Estimates of early outbreak-specific SARS-CoV-2 epidemiological parameters from genomic data

Author:

Vaughan Timothy G.12ORCID,Scire Jérémie12,Nadeau Sarah A.12ORCID,Stadler Tanja12ORCID

Affiliation:

1. Department of Biosystems Science and Engineering, Eidgenössiche Technische Hochschule Zurich, Basel 4058, Switzerland

2. Computational Evolution Group, Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland

Abstract

We estimate the basic reproductive number and case counts for 15 distinct Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks, distributed across 11 populations (10 countries and one cruise ship), based solely on phylodynamic analyses of genomic data. Our results indicate that, prior to significant public health interventions, the reproductive numbers for 10 (out of 15) of these outbreaks are similar, with median posterior estimates ranging between 1.4 and 2.8. These estimates provide a view which is complementary to that provided by those based on traditional line listing data. The genomic-based view is arguably less susceptible to biases resulting from differences in testing protocols, testing intensity, and import of cases into the community of interest. In the analyses reported here, the genomic data primarily provide information regarding which samples belong to a particular outbreak. We observe that once these outbreaks are identified, the sampling dates carry the majority of the information regarding the reproductive number. Finally, we provide genome-based estimates of the cumulative number of infections for each outbreak. For 7 out of 11 of the populations studied, the number of confirmed cases is much bigger than the cumulative number of infections estimated from the sequence data, a possible explanation being the presence of unsequenced outbreaks in these populations.

Publisher

Proceedings of the National Academy of Sciences

Subject

Multidisciplinary

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