VIRTUS

VIRTUS quantifies and identifies viral transcripts from conventional and single-cell RNA-seq data to characterize viral transcriptional activity within human cells.

Key Features:

• Comprehensive virus detection: Detects 763 different viruses, including herpesviruses, retroviruses, and SARS-CoV-2.
• Splice-aware transcript-level analysis: Identifies and quantifies viral transcripts by analyzing splicing events rather than genome copy numbers.
• Co-infection and host integration: Enables detection of infected cells and analysis of multiple co-infecting viruses alongside host gene expression profiles.
• Support for bulk and single-cell data: Applicable to conventional (bulk) RNA-seq and single-cell RNA-seq of human cells.
• Workflow implementation: Implemented using the Common Workflow Language (CWL) and Rabix with configurable parameters via YAML/JSON.

Scientific Applications:

• Detection of covert infections: Identification of viral transcriptional signatures that may indicate covert or active infections affecting disease progression.
• Virus–host interaction studies: Joint analysis of viral and host transcriptomes to investigate transcriptional responses and interactions.
• Co-infection and viral ecosystem analysis: Characterization of composition and transcriptional activity of multiple co-infecting viruses within cells.
• Translational research: Generation of transcriptional evidence that can inform development of therapeutic strategies targeting viral activity.

Methodology:

Uses RNA-seq data to identify and quantify viral transcripts by analyzing splicing events rather than genome copy numbers and is implemented in CWL with Rabix and YAML/JSON-configurable parameters.