Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York
- Creators
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West, Anthony P., Jr.
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Wertheim, Joel O.
- Wang, Jade C.
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Vasylyeva, Tetyana I.
- Havens, Jennifer L.
- Chowdhury, Moinuddin A.
- Gonzalez, Edimarlyn
- Fang, Courtney E.
- Di Lonardo, Steve S.
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Hughes, Scott
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Rakeman, Jennifer L.
- Lee, Henry H.
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Barnes, Christopher O.
- Gnanapragasam, Priyanthi N. P.
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Yang, Zhi
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Gaebler, Christian
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Caskey, Marina
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Nussenzweig, Michel C.
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Keeffe, Jennifer R.
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Bjorkman, Pamela J.
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.
Additional Information
© The Author(s) 2021. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. Received 10 June 2021; Accepted 28 July 2021; Published 09 August 2021. We thank the Global Initiative on Sharing Avian Influenza Data (GISAID) and the originating and submitting laboratories for sharing the SARS-CoV-2 genome sequences; see Supplementary Data 4 for a list of sequence contributors. We thank Andrew Rambaut and Áine O'Toole for lineage designation. This work was supported by the Caltech Merkin Institute for Translational Research (P.J.B.). This work was supported, in whole or in part, by the Bill & Melinda Gates Foundation [grant INV-002143 to P.J.B.]. Under the grant conditions of the Foundation, a Creative Commons Attribution 4.0 Generic License has already been assigned to the Author Accepted Manuscript version that might arise from this submission. J.O.W. acknowledges funding from the National Institutes of Health (AI135992 and AI136056). T.I.V. is funded by a Branco Weiss Fellowship. M.C.N. is an HHMI Investigator. Data availability: The SARS-CoV-2 genomes generated in this study have been deposited in GenBank under accession codes MZ637509-MZ642234 (see Supplementary Data 1) and GISAID (see Supplementary Data 2 for a list of genomes used in phylogenetic analysis and Supplementary Data 3 for genomes used in geographic distribution analysis). The data analyzed as part of this project were obtained from the GISAID database and through a Data Use Agreement between NYC DOHMH and the University of California San Diego. Sequences analyzed by using the vdb tool were downloaded from GISAID. No personally identifying information were included as part of these analyses. Data for Fig. 5 are provided in Supplementary Tables 2 and 3. Code availability: The source code for the vdb program is available at the GitHub repository46: https://github.com/variant-database/vdb. Author Contributions: A.P.W., J.O.W., J.L.H., T.I.V., H.H.L., S.H. and J.C.W. analyzed data. J.C.W., M.A.C., E.G. and H.H.L. performed genome sequencing and assembly. J.O.W. curated data. C.G., M. Caskey and M.C.N. provided clinical samples. P.N.P.G. and J.R.K. carried out experiments. A.P.W., C.O.B., Z.Y., S.H., S.S.D., C.E.F., T.I.V, J.L.H. and J.O.W. prepared figures. A.P.W., J.O.W., T.I.V., C.O.B., J.C.W. and S.H. wrote the manuscript with input from all co-authors. A.P.W., P.J.B., J.O.W., J.L.R. and S.H. supervised the study. Competing interests: P.J.B. is a co-inventor on a provisional application from the California Institute of Technology for the use of mosaic nanoparticles as coronavirus immunogens. M.C.N., P.J.B. and C.O.B. are co-inventors on provisional applications for several anti-SARS-CoV-2 monoclonal antibodies. J.O.W. has received funding from Gilead Sciences, LLC (completed) and the CDC (ongoing) via grants and contracts to his institution unrelated to this research. All other authors declare no competing interests. Peer review information: Nature Communications thanks the anonymous reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available.Attached Files
Published - s41467-021-25168-4.pdf
Submitted - 20210214-431043v3full.pdf
Supplemental Material - 41467_2021_25168_MOESM1_ESM.pdf
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Supplemental Material - 41467_2021_25168_MOESM5_ESM.txt
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Additional details
- Alternative title
- SARS-CoV-2 lineage B.1.526 emerging in the New York region detected by software utility created to query the spike mutational landscape
- PMCID
- PMC8352861
- Eprint ID
- 108067
- Resolver ID
- CaltechAUTHORS:20210216-123229308
- Caltech Merkin Institute for Translational Research
- INV-002143
- Bill and Melinda Gates Foundation
- AI135992
- NIH
- AI136056
- NIH
- Branco Weiss Fellowship
- Howard Hughes Medical Institute (HHMI)
- Created
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2021-02-16Created from EPrint's datestamp field
- Updated
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2023-10-02Created from EPrint's last_modified field
- Caltech groups
- COVID-19, Richard N. Merkin Institute for Translational Research, Division of Biology and Biological Engineering