Title Metagenomic sequencing detects human respiratory and enteric viruses in air samples collected from congregate settings.
Author Minor, Nicholas R; Ramuta, Mitchell D; Stauss, Miranda R; Harwood, Olivia E; Brakefield, Savannah F; Alberts, Alexandra; Vuyk, William C; Bobholz, Max J; Rosinski, Jenna R; Wolf, Sydney; Lund, Madelyn; Mussa, Madison; Beversdorf, Lucas J; Aliota, Matthew T; O'Connor, Shelby L; O'Connor, David H
Journal Sci Rep Publication Year/Month 2023-Dec
PMID 38049453 PMCID PMC10696062
Affiliation + expend 1.Wisconsin National Primate Research Center, Madison, WI, USA.

Innovative methods for evaluating virus risk and spread, independent of test-seeking behavior, are needed to improve routine public health surveillance, outbreak response, and pandemic preparedness. Throughout the COVID-19 pandemic, environmental surveillance strategies, including wastewater andair sampling, have been used alongside widespread individual-based SARS-CoV-2 testing programs to provide population-level data. These environmental surveillance strategies have predominantly relied on pathogen-specific detection methods to monitor viruses through space and time. However, this provides a limited picture of the virome present in an environmental sample, leaving us blind to most circulating viruses. In this study, we explore whether pathogen-agnostic deep sequencing can expand the utility of air sampling to detect many human viruses. We show that sequence-independent single-primer amplification sequencing of nucleic acids from air samples can detect common and unexpected human respiratory and enteric viruses, including influenza virus type A and C, respiratory syncytial virus, human coronaviruses, rhinovirus, SARS-CoV-2, rotavirus, mamastrovirus, and astrovirus.

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    National Institute of Pathogen Biology, CAMS & PUMC, Bejing, China
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