Whole genome sequencing of reassortant influenza A viruses recovered from individual pigs in farm conditions

We evaluated the diversity and replicative fitness of reassortant influenza plaques obtained from individual pigs raised in commercial farms to understand influenza A viruses' emergence, persistence, and subsidence. Up to 244 influenza plaques were isolated from 24 pigs on the same farm, and all the plaques were subjected to whole genome sequencing to identify the genotypes.