ABSTRACT
Dengue and Zika viral infections affect millions of people annually and can be complicated by shock and hemorrhage or neurological manifestations, respectively. Yet, a thorough understanding of the host response to these viruses is still lacking, in part because conventional approaches do not enable one to resolve heterogeneity in viral loads and cellular response between different individual cells. Here we present viscRNA-Seq (virus-inclusive single-cell RNA-Seq), an approach to probe the whole host transcriptome together with intracellular viral RNA at the single cell level that is applicable to both polyadenylated and non-polyadenylated viruses. We applied viscRNA-Seq to monitor dynamics of dengue and Zika virus infection in cultured cells and discovered a high heterogeneity of intracellular viral load which affects the virus-triggered host response. The single-cell distributions of both intracellular viral load and gene expression indicate that mean values measured in conventional bulk assays tend to over-represent highly infected cells. When these effects are accounted for, we discovered that several host factors show complex dynamics and a high degree of specificity for either virus. These host factors include both known and novel members of the endoplasmic reticulum translocon and proteins involved in signal peptide processing and intracellular membrane trafficking. We used loss-of-function and gain-of-function experiments to validate the viscRNA-Seq hits and discovered novel proviral and antiviral factors. Overall, viscRNA-Seq is a powerful approach to quantitatively assess the complex interplay between virus and host at the single cell level and at a genome-wide scale, and to elucidate the cellular pathways involved in viral infection.
