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Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York.
West, 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.
  • West AP; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA. apwest@caltech.edu.
  • Wertheim JO; Department of Medicine, University of California San Diego, La Jolla, CA, USA.
  • Wang JC; New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA.
  • Vasylyeva TI; Department of Medicine, University of California San Diego, La Jolla, CA, USA.
  • Havens JL; Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA.
  • Chowdhury MA; New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA.
  • Gonzalez E; New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA.
  • Fang CE; New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA.
  • Di Lonardo SS; New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA.
  • Hughes S; New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA.
  • Rakeman JL; New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA.
  • Lee HH; Pandemic Response Laboratory, Long Island City, NY, USA.
  • Barnes CO; Department of Genetics, Harvard Medical School, Boston, MA, USA.
  • Gnanapragasam PNP; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
  • Yang Z; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
  • Gaebler C; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
  • Caskey M; Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA.
  • Nussenzweig MC; Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA.
  • Keeffe JR; Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA.
  • Bjorkman PJ; Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
Nat Commun ; 12(1): 4886, 2021 08 09.
Article in English | MEDLINE | ID: covidwho-1349666
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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Diagnostic study Topics: Vaccines / Variants Limits: Humans Country/Region as subject: North America Language: English Journal: Nat Commun Journal subject: Biology / Science Year: 2021 Document Type: Article Affiliation country: S41467-021-25168-4

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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Diagnostic study Topics: Vaccines / Variants Limits: Humans Country/Region as subject: North America Language: English Journal: Nat Commun Journal subject: Biology / Science Year: 2021 Document Type: Article Affiliation country: S41467-021-25168-4