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

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, Jennifer L. Rakeman, Henry H. Lee, Christopher O. Barnes, Priyanthi N. P. Gnanapragasam, Zhi Yang, Christian Gaebler, Marina Caskey, Michel C. Nussenzweig, Jennifer R. Keeffe and Pamela J. Bjorkman
Additional contact information
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
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
Jennifer R. Keeffe: California Institute of Technology
Pamela J. Bjorkman: California Institute of Technology

Nature Communications, 2021, vol. 12, issue 1, 1-10

Abstract: 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.

Date: 2021
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DOI: 10.1038/s41467-021-25168-4

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