University of Massachusetts Medical School Faculty Publications
Title
Single-cell analysis of upper airway cells reveals host-viral dynamics in influenza infected adults
UMMS Affiliation
Graduate School of Biomedical Sciences; Program in Bioinformatics and Integrative Biology; Department of Medicine, Division of Infectious Diseases and Immunology; Program in Molecular Medicine
Publication Date
2020-04-17
Document Type
Article Preprint
Disciplines
Bioinformatics | Computational Biology | Genomics | Immunology and Infectious Disease | Infectious Disease | Respiratory Tract Diseases | Virology | Virus Diseases
Abstract
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.
Keywords
Genomics, influenza virus infection, virus-host interactions, RNA sequencing, goblet cell population, viral variation
Rights and Permissions
The copyright holder for this preprint (which was not peer-reviewed) is the author/funder.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.
DOI of Published Version
10.1101/2020.04.15.042978
Source
bioRxiv 2020.04.15.042978; doi: https://doi.org/10.1101/2020.04.15.042978. Link to preprint on bioRxiv service
Journal/Book/Conference Title
bioRxiv
Repository Citation
Cao Y, Guo Z, Vangala P, Donnard E, Liu P, McDonel P, Ordovas Montanes J, Shalek AK, Finberg RW, Wang JP, Garber M. (2020). Single-cell analysis of upper airway cells reveals host-viral dynamics in influenza infected adults. University of Massachusetts Medical School Faculty Publications. https://doi.org/10.1101/2020.04.15.042978. Retrieved from https://escholarship.umassmed.edu/faculty_pubs/1676
Creative Commons License
This work is licensed under a Creative Commons Attribution-No Derivative Works 4.0 License.
Included in
Bioinformatics Commons, Computational Biology Commons, Genomics Commons, Immunology and Infectious Disease Commons, Infectious Disease Commons, Respiratory Tract Diseases Commons, Virology Commons, Virus Diseases Commons