SUMMARYVirus infection is frequently characterized using bulk cell populations. How these findings correspond to infection in individual cells remains unclear. Here, we integrate high-dimensional single-cell approaches to quantify viral and host RNA and protein expression signatures using de novo infection with a well-characterized model gammaherpesvirus. While infected cells demonstrated genome-wide transcription, individual cells revealed pronounced variation in gene expression, with only 9 of 80 annotated viral open reading frames uniformly expressed in all cells, and a 1000-fold variation in viral RNA expression between cells. Single-cell analysis further revealed positive and negative gene correlations, many uniquely present in a subset of cells. Beyond variation in viral gene expression, individual cells demonstrated a pronounced, dichotomous signature in host gene expression, revealed by measuring host RNA abundance and post-translational protein modifications. These studies provide a resource for the high-dimensional analysis of virus infection, and a conceptual framework to define virus infection as the sum of virus and host responses at the single-cell level.HIGHLIGHTSCyTOF and scRNA-seq identify wide variation in gene expression between infected cells.Host RNA expression and post-translational modifications stratify virus infection.Single cell RNA analysis reveals new relationships in viral gene expression.Simultaneous measurement of virus and host defines distinct infection states.
Single-Cell Analysis of RNA Virus Infection Identifies Multiple Genetically Diverse Viral Genomes within Single Infectious Units