PT  - JOURNAL ARTICLE
AU  - Fabio Zanini
AU  - Szu-Yuan Pu
AU  - Elena Bekerman
AU  - Shirit Einav
AU  - Stephen R. Quake
TI  - Single-cell transcriptional dynamics of flavivirus infection
AID  - 10.1101/203331
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 203331
4099  - http://biorxiv.org/content/early/2018/01/18/203331.short
4100  - http://biorxiv.org/content/early/2018/01/18/203331.full
AB  - Dengue and Zika viral infections affect millions of people annually and can be complicated by hemorrhage or neurological manifestations, respectively. However, a thorough understanding of the host response to these viruses is lacking, partly because conventional approaches ignore heterogeneity in virus abundance across cells. We present viscRNA-Seq (virus-inclusive single cell RNA-Seq), an approach to probe the host transcriptome together with intracellular viral RNA at the single cell level. We applied viscRNA-Seq to monitor dengue and Zika virus infection in cultured cells and discovered extreme heterogeneity in virus abundance. We exploited this variation to identify host factors that show complex dynamics and a high degree of specificity for either virus, including proteins involved in the endoplasmic reticulum translocon, signal peptide processing, and membrane trafficking. We validated the viscRNA-Seq hits and discovered novel proviral and antiviral factors. viscRNA-Seq is a powerful approach to assess the genome-wide virus-host dynamics at single cell level.