The transcriptomic landscape of pediatrics with dengue virus infection reveals the severity-dependent immune response

We performed virus inclusive single cell RNA sequencing of children with diverse DENV infection severity and profiled both cell type abundances and gene expression within each cell type. Overall design: We collected PBMC samples of 20 DENV-infected children (ages: 2 to 16) and 4 healthy donors from a established cohort in Colombia.The 20 patients were classified into 3 clinical conditions: uncomplicated dengue without warning signs (D, n = 8), dengue with warning sign (DWS, n = 4), severe dengue (SD, n = 8) which were identified based on the discharge diagnoses using the WHO 2009 criteria. we adapted the commercial 5'-end droplet-based scRNA-seq (10X Genomics) by adding a capture oligonucleotide for the positive strand of DENV. each sample was first depleted of dead cells and subsequently split in two aliquots. The first aliquot was processed with the magnetic beads coated with CD3 antibody to remove T cells before remixing with the second, unprocessed one to decrease the T cell population to 30%-40%.