Founder effect contributes to the unique pattern of SARS-CoV-2 variant B.1.1.519 emergence in Alaska

Abstract

Alaska is the largest geographic state in the United States with the lowest population density and a mix of urban centers and isolated rural communities. The differences in population dynamics in Alaska from the contiguous United States may have contributed to a unique pattern of emergence and spread of SARS-CoV-2 variants observed in early 2021. Here we examined 2,323 virus genomes from Alaska and 278,635 virus genomes from the contiguous United States collected between the first week of December 2020 through the last week of June 2021. We focused on this timeframe because of the notable emergence and spread of the SARS-CoV-2 lineage B.1.1.519 observed in Alaska. We found that this variant was consistently detected in Alaska from the end of January through June of 2021 with a peak prevalence in April of 77.9% unlike the rest of the United States with a peak prevalence of 4.6%. In Alaska, the earlier emergence of B.1.1.519 coincided with a later peak of Alpha (B.1.1.7) when compared to the rest of the United States. We also observed differences in the composition of lineages and variants over time between the two most populated regions of Alaska. Although there was a modest increase in COVID-19 cases during the peak incidence of B.1.1.519, it is difficult to disentangle how social dynamics conflated changes in COVID-19 during this time. We suggest that the viral characteristics, such as amino acid substitutions in the spike protein, and a founder effect likely contributed to the unique spread of B.1.1.519 in Alaska.

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

“…This was suggested because of the inconclusive results over the positive selection of those mutations and coinciding timing with the nexus of dispersal from Asia to Europe associated with the D614G mutation (Grubaugh et al, 2020). Given the emergence of other lineages in the Lower 48 even though BA.2.3 was detected around the same time for many locations, Alaska’s emergence of BA.2.3, and B.1.1.519 earlier in the pandemic, implicates repeat occurrences of variant emergence influenced by the founder effect (Haan et al, 2022).…”

“…During this wave, the Alpha variant (lineage B.1.1.7; Rambaut et al, 2020), which showed evidence of increased transmissibility, became the most prevalent variant for most places globally (Volz et al, 2021). Unlike other regions, including within the contiguous 48 states of the United States (hereafter referred to as Lower 48), Alaska’s dominant lineage was B.1.1.519 throughout early 2021, which was similar to Mexico in late 2020 (Haan et al, 2022; Rodríguez-Maldonado et al, 2021). The timeline in which Alpha and B.1.1.519 emerged in Alaska paired with the striking difference in prevalence between Alaska, which had a peak B.1.1.519 prevalence of 77.9%, and the Lower 48, which had a peak prevalence of 4.9%, was indicative of a B.1.1.519 founder event in Alaska (Haan et al, 2022).…”

“…Unlike other regions, including within the contiguous 48 states of the United States (hereafter referred to as Lower 48), Alaska’s dominant lineage was B.1.1.519 throughout early 2021, which was similar to Mexico in late 2020 (Haan et al, 2022; Rodríguez-Maldonado et al, 2021). The timeline in which Alpha and B.1.1.519 emerged in Alaska paired with the striking difference in prevalence between Alaska, which had a peak B.1.1.519 prevalence of 77.9%, and the Lower 48, which had a peak prevalence of 4.9%, was indicative of a B.1.1.519 founder event in Alaska (Haan et al, 2022). Since this initial deviation from the Lower 48, Alaska has displayed similar patterns of variant emergence and spread both with the sweep of the Delta variant in early August 2021 followed by the sweep of Omicron beginning in December 2021 (CDC, 2021).…”

“…The Omicron sublineage reported in this study, BA.2.3, encodes several key amino acid changes including A2909V in ORF1a and L140F in ORF3a. These changes may have provided growth advantages such as antibody evasion and increased reproductive rate that allowed Omicron lineages to displace Delta initially (Iketani et al, 2022; Smith et al, 2022).…”

“…We contrast this pattern with observations in the Lower 48 and several major US states including California, New York, and Washington. Using data generated through genomic surveillance efforts, we explore the pattern in Omicron sublineages of Alaska similar to that of the founder event that occurred with B.1.1.519 in early 2021 (Haan et al, 2022). These repetitive patterns of variant emergence are suggestive of repeat founder events in Alaska.…”