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

• DOI: 10.1038/s41467-022-28246-3
• Publication Date: 2022-02-03T11:07:29Z
• Authors: Davida S. Smyth; Monica Trujillo; Devon A. Gregory; Kristen Cheung; Anna Gao; Maddie Graham; Yue Guan; Caitlyn Guldenpfe...; 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; John J. Dennehy
• Keywords: Coding region

Tracking SARS-CoV-2 genetic diversity is strongly indicated because diversifying selection may lead to the emergence of novel variants resistant naturally acquired or vaccine-induced immunity. To monitor New York City (NYC) for presence variants, we deep sequence most receptor binding domain coding S protein isolated from wastewater. Here report detecting increasing frequencies cryptic lineages not recognized in GISAID's EpiCoV database. These contain mutations that had been rarely observed clinical samples, including Q493K, Q498Y, E484A, and T572N share many with Omicron variant concern. Some these expand tropism pseudoviruses by allowing infection cells expressing human, mouse, rat ACE2 receptor. Finally, containing spike amino acid were different classes neutralizing monoclonal antibodies. We offer several hypotheses anomalous lineages, possibility are derived unsampled human COVID-19 infections they indicate a non-human animal reservoir.