SurVirus

SurVirus detects virus integration sites in human genomes by correcting read misalignments in repetitive regions to reduce false positives and false negatives in integration calling for studies of virus-associated disease.

Key Features:

• Repeat-Aware Alignment Correction: Corrects incorrect read alignments in repetitive genomic regions to improve localization of virus-host junctions.
• Precision and Novelty Detection: Demonstrates superior precision relative to existing callers and identifies novel integrations missed by other methods.
• Validation of Novel Integrations: A subset of newly identified integrations has been validated, confirming high accuracy of detected events.
• Enrichment Analysis: Reveals enrichment of Human Papillomavirus (HPV) and Hepatitis B Virus (HBV) integrations within LINEs (Long Interspersed Nuclear Elements) and Satellite DNA regions.
• Discovery of Recurrent Breakpoints: Detects recurrent breakpoints in human genome–virus fusion transcripts, particularly involving HBV and HPV.

Scientific Applications:

• Mapping integration landscapes: Provides more accurate maps of virus integration sites in human genomes for studies of virus-associated cancers and other diseases.
• Detection of novel integrations in repetitive regions: Enables discovery of previously undetected integrations within LINE and Satellite regions.
• Characterization of fusion transcripts and breakpoints: Facilitates identification of recurrent breakpoints in virus–host fusion transcripts to study mechanisms of viral oncogenesis and to inform potential targeted therapies.

Methodology:

Processes high-throughput sequencing datasets and corrects misaligned reads in repetitive genomic regions to identify virus-host integration sites, thereby reducing false positives and false negatives.