Genomics used in new bird flu study

ChickenHeads_closeup_blogCanadian scientists are fast-tracking a genomic surveillance system to detect new, virulent avian flu viruses in wild birds in order to predict and hopefully prevent outbreaks in domestic birds, a new report states.

Recently, a new strain of avian flu swept through poultry farms in British Columbia and contained a blend of genetic material from a North American avian flu and the pathogenic Eurasian H5N8 virus, the first of its kind to be detected in North America. The H5N2 virus is particularly deadly for domestic poultry and has led to the destruction of 245,000 birds in British Columbia alone.

In the U.S., two new outbreaks of the same H5N2 variant have been reported and confirmed in commercial turkeys – one in Barron County, Wisconsin (affecting 126,000 birds) and the other in Roseau County, Minnesota (26,000 birds).  Other outbreaks of avian influenza have occurred most recently in Iowa, Missouri, Arkansas, the Dakotas and Kansas leading to the depopulation of more than one million turkeys and chickens since January.

However, this new research is important because it can detects genetic material from entire communities of microbes, including influenza viruses that might be lurking in wetlands frequented by migratory birds. This is important in the fight against avian flu because the migratory routes of birds from North and South America, Europe and Asia overlap at several locations.

According to the article, this is likely where the viruses intermingled and formed new and highly pathogenic avian influenza strains. Also, climate change could alter those flyways and lead to more mixing of potential pathogens, Chelsea Himsworth, a veterinary pathologist with the Ministry of Agriculture, said in the article.

The research team has analyzed 250 water and sediment samples from 20 locations across the Fraser Valley in British Columbia to catalogue which avian flu viruses are normally found in the fecal matter of wild birds. This method will reveal which viruses are present in entire populations of birds. This strategy is beneficial because catching and testing individual birds is too hit-and-miss, the article states, as any given bird may or may not have a flu virus that is present in other members of a flock.

The first round of samples could also tell researchers whether wild waterfowl were responsible for transmitting the H5N2 into the Fraser Valley poultry flocks and whether there are geographical hot spots for flu transmission. While H5N2 is not a threat to people, other H5 strains have infected humans and led to serious illness and death in the past.

The project is expected to result in a working surveillance system up which should be ready in time for the autumn influx of migrating birds. Then, by re-sampling at the wetlands when migratory birds arrive and running a meta-genomic analysis, the scientists can learn whether known pathogenic avian flu viruses are present or if a new variant of the flu has arrived.

Warning farmers when new threats are present will allow them to take extra biosecurity measures and help prevent the transmission of another potentially dangerous virus to domestic flocks.

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