Abstract Title
Avian influenza surveillance in wild birds using sediment specimens from wetland habitats
Abstract
Introduction: Surveillance for highly pathogenic avian influenza (HPAI) is traditionally conducted by testing wild birds, but these programs struggle to obtain sufficient and representative samples of animals. Consequently, HPAI arrivals are not always detected, especially when they are not lethal to their wildlife hosts. To enhance local surveillance programs, we developed and deployed a novel environmental surveillance strategy wherein we tested wetlands sediment from wild bird habitats for avian influenza virus (AIV) contamination.
Methods: Sediment specimens (n=1,236) were collected from 32 wetland habitats along the North American Pacific flyway in British Columbia, Canada between Oct 2021 and Dec 2023 (three fall/winter seasons). RNA was extracted, screened by qPCR, then sequenced using a custom targeted enrichment method.
Results: AIV sequences were recovered from 23.7% of sediment specimens. Greater subtype diversity was observed through environmental surveillance than through contemporary passive surveillance of wildlife: 12 vs 6 HA subtypes and 9 vs 6 NA subtypes. All HPAI lineages responsible for local poultry outbreaks were detected in sediment specimens. During a wave of poultry farm outbreaks in fall 2023, HPAI detections in sediment preceded HPAI detections in wild birds by one week and preceded the first farm outbreak by two weeks. Throughout this season, the sediment HPAI-positivity rate reflected the incidence of HPAI in wildlife and poultry farms.
Conclusion: Environmental surveillance is a promising complementary approach to traditional animal-based HPAI surveillance that detects greater AIV diversity, provides early detection of HPAI arrivals, and does not depend on wildlife host mortality.
Methods: Sediment specimens (n=1,236) were collected from 32 wetland habitats along the North American Pacific flyway in British Columbia, Canada between Oct 2021 and Dec 2023 (three fall/winter seasons). RNA was extracted, screened by qPCR, then sequenced using a custom targeted enrichment method.
Results: AIV sequences were recovered from 23.7% of sediment specimens. Greater subtype diversity was observed through environmental surveillance than through contemporary passive surveillance of wildlife: 12 vs 6 HA subtypes and 9 vs 6 NA subtypes. All HPAI lineages responsible for local poultry outbreaks were detected in sediment specimens. During a wave of poultry farm outbreaks in fall 2023, HPAI detections in sediment preceded HPAI detections in wild birds by one week and preceded the first farm outbreak by two weeks. Throughout this season, the sediment HPAI-positivity rate reflected the incidence of HPAI in wildlife and poultry farms.
Conclusion: Environmental surveillance is a promising complementary approach to traditional animal-based HPAI surveillance that detects greater AIV diversity, provides early detection of HPAI arrivals, and does not depend on wildlife host mortality.
Co-Author(s)
Kevin S. Kuchinski, University of British ColumbiaMichelle Coombe, British Columbia Ministry of AgricultureSarah C. Mansour, British Columbia Centre for Disease ControlGabrielle Angelo P. Cortez, University of British ColumbiaMarzieh Kalhor, University of British ColumbiaEthan Kenmuir, University of British ColumbiaJake Miller, University of British ColumbiaChelsea G. Himsworth, British Columbia Ministry of AgricultureNatalie A. Prystajecky, British Columbia Centre for Disease Control
Abstract Category
Notable outbreaks, field and molecular epidemiology, and surveillance in wild birds