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

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 r...

Full description

Saved in:

Bibliographic Details
Published in:	Nature communications 2021-08, Vol.12 (1), p.4886-4886, Article 4886
Main Authors:	West, Jr, Anthony P, Wertheim, Joel O, Wang, Jade C, 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, Keeffe, Jennifer R, Bjorkman, Pamela J
Format:	Article
Language:	eng
Subjects:	Computer programs COVID-19 COVID-19 - epidemiology COVID-19 - virology Gene sequencing Genome, Viral Genomes Humans Models, Molecular Mutation Neutralization New York - epidemiology Pandemics Phylogeny Public health SARS-CoV-2 - classification SARS-CoV-2 - genetics SARS-CoV-2 - isolation & purification Severe acute respiratory syndrome Severe acute respiratory syndrome coronavirus 2 Software Software development tools Spike Glycoprotein, Coronavirus - genetics Spikes Viral diseases
Online Access:	Get full text
Tags:	Add Tag No Tags, Be the first to tag this record!

Description
Summary:	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.
ISSN:	2041-1723 2041-1723