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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
doi: https://doi.org/10.1101/2021.02.14.431043
Anthony P. West Jr.
1Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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  • For correspondence: apwest@caltech.edu
Joel O. Wertheim
2Department of Medicine, University of California San Diego, La Jolla, CA 92093
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Jade C. Wang
3New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, 10016 USA
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Tetyana I. Vasylyeva
2Department of Medicine, University of California San Diego, La Jolla, CA 92093
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Jennifer L. Havens
4Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA 92093
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Moinuddin A. Chowdhury
3New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, 10016 USA
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Edimarlyn Gonzalez
3New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, 10016 USA
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Courtney E. Fang
3New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, 10016 USA
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Steve S. Di Lonardo
3New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, 10016 USA
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Scott Hughes
3New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, 10016 USA
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Jennifer L. Rakeman
3New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, 10016 USA
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Henry H. Lee
5Pandemic Response Laboratory, Long Island City, NY 11101
6Department of Genetics, Harvard Medical School, Boston, MA 02115
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Christopher O. Barnes
1Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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Priyanthi N. P. Gnanapragasam
1Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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Zhi Yang
1Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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Christian Gaebler
7Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
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Marina Caskey
7Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
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Michel C. Nussenzweig
7Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
8Howard Hughes Medical Institute, The Rockefeller University, New York, NY, 10065 USA
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Jennifer R. Keeffe
1Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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Pamela J. Bjorkman
1Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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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.

Competing Interest Statement

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.

Footnotes

  • This version has additional phylogenetic and phylodynamic analysis, geographic analysis, and plasma pseudovirus neutralization assays.

Copyright 
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.
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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
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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

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