ArticleNucleic acids research2021
SurVirus: a repeat-aware virus integration caller.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 28 citations in OpenAlex.
- Revisiting HPV integration landscapes using telomere-to-telomere human genome reference closes the gaps in HPV integration sites search.Virology journal · 2026Article
- Proteogenomic characterization of cervical cancer identifies molecular subtypes predictive of clinical outcomes and subtype-specific targets.The Journal of clinical investigation · 2026Article
- HPV Integration in Head and Neck Cancer: Downstream Splicing Events and Expression Ratios Linked with Poor Outcomes.Clinical cancer research : an official journal of the American Association for Cancer Research · 2026Article
- Challenges in the detection and assembly of virus integration structures in human genomes.Frontiers in oncology · 2026Review
- Review
- Splicing of HPV16 E6 promotes aggressive invasion in oropharyngeal cancer via endocytosis of E-cadherin.bioRxiv : the preprint server for biology · 2025Article
- AVID enables sensitive and accurate viral integration detection across human cancers.Cell reports methods · 2025Article
- Multiple DNA Viruses and HPV Integration in Inverted Papilloma and Associated Sinonasal Carcinoma.The Laryngoscope · 2025Article
- Intratumor heterogeneity of HPV integration in HPV-associated head and neck cancer.Nature communications · 2025Article
- Virusplot: a web server for viral integration analysis and visualization.Frontiers in oncology · 2025Article
- Risk assessment and triage strategy of cervical cancer primary screening on HPV integration status: 5-year follow-up of a prospective cohort study.Journal of the National Cancer Center · 2024Article
- Intra-host genomic diversity and integration landscape of human tissue-resident DNA virome.Nucleic acids research · 2024Article
- Occult Hepatitis B Virus Infection in Hepatic Diseases and Its Significance for the WHO's Elimination Plan of Viral Hepatitis.Pathogens (Basel, Switzerland) · 2024Review
- ViroISDC: a method for calling integration sites of hepatitis B virus based on feature encoding.BMC bioinformatics · 2024Article
- Nonproductive Hepatitis B Virus Covalently Closed Circular DNA Generates HBx-Related Transcripts from the HBx/Enhancer I Region and Acquires Reactivation by Superinfection in Single Cells.Journal of virology · 2023Article
- Multi-omics characterization of silent and productive HPV integration in cervical cancer.Cell genomics · 2023Article
- AlcoR: alignment-free simulation, mapping, and visualization of low-complexity regions in biological data.GigaScience · 2022Article
- Analysis of Human Papilloma Virus Content and Integration in Mucoepidermoid Carcinoma.Viruses · 2022Article
- The complexity landscape of viral genomes.GigaScience · 2022Article
- Revolutionized virome research using systems microbiology approaches.Experimental biology and medicine (Maywood, N.J.) · 2022Review
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A significant portion of human cancers are due to viruses integrating into human genomes. Therefore, accurately predicting virus integrations can help uncover the mechanisms that lead to many devastating diseases. Virus integrations can be called by analysing second generation high-throughput sequencing datasets. Unfortunately, existing methods fail to report a significant portion of integrations, while predicting a large number of false positives. We observe that the inaccuracy is caused by incorrect alignment of reads in repetitive regions. False alignments create false positives, while missing alignments create false negatives. This paper proposes SurVirus, an improved virus integration caller that corrects the alignment of reads which are crucial for the discovery of integrations. We use publicly available datasets to show that existing methods predict hundreds of thousands of false positives; SurVirus, on the other hand, is significantly more precise while it also detects many novel integrations previously missed by other tools, most of which are in repetitive regions. We validate a subset of these novel integrations, and find that the majority are correct. Using SurVirus, we find that HPV and HBV integrations are enriched in LINE and Satellite regions which had been overlooked, as well as discover recurrent HBV and HPV breakpoints in human genome-virus fusion transcripts.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.