Host Transcriptomic Response to Acute Respiratory Viral Infection
The objective of this study is to examine clinical respiratory viral infections to elucidate gene expression patterns that may underlie clinical disease. We will delineate if the host gene response to respiratory viral infection is virus specific and evaluate the impact of specific virus strain and viral co-infections on the host transcriptomic response. To accomplish these aims, we will conduct unbiased RNA sequencing (RNA-seq) from clinical nasopharyngeal samples of 48 patients infected with nine different respiratory viruses. The viruses from these patients have previously undergone extensive genomic and phylogenetic characterization. Furthermore, to ascertain whether the host response is altered by the specific strain of virus we will conduct RNA-seq on an extra 48 samples to include additional subtypes and strains of and 8 samples with co-infections common respiratory viruses. Together this data will allow for unprecedented examination of both the pathogen and the immune response in humans. The results of this study will expand our knowledge of both viral and host genomic factors that control infection and provide critical insight into the pathogenesis of infection, the host immune response, and clinical disease. Moreover, we anticipate demonstrating that deep, next generation sequencing of viruses and the host transcriptome can provide critical information that will lead to improved clinical understanding of the disparate clinical outcomes in respiratory viral infections.