcement of community containment was a restriction on the movement of people throughout the community, minimizing human contact .
2020-03-23 Amariles et al How to link patients with suspicious COVID-19 to health system from the community pharmacies? A route proposal
Research in Social and Administrative Pharmacy
IV. Other 4 Community pharmacies and pharmacy staff play a crucial role in minimizing the stage of "community transmission" of COVID-19, through properly detection, referral and management of possible cases and customer education about self-care to prevent the infection transmission, including hand hygiene, correct use of face masks, and evaluation of symptoms, accordingly to the government instructions.
2020-03-25 Vahia et al COVID-19, Mental Health and Aging: A Need for New Knowledge to Bridge Science and Service
The American Journal of Geriatric Psychiatry
IV. Other We believe that a range of measures may have been implemented across various care settings worldwide, including inpatient and outpatient care and large tertiary care centers, community-based hospitals, primary care settings, nursing homes as well as residential environments such as assisted living facilities.
2020-03-25 Su et al The different clinical characteristics of corona virus disease cases between children and their families in China – the character of children with COVID-19
Emerg Microbes Infect
IV. Other Public health measures such as home isolation should be aimed at minimizing such risk factors when addressing household transmission of serious infections spread through droplet transmission.
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.
5.1 Infection control measures to prevent spread of influenza: Standard precautions are a group of infection prevention practices always used in healthcare settings, and in RCFs with a suspected or confirmed influenza outbreak.

03 Although not regulatory in scope, these guidelines support infection prevention and control (IP&C) professionals, health care organizations and health care providers in developing, implementing and evaluating IP&C policies, procedures and programs to improve the quality and safety of health care and patient outcomes.

Manitoba Health Seniors and Active Living, 2019; Country: Canada, Sponsor: Not reported Scope: these guidelines support infection prevention and control (IP&C) professionals, health care organizations and health care providers in developing, implementing and evaluating IP&C policies, procedures and programs to improve the quality and safety of health care and patient outcomes Active surveillance for additional cases should be implemented as soon as possible when one healthcare-associated laboratoryconfirmed influenza case is identified in a hospital or one case of laboratory-confirmed influenza is identified in a long-term care facility (A-III).

All staff in a residential care facility should receive general education on policies, including the principles of infection prevention and control.
2020-03-27 Foddai et al Surveillance to improve evidence for community control decisions during the COVID-19 pandemic – Opening the animal epidemic toolbox for public health
One Health
IV. Prevalence Study Countries are implementing different community control measures.
2020-03-27 Zhang et al Familial cluster of COVID-19 infection from an asymptomatic
Crit Care
IV. Other Therefore, to identify and control the asymptomatic cases, as well as early quarantine for their close contacts, especially in families are important measures to prevent transmission of the COVID-19 infection.
2020-03-30 Zhou et al Forecasting the Worldwide Spread of COVID-19 based on Logistic Model and SEIR Model
medrxiv
IV. Computer Model Countries had different start time and level of interventions and measures to reduce risk of domestic secondary infections of COVID-19.
2020-03-30 Cheng et al China's fight against COVID-19: What we have done and what we should do next?
medrxiv
IV. Other The prevention and control measures were conducted in the community, with precise management and it was imperative to make full use of the power at the community level to curb spread from communities.
2020-03-30 Lin et al Which Measures are Effective in Containing COVID-19? Empirical Research Based on Prevention and Control Cases in China
medrxiv
IV. Prevalence Study When infectious disease outbreaks, various countries adopt public health intervention policies, in which one is to control human contacts, such as isolation, quarantine, and social distancing; the other is to control population mobility, such as travel restrictions.
2020-03-31 Lyu et al Expert consensus on the procedure of interventional diagnosis and treatment of cancer patients during the COVID-19 epidemic
Journal of Interventional Medicine
IV. Prevalence Study These measures may prevent nosocomial infections substantially.
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.
4 , the national healthcare system capacity with high level of control measures helps to reduce spread of diseases.

13 Effectiveness of personal protective equipment (PPE) and its usefulness to reduce risk of transmission in health care and community settings

13.0.0.1 Highlights

13.0.0.2 Articles

Date Authors Title LOE(?) & Sample Matches
2020 MacIntyre et al Wuhan novel coronavirus 2019nCoV
Global Biosecurity
IV. Other Triage, isolation and infection control are key, as well as personal protective equipment (PPE) for health care workers.
2020-01-31 Koenig et al 2019-nCoV: The Identify-Isolate-Inform (3I) Tool Applied to a Novel Emerging Coronavirus
West J Emerg Med
IV. Prevalence Study

One preliminary, small-scale study of 41 patients in Wuhan China, reported 6 deaths (15% mortality) with a median age of 49.0 years.
The mode of transmission has implications for the types of personal protective equipment (PPE) needed to protect healthcare providers in the prehospital, clinic, and hospital settings.
2020-02-07 Kruse et al Therapeutic strategies in an outbreak scenario to treat the novel coronavirus originating in Wuhan, China
F1000Res
IV. Prevalence Study

Like some of the therapeutic options discussed below, the ability to express any lead candidates in lower organisms for protein expression (bacteria, yeast, insect cells) would facilitate faster production of therapy for patients 19 .
Healthcare workers were also at risk, and despite extensive personal protective equipment measures, clinical providers did get infected in both outbreaks 9 .
2020-02-12 Wu et al Facemask shortage and the coronavirus disease (COVID-19) outbreak: Reflection on public health measures
medrxiv
IV. Computer Model The World Health Organization's (WHO) guidance on prevention and control of the COVID-19 outbreak recommends hand, and respiratory hygiene and the use of appropriate personal protective equipment for healthcare workers in practice and patients with suspected SARS-CoV-2 infection should be offered a medical mask 8 .
2020-02-13 Cowling et al Epidemiological research priorities for public health control of the ongoing global novel coronavirus (2019-nCoV) outbreak
Euro Surveill
IV. Other Face masks are essential components of personal protective equipment in healthcare settings, and should be recommended for ill persons in the community or for those who care for ill persons.
2020-02-21 Huang et al Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China
The Lancet
III-2. Cross Sectional Control

14 Of 59 suspected cases, 41 patients were confirmed to be infected with 2019-nCoV.
19 Airborne precautions, such as a fit-tested N95 respirator, and other personal protective equipment are strongly recommended.
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.
15 Concerns were raised about infections in healthcare workers despite apparently appropriate personal protective equipment (PPE).

21 Healthcare workers were exposed to risk of infection before PPE was used.
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).
c) Training in the use of personal protective equipment protects the safety of HCWs .
2020-03-03 Peng et al Transmission routes of 2019-nCoV and controls in dental practice
Int J Oral Sci
IV. Other Since airborne droplet transmission of infection is considered as the main route of spread, particularly in dental clinics and hospitals, barrier-protection equipment, including protective eyewear, masks, gloves, caps, face shields, and protective outwear, is strongly recommended for all healthcare givers in the clinic/hospital settings during the epidemic period of 2019-nCoV.
2020-03-05 Xiao et al Taking the right measures to control COVID-19
The Lancet Infectious Diseases
IV. Prevalence Study 3, 4 Second, in the use of personal protective equipment, we should try to distinguish different risk factors, adopt different epidemic prevention measures, and reduce the waste of personal protective equipment, as these resources are already in short supply.

High-filtration masks such as N95 masks and protective clothing (goggles and gowns) should be used in hospitals where health-care workers are in direct contact with infected patients.5 Third, the practice of blocking traffic and lockdown of villages is of no value for the prevention and control of COVID-19.
2020-03-07 Baker et al Preparing for a Surge of Coronavirus Cases
The Joint Commission Journal on Quality and Patient Safety
IV. Other  Implement all elements of standard precautions as outlined in the CDC Core Practices, including o Hand hygiene o Environmental cleaning and disinfection o Risk assessment with use of appropriate personal protective equipment (such as gloves, gowns, face masks) based on activities being performed o Reprocessing of reusable medical equipment between each patient and when soiled  Hand-off communications, both inter-and intrafacility, should include notification of colonization or infection with a potentially transmissible pathogen.
2020-03-11 Chopra et al How Should U.S. Hospitals Prepare for Coronavirus Disease 2019 (COVID-19)?
Ann Intern Med
IV. Other Health care personnel should receive training on proper donning and doffing of personal protective equipment, including fit testing of N95 masks and use of powered air-purifying respirators, as well as basic infection prevention tenets, such as hand hygiene.
2020-03-13 Ghinai et al First known person-to-person transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the USA
The Lancet
IV. Prevalence Study Facemasks or other personal protective equipment (PPE) were not used at the home.
2020-03-13 Li et al The demand for inpatient and ICU beds for COVID-19 in the US: lessons from Chinese cities
medrxiv
IV. Prevalence Study

During the peak of the epidemic from mid to late February, a maximum of 19,425 patients (24.5 per 10,000 adults) were hospitalized, 9,689 patients (12.2 per 10,000 adults) were considered to be in "serious" condition, and 2,087 patients (2.6 per 10,000 adults) needed critical care per day.
In several countries with high-performing healthcare systems where SARS-CoV-2 transmission has been established earlier, both supplies of personal protective equipment in hospitals and the availability of services has been problematic for COVID-19 care, and in all locations, ICU bed capacity is limited.
2020-03-14 Repici et al Coronavirus (COVID-19) outbreak: what the department of endoscopy should know
Gastrointestinal Endoscopy
IV. Prevalence Study Personal protective equipment (PPE) is worn to reduce exposure to hazards that cause workplace injuries and illnesses.
2020-03-15 Xiang et al The COVID-19 outbreak and psychiatric hospitals in China: managing challenges through mental health service reform
Int J Biol Sci
IV. Other Clearly, preventive measures such as the provision of adequate medical supplies and protective equipment, public education on the risks of COVID-19 for hospital staff and patients, and restricting family visits to hospitals, are essential to reduce the likelihood of disease transmission in major psychiatric hospitals.
2020-03-16 Teslya et al Impact of self-imposed prevention measures and short-term government intervention on mitigating and delaying a COVID-19 epidemic
medrxiv
IV. Computer Model The efficacy of handwashing and mask-wearing are given by the reduction in susceptibility and infectivity, respectively.
2020-03-16 Ye et al Environmental contamination of the SARS-CoV-2 in healthcare premises: An urgent call for protection for healthcare workers
medrxiv
IV. Other 1 Early on during the COVID-19 outbreak, healthcare workers (HCW) were found to beat high risk of developing COVID-19, even when infection prevention measures were in place, including usage of personal protective equipment (PPE: eye protection/face shield, respiratory protection, isolation gowns, and gloves), hand hygiene, and patient placement in negative-pressure isolation rooms.
2020-03-18 Wang et al COVID-19 infection epidemic: the medical management strategies in Heilongjiang Province, China
Crit Care
IV. Other The content of training included personal protection such as hand hygiene, wearing personal protective equipment (PPE), safe waste disposal, and emergency handling protocols.
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 All ECMO centres should have designated areas for putting on and removing of personal protective equipment (PPE) and power air-purifying respirators (PAPR).
2020-03-20 Legido-Quigley et al Are high-performing health systems resilient against the COVID-19 epidemic?
The Lancet
IV. Prevalence Study Fifth, in all locations, critical care treatment and medicines have been available for patients with COVID-19, but adequate supplies of personal protective equipment in hospitals and face masks in the community are a key concern.
2020-03-20 Elachola et al COVID-19: Facemask use prevalence in international airports in Asia, Europe and the Americas, March 2020
Travel Medicine and Infectious Disease
IV. Prevalence Study Studies have indicated that facemasks reduce the risk of contracting influenza-like illnesses in households, especially when combined with proper wearing, handwashing and social distance .
2020-03-20 Zhang et al Estimating Preventable COVID19 Infections Related to Elective Outpatient Surgery in Washington State: A Quantitative Model
medrxiv
IV. Prevalence Study

Thus we multiplied our ratio with 3047 total patients per day and 2742 total HCW to arrive at the initial values of 0.18 asymptomatic infected patients per day, 3046.82 uninfected patients per day, 0.16 asymptomatic infected HCW, and 2741.84 uninfected HCW.
Since COVID-19 would not be suspected in these patients, healthcare workers interacting with them typically would not use the level of personal protective equipment (PPE) or precautions necessary to prevent COVID-19 transmission, especially if there were also restrictions due to PPE shortages within the clinical institution.
2020-03-23 Amariles et al How to link patients with suspicious COVID-19 to health system from the community pharmacies? A route proposal
Research in Social and Administrative Pharmacy
IV. Other 4 Community pharmacies and pharmacy staff play a crucial role in minimizing the stage of "community transmission" of COVID-19, through properly detection, referral and management of possible cases and customer education about self-care to prevent the infection transmission, including hand hygiene, correct use of face masks, and evaluation of symptoms, accordingly to the government instructions.
2020-03-23 Wang et al Effectiveness and cost-effectiveness of public health measures to control COVID-19: a modelling study
medrxiv
IV. Prevalence Study The cost of personal protection included masks and handwashing (water and soap).
2020-03-26 Rios et al Preventing respiratory illness in older adults aged 60 years and above living in long-term care: A rapid overview of reviews
medrxiv
I. Systematic Review

During full text review, articles were included if they contained the number of influenza cases occurring on a specific date or within a 3-day period, such as through an epidemic curve or a line list of symptom onset dates 37 studies N = NR Long term care facilitiesdefined as any residential environment that housed older adults or elderly individuals with the assistance of medical staff and included facilities referred to as 'assisted living' or 'nursing homes' but excluded community centers and daytime-only facilities serving older adults living in the outside community.
For the rest of the strategies, there was either no evidence of effectiveness (e.g., social isolation) or mixed evidence of effectiveness (e.g., rimantadine, zanamivir, hand hygiene, personal protective equipment).

One moderate quality SR with meta-analysis found a moderate non-statistically significant effect for personal protective equipment (PPE) in preventing infection and found no statistically significant results for the effectiveness of social isolation.
2020-03-26 Rios et al Guidelines for preventing respiratory illness in older adults aged 60 years and above living in long-term care: A rapid review of clinical practice guidelines
medrxiv
IV. Prevalence Study

If one or more respiratory samples from ILI cases in a suspected outbreak returns a positive laboratory result for influenza, then an influenza outbreak is confirmed.
Preventing respiratory illness in long-term care facilities: Two or more clinical practice guidelines recommended the following: hand hygiene (n=13), wearing personal protective equipment (n=13), social distancing/isolation (n=13), disinfecting surfaces (n=12), droplet precautions (n=12), surveillance and evaluation (n=11), conducting diagnostic testing to confirm suspected respiratory illness (n=10), policies and procedures for visitors (n=9), respiratory hygiene/cough etiquette (n=9), policies and procedures for staff and/or residents (n=9), providing supplies (n=9), education of staff and/or residents (n=8), increasing communication (n=6), consulting or notifying health professionals (n=6), appropriate ventilation practices (n=2), and cohorting equipment (n=2) ( Table 2 , Appendix 6).
2020-03-26 Carico et al Community pharmacists and communication in the time of COVID-19: Applying the health belief model
Research in Social and Administrative Pharmacy
IV. Other Community pharmacists can help patients who express difficulties with perceived self-efficacy with respect to COVID-19 prevention behaviors.
2020-03-27 Card et al UV Sterilization of Personal Protective Equipment with Idle Laboratory Biosafety Cabinets During the Covid-19 Pandemic
medrxiv
IV. Other Personal protective equipment (PPE), including surgical masks and N95 respirators, is crucially important to the safety of both patients and medical personnel, particularly in the event of infectious pandemics.
2020-03-27 Dinh et al Radiation Therapy in King County, Washington During The COVID-19 Pandemic: Balancing Patient Care, Transmission Mitigation and Resident Training
Advances in Radiation Oncology
IV. Other The rate of consumption of personal protective equipment (PPE) has been high and is expected to 78 greatly increase in our facilities.
2020-03-27 Huang et al Special attention to nurses’ protection during the COVID-19 epidemic
Crit Care
IV. Other We provide adequate education to nurses, and training content includes the use of personal protective equipment (PPE), hand hygiene, ward disinfection, medical waste management, and sterilization of patient-care devices and management of occupational exposure.
2020-03-27 Christian et al COVID-19 in Canada: Predictions for the future and control lessons from Asia
medrxiv
IV. Other These numbers will pose significant threats to ICU bed capacity, and the ability of hospitals to provide front-line medical staff with maximum personal protective equipment (PPE).
2020-03-27 Soetikno et al Considerations in performing endoscopy during the COVID-19 pandemic
Gastrointestinal Endoscopy
IV. Other As the outbreaks continue to occur, masks and personal protective equipment (PPE) may become scarce in quantity.
2020-03-27 Breslin et al COVID-19 in pregnancy: early lessons
American Journal of Obstetrics & Gynecology MFM
IV. Other An estimated 15 healthcare providers were exposed to this patient prior to diagnosis, including during intubation, all with inadequate personal protective equipment (PPE).
2020-03-30 Thomas et al Physiotherapy management for COVID-19 in the acute hospital setting: clinical practice recommendations
Journal of Physiotherapy
IV. Prevalence Study

12 In adult patients with COVID-19 and severe ARDS, prone ventilation for 12 to 16 hours per day is recommended.
The risk of airborne transmission to staff is low when optimal PPE and other infection control precautions are being used.
2020-03-30 Lin et al Which Measures are Effective in Containing COVID-19? Empirical Research Based on Prevention and Control Cases in China
medrxiv
IV. Prevalence Study On the other hand, the difference transmission can significantly affect the speed of disease spreading and the choice of personal protective equipment (PPE).
2020-03-31 Guerci et al COVID-19: HOW CAN A DEPARTMENT OF GENERAL SURGERY SURVIVE TO A PANDEMIC?
Surgery
IV. Other To avoid nosocomial transmission of the virus, the members of the medical and nursing staff always use personal protective equipment (PPE).
2020-03-31 Belingheri et al Beyond the assistance: additional exposure situations to COVID-19 for healthcare workers
Journal of Hospital Infection
IV. Other WHO has recommended that HCWs should use proper personal protective equipment (PPE), such as medical masks, gowns, gloves and eye protection .
2020-03-31 Papachristofilou et al Contingency plans in a radiation oncology department amid the 2019-nCoV outbreak in Switzerland
Advances in Radiation Oncology
IV. Other Strict compliance with hospital-wide hygiene measures is mandatory, and this included the use of personal protective equipment (PPE) from an early stage, as well as regular disinfection procedures, distribution of hand sanitizers, and instruction of both patients and staff.
2020-03-31 Porzio et al Home care for cancer patients during COVID-19 pandemic: the “double triage” protocol.
Journal of Pain and Symptom Management
IV. Other Of course, physicians and nurses wear personal protective equipment (masks, gloves, disposable gowns) during the home visits.
2020-03-31 Berghella et al NOW!: Protection for Obstetrical providers and Patients
American Journal of Obstetrics & Gynecology MFM
IV. Other Personal protective equipment (PPE) such as surgical masks as well as N-95 masks or equivalent should be prioritized by the fed and individual states for healthcare workers.
2020-03-31 Olivia Li et al Preparedness among Ophthalmologists: During and Beyond the COVID-19 Pandemic
Ophthalmology
IV. Other In particular, front-line health care workers -emergency medicine physicians, intensivists, anesthesiologists, nurses, and many others -have continued to care for massive surges of COVID-19 patients in the setting of health systems illprepared for the level of disease severity with dangerous, worldwide shortages of personal protective equipment (PPE) and protocols that might attenuate health worker risk overwhelmed.
2020-03-31 Fausto et al Creating a Palliative Care Inpatient Response Plan for COVID19 – The UW Medicine Experience
Journal of Pain and Symptom Management
IV. Other A second consideration was the implementation of Personal Protective Equipment (PPE) preservation, which has been a core strategy to maintain healthcare worker safety.
2020-04-01 Lakkireddy et al Guidance for Cardiac Electrophysiology During the Coronavirus (COVID-19) Pandemic from the Heart Rhythm Society COVID-19 Task Force; Electrophysiology Section of the American College of Cardiology; and the Electrocardiography and Arrhythmias Committee of the Council on Clinical Cardiology, American Heart Association
Heart Rhythm
IV. Prevalence Study Reducing contact between health care personnel and COVID-19 patients is an integral step in limiting its spread and resource utilization, including use of personal protective equipment (PPE).
2020-04-01 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.
All zones must provide personal protective equipment (PPE), such as protective clothing, helmets, goggles, or other garments and equipment.
2020-04-01 Sultan et al AGA Institute Rapid Recommendations for Gastrointestinal Procedures During the COVID-19 Pandemic
Gastroenterology
I. Systematic Review

58, 59 First, the systematic reviews by Offeddu et al included a meta-analysis of 3 observational studies that showed a benefit in using N95 respirators over standard masks in protecting health care workers from SARS (OR = 0.86; 95% CI: 0.
In the setting of a pandemic, the limited availability of resources (such as critical shortages of PPE) combined with the risk of potential exposure and spread of infection to patients and the availability of appropriate health care workers, often become the main drivers for provision of health care services.
2020-05-31 Chughtai et al Policies on the use of respiratory protection for hospital health workers to protect from coronavirus disease (COVID-19)
International Journal of Nursing Studies
IV. Other All guidelines however highlight the importance of training for respiratory (and other personal protective equipment) use.

14 Role of the environment in transmission

14.0.0.1 Highlights

14.0.0.2 Articles

Date Authors Title LOE(?) & Sample Matches
2020 Cao et al SARS-CoV-2 infection in children: Transmission dynamics and clinical characteristics
Journal of the Formosan Medical Association
IV. Other In conclusion, understanding the role of pediatric population in the transmission dynamics of the outbreak is important, as children may become a significant spreader at the explosion stage of the outbreak.
2020 Rocklöv et al COVID-19 outbreak on the Diamond Princess cruise ship: estimating the epidemic potential and effectiveness of public health countermeasures
Journal of Travel Medicine
IV. Other 1 Thus, cruise ships present a unique environment for transmission of human-to-human transmitted infections.
2020 Hui et al The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health — The latest 2019 novel coronavirus outbreak in Wuhan, China - International Journal of Infectious Diseases
International Journal of Infectious Diseases
IV. Other While it appears to be transmitted to humans via animals, the specific animals and other reservoirs need to be identified, the transmission route, the incubation period and characteristics of the susceptible population and survival rates.
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.
It is reported that both symptomatic and asymptomatic patients with 2019-nCov can play a role in disease transmission via airborne and contact.
2020 Shang et al The outbreak of SARS-CoV-2 pneumonia calls for viral vaccines
WHO
IV. Other Respiratory droplets and direct contact are conventional transmission routes for SARS-CoV-2, and fecal-to-oral transmission might also have a role3.
2020-02-09 Guan et al Clinical characteristics of 2019 novel coronavirus infection in China
medrxiv
III-2. Retrospective Cohort

The core data sets (including clinical outcomes and symptoms) of 3 patients were lacking due to the incompleteness of original reports, hence this report delineates 1,099 patients with 2019-nCoV ARD from 552 hospitals in 31 provinces/province-level municipalities (Fig.
Evidence pointing to the person-to-person transmission in hospital and family settings has been accumulating .
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 .
2020-02-17 Neher et al Potential impact of seasonal forcing on a SARS-CoV-2 pandemic
medrxiv
IV. Prevalence Study

The dataset included a total of 52,158 patient samples with 190,257 diagnostic tests, of which 2,084 were positive for any of the coronaviruses (229E = 319; NL63 = 499; OC43 = 604; HKU1 = 355; OC43/HKU1 = 307).
The strength of variation of the transmission rate through the year could be of high relevance to the spread of SARS-CoV-2 in 2020 and following years.
2020-02-17 Luo et al The role of absolute humidity on transmission rates of the COVID-19 outbreak
medrxiv
IV. Other In addition to population mobility and human-to-human contact, environmental factors can impact droplet transmission and survival of viruses (e.g., influenza) but have not yet been examined for this novel pathogen.
2020-02-18 Danchin et al A new transmission route for the propagation of the SARS-CoV-2 coronavirus
medrxiv
IV. Computer Model Elaborating on the behavior of previous coronavirus outbreaks, we worked out the hypothesis that an alternative infection tropism (the gut tropism) linked to a secondary propagation route (through environment) is affecting the development of the present 2019-nCoV epidemic.

The model indicates that Wuhan quarantine measures were effective but that alternative virus forms (gut tropism) and a second propagation route (through environment) was present.
2020-02-21 Chang et al Coronavirus Disease 2019: Coronaviruses and Blood Safety
Transfusion Medicine Reviews
IV. Prevalence Study

In a study on the viral load in different samples among 37 MERS patients, investigators found that nearly half of serum samples tested yielded a viral RNA signal during the first week after diagnosis and that the viral load ranged from about 2.1×10 2 to 2.51×10 5 copies/mL.
Infected feces also played an important role in some cluster outbreak cases .
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.
2020-02-25 Zhang et al Characterizing the transmission and identifying the control strategy for COVID-19 through epidemiological modeling
medrxiv
IV. Other In an enclosed and crowded environment, the transmission of SARS-CoV-2 was thought to significantly increase.
2020-02-27 Al-Tawfiq et al Asymptomatic coronavirus infection: MERS-CoV and SARS-CoV-2 (COVID-19)
Travel Medicine and Infectious Disease
IV. Other Those asymptomatic cases may play a role in the transmission and thus pose a significant infection control challenge.

However, the contribution of asymptomatic cases in the transmission of these viruses is not well known and deserve further studies to examine the extent of occurrence and the role in transmission.
2020-02-27 Tian et al Characteristics of COVID-19 infection in Beijing
Journal of Infection
IV. Other Therefore, person-to-person transmission is the main route of transmission.
2020-02-28 Kam et al A Well Infant with Coronavirus Disease 2019 (COVID-19) with High Viral Load
Clinical Infectious Diseases
IV. Other These patients may play important roles in human-to-human transmission in the community.
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 This means that the transmission route was mainly from person to person rather than from reservoir to person in the early stage of the transmission in Wuhan City.
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 These findings underscore the role of human-to-human transmission of 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 Meanwhile, cases of familial clustering increased to be predominant (76, 61.3%), indicating that local transmission in the family environment was important route of transmission.

As transmission of infectious disease requires links between three parts of the cycle, the source of infection, route of transmission and susceptible population.
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).
The E protein plays a role in virus assembly and release, and is required for pathogenesis .
2020-03-06 Wu et al Key Points of Clinical and CT Imaging Features of 2019 Novel Coronavirus (2019-nCoV) Imported Pneumonia Based On 21 Cases Analysis
medrxiv
IV. Other Person-to-person transmission of NCP has been confirmed and with several ways of transmission, moreover the asymptomatic individual is identified as a potential source of infection.
2020-03-06 Tang et al Prediction of New Coronavirus Infection Based on a Modified SEIR Model
medrxiv
IV. Other The transmission method is person-to-person.
2020-03-12 Ferretti et al Quantifying dynamics of SARS-CoV-2 transmission suggests that epidemic control and avoidance is feasible through instantaneous digital contact tracing
medrxiv
III-3. Time Series Analysis Environmental transmission: transmission via contamination, and specifically in a way that would not typically be attributable to contact with the source in a contact survey (i.e., this does not include transmission pairs who were in extended close contact, but for whom in reality the infectious dose passed via the environment instead of more directly).
2020-03-12 Wu et al The SARS-CoV-2 outbreak: what we know
International Journal of Infectious Diseases
IV. Other In addition, J o u r n a l P r e -p r o o f we should actively study its origin, tropism, and pathogenesis with the aim of providing some guidance in dealing with this rapidly spreading epidemic.
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.
SARS-CoV-2 was detected from the working environment of the market, supporting the existence of a live animal source.
2020-03-15 Ye et al Zoonotic origins of human coronaviruses
Int J Biol Sci
IV. Prevalence Study Whether fecal-oral transmission of SARS-CoV-2 plays an important role as in the case of SARS-CoV at least under some circumstance remains to be clarified by future studies.
2020-03-16 Hemida et al The SARS-CoV-2 outbreak from a one health perspective
One Health
IV. Prevalence Study In the light of the One Health concept, control of this emerging virus requires the reduction of the viral shedding to the environment from the main reservoirs, for animal-person transmission and from humans for person-person transmission .

The environment serves as the intermediate vessels between the animals and humans.
2020-03-16 Shi et al Immunopathological characteristics of coronavirus disease 2019 cases in Guangzhou, China
medrxiv
IV. Prevalence Study

Increased serum IL-6, IP-10, MCP-1, MIP-1A, and TNFα were observed in COVID-19 patients 8 .
The outbreak of COVID-19 poses an urgent demand of understanding the role of immunity in the progression of viral infection and subsequent pneumonia.
2020-03-16 Araujo et al Spread of SARS-CoV-2 Coronavirus likely to be constrained by climate
medrxiv
IV. Computer Model Coronavirus should continue to spread owing to seasonal changes of climate suitability and increased abundance of the viral pool.
2020-03-17 Bedford et al COVID-19: towards controlling of a pandemic
The Lancet
IV. Other 4, 5 These findings suggest that close and unprotected exposure is required for transmission by direct contact or by contact with fomites in the immediate environment of those with infection.
2020-03-17 Pujari et al Multi-city modeling of epidemics using spatial networks: Application to 2019-nCov (COVID-19) coronavirus in India
medrxiv
III-3. Time Series Analysis Our work also shows that because of the contagious nature of the COVID19 and the crucial role of the domestic transportation networks, even a small infected population is sufficient to sustain and spread the pandemic.
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 .
Aerosol transmission might also be a way of transmission.

Chinese medicine also played an important role in the treatment of SARS-CoV-2 infection.
2020-03-20 Liu et al Assessing the Global Tendency of COVID-19 Outbreak
medrxiv
IV. Computer Model In addition, in the second phase of epidemic transmission, human-to-human transmission plays an important role.
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 Amongst other factors, sequence of the host invasion factors of the virus strain may possibly play an important role in degree of transmission, virulence and pathogenicity of the virus.
2020-03-24 Wigginton et al Environmental Engineers and Scientists Have Important Roles to Play in Stemming Outbreaks and Pandemics Caused by Enveloped Viruses
Environ Sci Technol
IV. Other Virus particles in the air and on fomites are exposed to a range of environmental conditions that influence their persistence.
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
The route of transmission was by close contact with family members (32 [89%]) or a history of exposure to the epidemic area (12 [33%]); eight (22%) patients had both exposures.
2020-03-26 Santarpia et al Transmission Potential of SARS-CoV-2 in Viral Shedding Observed at the University of Nebraska Medical Center
medrxiv
IV. Other Nosocomial transmission 15 of SARS-CoV-2 has been reported, but the role of aerosol transmission and environmental contamination remains unclear .
2020-03-30 Muller et al Mobility traces and spreading of COVID-19
medrxiv
IV. Computer Model Still, the contagion effect of public transport clearly plays a role.

Infections in public transport play an important role.
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 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 Goh et al Shell disorder analysis predicts greater resilience of the SARS-CoV-2 (COVID-19) outside the body and in body fluids
Microbial Pathogenesis
IV. Other The ability to stay longer in the environment could, however, provide advantages to a virus with greater respiratory transmission potential, especially with respect to spread via airborne virus from feces or body fluids.
2020-03-31 Acuna-Zegarra et al The SARS-CoV-2 epidemic outbreak: a review of plausible scenarios of containment and mitigation for Mexico
medrxiv
IV. Prevalence Study

Observe that the peak incidence is approximately 4 935 individuals and it occurs 2 days after isolation began (January 26th, ) Figure 14(b) ).
The role of asymptomatic cases has been under study in the literature particularly as their likely important role in driving the epidemic appears clearer.
2020-03-31 Byass et al Eco-epidemiological assessment of the COVID-19 epidemic in China, January-February 2020
medrxiv
IV. Computer Model Where a new disease is involved, such as COVID-19, it is particularly important to chart an unknown infectious agent's interactions with environments in which transmission has occurred.
2020-04-30 Yeo et al Enteric involvement of coronaviruses: is faecal–oral transmission of SARS-CoV-2 possible?
The Lancet Gastroenterology & Hepatology
IV. Other The viability of SARS-CoV and MERS-CoV under various conditions and their prolonged presence in the environment suggest the potential for coronaviruses to be transmitted via contact or fomites.
×
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