Influenza Genome Sequencing to study Human transmission kinetics. Influenza A virus

This study uses whole genome sequencing of influenza virus from nasal washes to determine viral transmission kinetics during natural infection. The longitudinal nature of this study allows us to examine whether the virus transmitted from the alleged index case is the dominant virus in a quasispecies population. Individual viruses detected in the same subject over time can be assessed for the presence of genetic changes either associated with antigenic drift (in B cell or T cell epitopes) and/or adaptation to the human host. By evaluating virus shedding in nasal washes from both cases and contacts, we may be able to characterize virus sequentially through several passages in humans. Because many index cases received treatment with antiviral agents (oseltamivir), we will be able to assess the frequency of emergence of resistance, or resistant subpopulations.