Phylodynamics of a regional SARS-CoV-2 rapid spreading event in Colorado in late 2020

  1. Kristen J. Wade
  2. Samantha Tisa
  3. Chloe Barrington
  4. Jesslyn C. Henriksen
  5. Kristy R. Crooks
  6. Christopher R. Gignoux
  7. Austin T. Almand
  8. J. Jordan Steel
  9. John C. Sitko
  10. Joseph W. Rohrer
  11. Douglas P. Wickert
  12. Erin A. Almand
  13. David D. Pollock
  14. Olivia S. Rissland

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Abstract

Since the initial reported discovery of SARS-CoV-2 in late 2019, genomic surveillance has been an important tool to understand its transmission and evolution. Here, we sought to describe the underlying regional phylodynamics before and during a rapid spreading event that was documented by surveillance protocols of the United States Air Force Academy (USAFA) in late October-November of 2020. We used replicate long-read sequencing on Colorado SARS-CoV-2 genomes collected July through November 2020 at the University of Colorado Anschutz Medical campus in Aurora and the United States Air Force Academy in Colorado Springs. Replicate sequencing allowed rigorous validation of variation and placement in a phylogenetic relatedness network. We focus on describing the phylodynamics of a lineage that likely originated in the local Colorado Springs community and expanded rapidly over the course of two months in an outbreak within the well-controlled environment of the United States Air Force Academy. Divergence estimates from sampling dates indicate that the SARS-CoV-2 lineage associated with this rapid expansion event originated in late October 2020. These results are in agreement with transmission pathways inferred by the United States Air Force Academy, and provide a window into the evolutionary process and transmission dynamics of a potentially dangerous but ultimately contained variant.

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  1. Version published to 10.1371/journal.pone.0274050
  2. ScreenIT

    SciScore for 10.1101/2021.09.28.21262976: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    RandomizationSamples were processed in random order in two replicates.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Summary statistics describing read length, error rate, total number of reads, number of reads mapped and other quality metrics were generated using samtools stats.
    samtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    Following previous publications (Hourdel et al. 2020; Paden et al. 2020), positions with coverage less than or equal to 30X were marked as ‘N’ in the consensus genome sequence using bedtools maskfasta.
    bedtools
    suggested: (BEDTools, RRID:SCR_006646)

    Results from OddPub: Thank you for sharing your code.

    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.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  3. Version published to 10.1101/2021.09.28.21262976v1 on medRxiv