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

West, Anthony P., Jr. and Wertheim, Joel O. and Wang, Jade C. and Vasylyeva, Tetyana I. and Havens, Jennifer L. and Chowdhury, Moinuddin A. and Gonzalez, Edimarlyn and Fang, Courtney E. and Di Lonardo, Steve S. and Hughes, Scott and Rakeman, Jennifer L. and Lee, Henry H. and Barnes, Christopher O. and Gnanapragasam, Priyanthi N. P. and Yang, Zhi and Gaebler, Christian and Caskey, Marina and Nussenzweig, Michel C. and Keeffe, Jennifer R. and Bjorkman, Pamela J. (2021) Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20210216-123229308

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Abstract

Wide-scale SARS-CoV-2 genome sequencing is critical to tracking viral evolution during the ongoing pandemic. Variants first detected in the United Kingdom, South Africa, and Brazil have spread to multiple countries. We developed the software tool, Variant Database (VDB), for quickly examining the changing landscape of spike mutations. Using VDB, we detected 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 when it represented <1% of sequenced coronavirus genomes that were collected in New York City (NYC). By February 2021, genomes from this lineage accounted for ~32% of 3288 sequenced genomes from NYC specimens. Phylodynamic inference confirmed the rapid growth of the B.1.526 lineage in NYC, notably the sub-clade defined by the spike mutation E484K, which has outpaced the growth of other variants in NYC. Pseudovirus neutralization experiments demonstrated that B.1.526 spike mutations adversely affect the neutralization titer of convalescent and vaccinee plasma, indicating the public health importance of this lineage.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/2021.02.14.431043DOIDiscussion Paper
https://github.com/variant-database/vdbRelated ItemCode
ORCID:
AuthorORCID
Barnes, Christopher O.0000-0003-2754-5951
Yang, Zhi0000-0001-8680-3784
Gaebler, Christian0000-0001-7295-8128
Caskey, Marina0000-0003-1727-8693
Nussenzweig, Michel C.0000-0003-0592-8564
Keeffe, Jennifer R.0000-0002-5317-6398
Bjorkman, Pamela J.0000-0002-2277-3990
Alternate 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
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. Version 1: February 15, 2021; Version 2: February 23, 2021; Version 3: April 22, 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 Table 3 for a list of sequence contributors. We thank Andrew Rambaut and Aine O’Toole for lineage designation. This work was supported by the Caltech Merkin Institute for Translational Research (P.J.B.) and the Bill and Melinda Gates Foundation Collaboration for AIDS Vaccine Discovery (CAVD) (INV-002143). 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 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. SARS-CoV-2 genomes included in these analyses have been deposited in GISAID. See Supplementary Data 1 for a list of genomes, including which genomes were excluded from the phylogenetic analysis. Data for Figure 5 are provided in Supplementary Table 2. Code availability: The source code for the vdb program is available at the Github repository: 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. 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.
Group:COVID-19, Richard N. Merkin Institute for Translational Research
Funders:
Funding AgencyGrant Number
Caltech Merkin Institute for Translational ResearchUNSPECIFIED
Bill and Melinda Gates FoundationINV-002143
NIHAI135992
NIHAI136056
Branco Weiss FellowshipUNSPECIFIED
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
Record Number:CaltechAUTHORS:20210216-123229308
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20210216-123229308
Official Citation:Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. Anthony P West Jr., Joel O. Wertheim, Jade C. Wang, Tetyana I. Vasylyeva, Jennifer L. Havens, Moinuddin A. Chowdhury, Edimarlyn Gonzalez, Courtney E. Fang, Steve S. Di 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, Pamela J Bjorkman. bioRxiv 2021.02.14.431043; doi: https://doi.org/10.1101/2021.02.14.431043
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:108067
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:16 Feb 2021 21:26
Last Modified:23 Apr 2021 22:39

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