Genome-wide RNA-seq and ATAC-seq analysis of an in vivo human immune response to acute Zika virus infection

A longitudinal systems immunologic investigation of acute Zika virus infection in an individual infected with ZIKV while traveling to Caracas, Venezuela during the zika virus epidemic. Includes longitudinal RNA-seq and ATAC-seq characterization of innate and adaptive immune responses during an acute ZIKV infection. Overall design: Blood was collected from an individual with NAAT confirmed acute Zika virus infection on four occasions d3, d6, d17, and d48 post-onset of symptoms (POS). Peripheral blood mononuclear cells were isolated from heparinized blood using Histopaque-1077 per manufacturers instructions and subjected to flow activated cell sorting (FACS) to characterize and isolate innate and adaptive immune cell populations. 5000-15,000 live PBMCs or individual cell populations were used to perform low input RNA-seq using the Smart-seq2 method with some modifications. 50,000 FACS isolated live classical monocytes or NK cells were used for ATAC-seq analysis.