Longitudinal COVID-19 Surveillance and Characterization in the Workplace with Public Health and Diagnostic Endpoints

  1. Manjula Gunawardana
  2. Jessica Breslin
  3. John M. Cortez
  4. Sofia Rivera
  5. Simon Webster
  6. F. Javier Ibarrondo
  7. Otto O. Yang
  8. Richard B. Pyles
  9. Christina M. Ramirez
  10. Amy P. Adler
  11. Peter A. Anton
  12. Marc M. Baum

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Abstract

The rapid spread of SARS-CoV-2 and the associated COVID-19 has precipitated a global pandemic heavily challenging our social behavior, economy, and health care infrastructure. In the absence of widespread, worldwide access to safe and effective vaccines and therapeutics, public health measures represent a key intervention for curbing the devastating impacts from the pandemic.

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  1. Version published to 10.1128/msphere.00542-21
  2. ScreenIT

    SciScore for 10.1101/2020.07.25.20160812: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementConsent: All 54 study participants provided written informed consent or assent.
    IRB: Volunteers who met the inclusion criteria were asked to provide written consent (or assent in the case of minors) to participate in the study, under an institutional review board approved protocol.
    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
    Confluent Caco-2 cells were used as a human specimen control (HSC) according to CDC guidelines [9].
    Caco-2
    suggested: None
    Software and Algorithms
    SentencesResources
    The plates were run on a CFX96 Touch Real-Time PCR Detection System (Bio-Rad Laboratories, Inc., Hercules, CA) using the following cycling conditions: Stage 1, 25°C, 2 min (1 cycle); Stage 2, 50°C, 15 min (1 cycle); Stage 3, 95°C, 2 min (1 cycle); Stage 4, Step 1, 95°C, 3 s
    Bio-Rad Laboratories
    suggested: (Bio-Rad Laboratories, RRID:SCR_008426)
    Data Analysis: Datasets were analyzed using GraphPad Prism (version 8.4.3, GraphPad Software, Inc., La Jolla, CA).
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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: We detected the following sentences addressing limitations in the study:
    There are some caveats to interpreting our antibody data. We measured only IgM, IgG, and IgA against RBD and not the whole spike or E proteins, as discussed in more detail elsewhere [33]. The IgM assay is subject to greater uncertainty compared to IgA and IgG at low concentrations (ca. 0.25 µg mL-1, or lower) need to be interpreted with caution. However, all serum samples were analyzed at three levels of dilution (1:100, 1:40, and 1:20) and only detectable concentrations in at least 2 of the 3 diluted samples are reported. The clinical study described here has met its goals to date by providing a safe work environment for employees of a small academic institute. The ability to perform routine, frequent COVID-19 testing not only has allowed us to responsibly maintain a productive work environment during the pandemic, but also provided continuous reassuring data for the participating households, many including vulnerable individuals. This had the important mental health benefits of reducing anxiety and providing a sense of normalcy in the workplace (i.e., safe zone) during an acutely stressful period. Modeling local study impacts predicted that without our intervention up to 7 employees or household contacts could have become infected with SARS-CoV-2 by July 7, 2020. Our finding that only 2 subjects contracted COVID-19, one prior to the start of the study, suggests that workplace disease surveillance based on frequent, longitudinal testing combined with recommended public healt...

    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. ScreenIT

    SciScore for 10.1101/2020.07.25.20160812: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementAll 54 study participants provided written informed consent or assent.Randomizationnot detected.Blindingnot detected.Power Analysisnot detected.Sex as a biological variable(21-68) 40 (11-80) Female, n (%) 13 (48) 16 (59) Male, n (%) 14 (52) 11 (41) Black or African American 0 0 White 23 (85) 25 (93) Hispanic 10 (37) 14 (52Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    The plates were washed three times with TPBS, and the secondary antibody anti-human IgG-horseradish peroxidase (Bethyl Laboratories, Montgomery, TX) –or anti-human IgM-horseradish peroxidase, or anti-IgAhorseradish peroxidase– was added in PBS at a 1:50,000 dilution for incubation at room temperature for one hour.
    anti-human IgG-horseradish
    suggested: None
    anti-human IgM-horseradish peroxidase ,
    suggested: None
    anti-IgAhorseradish
    suggested: None
    Each plate also contained wells with the control anti-RBD monoclonal IgG antibody CR3022 (Creative Biolabs, New York, NY) plated in serial dilutions to establish a standard curve, or an IgM or IgA monoclonal antibody with the same variable region as CR3022 produced in-house.
    anti-RBD
    suggested: None
    IgA
    suggested: None
    Blood draws on May 14, 15, and 26 from the subject produced serum samples that were below the analytical LLD for 2 of the measured anti-SARS-CoV-2 monoclonal antibodies (IgM and IgG).
    anti-SARS-CoV-2
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Confluent Caco-2 cells were used as a human specimen control (HSC) according to CDC guidelines [9].
    Caco-2
    suggested: CLS Cat# 300137/p1665_CaCo-2, RRID:CVCL_0025
    Software and Algorithms
    SentencesResources
    The plates were run on a CFX96 Touch Real-Time PCR Detection System (Bio-Rad Laboratories, Inc., Hercules, CA) using the following cycling conditions: Stage 1, 25°C, 2 min (1 cycle); Stage 2, 50°C, 15 min (1 cycle); Stage 3, 95°C , 2 min (1 cycle); Stage 4, Step 1, 95°C, 3 s, Step 2, 55°C, 30
    Bio-Rad Laboratories
    suggested: (Bio-Rad Laboratories, RRID:SCR_008426)
    Data Analysis Datasets were analyzed using GraphPad Prism (version 8.4.3, GraphPad Software, Inc., La Jolla, CA).
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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: We detected the following sentences addressing limitations in the study:

    There are some caveats to interpreting our antibody data. We measured only IgM, IgG, and IgA against RBD and not the whole spike or E proteins, as discussed in more detail elsewhere [33]. The IgM assay is subject to greater uncertainty compared to IgA and IgG at low concentrations (ca. 0.25 µg mL-1, or lower) need to be interpreted with caution. However, all serum samples were analyzed at three levels of dilution (1:100, 1:40, and 1:20) and only detectable concentrations in at least 2 of the 3 diluted samples are reported. The clinical study described here has met its goals to date by providing a safe work environment for employees of a small academic institute. The ability to perform routine, frequent COVID-19 testing not only has allowed us to responsibly maintain a productive work environment during the pandemic, but also provided continuous reassuring data for the participating households, many including vulnerable individuals. This had the important mental health benefits of reducing anxiety and providing a sense of normalcy in the workplace (i.e., safe zone) during an acutely stressful period. Modeling local study impacts predicted that without our intervention up to 7 employees or household contacts could have become infected with SARS-CoV-2 by July 7, 2020. Our finding that only 2 subjects contracted COVID-19, one prior to the start of the study, suggests that workplace disease surveillance based on frequent, longitudinal testing combined with recommended public health practices (social distancing, frequent hand sanitizing, and mask wearing on select days), when feasible, can be effective at creating a safe zone or bubble preventing COVID-19 from entering into the workplace. Our simulations predicted an important, local public health benefit from our scalable surveillance plan. Similar approaches are being adopted by professional sports leagues (e.g., the National Hockey League), the entertainment industry, and others to support responsible resumption of their activities. The study also generated important, new scientific data on the SARS-CoV-2 host dynamics enabled by its longitudinal, intense sampling design. Our clinical study represents a powerful example on how an innovative public health initiative can be dovetailed with scientific discovery.

    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.

    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.

  4. ScreenIT

    SciScore for 10.1101/2020.07.25.20160812: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementAll 54 study participants provided written informed consent or assent.Randomizationnot detected.Blindingnot detected.Power Analysisnot detected.Sex as a biological variablenot detected.Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Serum virus-specific antibody concentrations (IgG, IgM, and IgA) were measured using a selective, sensitive, and quantitative ELISA assay developed in house.
    IgA
    suggested: None
    The plates were washed three times with TPBS, and the secondary antibody anti-human IgG-horseradish peroxidase (Bethyl Laboratories, Montgomery, TX) –or anti-human IgM-horseradish peroxidase, or anti-IgAhorseradish peroxidase– was added in PBS at a 1:50,000 dilution for incubation at room temperature for one hour.
    anti-human IgG-horseradish
    suggested: None
          <div style="margin-bottom:8px">
        <div><b>anti-human IgM-horseradish peroxidase ,</b></div>
        <div>suggested: None</div>
      </div>
    
      <div style="margin-bottom:8px">
        <div><b>anti-IgAhorseradish</b></div>
        <div>suggested: None</div>
      </div>
    </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Each plate also contained wells with the control anti-RBD monoclonal IgG antibody CR3022 (Creative Biolabs, New York, NY) plated in serial dilutions to establish a standard curve, or an IgM or IgA monoclonal antibody with the same variable region as CR3022 produced in-house.</td><td style="min-width:100px;border-bottom:1px solid lightgray">
      <div style="margin-bottom:8px">
        <div><b>anti-RBD</b></div>
        <div>suggested: None</div>
      </div>
    </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Blood draws on May 14, 15, and 26 from the subject produced serum samples that were below the analytical LLD for 2 of the measured anti-SARS-CoV-2 monoclonal antibodies (IgM and IgG).</td><td style="min-width:100px;border-bottom:1px solid lightgray">
      <div style="margin-bottom:8px">
        <div><b>anti-SARS-CoV-2</b></div>
        <div>suggested: None</div>
      </div>
    </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Subject 18, a self-quarantined employee who had just recovered from suspected COVID-19 (based on symptomology) at the start of the study, repeatedly tested negative for SARS-CoV-2 RNA, but tested positive for IgM antibodies that rapidly declined (τ1/2 = 8.8 d, Fig. 4A).</td><td style="min-width:100px;border-bottom:1px solid lightgray">
      <div style="margin-bottom:8px">
        <div><b>IgM</b></div>
        <div>suggested: None</div>
      </div>
    </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2"><b>Experimental Models: Cell Lines</b></td></tr><tr><td style="min-width:100px;text=align:center"><i>Sentences</i></td><td style="min-width:100px;text-align:center"><i>Resources</i></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Confluent Caco-2 cells were used as a human specimen control (HSC) according to CDC guidelines [9].</td><td style="min-width:100px;border-bottom:1px solid lightgray">
      <div style="margin-bottom:8px">
        <div><b>Caco-2</b></div>
        <div>suggested: CLS Cat# 300137/p1665_CaCo-2, <a href="https://scicrunch.org/resources/Any/search?q=CVCL_0025">CVCL_0025</a></div>
      </div>
    </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2"><b>Software and Algorithms</b></td></tr><tr><td style="min-width:100px;text=align:center"><i>Sentences</i></td><td style="min-width:100px;text-align:center"><i>Resources</i></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Data Analysis Datasets were analyzed using GraphPad Prism (version 8.4.3, GraphPad Software, Inc., La Jolla, CA).</td><td style="min-width:100px;border-bottom:1px solid lightgray">
      <div style="margin-bottom:8px">
        <div><b>GraphPad Prism</b></div>
        <div>suggested: (GraphPad Prism, <a href="https://scicrunch.org/resources/Any/search?q=SCR_002798">SCR_002798</a>)</div>
      </div>
    
      <div style="margin-bottom:8px">
        <div><b>GraphPad</b></div>
        <div>suggested: (GraphPad Prism, <a href="https://scicrunch.org/resources/Any/search?q=SCR_002798">SCR_002798</a>)</div>
      </div>
    </td></tr></table>

    Data from additional tools added to each annotation on a weekly basis.

    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 10.1101/2020.07.25.20160812 on medRxiv