Single cell analysis of de novo infection of permissive cells with MHV-68.

This analysis focused on virally-infected cells demonstrating viral protein expression, defined through use of a viral fusion protein capable of being detected and purified by fluorescence activated cell sorting.

Single cell RNA Seq analysis demonstrated distinct cellular and viral profiles within a permissive fibroblast cell line infected with a uniform virus inoculum and incubation period. These studies reveal: i) pronounced variation in gene expression, with only a small fraction of viral open reading frames uniformly detected in all cells, and a 1000-fold variation in viral RNA expression between cells, ii) positive and negative gene correlations, many uniquely present in a subset of cells, and iii) a dichotomous signature of host gene expression, further revealed by accompanying CyTOF data in the accompanying manuscript.