Abstract Title
Phylogenetic analysis of free-ranging waterfowl and environmental samples from Ontario wetlands reveals clustering of Ontario low-pathogenic avian influenza virus gene segments with Canadian highly pathogenic avian influenza viruses
Abstract
Current methods used for sampling avian influenza viruses (AIVs) primarily include sampling animals, which is limited by resources and accessibility. Our study aimed to test the efficacy of a novel environmental AIV surveillance method in bodies of water using a device termed “the torpedo” loaded with sorbent materials allowing for water sampling on immersion and towing from a watercraft.
Six Ontario wetlands were sampled from 17 August to 20 September 2023. Oral and cloacal swab samples from free-ranging waterfowl were collected in parallel with torpedo-collected water samples. 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.
We collected 200 swab samples and 72 water samples. AIV was detected in 32 swab samples and 16 water samples. Ct values ranged from 27.18 to 35.96 in waterfowl samples and from 36.57 to 38.92 in torpedo samples. H5 was detected in 1 waterfowl sample with a ct of 31.72 and no water samples. Whole viral genome sequences were obtained from both swab and torpedo samples, and 7 unique subtypes were detected. The average depth of sequencing coverage was 91.55 for torpedo samples and 544.08 for waterfowl samples. Phylogenetic analysis showed clustering of 2-4 internal gene segments from each sequence with Canadian H5 highly pathogenic AIV sequences. We concluded that the torpedo environmental sampling method is capable of detecting AIV in water in a field setting.
Six Ontario wetlands were sampled from 17 August to 20 September 2023. Oral and cloacal swab samples from free-ranging waterfowl were collected in parallel with torpedo-collected water samples. 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.
We collected 200 swab samples and 72 water samples. AIV was detected in 32 swab samples and 16 water samples. Ct values ranged from 27.18 to 35.96 in waterfowl samples and from 36.57 to 38.92 in torpedo samples. H5 was detected in 1 waterfowl sample with a ct of 31.72 and no water samples. Whole viral genome sequences were obtained from both swab and torpedo samples, and 7 unique subtypes were detected. The average depth of sequencing coverage was 91.55 for torpedo samples and 544.08 for waterfowl samples. Phylogenetic analysis showed clustering of 2-4 internal gene segments from each sequence with Canadian H5 highly pathogenic AIV sequences. We concluded that the torpedo environmental sampling method is capable of detecting AIV in water in a field setting.
Co-Author(s)
Juliette Blais-Savoie, University of Toronto, Sunnybrook Research Institute;
Ayden McGuire Sherritt, Ontario Ministry of Natural Resources and Forestry;
Munir Bhatti, University of Guelph;
Md Tashnimul Hasan, University of Guelph;
Winfield Yim, Sunnybrook Research Institute;
Renee Schryer, Sunnybrook Research Institute;
Emily Chien, Sunnybrook Research Institute;
Lily Yip, Sunnybrook Research Institute;
Joseph Train, University of Guelph;
Trevor Townsend, University of Guelph;
Alyssa Leonard, University of Guelph;
Davor Ojkic, University of Guelph;
Yohannes Berhane, Canadian Food Inspection Agency;
Anthony Signore, Canadian Food Inspection Agency;
Larissa Nituch, Ontario Ministry of Natural Resources and Forestry;
Edward McBean, University of Guelph;
Samira Mubareka, University of Toronto, Sunnybrook Research Institute;
Claire Jardine, University of Guelph, Canadian Wildlife Health Cooperative
Abstract Category
Notable outbreaks, field and molecular epidemiology, and surveillance in wild birds