Elucidate influenza-host-microbiome determinants that influence pathogenesis. Influenza A virus

The aim of this study is to use next-gen sequencing techniques to characterize the genotype of Influenza A virus (IAV) isolated from infected individual at serial time points; determine the changes in diversity that microbial communities undergo during an IAV infection; and use RNA-seq to determine the local upper respiratory tract gene expression levels of the host, virus, and microbiota throughout the course of infection from a subset of the samples. The proposed sequential sampling will allow us to evaluate the 16S, and viral genotype and intra-host diversity over the course of a human IAV infection. Finally, the sample collected on day 28 will be useful to evaluate whether the individual’s microbiota have returned to baseline levels after the infection or if a new baseline is set by the infection.