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Estimating R e and overdispersion in secondary cases from the size of identical sequence clusters of SARS-CoV-2

Abstract The wealth of genomic data that was generated during the COVID-19 pandemic provides an exceptional opportunity to obtain information on the transmission of SARS-CoV-2. Specifically, there is great interest to better understand how the effective reproduction number R e and the overdispersion of secondary cases, which can be quantified by the negative binomial dispersion parameter k , changed over time and across regions and viral variants. The aim of our study was to develop a Bayesian framework to infer R e and k from viral sequence data. First, we developed a mathematical model for the distribution of the size of identical sequence clusters, in which we integrated viral transmission, the mutation rate of the virus, and incomplete case-detection. Second, …

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