Final Report Summary - FERFLU EXPRESS (Investigation of influenza immune responses and vaccine efficacy correlates by global expression profiling and immunological analyses in the ferret model of influenza) In this project, we proposed to elucidate the mechanisms involved in host response to influenza infection and determine the key immune responses triggered by different influenza viruses. We suggested a comprehensive analysis of gene expression changes in influenza infected ferrets (Objective 1). These responses were then be compared to the key transcriptional changes with regard to influenza challenge after vaccination in the ferret model (Objective 2) to identify key genetic biomarkers correlating with vaccine protection. We utilized de-novo transcriptome sequencing of a normalized cDNA library from influenza infected ferrets. This allowed us to identify more than 19000 partial ferret transcripts, including more than 1000 gene orthologs known to be involved in the innate and the adaptive immune response. This study shows that utilizing next generation sequencing of a cDNA library is a fast and effective way to generate molecular analysis tools for non-standard animal models. We also analyzed the gene expression changes induced by different closely related influenza strains in the ferret model. The analysis revealed a common set of genes being either up or down regulated by all three strains investigated. However, the bulk of the identified expression changes showed strain specific patterns. Using sophisticated statistical algorithms, we were able to isolate a small number of genes that could predict both the infectious strain and the lung pathology in a set of unknown samples. The results show promise for further development of diagnostic tools, based on gene expression profiles of genetic biomarkers in blood. Such diagnostic tools could be used for early identification of patients infected with highly pathogenic strains, which could prevent transmission of more virulent virus strains, and more importantly, increasing the possibility of starting early treatment in these patients will spare both life and health care resources.