Single-cell analysis of upper airway cells reveals host-viral dynamics in influenza infected adults [preprint]
Authors
Cao, YumingGuo, Zhiru
Vangala, Pranitha
Donnard, Elisa
Liu, Ping
McDonel, Patrick
Ordovas Montanes, Jose
Shalek, Alex K.
Finberg, Robert W.
Wang, Jennifer P.
Garber, Manuel
UMass Chan Affiliations
Program in Molecular MedicineDepartment of Medicine, Division of Infectious Diseases and Immunology
Program in Bioinformatics and Integrative Biology
Graduate School of Biomedical Sciences
Document Type
PreprintPublication Date
2020-04-17Keywords
Genomicsinfluenza virus infection
virus-host interactions
RNA sequencing
goblet cell population
viral variation
Bioinformatics
Computational Biology
Genomics
Immunology and Infectious Disease
Infectious Disease
Respiratory Tract Diseases
Virology
Virus Diseases
Metadata
Show full item recordAbstract
Influenza virus infections are major causes of morbidity and mortality. Research using cultured cells, bulk tissue, and animal models cannot fully capture human disease dynamics. Many aspects of virus-host interactions in a natural setting remain unclear, including the specific cell types that are infected and how they and neighboring bystander cells contribute to the overall antiviral response. To address these questions, we performed single-cell RNA sequencing (scRNA-Seq) on cells from freshly collected nasal washes from healthy human donors and donors diagnosed with acute influenza during the 2017-18 season. We describe a previously uncharacterized goblet cell population, specific to infected individuals, with high expression of MHC class II genes. Furthermore, leveraging scRNA-Seq reads, we obtained deep viral genome coverage and developed a model to rigorously identify infected cells that detected influenza infection in all epithelial cell types and even some immune cells. Our data revealed that each donor was infected by a unique influenza variant and that each variant was separated by at least one unique non-synonymous difference. Our results demonstrate the power of massively-parallel scRNA-Seq to study viral variation, as well as host and viral transcriptional activity during human infection.Source
bioRxiv 2020.04.15.042978; doi: https://doi.org/10.1101/2020.04.15.042978. Link to preprint on bioRxiv service
DOI
10.1101/2020.04.15.042978Permanent Link to this Item
http://hdl.handle.net/20.500.14038/29451Rights
The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It is made available under a CC-BY-ND 4.0 International license.Distribution License
http://creativecommons.org/licenses/by-nd/4.0/ae974a485f413a2113503eed53cd6c53
10.1101/2020.04.15.042978
Scopus Count
Except where otherwise noted, this item's license is described as The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It is made available under a CC-BY-ND 4.0 International license.