Document Type
Article
Publication Date
2-2022
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.
Digital Object Identifier (DOI)
https://doi.org/10.1038/s41467-022-28246-3
Repository Citation
Smyth, Davida S.; Trujillo, Monica; Gregory, Devon A.; Johnson, Marc C.; Dennehy, John J.; and et al., "Tracking Cryptic SARS-CoV-2 Lineages Detected in NYC Wastewater" (2022). Biology Faculty Publications. 29.
https://digitalcommons.tamusa.edu/bio_faculty/29
Comments
Originally published as:
Smyth, D.S., Trujillo, M., Gregory, D.A. et al. Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater. Nat Commun 13, 635 (2022). https://doi.org/10.1038/s41467-022-28246-3
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.