Résumé
Since 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 spread
rapidly, outcompeting 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 differed 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 dynamics as a function
of the Stringency Index, a measure of the amount of Non-Pharmaceutical
Interventions. Assuming that these control measures reduce contact rates
and transmission, we developed a two-step approach based on SEIR models
and the analysis of a combination of epidemiological and evolutionary
information. First, we quantify the link between the Stringency Index and
the reduction in viral transmission. Secondly, based on a novel
theoretical derivation of the selection gradient in an SEIR model, we
infer the phenotype of the Alpha variant from its frequency changes. We
show that its selective advantage is more likely to result from a higher
transmission than from a longer infectious period. Our work illustrates
how the analysis of the joint epidemiological and evolutionary dynamics of
infectious diseases can help understand the phenotypic evolution driving
pathogen adaptation.