EVOLUTION OF SARS-CoV-2 VARIANTS IN GEOGRAPHIC LOCATIONS WITH VARYING CASE INCIDENCE

Date
2022
Authors
Fraser, Claire Jisu
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Butler, Marguerite A.
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Microbiology
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The evolutionary dynamics of SARS-CoV-2 over the course of the pandemic are of great concern. Prior studies have identified accelerated protein evolution early in the pandemic, followed by a period of increased selective constraints. While there are expected changes in rates of mutation influenced by viral spread, the translation to selection is not well studied. In addition, new variants are emerging as SARS-CoV-2 continues to evolve and some are spreading more rapidly due to mutations that provide a viral advantage. A comparative analysis between Los Angeles County and Hawai'i, localities with rigorous surveillance sequencing programs and varying case incidence, was conducted to test whether there are evolutionary differences of B.1.1.7, the first identified variant of concern, and B.1.243, a rapidly spreading variant in Hawai'i, across localities. Of these four locality-variant scenarios, only B.1.243 in LA County occurred at low case incidence and the remaining three scenarios were at high case incidence. With the rapid spread of virus, I generally found elevated rates of evolution - both synonymous and nonsynonymous substitution. The two variants had very different histories, with B.1.243 evolving locally in Hawaii before being introduced into LA County in a single migration event, whereas B.1.1.7 travelled between localities repeatedly. Yet, there were great differences in diversity of genome sequences overall and elevation of number of sites under positive and negative selection in Los Angeles County relative to the same variant in Hawaii. Within each local outbreak of each variant, I found little evidence for an early phase of protein adaptation followed by an increase in constraints as found in a previous study across the US. Instead, I find that in general more sites are under negative selection than positive selection at this point of the pandemic. Overall, these results show support for variability in evolutionary dynamics across localities and suggest differences in selective pressures across different populations.
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Evolution & development, Virology, diversity, evolution, phylogenetics, SARS-CoV-2, selection, variants
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45 pages
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