Extreme heterogeneity of influenza virus infection in single cells

Abstract

Viral infection can dramatically alter a cell's transcriptome. However, these changes 8 have mostly been studied by bulk measurements on many cells. Here we use single-cell mRNA 9 sequencing to examine the transcriptional consequences of influenza virus infection. We find 10 extremely wide cell-to-cell variation in production of viral gene transcripts -viral transcripts 11 compose less than a percent of total mRNA in many infected cells, but a few cells derive over half 12

Distinct antiviral signatures revealed by the magnitude and round of influenza virus replication in vivo

“…Multiple studies using single-cell sequencing have revealed heterogeneity in IAV replication and the antiviral response in vitro (14,15). These data are consistent with previous reports demonstrating stochasticity in single-cell responses to infection (16,(30)(31)(32).…”

“…Prolonged presence of infectious particles in the lungs could result in varied time of infection and lead to replication disparity. This is unlikely, given the speed of IAV entry in vitro and that virus dose and duration of infection did not impact heterogeneity in single-cell analyses (15,19,20). However, the half-life of an infectious particle in vivo has never been experimentally determined.…”

“…While these analyses have been critical for evaluating host factors that support or inhibit IAV, the understanding of the complex interplay between different cell types, anatomical locations, and immune responses in the context of virus infection in vivo is still incomplete. Single-cell analyses can help bridge this gap and have demonstrated the heterogeneity in IAV replication and the antiviral response in vitro (14)(15)(16). Unfortunately, current single-cell mRNA-seq strategies using WT virus cannot distinguish between newly infected cells and cells in which replication has been controlled in vivo.…”

Single-cell transcriptional dynamics of flavivirus infection

“…1D). The addition of a virus-specific oligo overcomes limitations of other approaches and enables studying of viruses that are not polyadenylated (A. B. Russell, Trapnell, and Bloom 2017) .…”

The Transcriptome of Latent Human Cytomegalovirus

“…In addition, HCMV latency may represent multiple programs, which will also be lost in bulk analyses. Single-cell RNA-seq (scRNAseq) is a powerful methodology which can define cellular heterogeneity and has proven to be instrumental in studying viral infections, as their dynamics and progression rely, to a great extent, on the host cell (35)(36)(37). The scRNA-seq we applied to HCMV-infected CD14 ϩ monocytes and CD34 ϩ HPCs (30) should be considered as a sampling procedure where the reads per cell reflect random sampling from a pool of approximately 100,000 mRNA molecules, which differs between cells depending on the cell type or regulatory state.…”