Evolution of new variants of SARS-COV-2 during the pandemic: mutation limited or selection limited?

Abstract

The recent pandemic caused by SARS-Cov-2 has witnessed an evolving succession of variants of the virus. While the phenomenon of invasion by immunity evading variants is known for other viruses such as influenza, the dynamics of the ecological and evolutionary process in the succession is little known. Since during the Covid-19 pandemic, large scale epidemiological data were collected and made available in the public domain, it is possible to seek answers to a number of evolutionary questions, which will also have public health implications. We list multiple alternative hypotheses about the origin and invasion of the variants and evaluate them in the light of epidemiological data. Our analysis shows that invasion by novel variants is selection limited and not mutation limited. Further novel variants are not the necessary and sufficient causes of the repeated waves during the pandemic. Rather there is substantial overlap between the conditions leading to a wave and those favoring selection of a partial immune evading variant. This is likely to lead to an association between invasion by new variant and the rise of a new wave. But the association is not sufficiently strong and does not support a causal role of the new variant. The dynamics of interaction between epidemiological processes and selection on viral variants have many public health implications that can guide future policies for effective control of infectious epidemics.