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Updated: May 18, 2026
Tissue Collection of Bats for -Omics Analyses and Primary Cell Culture
Published on: October 23, 2019
Optimization of environmental air sampling for viral metagenomics in a cave-roosting bat assemblage
Caleb A Huntington1, Cassandra M Bonavita2, Heather L Wells2
1Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA. chunting@ucdavis.edu.
Background:
Environmental air sampling holds significant potential as a tool for viral surveillance. Its use in agricultural and indoor settings has demonstrated its feasibility and effectiveness but despite this, it has rarely been used in wildlife settings.
Methods:
To enable future applications, we optimized key parameters in air sampling methodology using a cave-roosting bat assemblage as a model system. We systematically investigated the impact of sampling conditions (flow rate, sampling duration, and sampling location/deployment time) and post-sampling treatments (DNA/RNA Shield ratios and secondary filtration) on three viral metrics - total mammalian virus abundance, mammalian RNA virus abundance, and Shannon diversity index - generated from next-generation sequencing data.
Results:
We first showed that air sampling can recover broad viral diversity, including alphacoronaviruses and betacoronaviruses. The sampling conditions for maximizing viral metrics were larger air sample volumes (≥24,000 liters) and sampling inside the cave while the bats were roosting, as opposed to at the cave entrance during emergence. Post-sampling treatments had limited impact on viral metrics, but their application may vary depending on the objectives of the study.
Conclusion:
This work provides a proof-of-concept for applying air sampling for wildlife viral surveillance in a cave-roosting bat assemblage and identifies key sampling parameters.
