Metatranscriptomic RNA-Seq Data Analysis of Virus-Infected Host Cells

Nooran Abu Mazen¹, Jessica Luc¹, Briallen Lobb¹, Jeremy Alexander Hirota^{1

2

3

4

5}, Arinjay Banerjee^{1

6

7

8

9}, Andrew C Doxey^{10

11

12}

Affiliations

¹ Department of Biology, University of Waterloo, Waterloo, ON, Canada.
² Firestone Institute for Respiratory Health - Division of Respirology, Department of Medicine, McMaster University, Hamilton, ON, Canada.
³ School of Biomedical Engineering, McMaster University, Hamilton, ON, Canada.
⁴ McMaster Immunology Research Centre, McMaster University, Michael G. DeGroote Centre for Learning and Discovery, Hamilton, ON, Canada.
⁵ Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.
⁶ Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada.
⁷ Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK, Canada.
⁸ Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
⁹ Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.
¹⁰ Department of Biology, University of Waterloo, Waterloo, ON, Canada. acdoxey@uwaterloo.ca.
¹¹ Firestone Institute for Respiratory Health - Division of Respirology, Department of Medicine, McMaster University, Hamilton, ON, Canada. acdoxey@uwaterloo.ca.
¹² Waterloo Centre for Microbial Research, Waterloo, ON, Canada. acdoxey@uwaterloo.ca.

PMID: 38888771
DOI: 10.1007/978-1-0716-3890-3_5

Metatranscriptomic RNA-Seq Data Analysis of Virus-Infected Host Cells

Nooran Abu Mazen et al. Methods Mol Biol. 2024.

. 2024:2813:79-94.

doi: 10.1007/978-1-0716-3890-3_5.

Authors

Nooran Abu Mazen¹, Jessica Luc¹, Briallen Lobb¹, Jeremy Alexander Hirota^{1

2

3

4

5}, Arinjay Banerjee^{1

6

7

8

9}, Andrew C Doxey^{10

11

12}

Affiliations

¹ Department of Biology, University of Waterloo, Waterloo, ON, Canada.
² Firestone Institute for Respiratory Health - Division of Respirology, Department of Medicine, McMaster University, Hamilton, ON, Canada.
³ School of Biomedical Engineering, McMaster University, Hamilton, ON, Canada.
⁴ McMaster Immunology Research Centre, McMaster University, Michael G. DeGroote Centre for Learning and Discovery, Hamilton, ON, Canada.
⁵ Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.
⁶ Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada.
⁷ Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK, Canada.
⁸ Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
⁹ Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.
¹⁰ Department of Biology, University of Waterloo, Waterloo, ON, Canada. acdoxey@uwaterloo.ca.
¹¹ Firestone Institute for Respiratory Health - Division of Respirology, Department of Medicine, McMaster University, Hamilton, ON, Canada. acdoxey@uwaterloo.ca.
¹² Waterloo Centre for Microbial Research, Waterloo, ON, Canada. acdoxey@uwaterloo.ca.

PMID: 38888771
DOI: 10.1007/978-1-0716-3890-3_5

Abstract

RNA sequencing (RNA-seq) analysis of virus-infected host cells enables researchers to study a wide range of phenomena involving host-virus interactions. This includes genomic analysis of the viral population itself, as well as analysis of the transcriptional dynamics of the virus and host during infection. In this chapter, we provide a guide for researchers interested in performing RNA-seq data analysis of virus-infected host cells or cell lines. We outline several bioinformatic protocols for quantifying viral abundance, assembling viral genomes from mixed samples, and performing differential expression analysis, among other common workflows. These workflows can be used as starting points for researchers aiming to analyze RNA-seq datasets of mixed samples containing both host and viral RNA, such as virus-infected cell lines or clinical samples.

Keywords: BioinformaticsBioinformatics; Host response to virus; Metatranscriptomics; RNA sequencing; Taxonomic profiling; Viral abundance; Viral genome assembly; Viral infection; Viral strain variation.

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References

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Metatranscriptomic RNA-Seq Data Analysis of Virus-Infected Host Cells

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Metatranscriptomic RNA-Seq Data Analysis of Virus-Infected Host Cells

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