Metagenomic sequencing detects human respiratory and enteric viruses in air samples collected from congregate settings.

Publication date: Dec 04, 2023

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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Concepts Keywords
Coronaviruses Air
Environmental Cov
Mamastrovirus Enteric
Pandemic Environmental
Routine Including


Type Source Name
disease VO Viruses
drug DRUGBANK Medical air
disease MESH COVID-19 pandemic
disease VO population
disease IDO pathogen
disease VO time
drug DRUGBANK Influenza A virus
disease VO Respiratory syncytial virus
disease VO Rotavirus
drug DRUGBANK Coenzyme M
disease MESH influenza
disease MESH infection
disease IDO process
disease VO USA
disease IDO bacteria
disease VO Fungi
disease MESH genetic marker
disease IDO assay
disease IDO facility
disease MESH emergency
disease IDO host
disease VO Optaflu
drug DRUGBANK Pentaerythritol tetranitrate
disease IDO pathogen surveillance
disease VO gene
disease VO effective
drug DRUGBANK Ranitidine
disease IDO cell
disease VO effectiveness
drug DRUGBANK Methyltestosterone
disease VO volume
drug DRUGBANK Water
drug DRUGBANK Dimethyl sulfoxide
disease IDO replication
drug DRUGBANK Ademetionine
drug DRUGBANK Thiocolchicoside
disease IDO algorithm
disease VO protocol
disease VO report
disease MESH gastroenteritis
disease VO Monkeypox virus
disease MESH monkeypox
disease MESH Allergy
disease MESH Infectious Diseases
disease VO organization

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