Multiple Introductions of SARS-CoV-2 Alpha and Delta Variants into White-Tailed Deer in Pennsylvania

  1. Andrew D. Marques
  2. Scott Sherrill-Mix
  3. John K. Everett
  4. Hriju Adhikari
  5. Shantan Reddy
  6. Julie C. Ellis
  7. Haley Zeliff
  8. Sabrina S. Greening
  9. Carolyn C. Cannuscio
  10. Katherine M. Strelau
  11. Ronald G. Collman
  12. Brendan J. Kelly
  13. Kyle G. Rodino
  14. Frederic D. Bushman
  15. Roderick B. Gagne
  16. Eman Anis

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Abstract

Coronaviruses have been documented to replicate in numerous species of vertebrates, and multiple spillovers of coronaviruses from animals into humans have founded human epidemics. The COVID-19 epidemic likely derived from a spillover of SARS-CoV-2 from bats into humans, possibly via an intermediate host.

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  1. Version published to 10.1128/mbio.02101-22
  2. Version published to 10.1101/2022.02.17.22270679v4 on medRxiv
  3. Version published to 10.1101/2022.02.17.22270679v3 on medRxiv
  4. ScreenIT

    SciScore for 10.1101/2022.02.17.22270679: (What is this?)

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

    Table 1: Rigor

    EthicsField Sample Permit: Samples were shipped to the University of Pennsylvania within one week of collection and stored at -80°C until RNA extraction.
    IRB: For most samples, the University of Pennsylvania Institutional Review Board (IRB) reviewed the research protocol and deemed the limited data elements extracted to be exempt from human subject research per 45 CFR 46.104, category 4 (IRB #848605).
    Consent: For hospitalized subjects, following informed consent (IRB protocol #823392), patients were sampled by collection of saliva, oropharyngeal and/or nasopharyngeal swabs, or endotracheal aspirates if intubated, as previously described 18.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Chi-squared tests were performed using R Statistical software (v4.0.5)15 (R Core Development Team 2021) to test for differences in proportions of positive deer by gender, age, source of deer (i.e., from volunteer compared to technician collectors as well as between hunter harvested, road-killed, or all other causes of death).
    R Statistical
    suggested: (R Project for Statistical Computing, RRID:SCR_001905)
    BWA aligner tool (v0.7.17) was used to align subject sequences to the Wuhan reference sequence (NC_045512.2)19.
    BWA
    suggested: (BWA, RRID:SCR_010910)
    Samtools package (v1.10) was used to filter alignments20.
    Samtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    Mutation Analysis: 108 deer-derived SARS-CoV-2 genomes were downloaded from GISAID and compared with the 7 deer sequenced in this publication and the human dataset.
    Mutation Analysis
    suggested: None
    IQ-TREE (v1.6.12) was used to infer a tree using maximum-likelihood methods using 1,000 bootstrap replicates27.
    IQ-TREE
    suggested: (IQ-TREE, RRID:SCR_017254)
    Visualization of the inferred tree was performed using FigTree (v.1.4.4)28.
    FigTree
    suggested: (FigTree, RRID:SCR_008515)

    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.

    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.

  5. Version published to 10.1101/2022.02.17.22270679v2 on medRxiv
  6. Version published to 10.1101/2022.02.17.22270679v1 on medRxiv