Evaluating sampling strategies for the detection of avian influenza viruses in the environment

Miller, A. K.; Heremia, L.; Waller, S. J.; Blanchard, S.-L.; Taylor, J. T.; Wille, M.; Gemmell, N.; Winter, D.; Dowle, E. J.; Geoghegan, J. L.

doi:10.1101/2025.09.18.677014

bioRxiv · 10.1101/2025.09.18.677014

Evaluating sampling strategies for the detection of avian influenza viruses in the environment

Miller, A. K.·Heremia, L.·Waller, S. J.·Blanchard, S.-L.·Taylor, J. T.·Wille, M.·Gemmell, N.·Winter, D.·Dowle, E. J.·Geoghegan, J. L.

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Abstract

Highly pathogenic avian influenza (HPAI) viruses threaten humans, livestock and wildlife, highlighting the urgent need for early warning surveillance. Environmental RNA (eRNA) monitoring provides a safer, cost-effective and non-invasive alternative to direct pathogen testing, yet the effectiveness of different sample types for avian influenza viruses (AIVs) is unclear. We evaluated four eRNA-based sampling methods in urban waterfowl ponds over approximately one year. All methods combined with RT-qPCR and metagenomic sequencing detected AIV, but detections were asynchronous, likely reflecting low viral concentrations or detection limits. These results highlight both the promise and the current limitations of eRNA-based AIV surveillance. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=156 SRC="FIGDIR/small/677014v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@e8e189org.highwire.dtl.DTLVardef@12f17fforg.highwire.dtl.DTLVardef@d09f5forg.highwire.dtl.DTLVardef@8f55fd_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Miller, A. K., Heremia, L., Waller, S. J., Blanchard, S.-L., Taylor, J. T., Wille, M., Gemmell, N., Winter, D., Dowle, E. J., Geoghegan, J. L.. 2025-09-18. Evaluating sampling strategies for the detection of avian influenza viruses in the environment. https://doi.org/10.1101/2025.09.18.677014

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