Tonight I watched another PAG Industry Workshop session by Oxford Nanopore Technologies. This one was titled “Pasteurized retail dairy enables genomic surveillance of H5N1 avian influenza in the United States.” Andrew Lail from the University of Wisconsin-Madison was the presenter. Lail explained that influenza is an RNA virus with 8 RNA segments. H5N1 influenza is native to wild birds… and migratory birds. This H5N1 was transmitted through through migratory birds and made its way to the United States. The FDA noted an outbreak in the United States. Lail’s lab wanted to evaluate whether they could identify H5N1 in store-purchased milk. They have assessed 256 cartons of milk and found sequences using a 250 bp tiled amplicon scheme. They used PrimalScheme to create a tiling scheme. The tiled amplicon approach provides high genome coverage, with some lower coverage regions. The team then asked: are we detecting concerning mutations? They are picking up mutations but not some of the more worrisome ones! Lail noted that performing increased testing of dairy cows and bulk tank is important. This involves on-farm initial testing.
