Pattern of SARS-CoV-2 variant B.1.1.519 emergence in Alaska

  1. Tracie J. Haan
  2. Lisa K. Smith
  3. Stephanie DeRonde
  4. Elva House
  5. Jacob Zidek
  6. Diana Puhak
  7. Matthew Redlinger
  8. Jayme Parker
  9. Brian M. Barnes
  10. Jason L. Burkhead
  11. Cindy Knall
  12. Eric Bortz
  13. Jack Chen
  14. Devin M. Drown

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Abstract

Alaska has the lowest population density in the United States (US) with a mix of urban centers and isolated rural communities. Alaska’s distinct population dynamics compared to the contiguous US may have contributed to unique patterns of SARS-CoV-2 variants observed in early 2021. Here we examined 2323 SARS-CoV-2 genomes from Alaska and 278,635 from the contiguous US collected from December 2020 through June 2021 because of the notable emergence and spread of lineage B.1.1.519 in Alaska. We found that B.1.1.519 was consistently detected from late January through June of 2021 in Alaska with a peak prevalence in April of 77.9% unlike the rest of the US at 4.6%. The earlier emergence of B.1.1.519 coincided with a later peak of Alpha (B.1.1.7) compared to the contiguous US. We also observed differences in variant composition over time between the two most populated regions of Alaska and a modest increase in COVID-19 cases during the peak incidence of B.1.1.519. However, 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, likely contributed to the unique spread of B.1.1.519 in Alaska.

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  1. Version published to 10.1038/s41598-022-25373-1
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    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Visualizations and Statistical Analyses: We generated visualizations in RStudio (v 1.4.1106) using packages ggplot2 (v 3.3.5), ggpubr (v 0.4.0), tidyverse (v 1.3.1), and lubridate (v 1.7.10).
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    suggested: (ggplot2, RRID:SCR_014601)

    Results from OddPub: Thank you for sharing your data.

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.

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  3. Version published to 10.1101/2022.03.17.22272446 on medRxiv