unidentified influenza virus Raw sequence reads
Avian influenza viruses (AIVs) are associated with more severe disease but less ransmissibility after infection of humans than are seasonal influenza viruses. Animal models and limited studies of single or small clusters of AIV human cases have been utilized to understand the underlying mechanisms with varying success and inference. Hampering scientific progress to a substantial degree has been the historically sporadic nature of human AIV cases, making comparative and extensive prospective studies unfeasible. The emergence of the H7N9 AIV in China has now changed this. These H7N9 cases are associated with a predictable spatial and temporal pattern that makes it feasible to consider a cohort study. Here, we propose to conduct a longitudinal study to identify the immunological and virological hallmarks of AIV infections in humans. Our study will test two hypotheses: replication of AIVs in the mammalian host limits virus population diversity which in turn limits onwardsransmission. Southern China is a particularly important region for human cases of AIV due to its high density of humans and domestic poultry. The completion of the above aims will lead to the most omprehensive analysis of AIV infections in humans to date and also to a direct side-by-side comparison with seasonal influenza.