A repeat pattern of founder events for SARS-CoV-2 variants in Alaska

Abstract

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 2022-02-27, 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.

The relative prevalence of the Omicron variant within SARS-CoV-2 infected cohorts in different countries: A systematic review

“…Haan et al 52 investigated the differences in patterns of the emergence of the SARS-CoV-2 variants in Alaska as compared to other regions of the USA. A total of 11,971 sequences were downloaded from Alaskan samples, along with metadata limited to the period of time from November 28, 2021, to April 12, 2022, from lower 48 contiguous states from GISAID.…”

“…However, the prevalence of BA.2.3 in Alaska is much higher than the other regions. Haan et al 52 concluded that the pattern of emergence in Alaska was unique and suggestive of founder event for BA.2.3 due to an absence of other lineages from BA.2, along with being influenced by its geographical and population differences compared to contiguous United States. Phan et al, was the first to report the presence of BA.5 circulating in Western Pennsylvania in May 2022.…”