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Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater.
Smyth, Davida S; Trujillo, Monica; Gregory, Devon A; Cheung, Kristen; Gao, Anna; Graham, Maddie; Guan, Yue; Guldenpfennig, Caitlyn; Hoxie, Irene; Kannoly, Sherin; Kubota, Nanami; Lyddon, Terri D; Markman, Michelle; Rushford, Clayton; San, Kaung Myat; Sompanya, Geena; Spagnolo, Fabrizio; Suarez, Reinier; Teixeiro, Emma; Daniels, Mark; Johnson, Marc C; Dennehy, John J.
  • Smyth DS; Department of Life Sciences, Texas A&M University-San Antonio, San Antonio, TX, 78224, USA.
  • Trujillo M; Department of Biological Sciences and Geology, Queensborough Community College of The City University of New York, Queens, NY, 11364, USA.
  • Gregory DA; Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA.
  • Cheung K; Biology Department, Queens College and The Graduate Center of The City University of New York, Queens, NY, 11367, USA.
  • Gao A; Biology Department, Queens College and The Graduate Center of The City University of New York, Queens, NY, 11367, USA.
  • Graham M; Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA.
  • Guan Y; Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA.
  • Guldenpfennig C; Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA.
  • Hoxie I; Biology Department, Queens College and The Graduate Center of The City University of New York, Queens, NY, 11367, USA.
  • Kannoly S; Biology Department, Queens College and The Graduate Center of The City University of New York, Queens, NY, 11367, USA.
  • Kubota N; Biology Department, Queens College and The Graduate Center of The City University of New York, Queens, NY, 11367, USA.
  • Lyddon TD; Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA.
  • Markman M; Biology Department, Queens College and The Graduate Center of The City University of New York, Queens, NY, 11367, USA.
  • Rushford C; Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA.
  • San KM; Biology Department, Queens College and The Graduate Center of The City University of New York, Queens, NY, 11367, USA.
  • Sompanya G; Department of Life Sciences, Texas A&M University-San Antonio, San Antonio, TX, 78224, USA.
  • Spagnolo F; Department of Biological & Environmental Sciences, Long Island University-Post, Greenvale, New York, 11548, USA.
  • Suarez R; Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA.
  • Teixeiro E; Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA.
  • Daniels M; Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA.
  • Johnson MC; Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA. marcjohnson@missouri.edu.
  • Dennehy JJ; Biology Department, Queens College and The Graduate Center of The City University of New York, Queens, NY, 11367, USA. john.dennehy@qc.cuny.edu.
Nat Commun ; 13(1): 635, 2022 02 03.
Article in English | MEDLINE | ID: covidwho-1671556
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ABSTRACT
Tracking SARS-CoV-2 genetic diversity is strongly indicated because diversifying selection may lead to the emergence of novel variants resistant to naturally acquired or vaccine-induced immunity. To monitor New York City (NYC) for the presence of novel variants, we deep sequence most of the receptor binding domain coding sequence of the S protein of SARS-CoV-2 isolated from the New York City wastewater. Here we report detecting increasing frequencies of novel cryptic SARS-CoV-2 lineages not recognized in GISAID's EpiCoV database. These lineages contain mutations that had been rarely observed in clinical samples, including Q493K, Q498Y, E484A, and T572N and share many mutations with the Omicron variant of concern. Some of these mutations expand the tropism of SARS-CoV-2 pseudoviruses by allowing infection of cells expressing the human, mouse, or rat ACE2 receptor. Finally, pseudoviruses containing the spike amino acid sequence of these lineages were resistant to different classes of receptor binding domain neutralizing monoclonal antibodies. We offer several hypotheses for the anomalous presence of these lineages, including the possibility that these lineages are derived from unsampled human COVID-19 infections or that they indicate the presence of a non-human animal reservoir.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Water Microbiology / Wastewater / SARS-CoV-2 Type of study: Prognostic study Topics: Vaccines / Variants Limits: Adult / Aged / Animals / Female / Humans / Male / Middle aged / Young adult Country/Region as subject: North America Language: English Journal: Nat Commun Journal subject: Biology / Science Year: 2022 Document Type: Article Affiliation country: S41467-022-28246-3

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Water Microbiology / Wastewater / SARS-CoV-2 Type of study: Prognostic study Topics: Vaccines / Variants Limits: Adult / Aged / Animals / Female / Humans / Male / Middle aged / Young adult Country/Region as subject: North America Language: English Journal: Nat Commun Journal subject: Biology / Science Year: 2022 Document Type: Article Affiliation country: S41467-022-28246-3