OAHN Wildlife Network Project: Assessing the use of passive water samples for the detection of influenza viruses

Project Lead: Dr. Claire Jardine

Collaborators:  Dr. Alex Reid

Project Summary

The overall objective of this project was to refine, test, and validate the use of a passive sampler for avian influenza virus (AIV) detection via PCR in water.

Our first step was to ensure that the sorbent material within the passive sampler could capture influenza virus from the environment. Three unique sorbent materials were compared: Swiffer pads, gauze pads, and polycarbonate filters. Swiffer and gauze pads produced equal numbers of matrix gene-positive samples by qPCR and were used for the field sampling.

The second step of this pilot project was to test and validate the use of the passive water sampler in the field. Sampling was conducted at six Ontario wetlands from August 17 to September 20, 2023. Oral and cloacal swab samples from free-ranging waterfowl were collected in parallel with the wetland water samples that were collected using the passive sampler. All samples were tested by qPCR with universal influenza A matrix gene and H5 gene targets. Samples that were matrix gene-positive and H5-negative underwent whole-genome sequencing using the Illumina MiniSeq platform. H5-positives were sent to the National Centre for Foreign Animal Disease for further analysis.

Two hundred swab samples from wild waterfowl and 72 sorbent material samples from 28 passive samplers were collected. AIV was detected in 32 swab samples and 16 sorbent materials from 5 passive samplers. H5 was detected in 1 waterfowl sample with a Ct of 31.72 and no torpedo samples. Whole genome viral sequences were obtained from both swab and sorbent samples, and 7 unique subtypes were detected. Additional work to further characterize the subtypes is underway. We concluded that the torpedo environmental sampling method is capable of detecting AIV in water in a field setting.