Profiling and network modeling of innate immunity to human Zika virus infection

This supplemental project will focus on profiling and network modeling of innate immunity to human Zika virus infection. These studies will be conducted in children - Dengue neg and Dengue pos children from long-standing Nicaraguan cohorts. Deep sequencing RNA for both mapping and quantifying transcriptomes (RNA-seq) is an unbiased way to catalog all transcript species (mRNAs and non-coding RNAs) and resolve the transcriptional structure of genes (start sites, 5' and 3' ends, splicing patterns and other post-transcriptional modifications). With this approach, we catalog various classes of transcript, determine their transcriptional structure, and quantify their changing expression levels with high levels of reproducibility over a large dynamic range to create a global picture of cell function. We can simultaneously analyze expression patterns, including the analysis of gene regulation through allelic expression and lncRNAs, in cells from the same person before, during and after a naturally acquired infection. Compared to microarrays, RNA-seq is more specific and has a greater dynamic range and sensitivity. We are using this approach to gain a global survey of gene activity in blood from Dengue virus (DENV)-infected and Chikungunya virus (CHIKV)-infected children in Nicaragua with completeness and specificity not attainable by highdensity arrays that allow us to see complex expression patterns not seen before. Here, we will extend this approach to human samples of Zika virus infections from the same hospital-based study as for dengue and CHIKV, enabling an in-depth profile of Zika virus infection to be obtained for network modeling of Zika virus infection, which will be compared to similar analyses of dengue and CHIKV patients. The Wolinsky group has already successfully collaborated with Dr. Harris and the Nicaraguan team on a study of host genetic markers of susceptibility to severe dengue.