Early Adoption of Longitudinal Surveillance for SARS-CoV-2 among Staff in Long-Term Care Facilities: Prevalence, Virologic and Sequence Analysis

  1. Emily N. Gallichotte
  2. Kendra M. Quicke
  3. Nicole R. Sexton
  4. Emily Fitzmeyer
  5. Michael C. Young
  6. Ashley J. Janich
  7. Karen Dobos
  8. Kristy L. Pabilonia
  9. Gregory Gahm
  10. Elizabeth J. Carlton
  11. Gregory D. Ebel
  12. Nicole Ehrhart

Reviewed by

Read the full article See related articles

Listed in

Log in to save this article

Abstract

Our work comprises unique data on the characteristics of SARS-CoV-2 dynamics among staff working at LTCFs in the early months of the SARS-CoV-2 pandemic prior to mandated staff surveillance testing. During this time period, LTCF residents were largely sheltering-in-place.

Article activity feed

  1. Version published to 10.1128/spectrum.01003-21
  2. ScreenIT

    SciScore for 10.1101/2020.06.08.20125989: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementConsent: Study sites: Staff at LTCFs provided consent to participate in this study.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    Plaque assay: Plaque assays were performed on African Green Monkey Kidney (Vero) cells (ATCC CCL-81) according to standard methods [28].
    Vero
    suggested: None
    Software and Algorithms
    SentencesResources
    Symptom reporting: Symptom data were collected and managed with REDCap electronic data capture tools hosted at the Colorado Clinical and Translational Sciences Institute (CCTSI) at University of Colorado Anschutz Medical Campus [29, 30].
    REDCap
    suggested: (REDCap, RRID:SCR_003445)
    MiSeq reads were demultiplexed, quality checked by FASTQC, paired-end reads were processed to remove Illumina primers and quality trimmed with Cutadapt; duplicate reads were removed.
    MiSeq
    suggested: (A5-miseq, RRID:SCR_012148)
    FASTQC
    suggested: (FastQC, RRID:SCR_014583)
    Consensus sequences were aligned in Geneious and a maximum-likelihood tree generated using PhyML in Geneious with the Wuhan-Hu-1 reference sequence (GeneBank: MN908947.3) as an outgroup and 100 bootstrap replicates.
    PhyML
    suggested: (PhyML, RRID:SCR_014629)
    Geneious
    suggested: (Geneious, RRID:SCR_010519)

    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.

    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 10.1101/2020.06.08.20125989v2 on medRxiv
  4. ScreenIT

    SciScore for 10.1101/2020.06.08.20125989: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementParticipants provided consent to participate in the study and were promptly informed of test results and, if positive, instructed to self-isolate for a period of ten days.Randomizationnot detected.Blindingnot detected.Power AnalysisAdditional data on the degree of viral genetic diversity in the larger community would add significant power to our ability to discriminate between these two non-mutually exclusive scenarios.Sex as a biological variablenot detected.Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    Plaque assays were performed on African Green Monkey Kidney (Vero) cells (ATCC CCL-81) according to standard methods (5).
    Vero
    suggested: None
    Software and Algorithms
    SentencesResources
    MiSeq reads were demultiplexed, quality checked by FASTQC, paired-end reads were processed to remove Illumina primers and quality trimmed with Cutadapt, duplicate reads were removed.
    MiSeq
    suggested: (A5-miseq, SCR_012148)
          <div style="margin-bottom:8px">
        <div><b>FASTQC</b></div>
        <div>suggested: (FastQC, <a href="https://scicrunch.org/resources/Any/search?q=SCR_014583">SCR_014583</a>)</div>
      </div>
    
      <div style="margin-bottom:8px">
        <div><b>Cutadapt</b></div>
        <div>suggested: (cutadapt, <a href="https://scicrunch.org/resources/Any/search?q=SCR_011841">SCR_011841</a>)</div>
      </div>
    </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Consensus sequences were aligned in Geneious and a neighbor-joining tree generated with the Reference sequence as an outgroup and 1000 bootstrap replicates.</td><td style="min-width:100px;border-bottom:1px solid lightgray">
      <div style="margin-bottom:8px">
        <div><b>Geneious</b></div>
        <div>suggested: (Geneious, <a href="https://scicrunch.org/resources/Any/search?q=SCR_010519">SCR_010519</a>)</div>
      </div>
    </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Clinical characteristics of 24 asymptomatic infections with COVID-19 screened among close contacts in Nanjing, China. Sci China Life Sci 63:706711. 4. Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DKW, Bleicker T, Brunink S, Schneider J, Schmidt ML, Mulders D, Haagmans BL, van der Veer B, van den Brink S, Wijsman L, Goderski G, Romette JL, Ellis J, Zambon M, Peiris M, Goossens H, Reusken C, Koopmans MPG, Drosten C. 2020. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR.</td><td style="min-width:100px;border-bottom:1px solid lightgray">
      <div style="margin-bottom:8px">
        <div><b>Schneider J</b></div>
        <div>suggested: (ARLEQUIN, <a href="https://scicrunch.org/resources/Any/search?q=SCR_009051">SCR_009051</a>)</div>
      </div>
    </td></tr></table>

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

    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 is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, including references cited, please follow this link.

  5. Version published to 10.1101/2020.06.08.20125989v1 on medRxiv