A Method for Variant Agnostic Detection of SARS-CoV-2, Rapid Monitoring of Circulating Variants, and Early Detection of Emergent Variants Such as Omicron

  1. Eric Lai
  2. Emily B. Kennedy
  3. Jean Lozach
  4. Kathleen Hayashibara
  5. Jeremy Davis-Turak
  6. David Becker
  7. Pius Brzoska
  8. Tyler Cassens
  9. Evan Diamond
  10. Manoj Gandhi
  11. Alexander L. Greninger
  12. Pooneh Hajian
  13. Nicole A. Leonetti
  14. Jason M. Nguyen
  15. K. M. Clair O’Donovan
  16. Troy Peck
  17. Jimmy M. Ramirez
  18. Pavitra Roychoudhury
  19. Efren Sandoval
  20. Cassandra Wesselman
  21. Timothy Wesselman
  22. Simon White
  23. Stephen Williams
  24. David Wong
  25. Yufei Yu
  26. Richard S. Creager

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Abstract

The rapid emergence of SARS-CoV-2 variants raised public health questions concerning the capability of diagnostic tests to detect new strains, the efficacy of vaccines, and how to map the geographical distribution of variants to understand transmission patterns and loads on healthcare resources. Next-generation sequencing (NGS) is the primary method for detecting and tracing new variants, but it is expensive, and it can take weeks before sequence data are available in public repositories.

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  1. Version published to 10.1128/jcm.00342-22
  2. ScreenIT

    SciScore for 10.1101/2022.01.08.22268865: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: Samples: SARS-CoV-2 positive subject samples used in this investigation were collected in November 2021 and December 2021 by Helix OpCo and The University of Washington (UW), both Clinical Laboratory Improvement Amendments (CLIA)-certified labs participating in the CDC National SARS-CoV-2 Strain Surveillance (NS3) sequencing program to monitor variant distribution in the United States.26 Western Institutional Review Board-Copernicus Group (WCG), the Institutional Review Board (IRB) of record for the Helix Respiratory Registry, gave ethical approval for the use of Helix OpCo de-identified remnants of clinical testing.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Pairwise whole-genome alignments of all sequences were performed using LASTZ v1.04.02 with NCBI Reference Sequence: NC_045512.2 as the SARS-CoV-2 reference genome.20,21 The Bioconductor package for genetic variants, VariantAnnotation v1.20.2, was then used for the translation into amino acids in R v3.3.2, and the identification of amino acid substitutions or frameshifts were used to call a unique mutation incident.22,23 Selection of the lineages considered for the marker panel was performed by combining the top 100 most frequent lineages reported worldwide for the 120-day period between May 12, 2021 and September 11, 2021 (data not shown). 1,200,791 sequences representing 393 lineages were analyzed.
    LASTZ
    suggested: (LASTZ, RRID:SCR_018556)
    Bioconductor
    suggested: (Bioconductor, RRID:SCR_006442)
    VariantAnnotation
    suggested: (VariantAnnotation, RRID:SCR_000074)
    Samples: SARS-CoV-2 positive subject samples used in this investigation were collected in November 2021 and December 2021 by Helix OpCo and The University of Washington (UW), both Clinical Laboratory Improvement Amendments (CLIA)-certified labs participating in the CDC National SARS-CoV-2 Strain Surveillance (NS3) sequencing program to monitor variant distribution in the United States.26 Western Institutional Review Board-Copernicus Group (WCG), the Institutional Review Board (IRB) of record for the Helix Respiratory Registry, gave ethical approval for the use of Helix OpCo de-identified remnants of clinical testing.
    Clinical Laboratory
    suggested: None

    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.

    Results from scite Reference Check: We found no unreliable references.

    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 10.1101/2022.01.08.22268865v1 on medRxiv