Influenza A virus Genome sequencing

Next Generation Sequencing technology is now being increasingly applied to study the within and between host population dynamics of viruses. However, information on avian influenza virus evolution and transmission during a naturally occurring epidemic is still limited. In this stydy, we use deep sequencing data obtained from clinical samples collected from five industrial holdings and a backyard farm infected during the 2013 highly pathogenic avian influenza (HPAI) H7N7 epidemic in Italy to unravel i) the virus population diversity, ii) the evolution of virus pathogenicity, and iii) the pathways of viral transmission between different holdings and sheds.