Viruses (Jan 2023)

A Repeat Pattern of Founder Events for SARS-CoV-2 Variants in Alaska

  • Tracie J. Haan,
  • Lisa K. Smith,
  • Stephanie DeRonde,
  • Elva House,
  • Jacob Zidek,
  • Diana Puhak,
  • Logan Mullen,
  • Matthew Redlinger,
  • Jayme Parker,
  • Brian M. Barnes,
  • Jason L. Burkhead,
  • Cindy Knall,
  • Eric Bortz,
  • Jack Chen,
  • Devin M. Drown

DOI
https://doi.org/10.3390/v15010222
Journal volume & issue
Vol. 15, no. 1
p. 222

Abstract

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Alaska is a unique US state because of its large size, geographically disparate population density, and physical distance from the contiguous United States. Here, we describe a pattern of SARS-CoV-2 variant emergence across Alaska reflective of these differences. Using genomic data, we found that in Alaska, the Omicron sublineage BA.2.3 overtook BA.1.1 by the week of 27 February 2022, reaching 48.5% of sequenced cases. On the contrary, in the contiguous United States, BA.1.1 dominated cases for longer, eventually being displaced by BA.2 sublineages other than BA.2.3. BA.2.3 only reached a prevalence of 10.9% in the contiguous United States. Using phylogenetics, we found evidence of potential origins of the two major clades of BA.2.3 in Alaska and with logistic regression estimated how it emerged and spread throughout the state. The combined evidence is suggestive of founder events in Alaska and is reflective of how Alaska’s unique dynamics influence the emergence of SARS-CoV-2 variants.

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