Phenotypic evolution of SARS-CoV-2: a statistical inference approach

Abstract

AbstractSince its emergence in late 2019, the SARS-CoV-2 virus has spread globally, causing the ongoing COVID-19 pandemic. In the fall of 2020, the Alpha variant (lineage B.1.1.7) was detected in England and rapidly spread and outcompeted the previous lineage. Yet, very little is known about the underlying modifications of the infection process that can explain this selective advantage. Here, we try to quantify how the Alpha variant differs from its predecessor on two phenotypic traits: the transmission rate and the duration of infectiousness. To this end, we analysed the joint epidemiological and evolutionary dy-namics of SARS-CoV-2 as a function of the Stringency Index, a measure of the amount of Non-Pharmaceutical Interventions. We developed a two-step approach based on a SEIR model and the analysis of a combination of epidemiological and evolutionary information. First, we infer how the Stringency Index reduces the amount of viral transmission. Secondly, based on a novel theoretical derivation of the selection gradient in a SEIR model, we infer the phenotype of the Alpha variant from the analysis of the change in its frequency and we show that its selective advantage is more likely to result from a higher transmission than from a longer infectious period.