Detection and Interspecies Comparison of SARS-CoV-2 Delta Variant (AY.3) in Feces from a Domestic Cat and Human Samples

  1. Olivia C. Lenz
  2. Andrew D. Marques
  3. Brendan J. Kelly
  4. Kyle G. Rodino
  5. Stephen D. Cole
  6. Ranawaka A.P.M. Perera
  7. Susan R. Weiss
  8. Frederic D. Bushman
  9. Elizabeth M. Lennon

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Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have spilled over from humans to companion and wild animals since the inception of the global COVID-19 pandemic. However, whole genome sequencing data of the viral genomes that infect non-human animal species has been scant. Here, we detected and sequenced a SARS-CoV-2 delta variant (AY.3) in fecal samples from an 11-year-old domestic house cat previously exposed to an owner who tested positive for SARS-CoV-2. Molecular testing of two fecal samples collected 7 days apart yielded relatively high levels of viral RNA. Sequencing of the feline-derived viral genomes showed the two to be identical, and differing by between 4 and 14 single nucleotide polymorphisms in pairwise comparisons to human-derived lineage AY.3 sequences collected in the same geographic area and time period. However, several mutations unique to the feline samples reveal their divergence from this cohort on phylogenetic analysis. These results demonstrate continued spillover infections of emerging SARS-CoV-2 variants that threaten human and animal health, as well as highlight the importance of collecting fecal samples when testing for SARS-CoV-2 in animals. To the authors’ knowledge, this is the first published case of a SARS-CoV-2 delta variant in a domestic cat in the United States.

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    SciScore for 10.1101/2022.01.31.478506: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: The University of Pennsylvania Institutional Review Board (IRB) reviewed the human research protocol and deemed the limited data elements extracted with positive human SARS-CoV-2 specimens to be exempt from human subject research per 45 CFR 46.104, category 4 (IRB #848605).
    Consent: Informed owner consent was provided for all procedures involving the cat.
    IACUC: The University of Pennsylvania Institutional Animal Care and Use Committee (IACUC) and Privately Owned Animal Protocol (POAP) Committee approved the protocol (IACUC/POAP #806977).
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Alignment used the BWA aligner tool (v0.7.17) [20]
    BWA
    suggested: (BWA, RRID:SCR_010910)
    Samtools package (v1.10) was used to remove reads that did not align to the reference [21].
    Samtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    2.5 SARS-CoV-2 Whole Genome Sequencing: To construct phylogenetic trees, NextClade was used for alignment [24], IQ-Tree (v1.6.12) was used to generate the phylogenetic tree [25–28], and FigTree v1.4.4 was used to visualize the tree.
    IQ-Tree
    suggested: (IQ-TREE, RRID:SCR_017254)
    FigTree
    suggested: (FigTree, RRID:SCR_008515)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    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.

  2. Version published to 10.1101/2022.01.31.478506 on bioRxiv