A Tale of Two Lenses: #Emergency department indoor - #air hybrid-capture #metagenomics complements #wastewater by adding a human-focused respiratory #virus perspective

 

Abstract

Background: 

Continuous, non-invasive viral surveillance is essential to monitor emerging pathogens and guide public health responses. Most environmental surveillance studies use targeted qPCR approaches, and comparisons between wastewater and indoor air surveillance remain limited. We aimed to compare the utility of emergency department indoor air and urban wastewater for tracking circulating viruses and resolving genomic information. 

Methods: 

We conducted a matched-pair study comparing 19 weekly indoor air samples from the central ventilation exhaust shaft of an emergency department and 19 24-hour composite municipal wastewater samples in Leuven, Belgium, from December 2024 to April 2025. Both sample sets were processed using probe-based hybrid-capture viral metagenomics targeting over 3000 viral species, using influenza A as a clinically relevant test case. 

Findings: 

Wastewater captured higher overall viral diversity (233 versus 106 species) and more complete genomes compared to indoor air, showing a relatively stable composition, mainly of enteric and animal-associated viruses. Indoor air demonstrated lower overall diversity but was enriched for respiratory viruses, including influenza A, coronaviruses, metapneumovirus, and respiratory syncytial virus, and more frequently achieved high genome coverage for these pathogens. Although both sample types permitted influenza A subtype characterization, influenza A genomes from wastewater were often less well covered. When coverage thresholds were met, indoor air supported targeted antiviral resistance-site screening for influenza A and RSV-A. 

Interpretation: 

Wastewater and indoor air generate distinct but complementary viromes. Wastewater acts as a diverse, population-level monitor for One-Health applications, whereas indoor air serves as a targeted, human-centric sentinel system facilitating further genomic characterization for respiratory viruses.

Competing Interest Statement

The authors have declared no competing interest.

Funding Statement

Mustafa Karatas is supported by a Research Foundation Flanders (FWO) fundamental research scholarship (number: 11P7I24N). C.G., L.C., E.H., S.G. and E.A. acknowledge support from the DURABLE project. The DURABLE project has been funded by the European Union, under the EU4Health Programme (EU4H), project no. 101102733. Views and opinions expressed are however those of the authors only and do not necessarily reflect those of the European Union or the European Health and Digital Executive Agency. Neither the European Union nor the granting authority can be held responsible for them. The computing power in this work was provided by the VSC (Flemish Supercomputer Centre), financed by the FWO and the Flemish government department EWI.

Source: MedRxIV, https://www.medrxiv.org/

Link: https://www.medrxiv.org/content/10.64898/2026.03.13.26348311v1

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Citywide indoor #air #sampling mirrors #wastewater and clinical case #surveillance of respiratory viruses

 

Abstract

Wastewater surveillance of respiratory pathogens can provide timely estimates of viral activity and disease trends in a population. Indoor air surveillance could be used similarly with some advantages but remains largely unvalidated at the community-scale. Here, an indoor air surveillance program was employed as part of public health environmental surveillance in Chicago, Illinois, USA. Ten air samplers were placed in healthcare and congregate living settings across the city. Weekly air samples were evaluated for influenza A, influenza B, respiratory syncytial virus, and SARS-CoV-2 over two respiratory virus seasons. Citywide, aggregated air sample positivity and viral load were closely correlated with local clinical case and wastewater surveillance data across all respiratory viruses. Virus trends in air data often preceded clinical and wastewater, although this varied across pathogens and respiratory virus seasons. Further, whole-genome sequencing of SARS-CoV-2 showed close correlation of variant proportions across all datasets. At the building-scale, air samples obtained from a single sampling device provided efficient respiratory virus surveillance, with well-correlated estimates of respiratory pathogens. These data demonstrate that air surveillance can provide accurate estimates of respiratory virus infections and variants at a building or community-scale, serving as an alternative or complementary tool for public health environmental surveillance.

Competing Interest Statement

The authors have declared no competing interest.

Funding Statement

This project was supported by the Centers for Disease Control and Prevention of the U.S. Department of Health and Human Services (HHS) as part of a financial assistance award totaling $800,000 with 100% funded by CDC/HHS. The contents are those of the author(s) and do not necessarily represent the official views of, nor an endorsement, by CDC/HHS, or the U.S. Government. The project described was supported in part by cooperative agreement NU50CK000556 from CDC. Its contents are solely the responsibility of the authors and do not necessarily represent the official views of CDC. This work was also supported through a Center for Emerging Infectious Diseases at Rush University Medical Center award (1 GE1HS45832-01-00).

Source: MedRxIV, https://www.medrxiv.org/content/10.1101/2025.10.13.25337283v1

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