Estimating the strength of selection for new SARS-CoV-2 variants

van Dorp, Christiaan H.; Goldberg, Emma E.; Hengartner, Nick; Ke, Ruian; Romero-Severson, Ethan O.

A challenge to controlling the SARS-CoV-2 pandemic is the ability of the virus to adapt to its new human hosts, with novel and more transmissible strains of the virus being continually identified. Yet there are no generally accepted methods to consistently estimate the relative magnitude of the change in transmissiblity of newly emerging variants. In this paper we consider three methods for examining and quantifying positive selection of new and emerging strains of SARS-CoV-2 over an existing wild-type strain. We consider replication at the level of countries and allow for the action of other processes that can change variants’ frequencies, specifically migration and drift. We apply these methods to the D614G spike mutation and the variant designated B.1.1.7, in every country where there is sufficient sequence data. For each of D614G and B.1.1.7, we find evidence for strong selection (greater than 25% increased contagiousness) in more than half of countries analyzed. Our results also shows that the selective advantages of these strains are highly heterogeneous at the country level, suggesting the need for a truly global perspective on the molecular epidemiology of SARS-CoV-2.