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TARGETED RESEQUENCING OF WETLAND SEDIMENT AS A TOOL FOR AVIAN INFLUENZA VIRUS SURVEILLANCE.

Authors
  • Himsworth, Chelsea G1, 2, 3
  • Duan, Jun4
  • Prystajecky, Natalie4, 5
  • Coombe, Michelle1, 2, 3
  • Baticados, Waren4
  • Jassem, Agatha N4, 5
  • Tang, Patrick6
  • Sanders, Eric7
  • Hsiao, William4, 5
  • 1 Canadian Wildlife Health Cooperative British Columbia, 1767 Angus Campbell Road, Abbotsford, British Columbia V3G 2M3, Canada. , (Canada)
  • 2 Animal Health Centre, British Columbia Ministry of Agriculture, 1767 Angus Campbell Road, Abbotsford, British Columbia V3G 2M3, Canada. , (Canada)
  • 3 University of British Columbia, School of Population and Public Health, 2206 East Mall, Vancouver, British Columbia V6T 1Z9, Canada. , (Canada)
  • 4 University of British Columbia, Department of Pathology and Laboratory Medicine, 2211 Wesbrook Mall, Vancouver, British Columbia V6T 2B5, Canada. , (Canada)
  • 5 British Columbia Centre for Disease Control, Public Health Laboratory, 655 West 12th Avenue, Vancouver, British Columbia V5Z 4R4, Canada. , (Canada)
  • 6 Sidra Medical and Research Center, PO Box 26999, Doha, Qatar. , (Qatar)
  • 7 University of British Columbia, Department of Statistics, 2207 Main Mall, Vancouver, British Columbia V6T 1Z4, Canada. , (Canada)
Type
Published Article
Journal
Journal of wildlife diseases
Publication Date
Nov 21, 2019
Identifiers
PMID: 31750776
Source
Medline
Keywords
Language
English
License
Unknown

Abstract

Surveillance methods for avian influenza virus (AIV) based upon collecting and testing samples from individual wild birds have several significant limitations primarily related to the difficulties associated with obtaining samples. Because AIVs are shed in waterfowl feces, the use of environmental substrates where waterfowl feces accumulate may overcome some of these limitations. However, these substrates are difficult to analyze using traditional diagnostic techniques, such as virus culture and PCR, because of virus inactivation, RNA degradation, low concentration of target RNA, microbial complexity, presence of inhibitory substances, and other factors. We investigated the use of a genomics-based approach called targeted resequencing to detect and characterize AIVs in wetland sediments during the 2014-2015 North American highly pathogenic avian influenza outbreak. We identified AIV in 20.6% (71/345) sediment samples obtained from wetlands (n=15) and outdoor waterbodies on AIV-infected poultry farms (n=10) in British Columbia, Canada (the first area affected during the outbreak). Thirteen hemagglutinin (HA) and nine neuraminidase (NA) subtypes were detected, including H5, N1, and N2 sequences that clustered with other sequences associated with the North American outbreak. Additionally, as many as eight HA and eight NA subtypes could be detected in a single sediment sample. This proof-of-concept study shows the potential utility of sediment sampling coupled with genomics-based analysis as a tool for AIV surveillance.

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