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Series GSE135553 Query DataSets for GSE135553
Status Public on Jun 16, 2020
Title Viral transcriptomic analysis of single cell-sorted of DF1 or MDCK cell lines infected with influenza A virus
Organisms Gallus gallus; Canis lupus familiaris
Experiment type Expression profiling by high throughput sequencing
Summary Infection with a single influenza A virus (IAV) is only rarely sufficient to initiate productive infection. Here, we exploit both single cell approaches and whole-animal systems to show that the extent of IAV reliance on multiple infection varies with virus strain and host species. Influenza A/guinea fowl/HK/WF10/99 (H9N2) [GFHK99] virus exhibits strong dependence on collective interactions in mammalian systems. This reliance focuses viral progeny production within coinfected cells and therefore results in frequent genetic exchange through reassortment. In contrast, GFHK99 virus has greatly reduced dependence on multiple infection in avian systems, indicating a role for host factors in viral collective interactions. Genetic mapping implicated the viral polymerase as a major driver of multiple infection dependence. Mechanistically, quantification of incomplete viral genomes showed that their complementation only partly accounts for the observed reliance on coinfection. Indeed, even when all polymerase components are detected in single cell mRNA sequencing, robust polymerase activity of GFHK99 virus in mammalian cells is reliant on multiple infection. In sum, IAV collective interactions not only augment reassortment, but can also overcome species-specific barriers to infection. These findings underscore the importance of virus-virus interactions in IAV infection, evolution and emergence. We used a single-cell sequencing platform (10x Genomics) to elucidate the differential infection rate of an avian influenza A virus on an avian cell line (DF1) and a mammalian (MDCK) cell line. Our work on IAV reassortment has raised new questions about the fundamental strategies that drive influenza virus evolution. Our data indicate that a large majority of influenza virus genomesare incomplete within cells, comprising less than the eight complete segments normally found in a replication competent infectious viral particle. This led us to ask: what underlying mechanisms give rise to incomplete genomes? What constitute an infectious unit? What are the implications for viral diversification, evolution and spread. By addressing these questions, we will advance he field by deepening our understanding how viral infections are initiated and propagated.
Overall design Avian DF-1 cells or mammalian MDCK cells were infected with different multiplicity of infection using wildtype A/Guinea Fowl/Hong Kong/WF10/99 and barcoded A/Guinea Fowl/Hong Kong/WF10/99. At 8 hours post infection, cells were harvested for both experiments and processed for single-cell sorting and 3' transcript sequencing using the 10x Genomics platform.
Contributor(s) Phipps K, Ganti K, Carnaccini S, Manandhar M, Jacobs NT, Pickett BE, Tan GS, Ferreri LM, Perez DR, Lowen AC
Citation(s) 32632248
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 AI127799 Host dependence of influenza A virus reassortment EMORY UNIVERSITY Anice C Lowen
U19 AI110819 The J. Craig Venter Institute Genome Center for Infectious Diseases J. Craig Venter Institute William Charles Nierman
Submission date Aug 08, 2019
Last update date Sep 15, 2020
Contact name Gene Tan
Organization name J. Craig Venter Institute
Street address 4120 Capricorn Lane
City La Joll
ZIP/Postal code 92037
Country USA
Platforms (2)
GPL19787 Illumina NextSeq 500 (Gallus gallus)
GPL21400 Illumina NextSeq 500 (Canis lupus familiaris)
Samples (16)
GSM4134170 DF1_0_07_Run_1
GSM4134171 DF1_0_2_Run_1
GSM4134172 DF1_0_6_Run_1
BioProject PRJNA559274
SRA SRP217802

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Supplementary file Size Download File type/resource
GSE135553_CanFam98_3WF10.fa.gz 692.5 Mb (ftp)(http) FA
GSE135553_CanFam98_3WF10.gtf.gz 16.0 Mb (ftp)(http) GTF
GSE135553_CanFam98_WF10.fa.gz 692.5 Mb (ftp)(http) FA
GSE135553_CanFam98_WF10.gtf.gz 17.1 Mb (ftp)(http) GTF
GSE135553_GRCg6a_3WF10.fa.gz 305.6 Mb (ftp)(http) FA
GSE135553_GRCg6a_3WF10.gtf.gz 11.2 Mb (ftp)(http) GTF
GSE135553_GRCg6a_WF10.fa.gz 305.6 Mb (ftp)(http) FA
GSE135553_GRCg6a_WF10.gtf.gz 10.2 Mb (ftp)(http) GTF
GSE135553_RAW.tar 32.2 Mb (http)(custom) TAR (of MTX, TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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