Amplicon sequencing of barcoded influenza during transmission in guinea pigs

For many viruses, narrow bottlenecks acting during transmission sharply reduce genetic diversity in a recipient host relative to the donor. Observing the evolutionary dynamics that occur during transmission is critical to understanding the forces driving viral evolution at an epidemiologic scale. We used a novel barcoded virus library and a guinea pig model of transmission. We tracked the dynamics of viral barcodes throughout infections using amplicon sequencing from nasal wash samples.