key: cord-0885575-t7xjjxfd
authors: Haan, T. J.; Smith, L. K.; DeRonde, S.; House, E.; Zidek, J.; Puhak, D.; Redlinger, M.; Parker, J.; Barnes, B. M.; Burkhead, J. L.; Knall, C.; Bortz, E.; Chen, J.; Drown, D. M.
title: Founder effect contributes to the unique pattern of SARS-CoV-2 variant B.1.1.519 emergence in Alaska
date: 2022-03-18
journal: nan
DOI: 10.1101/2022.03.17.22272446
sha: 09b8f191abfed56997d8c4c7f0ffd7c75ab6474f
doc_id: 885575
cord_uid: t7xjjxfd

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.

Genomes that did not fall into these lineages were grouped together into the category 'Not 98

Emerging Lineage.' The number of Spike protein amino acid substitutions was determined using 99

Nextclade (v 1.13.2) with 'bad' quality genomes, as determined by Nextclade's algorithm for 100 quality, removed prior to analyses (Aksamentov et . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) Alaska emphasizes both how founder events impact regional differences in circulating SARS-263

CoV-2 lineages and the significance of having robust sequencing efforts in place to detect this 264 variation. There are several resources that compile SARS-CoV-2 sequence data to help examine 265 patterns of emergence and spread. One such resource, outbreak.info, uses genomic data from 266 the sequence repository GISAID to estimate prevalence, emergence, and spread of SARS-CoV- . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

The copyright holder for this preprint this version posted March 18, 2022. ; https://doi.org/10.1101/2022.03.17.22272446 doi: medRxiv preprint

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