Viral Sequencing to Investigate Sources of SARS-CoV-2 Infection in US Healthcare Personnel

  1. Katarina M Braun
  2. Gage K Moreno
  3. Ashley Buys
  4. Elizabeth D Somsen
  5. Max Bobholz
  6. Molly A Accola
  7. Laura Anderson
  8. William M Rehrauer
  9. David A Baker
  10. Nasia Safdar
  11. Alexander J Lepak
  12. David H O’Connor
  13. Thomas C Friedrich

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Abstract

Background

Healthcare personnel (HCP) are at increased risk of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We posit that current infection control guidelines generally protect HCP from SARS-CoV-2 infection in a healthcare setting.

Methods

In this retrospective case series, we used viral genomics to investigate the likely source of SARS-CoV-2 infection in HCP at a major academic medical institution in the Upper Midwest of the United States between 25 March and 27 December 2020. We obtained limited epidemiological data through informal interviews and review of the electronic health record and combined this information with healthcare-associated viral sequences and viral sequences collected in the broader community to infer the most likely source of infection in HCP.

Results

We investigated SARS-CoV-2 infection clusters involving 95 HCP and 137 possible patient contact sequences. The majority of HCP infections could not be linked to a patient or coworker (55 of 95 [57.9%]) and were genetically similar to viruses circulating concurrently in the community. We found that 10.5% of HCP infections (10 of 95) could be traced to a coworker. Strikingly, only 4.2% (4 of 95) could be traced to a patient source.

Conclusions

Infections among HCP add further strain to the healthcare system and put patients, HCP, and communities at risk. We found no evidence for healthcare-associated transmission in the majority of HCP infections evaluated. Although we cannot rule out the possibility of cryptic healthcare-associated transmission, it appears that HCP most commonly become infected with SARS-CoV-2 via community exposure. This emphasizes the ongoing importance of mask wearing, physical distancing, robust testing programs, and rapid distribution of vaccines.

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  3. Version published to 10.1093/cid/ciab281
  4. ScreenIT

    SciScore for 10.1101/2021.01.28.21250421: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: Study approvals: The University of Wisconsin-Madison Institutional Review Board deemed this study quality improvement, rather than research, and considered it exempt from review.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    When inspecting in Geneious, we aligned all sequences to a standard reference sequence – an early Wuhan sequence (Genbank: MN908947.3).
    Geneious
    suggested: (Geneious, RRID:SCR_010519)
    We used Pangolin’s command-line tool to assign sequences to Pangolin lineages (https://github.com/cov-lineages/pangolin).
    Pangolin’s
    suggested: None
    Figures 1A, 2A, and 3A were created with BioRender.com.
    BioRender
    suggested: (Biorender, RRID:SCR_018361)

    Results from OddPub: Thank you for sharing your code.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    Given this limitation, we were often able to exclude patient contacts and co-workers as likely sources of infection in HCP, but we were rarely able to pinpoint the exact source of infection, especially when it occurred outside of the healthcare setting. In addition, this study only examined SARS-CoV-2 infections in HCP from a single academic medical center so our conclusions may not be broadly generalizable. However, another recent study evaluated healthcare-associated infections in the Netherlands and similarly found no evidence for widespread nosocomial transmission of SARS-CoV-2, suggesting our conclusions may hold across institutions and healthcare systems 1. Further, we were not able to differentiate between routes of infection (airborne, droplet, contact) with the limited epidemiological data available to us in this study. Here we demonstrated how rapid whole-genome sequencing of current SARS-CoV-2 outbreaks in hospitals can be used retrospectively to reconstruct the likely source of HCP infection and prospectively to adjust and improve infection control practices and guidelines. The approach we describe here need not be limited to investigation of pandemic virus outbreaks. Key concepts from genome sequencing and routine pathogen surveillance can be applied to any nosocomial pathogen and inform changes to infection control practices. Overall, while we do find examples of patient-to-HCP and HCP-to-HCP spread, the majority of HCP infections appeared to be acquired through...

    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.

  5. Version published to 10.1101/2021.01.28.21250421v1 on medRxiv