Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York

  1. Anthony P. West
  2. Joel O. Wertheim
  3. Jade C. Wang
  4. Tetyana I. Vasylyeva
  5. Jennifer L. Havens
  6. Moinuddin A. Chowdhury
  7. Edimarlyn Gonzalez
  8. Courtney E. Fang
  9. Steve S. Di Lonardo
  10. Scott Hughes
  11. Jennifer L. Rakeman
  12. Henry H. Lee
  13. Christopher O. Barnes
  14. Priyanthi N. P. Gnanapragasam
  15. Zhi Yang
  16. Christian Gaebler
  17. Marina Caskey
  18. Michel C. Nussenzweig
  19. Jennifer R. Keeffe
  20. Pamela J. Bjorkman

Reviewed by

Read the full article See related articles

Listed in

Log in to save this article

Abstract

Wide-scale SARS-CoV-2 genome sequencing is critical to tracking viral evolution during the ongoing pandemic. We develop the software tool, Variant Database (VDB), for quickly examining the changing landscape of spike mutations. Using VDB, we detect an emerging lineage of SARS-CoV-2 in the New York region that shares mutations with previously reported variants. The most common sets of spike mutations in this lineage (now designated as B.1.526) are L5F, T95I, D253G, E484K or S477N, D614G, and A701V. This lineage was first sequenced in late November 2020. Phylodynamic inference confirmed the rapid growth of the B.1.526 lineage. In concert with other variants, like B.1.1.7, the rise of B.1.526 appears to have extended the duration of the second wave of COVID-19 cases in NYC in early 2021. Pseudovirus neutralization experiments demonstrated that B.1.526 spike mutations adversely affect the neutralization titer of convalescent and vaccinee plasma, supporting the public health relevance of this lineage.

Article activity feed

  1. Version published to 10.1038/s41467-021-25168-4
  2. Version published to 10.1101/2021.02.14.431043v3 on bioRxiv
  3. ScreenIT

    SciScore for 10.1101/2021.02.14.431043: (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.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Additional sequences downloaded from GISAID on February 13, 2021, were aligned with MAFFT v7.464 (Katoh and Standley, 2013).
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)

    Results from OddPub: Thank you for sharing your code.

    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.

  4. Version published to 10.1101/2021.02.14.431043v2 on bioRxiv
  5. Version published to 10.1101/2021.02.14.431043v1 on bioRxiv