SARS-CoV-2 detection and genomic sequencing from hospital surface samples collected at UC Davis

  1. David A. Coil
  2. Timothy Albertson
  3. Shefali Banerjee
  4. Greg Brennan
  5. A. J. Campbell
  6. Stuart H. Cohen
  7. Satya Dandekar
  8. Samuel L. Díaz-Muñoz
  9. Jonathan A. Eisen
  10. Tracey Goldstein
  11. Ivy R. Jose
  12. Maya Juarez
  13. Brandt A. Robinson
  14. Stefan Rothenburg
  15. Christian Sandrock
  16. Ana M. M. Stoian
  17. Daniel G. Tompkins
  18. Alexandre Tremeau-Bravard
  19. Angela Haczku

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Abstract

There is little doubt that aerosols play a major role in the transmission of SARS-CoV-2. The significance of the presence and infectivity of this virus on environmental surfaces, especially in a hospital setting, remains less clear.

Objectives

We aimed to analyze surface swabs for SARS-CoV-2 RNA and infectivity, and to determine their suitability for sequence analysis.

Methods

Samples were collected during two waves of COVID-19 at the University of California, Davis Medical Center, in COVID-19 patient serving and staff congregation areas. qRT-PCR positive samples were investigated in Vero cell cultures for cytopathic effects and phylogenetically assessed by whole genome sequencing.

Measurements and main results

Improved cleaning and patient management practices between April and August 2020 were associated with a substantial reduction of SARS-CoV-2 qRT-PCR positivity (from 11% to 2%) in hospital surface samples. Even though we recovered near-complete genome sequences in some, none of the positive samples (11 of 224 total) caused cytopathic effects in cultured cells suggesting this nucleic acid was either not associated with intact virions, or they were present in insufficient numbers for infectivity. Phylogenetic analysis suggested that the SARS-CoV-2 genomes of the positive samples were derived from hospitalized patients. Genomic sequences isolated from qRT-PCR negative samples indicate a superior sensitivity of viral detection by sequencing.

Conclusions

This study confirms the low likelihood that SARS-CoV-2 contamination on hospital surfaces contains infectious virus, disputing the importance of fomites in COVID-19 transmission. Ours is the first report on recovering near-complete SARS-CoV-2 genome sequences directly from environmental surface swabs.

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  1. Version published to 10.1371/journal.pone.0253578
  2. ScreenIT

    SciScore for 10.1101/2021.02.23.21252022: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    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
    Six-well plates of Vero E6 cells (∼60% confluent) were infected with either 300 uL of the viral transport medium from qRT-PCR positive environmental swab samples diluted 1:1 in D10-CoV medium, or 300 µL of mNeonGreen SARS-CoV-2 (icSARS-CoV-2-mNG) 10-fold serially diluted in D10-CoV medium to infect wells with 105 PFU to 100 PFU per well.
    Vero E6
    suggested: RRID:CVCL_XD71)
    Software and Algorithms
    SentencesResources
    All swab samples and positive controls were diluted in D10-CoV medium consisting of DMEM supplemented with 10% FBS, 100 IU/ml Pen-Strep, 250 µg/ml Amphotericin B (Gibco) and 250 µg/ml Gentamicin (Quality Biologicals).
    Quality Biologicals
    suggested: None
    We followed the ARTIC Network bioinformatics SOP, which in brief involved high accuracy basecalling and demultiplexing using ONT Guppy, mapping reads to the Wuhan-Hu-1 (accession MN908947) reference, polishing with Nanopolish, and consensus generation (code for analysis available https://github.com/sociovirology/sars_cov2_environmental_seq).
    Nanopolish
    suggested: (Nanopolish, RRID:SCR_016157)

    Results from OddPub: Thank you for sharing your code and data.

    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 10.1101/2021.02.23.21252022v1 on medRxiv