Genomic Analysis of Wetland Sediment as a Tool for Avian

Influenza Virus Surveillance in Wild Waterfowl

Chelsea Himsworth DVM, MVetSc, PhD, Dipl ACVPLeader, Veterinary Science and Diagnostics, Animal

Health Centre, BC Ministry of Agriculture

Why Sediment?• Traditional surveillance methods• Avian influenza reservoir

o Passiveo 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

Maps courtesy of Innovation and Adaptation Services Branch, Ministry of Agriculture

+ 41 samples taken on infected premises

RNA Extraction Parallel Sequencing- PCR-based- Flu RNA capture

= HxNx= HxNx

Bioinformatics

Matrix PCR

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

Animal Health Centre

Sustainable Poultry Farming Group