Evolution of RNA Viruses

Fast evolving RNA viruses, such as rotavirus, influenza virus, human immunodeficiency virus, and zika virus, are a leading cause of death worldwide and represent a major challenge for global disease control. Despite their small genome size, often comprised of only a few thousand nucleotides and a handful of genes, it remains exceedingly difficult to study the infection biology of RNA viruses using modern gene sequencing technologies. The De Vlaminck (Dept. of Biomedical Engineering) and Parker (Dept of Microbiology & Immunology) labs are focused on developing and using novel single-cell sequencing technologies to understand the evolutionary forces operating at the level of single cells that select RNA virus genotypes. The extreme heterogeneity of RNA virus infections is difficult to survey with current molecular technologies which are largely limited to analyzing populations of infected cells. To overcome this limitation, we have recently created a single cell RNA sequencing technology that combines multiplexed amplicon sequencing with single cell transcriptional profiling: Droplet Assisted RNA Targeting by single-cell Sequencing (DART-seq). With DART-seq it is possible to catalog the diversity of viral genome sequences within single infected cells, and at the same time record the cellular response to viral infection. The cost per-cell of DART-seq is less than one dollar, and a single DART-seq assay can yield measurements across thousands of cells in a biological sample. In proof-of-principle studies, we have used DART-seq to profile viral-host interactions and viral genome dynamics in single cells infected with mammalian orthoreovirus (REOV) strain Type 3 Dearing (T3D). Future experiments will  expand upon these initial technology development experiments to interrogate the infection biology of REOVs and other segmented RNA viruses including rotavirus, a common cause of gastroenteritis, and influenza A virus. We also plan to further develop the DART-seq approach as a tool to allow assessment of single-cell viral replication and recombination. This project provides the opportunity for a postdoctoral associate to develop new scRNA-seq technologies optimized for the study of RNA virus biology.

This project is a collaboration between the Parker, and Iwijn de Vlaminck labs.