Genomic Analysis of Wetland
Sediment as a Tool for Avian
Influenza Virus Surveillance in
Wild Waterfowl
Chelsea Himsworth DVM, MVetSc, PhD, Dipl ACVP
Leader, Veterinary Science and Diagnostics, Animal
Health Centre, BC Ministry of Agriculture
Why Sediment?
•
Avian influenza reservoir
•
Traditional surveillance methods
o Passive
o Hunter kills or Live bird capture
Why Sediment?
Why Sediment?
Aim 1: To characterize the ecology of waterfowl species in the Fraser
Valley and identify sentinel wetlands for sediment sampling.
Aim 2: To use analyze superficial sediment samples from the
aforementioned wetlands for the presence of H5N2 and other AI strains
of significance to poultry and public health.
Aim 3: To synthesize the ecological and molecular information in order to
develop a better understanding of the 2014/2015 outbreak and to
develop a strategy (with associated field and laboratory methodology)
through which sediment surveillance could be implemented in the
future.
Maps courtesy of Innovation and Adaptation Services Branch, Ministry of Agriculture
+ 41 samples taken on infected premises
Maps courtesy of Innovation and Adaptation Services Branch, Ministry of Agriculture
RNA Extraction
Parallel Sequencing
- PCR-based
- Flu RNA capture
Bioinformatics
Matrix PCR
= HxNx
= HxNx
8% of samples positive
and an additional 17% suspect positive
So what?
• We can detect AI in wetland sediment!
• But still need to figure out if AI in sediment is
representative of strains circulating in
waterfowl populations
46% of samples positive
and an additional 17% suspect positive
So what?
• There seems to be heavy environmental
contamination on infected premises
• Is this due to waterfowl or is it spillover from
the poultry barn?
Summer Sampling
• Need to start with a ‘clean slate’ each year for
sediment sampling to work as a surveillance
tool
• Repeat sampling at AI positive sites in
August/September 2015
So what?
• Wetlands appear to ‘self sterilize’ over the
summer
• Suggests that AI found in the fall represents
what has been brought in by that year’s
migration (vs. ‘left overs’ from the previous
year)
Next Steps
• Full genome sequencing to characterize AI
viruses in each sample
• Epidemiologic/ecologic study to provide
insight into virus ecology and sampling
methodology
Next Steps
• Refine and transfer technology
Next Steps
• Determine if AI in sediment is representative
of AI in wild waterfowl
• Compare and contrast different surveillance
techniques to identify the most efficient and
effective combination
Future Directions
Acknowledgements
Sustainable Poultry
Farming Group
Animal
Health
Centre