Genome Biology (Apr 2021)
PCIP-seq: simultaneous sequencing of integrated viral genomes and their insertion sites with long reads
- Maria Artesi,
- Vincent Hahaut,
- Basiel Cole,
- Laurens Lambrechts,
- Fereshteh Ashrafi,
- Ambroise Marçais,
- Olivier Hermine,
- Philip Griebel,
- Natasa Arsic,
- Frank van der Meer,
- Arsène Burny,
- Dominique Bron,
- Elettra Bianchi,
- Philippe Delvenne,
- Vincent Bours,
- Carole Charlier,
- Michel Georges,
- Linos Vandekerckhove,
- Anne Van den Broeke,
- Keith Durkin
Affiliations
- Maria Artesi
- Unit of Animal Genomics, GIGA, Université de Liège (ULiège)
- Vincent Hahaut
- Unit of Animal Genomics, GIGA, Université de Liège (ULiège)
- Basiel Cole
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital and Ghent University
- Laurens Lambrechts
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital and Ghent University
- Fereshteh Ashrafi
- Unit of Animal Genomics, GIGA, Université de Liège (ULiège)
- Ambroise Marçais
- Service d’hématologie, Hôpital Universitaire Necker, Université René Descartes, Assistance Publique Hôpitaux de Paris
- Olivier Hermine
- Service d’hématologie, Hôpital Universitaire Necker, Université René Descartes, Assistance Publique Hôpitaux de Paris
- Philip Griebel
- Vaccine and Infectious Disease Organization, VIDO-Intervac, University of Saskatchewan
- Natasa Arsic
- Vaccine and Infectious Disease Organization, VIDO-Intervac, University of Saskatchewan
- Frank van der Meer
- Faculty of Veterinary Medicine: Ecosystem and Public Health
- Arsène Burny
- Laboratory of Experimental Hematology, Institut Jules Bordet, Université Libre de Bruxelles (ULB)
- Dominique Bron
- Laboratory of Experimental Hematology, Institut Jules Bordet, Université Libre de Bruxelles (ULB)
- Elettra Bianchi
- Department of Pathology, University Hospital (CHU), University of Liège
- Philippe Delvenne
- Department of Pathology, University Hospital (CHU), University of Liège
- Vincent Bours
- Laboratory of Human Genetics, GIGA, Université de Liège (ULiège)
- Carole Charlier
- Unit of Animal Genomics, GIGA, Université de Liège (ULiège)
- Michel Georges
- Unit of Animal Genomics, GIGA, Université de Liège (ULiège)
- Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital and Ghent University
- Anne Van den Broeke
- Unit of Animal Genomics, GIGA, Université de Liège (ULiège)
- Keith Durkin
- Unit of Animal Genomics, GIGA, Université de Liège (ULiège)
- DOI
- https://doi.org/10.1186/s13059-021-02307-0
- Journal volume & issue
-
Vol. 22,
no. 1
pp. 1 – 24
Abstract
Abstract The integration of a viral genome into the host genome has a major impact on the trajectory of the infected cell. Integration location and variation within the associated viral genome can influence both clonal expansion and persistence of infected cells. Methods based on short-read sequencing can identify viral insertion sites, but the sequence of the viral genomes within remains unobserved. We develop PCIP-seq, a method that leverages long reads to identify insertion sites and sequence their associated viral genome. We apply the technique to exogenous retroviruses HTLV-1, BLV, and HIV-1, endogenous retroviruses, and human papillomavirus.
Keywords
