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Inference of person-to-person transmission of COVID-19 reveals hidden super-spreading events during the early outbreak phase.

ABSTRACT: Coronavirus disease 2019 (COVID-19) was first identified in late 2019 in Wuhan, Hubei Province, China and spread globally in months, sparking worldwide concern. However, it is unclear whether super-spreading events occurred during the early outbreak phase, as has been observed for other emerging viruses. Here, we analyse 208 publicly available SARS-CoV-2 genome sequences collected during the early outbreak phase. We combine phylogenetic analysis with Bayesian inference under an epidemiological model to trace person-to-person transmission. The dispersion parameter of the offspring distribution in the inferred transmission chain was estimated to be 0.23 (95% CI: 0.13-0.38), indicating there are individuals who directly infected a disproportionately large number of people. Our results showed that super-spreading events played an important role in the early stage of the COVID-19 outbreak.

SUBMITTER: Wang L

PROVIDER: S-EPMC7538999 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

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Inference of person-to-person transmission of COVID-19 reveals hidden super-spreading events during the early outbreak phase.

Wang Liang L Didelot Xavier X Yang Jing J Wong Gary G Shi Yi Y Liu Wenjun W Gao George F GF Bi Yuhai Y

Nature communications 20201006 1

Coronavirus disease 2019 (COVID-19) was first identified in late 2019 in Wuhan, Hubei Province, China and spread globally in months, sparking worldwide concern. However, it is unclear whether super-spreading events occurred during the early outbreak phase, as has been observed for other emerging viruses. Here, we analyse 208 publicly available SARS-CoV-2 genome sequences collected during the early outbreak phase. We combine phylogenetic analysis with Bayesian inference under an epidemiological m ...[more]

PMID: 33024095

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Project description:BackgroundIn current epidemiology of tuberculosis (TB), heterogeneity in infectiousness among TB patients is a challenge, which is not well studied. We aimed to quantify this heterogeneity and the presence of "super-spreading" events that can assist in designing optimal public health interventions.MethodsTB epidemiologic investigation data notified between 1 January 2005 and 31 December 2015 from Victoria, Australia were used to quantify TB patients' heterogeneity in infectiousness and super-spreading events. We fitted a negative binomial offspring distribution (NBD) for the number of secondary infections and secondary active TB disease each TB patient produced. The dispersion parameter, k, of the NBD measures the level of heterogeneity, where low values of k (e.g. k?<?1) indicate over-dispersion. Super-spreading was defined as patients causing as many or more secondary infections as the 99th centile of an equivalent homogeneous distribution. Contact infection was determined based on a tuberculin skin test (TST) result of ?10?mm. A NBD model was fitted to identify index characteristics that were associated with the number of contacts infected and risk ratios (RRs) were used to quantify the strength of this association.ResultsThere were 4190 (2312 pulmonary and 1878 extrapulmonary) index TB patients and 18,030 contacts. A total of 15,522 contacts were tested with TST, of whom 3213 had a result of ?10?mm. The dispersion parameter, k for secondary infections was estimated at 0.16 (95%CI 0.14-0.17) and there were 414 (9.9%) super-spreading events. From the 3213 secondary infections, 2415 (75.2%) were due to super-spreading events. There were 226 contacts who developed active TB disease and a higher level of heterogeneity was found for this outcome than for secondary infection, with k estimated at 0.036 (95%CI 0.025-0.046). In regression analyses, we found that infectiousness was greater among index patients found by clinical presentation and those with bacteriological confirmation.ConclusionTB transmission is highly over dispersed and super-spreading events are responsible for a substantial majority of secondary infections. Heterogeneity of transmission and super-spreading are critical issues to consider in the design of interventions and models of TB transmission dynamics.

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Inference of person-to-person transmission of COVID-19 reveals hidden super-spreading events during the early outbreak phase.

Publications

Inference of person-to-person transmission of COVID-19 reveals hidden super-spreading events during the early outbreak phase.

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