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Estimating Transmission Parameters for COVID-19 Clusters by Using Symptom Onset Data, Singapore, January-April 2020.

ABSTRACT: We estimated the generation interval distribution for coronavirus disease on the basis of serial intervals of observed infector-infectee pairs from established clusters in Singapore. The short mean generation interval and consequent high prevalence of presymptomatic transmission requires public health control measures to be responsive to these characteristics of the epidemic.

SUBMITTER: Ng SH

PROVIDER: S-EPMC7853533 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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Estimating Transmission Parameters for COVID-19 Clusters by Using Symptom Onset Data, Singapore, January-April 2020.

Ng Sheryl Hui-Xian SH Kaur Palvinder P Kremer Cécile C Tan Woan Shin WS Tan Aidan Lyanzhiang AL Hens Niel N Toh Matthias Paul MP Teow Kiok Liang KL Kannapiran Palvannan P

Emerging infectious diseases 20210201 2

We estimated the generation interval distribution for coronavirus disease on the basis of serial intervals of observed infector-infectee pairs from established clusters in Singapore. The short mean generation interval and consequent high prevalence of presymptomatic transmission requires public health control measures to be responsive to these characteristics of the epidemic. ...[more]

PMID: 33496243

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Presymptomatic Transmission of SARS-CoV-2 - Singapore, January 23-March 16, 2020.

Project description:Presymptomatic transmission of SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), might pose challenges for disease control. The first case of COVID-19 in Singapore was detected on January 23, 2020, and by March 16, a total of 243 cases had been confirmed, including 157 locally acquired cases. Clinical and epidemiologic findings of all COVID-19 cases in Singapore through March 16 were reviewed to determine whether presymptomatic transmission might have occurred. Presymptomatic transmission was defined as the transmission of SARS-CoV-2 from an infected person (source patient) to a secondary patient before the source patient developed symptoms, as ascertained by exposure and symptom onset dates, with no evidence that the secondary patient had been exposed to anyone else with COVID-19. Seven COVID-19 epidemiologic clusters in which presymptomatic transmission likely occurred were identified, and 10 such cases within these clusters accounted for 6.4% of the 157 locally acquired cases. In the four clusters for which the date of exposure could be determined, presymptomatic transmission occurred 1-3 days before symptom onset in the presymptomatic source patient. To account for the possibility of presymptomatic transmission, officials developing contact tracing protocols should strongly consider including a period before symptom onset. Evidence of presymptomatic transmission of SARS-CoV-2 underscores the critical role social distancing, including avoidance of congregate settings, plays in controlling the COVID-19 pandemic.

| S-EPMC7147908 | biostudies-literature

Patterns of Virus Exposure and Presumed Household Transmission among Persons with Coronavirus Disease, United States, January-April 2020.

Project description:We characterized common exposures reported by a convenience sample of 202 US patients with coronavirus disease during January-April 2020 and identified factors associated with presumed household transmission. The most commonly reported settings of known exposure were households and healthcare facilities; among case-patients who had known contact with a confirmed case-patient compared with those who did not, healthcare occupations were more common. Among case-patients without known contact, use of public transportation was more common. Within the household, presumed transmission was highest from older (>65 years) index case-patients and from children to parents, independent of index case-patient age. These findings may inform guidance for limiting transmission and emphasize the value of testing to identify community-acquired infections.

| S-EPMC8386767 | biostudies-literature

Effectiveness of non-pharmaceutical interventions on COVID-19 transmission in 190 countries from 23 January to 13 April 2020.

Project description:BackgroundTo evaluate and compare the effectiveness of four types of non-pharmaceutical interventions (NPIs) to contain the time-varying effective reproduction number (Rt) of coronavirus disease-2019 (COVID-19).MethodsThis study included 1,908,197 confirmed COVID-19 cases from 190 countries between 23 January and 13 April 2020. The implemented NPIs were categorised into four types: mandatory face mask in public, isolation or quarantine, social distancing and traffic restriction (referred to as mandatory mask, quarantine, distancing and traffic hereafter, respectively).ResultsThe implementations of mandatory mask, quarantine, distancing and traffic were associated with changes (95% confidence interval, CI) of -15.14% (from -21.79% to -7.93%), -11.40% (from -13.66% to -9.07%), -42.94% (from -44.24% to -41.60%) and -9.26% (from -11.46% to -7.01%) in the Rt of COVID-19 when compared with those without the implementation of the corresponding measures. Distancing and the simultaneous implementation of two or more types of NPIs seemed to be associated with a greater decrease in the Rt of COVID-19.ConclusionOur study indicates that NPIs can significantly contain the COVID-19 pandemic. Distancing and the simultaneous implementation of two or more NPIs should be the strategic priorities for containing COVID-19.

| S-EPMC7598763 | biostudies-literature

Worldwide Effects of Coronavirus Disease Pandemic on Tuberculosis Services, January-April 2020.

Project description:Coronavirus disease has disrupted tuberculosis services globally. Data from 33 centers in 16 countries on 5 continents showed that attendance at tuberculosis centers was lower during the first 4 months of the pandemic in 2020 than for the same period in 2019. Resources are needed to ensure tuberculosis care continuity during the pandemic.

| S-EPMC7588533 | biostudies-literature

Estimating the generation interval for coronavirus disease (COVID-19) based on symptom onset data, March 2020.

Project description:BackgroundEstimating key infectious disease parameters from the coronavirus disease (COVID-19) outbreak is essential for modelling studies and guiding intervention strategies.AimWe estimate the generation interval, serial interval, proportion of pre-symptomatic transmission and effective reproduction number of COVID-19. We illustrate that reproduction numbers calculated based on serial interval estimates can be biased.MethodsWe used outbreak data from clusters in Singapore and Tianjin, China to estimate the generation interval from symptom onset data while acknowledging uncertainty about the incubation period distribution and the underlying transmission network. From those estimates, we obtained the serial interval, proportions of pre-symptomatic transmission and reproduction numbers.ResultsThe mean generation interval was 5.20 days (95% credible interval (CrI): 3.78-6.78) for Singapore and 3.95 days (95% CrI: 3.01-4.91) for Tianjin. The proportion of pre-symptomatic transmission was 48% (95% CrI: 32-67) for Singapore and 62% (95% CrI: 50-76) for Tianjin. Reproduction number estimates based on the generation interval distribution were slightly higher than those based on the serial interval distribution. Sensitivity analyses showed that estimating these quantities from outbreak data requires detailed contact tracing information.ConclusionHigh estimates of the proportion of pre-symptomatic transmission imply that case finding and contact tracing need to be supplemented by physical distancing measures in order to control the COVID-19 outbreak. Notably, quarantine and other containment measures were already in place at the time of data collection, which may inflate the proportion of infections from pre-symptomatic individuals.

| S-EPMC7201952 | biostudies-literature

Estimating Risk for Death from Coronavirus Disease, China, January-February 2020.

Project description:Since December 2019, when the first case of coronavirus disease (COVID-19) was identified in the city of Wuhan in the Hubei Province of China, the epidemic has generated tens of thousands of cases throughout China. As of February 28, 2020, the cumulative number of reported deaths in China was 2,858. We estimated the time-delay adjusted risk for death from COVID-19 in Wuhan, as well as for China excluding Wuhan, to assess the severity of the epidemic in the country. Our estimates of the risk for death in Wuhan reached values as high as 12% in the epicenter of the epidemic and ≈1% in other, more mildly affected areas. The elevated death risk estimates are probably associated with a breakdown of the healthcare system, indicating that enhanced public health interventions, including social distancing and movement restrictions, should be implemented to bring the COVID-19 epidemic under control.

| S-EPMC7258458 | biostudies-literature

Three infection clusters related with potential pre-symptomatic transmission of coronavirus disease (COVID-19), Shanghai, China, January to February 2020.

Project description:We report three clusters related with potential pre-symptomatic transmission of coronavirus disease (COVID-19) between January and February 2020 in Shanghai, China. Investigators interviewed suspected COVID-19 cases to collect epidemiological information, including demographic characteristics, illness onset, hospital visits, close contacts, activities' trajectories between 14 days before illness onset and isolation, and exposure histories. Respiratory specimens of suspected cases were collected and tested for SARS-CoV-2 by real-time reverse-transcriptase polymerase chain reaction (rRT-PCR) assay. The interval between the onset of illness in the primary case and the last contact of the secondary case with the primary case in our report was 1 to 7 days. In Cluster 1 (five cases), illness onset in the five secondary cases was 2 to 5 days after the last contact with the primary case. In Cluster 2 (five cases) and Cluster 3 (four cases), the illness onset in secondary cases occurred prior to or on the same day as the onset in the primary cases. The study provides empirical evidence for transmission of COVID-19 during the incubation period and indicates that pre-symptomatic person-to-person transmission can occur following sufficient exposure to confirmed COVID-19 cases. The potential pre-symptomatic person-to-person transmission puts forward higher requirements for prevention and control measures.

| S-EPMC7441604 | biostudies-literature

A Brazilian classified data set for prognosis of tuberculosis, between January 2001 and April 2020.

Project description:After COVID-19, tuberculosis (TB) is the leading cause of death by an infectious disease in the world. This work presents a data set based on data collected from the Brazilian Information System for Notifiable Diseases (SINAN) for the period from January 2001 to April 2020 relating to patients diagnosed with tuberculosis in Brazil. The data from SINAN was pre-processed to generate a new data set with two distinct treatment outcome classes: CURED and DIED. The data set comprises 37 categorical attributes (including socio-demographic, clinical, and laboratory data) as well as the target class. There are 927,909 records of patients classified as CURED and 36,190 classified as DIED, totaling 964,099 records.

| S-EPMC9753864 | biostudies-literature

SARS-CoV-2 in asymptomatic Danish infants and their mothers from April 2020 to January 2022.

Project description: Not available

| S-EPMC9350021 | biostudies-literature

Completeness of reporting for COVID-19 case reports, January to April 2020: a meta-epidemiologic study.

Project description:BackgroundThe quality of case reports, which are often the first reported evidence for a disease, may be negatively affected by a rush to publication early in a pandemic. We aimed to determine the completeness of reporting (COR) for case reports published on coronavirus disease 2019 (COVID-19).MethodsWe conducted a systematic search of the PubMed database for all single-patient case reports of confirmed COVID-19 published from Jan. 1 to Apr. 24, 2020. All included case reports were assessed for adherence to the CARE (Case Report) 31-item checklist, which was used to create a composite COR score. The primary outcome was the mean COR score assessed by 2 independent raters. Secondary outcomes included whether there was a change in overall COR score with certain publication factors (e.g., publication date) and whether there was a linear relation between COR and citation count and between COR scores and social media attention.ResultsOur search identified 196 studies that were published in 114 unique journals. We found that the overall mean COR score was 54.4%. No one case report included all of the 31 CARE checklist items. There was no significant correlation between COR with either citation count or social media attention.InterpretationWe found that the overall COR for case reports on COVID-19 was poor. We suggest that journals adopt common case-reporting standards to improve reporting quality.

| S-EPMC8096411 | biostudies-literature

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