Identification of diagnostic and prognostic host biomarkers of Zika virus infection by transcriptome profiling There is currently an unprecedented ongoing outbreak of Zika virus (ZIKV) in the Americas, with more than 100,000 cases reported to date. Limitations to existing diagnostic tests include lack of specificity for antibody-based assays and a very narrow time window for PCR (<1 week). Better diagnostic tests are urgently needed to diagnose ZIKV infection. In addition, the weight of the combined evidence now shows that ZIKV is directly responsible for devastating adverse fetal outcomes in infected pregnant women, including in utero demise and microcephaly. There is currently no laboratory test to monitor infected women and assess their risk for fetal complications. Here we propose use transcriptome profiling analysis by RNA-Seq next-generation sequencing of blood, urine, and saliva samples from acutely infected patients to diagnose ZIKV infection, and of serially collected samples from ZIKV-infected pregnant women to monitoring the dynamics of the host response. The goal is to identify diagnostic and prognostic host biomarkers that may be correlated with active infection (for diagnosis) as well as fetal infection and outcomes in pregnant women, and that can be used to develop new assays for monitor ZIKV infection and disease.