Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater

Davida S. Smyth, Monica Trujillo, Devon A. Gregory, Kristen Cheung, Anna Gao, Maddie Graham, Yue Guan, Caitlyn Guldenpfennig, Irene Hoxie, Sherin Kannoly, Nanami Kubota, Terri D. Lyddon, Michelle Markman, Clayton Rushford, Kaung Myat San, Geena Sompanya, Fabrizio Spagnolo, Reinier Suarez, Emma Teixeiro, Mark Daniels, Marc C. Johnson () and John J. Dennehy ()
Additional contact information
Davida S. Smyth: Texas A&M University-San Antonio
Monica Trujillo: Queensborough Community College of The City University of New York
Devon A. Gregory: University of Missouri-School of Medicine
Kristen Cheung: Queens College and The Graduate Center of The City University of New York
Anna Gao: Queens College and The Graduate Center of The City University of New York
Maddie Graham: University of Missouri-School of Medicine
Yue Guan: University of Missouri-School of Medicine
Caitlyn Guldenpfennig: University of Missouri-School of Medicine
Irene Hoxie: Queens College and The Graduate Center of The City University of New York
Sherin Kannoly: Queens College and The Graduate Center of The City University of New York
Nanami Kubota: Queens College and The Graduate Center of The City University of New York
Terri D. Lyddon: University of Missouri-School of Medicine
Michelle Markman: Queens College and The Graduate Center of The City University of New York
Clayton Rushford: University of Missouri-School of Medicine
Kaung Myat San: Queens College and The Graduate Center of The City University of New York
Geena Sompanya: Texas A&M University-San Antonio
Fabrizio Spagnolo: Long Island University–Post, Greenvale
Reinier Suarez: University of Missouri-School of Medicine
Emma Teixeiro: University of Missouri-School of Medicine
Mark Daniels: University of Missouri-School of Medicine
Marc C. Johnson: University of Missouri-School of Medicine
John J. Dennehy: Queens College and The Graduate Center of The City University of New York

Nature Communications, 2022, vol. 13, issue 1, 1-9

Abstract: 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.

Date: 2022
References: View references in EconPapers View complete reference list from CitEc
Citations: View citations in EconPapers (8)

Downloads: (external link)
https://www.nature.com/articles/s41467-022-28246-3 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-28246-3

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-022-28246-3

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().