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

Author

Listed:
  • Anthony P. West

    (California Institute of Technology)

  • Joel O. Wertheim

    (University of California San Diego)

  • Jade C. Wang

    (New York City Department of Health and Mental Hygiene)

  • Tetyana I. Vasylyeva

    (University of California San Diego)

  • Jennifer L. Havens

    (University of California San Diego)

  • Moinuddin A. Chowdhury

    (New York City Department of Health and Mental Hygiene)

  • Edimarlyn Gonzalez

    (New York City Department of Health and Mental Hygiene)

  • Courtney E. Fang

    (New York City Department of Health and Mental Hygiene)

  • Steve S. Lonardo

    (New York City Department of Health and Mental Hygiene)

  • Scott Hughes

    (New York City Department of Health and Mental Hygiene)

  • Jennifer L. Rakeman

    (New York City Department of Health and Mental Hygiene)

  • Henry H. Lee

    (Pandemic Response Laboratory
    Department of Genetics, Harvard Medical School)

  • Christopher O. Barnes

    (California Institute of Technology)

  • Priyanthi N. P. Gnanapragasam

    (California Institute of Technology)

  • Zhi Yang

    (California Institute of Technology)

  • Christian Gaebler

    (The Rockefeller University)

  • Marina Caskey

    (The Rockefeller University)

  • Michel C. Nussenzweig

    (The Rockefeller University
    The Rockefeller University)

  • Jennifer R. Keeffe

    (California Institute of Technology)

  • Pamela J. Bjorkman

    (California Institute of Technology)

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.

Suggested Citation

  • Anthony P. West & Joel O. Wertheim & Jade C. Wang & Tetyana I. Vasylyeva & Jennifer L. Havens & Moinuddin A. Chowdhury & Edimarlyn Gonzalez & Courtney E. Fang & Steve S. Lonardo & Scott Hughes & Jenni, 2021. "Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-25168-4
    DOI: 10.1038/s41467-021-25168-4
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    Cited by:

    1. Yunxi Liu & Nicolae Sapoval & Pilar Gallego-García & Laura Tomás & David Posada & Todd J. Treangen & Lauren B. Stadler, 2024. "Crykey: Rapid identification of SARS-CoV-2 cryptic mutations in wastewater," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    2. Joel O. Wertheim & Jade C. Wang & Mindy Leelawong & Darren P. Martin & Jennifer L. Havens & Moinuddin A. Chowdhury & Jonathan E. Pekar & Helly Amin & Anthony Arroyo & Gordon A. Awandare & Hoi Yan Chow, 2022. "Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    3. Michael X. Wang & Esther G. Lou & Nicolae Sapoval & Eddie Kim & Prashant Kalvapalle & Bryce Kille & R. A. Leo Elworth & Yunxi Liu & Yilei Fu & Lauren B. Stadler & Todd J. Treangen, 2024. "Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens," Nature Communications, Nature, vol. 15(1), pages 1-12, December.

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