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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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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