HCA Data Explorer

Extreme heterogeneity of influenza virus infection in single cells

Updated September 15, 2022

Viral infection can dramatically alter a cell's transcriptome. However, these changes have mostly been studied by bulk measurements on many cells. Here we use single-cell mRNA sequencing to examine the transcriptional consequences of influenza virus infection. We find extremely wide cell-to-cell variation in production of viral gene transcripts -- viral transcripts compose less than a percent of total mRNA in many infected cells, but a few cells derive over half their mRNA from virus. Some infected cells fail to express at least one viral gene, and this gene absence partially explains variation in viral transcriptional load. Despite variation in total viral load, the relative abundances of viral mRNAs are fairly consistent across infected cells. Activation of innate immune pathways is rare, but some cellular genes co-vary in abundance with the amount of viral mRNA. Overall, our results highlight the complexity of viral infection at the level of single cells.

Alistair Brian RussellFred Hutchinson Cancer Research Centerabrussel@fredhutch.org
Alistair Brian Russell (Experimental Scientist)1
1Fred Hutchinson Cancer Research Center
Teresa Marquez

To reference this project, please use the following link:

https://explore.data.humancellatlas.org/projects/5bb1f67e-2ff0-4848-bbcf-17d133f0fd2d

Supplementary links are provided by contributors and represent items such as additional data which can’t be hosted here; code that was used to analyze this data; or tools and visualizations associated with this specific dataset.

1.ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108041/suppl/GSE108041_RAW.tar,ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108041/suppl/GSE108041_README.txt,ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108041/suppl/GSE108041_reference_fasta.fasta.gz,ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108041/suppl/GSE108041_reference_genes.gtf.gz
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Analysis Portals

None

Project Label

InfluenzaVirusInfectionSingleCells

Species

Unspecified

Sample Type

cellLines

Anatomical Entity

Unspecified

Organ Part

Unspecified

Selected Cell Types

Unspecified

Model Organ

lung

Disease Status (Specimen)

Unspecified

Disease Status (Donor)

Unspecified

Development Stage

Unspecified

Library Construction Method

10x technology

Nucleic Acid Source

single cell

Paired End

false

Analysis Protocol

analysis_protocol_1

File Format

3 file formats

Cell Count Estimate

15.0k

Donor Count

0
fastq.gz72 file(s)tar1 file(s)xlsx1 file(s)