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

Area of Science:

• Virology
• Bioinformatics
• Genomics

Background:

• RNA sequencing (RNA-seq) is crucial for understanding host-virus interactions during infection.
• Analyzing viral and host transcriptional dynamics provides insights into infection mechanisms.
• Existing methods require specific bioinformatic protocols for mixed RNA samples.

Purpose of the Study:

• To provide a comprehensive guide for RNA sequencing data analysis in virus-infected host cells.
• To outline bioinformatic workflows for common analyses of mixed host-viral RNA samples.
• To serve as a starting point for researchers analyzing RNA-seq datasets from infected cells or clinical samples.

Main Methods:

• Bioinformatic protocol development for viral abundance quantification.
• Methods for viral genome assembly from mixed RNA samples.
• Differential gene expression analysis workflows for host and viral transcripts.

Main Results:

• Established protocols for quantifying viral RNA in mixed samples.
• Demonstrated workflows for assembling viral genomes from complex datasets.
• Provided methods for differential expression analysis to identify host-virus transcriptional changes.

Conclusions:

• RNA-seq analysis offers a powerful approach to study host-virus interactions.
• The outlined bioinformatic workflows facilitate comprehensive analysis of infected samples.
• This guide empowers researchers to investigate viral dynamics and host responses effectively.