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. 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.