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

Author:

West Anthony P.ORCID,Wertheim Joel O.,Wang Jade C.ORCID,Vasylyeva Tetyana I.,Havens Jennifer L.,Chowdhury Moinuddin A.,Gonzalez Edimarlyn,Fang Courtney E.,Di Lonardo Steve S.,Hughes Scott,Rakeman Jennifer L.,Lee Henry H.,Barnes Christopher O.,Gnanapragasam Priyanthi N. P.,Yang Zhi,Gaebler Christian,Caskey Marina,Nussenzweig Michel C.ORCID,Keeffe Jennifer R.ORCID,Bjorkman Pamela J.ORCID

Abstract

AbstractWide-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.

Funder

Bill and Melinda Gates Foundation

Caltech Merkin Institute for Translational Research

Publisher

Springer Science and Business Media LLC

Subject

General Physics and Astronomy,General Biochemistry, Genetics and Molecular Biology,General Chemistry

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