Quantification of influenza within-host diversity and transmission in upper respiratory tracts from pigs with various vaccination statuses.

The goal of this project is to evaluate how vaccination affects the whole-genome wide influenza A virus (IAV) within-host evolutionary dynamics in nasal cavities during infection and the transmission of variants among the pigs. A total of 60 nasal swabs were successfully go through the next-generation sequencing which collected from 17 pigs vaccinated with different immunization regimens after being infected simultaneously with an H1N1 and an H3N2 IAV. From the sequenced samples, 23 H1N1 and 45 H3N2 IAV genomes were obtained for analysing the IAV within-host diversity and variant transmission in the upper respiratory tracts of pigs with various vaccination backgrounds.