The Incubation Period of Coronavirus Disease 2019 (COVID-19) From Publicly Reported Confirmed Cases: Estimation and Application

Background: A novel human coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was identified in China in December 2019. There is limited support for many of its key epidemiologic features, including the incubation period for clinical disease (coronavirus disease 2019 [COVID-19]), which has important implications for surveillance and control activities. Objective: To estimate the length of the incubation period of COVID-19 and describe its public health implications. Design: Pooled analysis of confirmed COVID-19 cases reported between 4 January 2020 and 24 February 2020. Setting: News reports and press releases from 50 provinces, regions, and countries outside Wuhan, Hubei province, China. Participants: Persons with confirmed SARS-CoV-2 infection outside Hubei province, China. Measurements: Patient demographic characteristics and dates and times of possible exposure, symptom onset, fever onset, and hospitalization. Results: There were 181 confirmed cases with identifiable exposure and symptom onset windows to estimate the incubation period of COVID-19. The median incubation period was estimated to be 5.1 days (95% CI, 4.5 to 5.8 days), and 97.5% of those who develop symptoms will do so within 11.5 days (CI, 8.2 to 15.6 days) of infection. These estimates imply that, under conservative assumptions, 101 out of every 10 000 cases (99th percentile, 482) will develop symptoms after 14 days of active monitoring or quarantine. Limitation: Publicly reported cases may overrepresent severe cases, the incubation period for which may differ from that of mild cases. Conclusion: This work provides additional evidence for a median incubation period for COVID-19 of approximately 5 days, similar to SARS. Our results support current proposals for the length of quarantine or active monitoring of persons potentially exposed to SARS-CoV-2, although longer monitoring periods might be justified in extreme cases

Molecular tracing of a suspected foodborne disease event caused by Bacillus cereus

ObjectiveTo trace Bacillus cereus （B. cereus） from foodborne disease outbreaks toidentify pathogens and cut off transmission.MethodsPulsed-field gel electrophoresis （PFGE） was performed. Furthermore， 12 isolates of B. cereus were subjected to PFGE. Subsequently， whole-genome sequencing （WGS） analysis was conducted on ten of these isolates. The WGS data were analyzed and assembled using BioNumerics software. Multilocus sequence typing （MLST）， virulence gene profiles， and single nucleotide polymorphisms （SNPs） were analyzed using assembled sequences.ResultsPFGE analysis classified the 12 B. cereus strains into nine pulsotypes. The three B. cereus isolates with the same PFGE pattern belonged to ST1435， and there were only three SNPs in the three ST1435 strains. The two B. cereus isolates with the same PFGE patterns were ST24 with one SNP between them， and the two ST24 isolates harbored hlbACD. These results indicate that the B. cereus isolates belonged to the same clone. The remaining three B. cereus strains also contained hlbACD.ConclusionFood-borne illness events caused by B. cereus are complex and are sources of contamination. Therefore， it will be necessary to strengthen the hygiene surveillance of food sources and workers and to pay more attention to cleaning and disinfecting environments and facilities， which will be important for preventing and controlling foodborne diseases

Assessing the global threat from Zika virus.

First discovered in 1947, Zika virus (ZIKV) infection remained a little-known tropical disease until 2015, when its apparent association with a considerable increase in the incidence of microcephaly in Brazil raised alarms worldwide. There is limited information on the key factors that determine the extent of the global threat from ZIKV infection and resulting complications. Here, we review what is known about the epidemiology, natural history, and public health effects of ZIKV infection, the empirical basis for this knowledge, and the critical knowledge gaps that need to be filled

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Setting-specific Transmission Rates: A Systematic Review and Meta-analysis.

BACKGROUND: Understanding the drivers of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission is crucial for control policies, but evidence of transmission rates in different settings remains limited. METHODS: We conducted a systematic review to estimate secondary attack rates (SARs) and observed reproduction numbers (Robs) in different settings exploring differences by age, symptom status, and duration of exposure. To account for additional study heterogeneity, we employed a beta-binomial model to pool SARs across studies and a negative-binomial model to estimate Robs. RESULTS: Households showed the highest transmission rates, with a pooled SAR of 21.1% (95% confidence interval [CI]:17.4-24.8). SARs were significantly higher where the duration of household exposure exceeded 5 days compared with exposure of ≤5 days. SARs related to contacts at social events with family and friends were higher than those for low-risk casual contacts (5.9% vs 1.2%). Estimates of SARs and Robs for asymptomatic index cases were approximately one-seventh, and for presymptomatic two-thirds of those for symptomatic index cases. We found some evidence for reduced transmission potential both from and to individuals younger than 20 years of age in the household context, which is more limited when examining all settings. CONCLUSIONS: Our results suggest that exposure in settings with familiar contacts increases SARS-CoV-2 transmission potential. Additionally, the differences observed in transmissibility by index case symptom status and duration of exposure have important implications for control strategies, such as contact tracing, testing, and rapid isolation of cases. There were limited data to explore transmission patterns in workplaces, schools, and care homes, highlighting the need for further research in such settings

Protection against cholera from killed whole-cell oral cholera vaccines: a systematic review and meta-analysis

BACKGROUND: Killed whole-cell oral cholera vaccines (kOCVs) are becoming a standard cholera control and prevention tool. However, vaccine efficacy and direct effectiveness estimates have varied, with differences in study design, location, follow-up duration, and vaccine composition posing challenges for public health decision making. We did a systematic review and meta-analysis to generate average estimates of kOCV efficacy and direct effectiveness from the available literature. METHODS: For this systematic review and meta-analysis, we searched PubMed, Embase, Scopus, and the Cochrane Review Library on July 9, 2016, and ISI Web of Science on July 11, 2016, for randomised controlled trials and observational studies that reported estimates of direct protection against medically attended confirmed cholera conferred by kOCVs. We included studies published on any date in English, Spanish, French, or Chinese. We extracted from the published reports the primary efficacy and effectiveness estimates from each study and also estimates according to number of vaccine doses, duration, and age group. The main study outcome was average efficacy and direct effectiveness of two kOCV doses, which we estimated with random-effect models. This study is registered with PROSPERO, number CRD42016048232. FINDINGS: Seven trials (with 695 patients with cholera) and six observational studies (217 patients with cholera) met the inclusion criteria, with an average two-dose efficacy of 58% (95% CI 42-69, I2=58%) and effectiveness of 76% (62-85, I2=0). Average two-dose efficacy in children younger than 5 years (30% [95% CI 15-42], I2=0%) was lower than in those 5 years or older (64% [58-70], I2=0%; p<0·0001). Two-dose efficacy estimates of kOCV were similar during the first 2 years after vaccination, with estimates of 56% (95% CI 42-66, I2=45%) in the first year and 59% (49-67, I2=0) in the second year. The efficacy reduced to 39% (13 to 57, I2=48%) in the third year, and 26% (-46 to 63, I2=74%) in the fourth year. INTERPRETATION: Two kOCV doses provide protection against cholera for at least 3 years. One kOCV dose provides at least short-term protection, which has important implications for outbreak management. kOCVs are effective tools for cholera control. FUNDING: The Bill & Melinda Gates Foundation.This study was funded by WHO by a grant from The Bill & Melinda Gates Foundation. ASA, JL and DAS were funded by The Bill & Melinda Gates Foundation (OPP10892431 for ASA and JL and OPP1053556 for ASA and DAS).S

Micro-scale Spatial Clustering of Cholera Risk Factors in Urban Bangladesh

<div><p>Close interpersonal contact likely drives spatial clustering of cases of cholera and diarrhea, but spatial clustering of risk factors may also drive this pattern. Few studies have focused specifically on how exposures for disease cluster at small spatial scales. Improving our understanding of the micro-scale clustering of risk factors for cholera may help to target interventions and power studies with cluster designs. We selected sets of spatially matched households (matched-sets) near cholera case households between April and October 2013 in a cholera endemic urban neighborhood of Tongi Township in Bangladesh. We collected data on exposures to suspected cholera risk factors at the household and individual level. We used intra-class correlation coefficients (ICCs) to characterize clustering of exposures within matched-sets and households, and assessed if clustering depended on the geographical extent of the matched-sets. Clustering over larger spatial scales was explored by assessing the relationship between matched-sets. We also explored whether different exposures tended to appear together in individuals, households, and matched-sets. Household level exposures, including: drinking municipal supplied water (ICC = 0.97, 95%CI = 0.96, 0.98), type of latrine (ICC = 0.88, 95%CI = 0.71, 1.00), and intermittent access to drinking water (ICC = 0.96, 95%CI = 0.87, 1.00) exhibited strong clustering within matched-sets. As the geographic extent of matched-sets increased, the concordance of exposures within matched-sets decreased. Concordance between matched-sets of exposures related to water supply was elevated at distances of up to approximately 400 meters. Household level hygiene practices were correlated with infrastructure shown to increase cholera risk. Co-occurrence of different individual level exposures appeared to mostly reflect the differing domestic roles of study participants. Strong spatial clustering of exposures at a small spatial scale in a cholera endemic population suggests a possible role for highly targeted interventions. Studies with cluster designs in areas with strong spatial clustering of exposures should increase sample size to account for the correlation of these exposures.</p></div

The high risk categories of 10 exposures and the summary statistics.

<p>All household level exposures were dichotomized into high risk and low risk categories based on previous literature.</p

Co-occurrence of different household level exposures within households and within matched-sets.

<p>Values above one suggested two exposures tend to appear in the same households or matched-set closer to each other (co-occurrence of two exposures), while values less than one suggested two exposures tend to not appear together. Confidence interval was calculated by 1000 bootstrap iterations. Shading of each grid cell indicated the estimates of co-occurrence of different exposures, and the estimates that were statistically significant based on 1000 bootstrap iterations were marked by asteroids. Use of municipal supplied water and use of tubewell water was structurally correlated, thus the result was not shown in the graph and was marked by a #. As a result, when co-occurrence with the use of supplied water was over 1, co-occurrence with the use of tubewell water tended to be under 1. Household level unhygienic practices were correlated with infrastructure that is suspected to increase cholera risk. No pairs of exposures exhibited significant clustering in the same households.</p

Insights into household transmission of SARS-CoV-2 from a population-based serological survey

Household-based studies can provide insights into SARS-CoV-2 transmission. Here, the authors fit transmission models to serological data from Geneva, Switzerland, and estimate that the risk of infection from single household exposure (17.3%) was higher than for extra-household exposure (5.1%)