Interregional SARS-CoV-2 spread from a single introduction outbreak in a meat-packing plant in northeast Iowa

  1. Craig S. Richmond
  2. Arick P. Sabin
  3. Dean A. Jobe
  4. Steven D. Lovrich
  5. Paraic A. Kenny

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Abstract

SARS-CoV-2 spread has proven to be especially difficult to mitigate in high risk settings, including nursing homes, cruises, prisons and various industrial settings. Among industrial settings, meat processing facilities in the United States have experienced particularly challenging outbreaks. We have sequenced SARS-CoV-2 whole viral genomes from individuals testing positive in an integrated regional healthcare system serving 21 counties in southwestern Wisconsin, northeastern Iowa and southeastern Minnesota, providing an overview of SARS-CoV-2 introduction and spread in a region spanning multiple jurisdictions with differing mitigation policies. While most viral introductions we detected were contained with only minor transmission chains, a striking exception was an outbreak associated with a meatpacking plant in Postville, IA. In this case, a single viral introduction led to unrestrained spread within the facility, affecting many staff and members of their households. Importantly, by surveilling viral sequences from the surrounding counties, we have documented the spread of this SARS-CoV-2 substrain from this epicenter to individuals in 13 cities in 7 counties in Iowa, Wisconsin and Minnesota, a region spanning 185 square miles. This study highlights the regional public health consequences of failures to rapidly act to mitigate viral spread in a single industrial setting.

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  1. ScreenIT

    SciScore for 10.1101/2020.06.08.20125534: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: This study includes positive cases diagnosed between 3/18/2020 and 5/24/2020) Ethical approval was obtained from the Gundersen Health System Institutional Review Board (#2-20-03-008; PI: Kenny) to perform additional next-generation sequencing on remnant specimens after completion of diagnostic testing.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Samples for this study include only those testing positive in Gundersen Healthcare System’s diagnostic laboratories and, as such, do not include other cases from the region which may have been tested in other healthcare systems and/or public health laboratories
    Gundersen Healthcare
    suggested: None
    To overcome difficulties caused by read soft-clipping by this non-splice aware aligner, individual sequence reads were extracted using samtools (4) and re-aligned to the SARS-CoV-2 genome using a splice-aware aligner, hisat2 (5).
    samtools
    suggested: (SAMTOOLS, RRID:SCR_002105)

    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.

  2. Version published to 10.1101/2020.06.08.20125534v1 on medRxiv