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PCIP-seq: simultaneous sequencing of integrated viral genomes and their insertion sites with long reads

  • Artesi, Maria1, 2, 3
  • Hahaut, Vincent1, 2
  • Cole, Basiel4
  • Lambrechts, Laurens4, 5
  • Ashrafi, Fereshteh1, 6
  • Marçais, Ambroise7
  • Hermine, Olivier7
  • Griebel, Philip8
  • Arsic, Natasa8
  • van der Meer, Frank9
  • Burny, Arsène2
  • Bron, Dominique2
  • Bianchi, Elettra10
  • Delvenne, Philippe10
  • Bours, Vincent3, 10
  • Charlier, Carole1
  • Georges, Michel1
  • Vandekerckhove, Linos4
  • Van den Broeke, Anne1, 2
  • Durkin, Keith1, 2
  • 1 GIGA, Université de Liège (ULiège), Avenue de l’Hôpital 11, Liège, 4000, Belgium , Liège (Belgium)
  • 2 Institut Jules Bordet, Université Libre de Bruxelles (ULB), Boulevard de Waterloo 121, Brussels, 1000, Belgium , Brussels (Belgium)
  • 3 Université de Liège (ULiège), Avenue de l’Hôpital 11, Liège, 4000, Belgium , Liège (Belgium)
  • 4 Ghent University Hospital and Ghent University, Ghent, 9000, Belgium , Ghent (Belgium)
  • 5 Ghent University, Ghent, Belgium , Ghent (Belgium)
  • 6 Ferdowsi University of Mashhad, Mashhad, Iran , Mashhad (Iran)
  • 7 Hôpital Universitaire Necker, Université René Descartes, Assistance Publique Hôpitaux de Paris, Paris, France , Paris (France)
  • 8 University of Saskatchewan, 120 Veterinary Road, Saskatoon, S7N 5E3, Canada , Saskatoon (Canada)
  • 9 Faculty of Veterinary Medicine: Ecosystem and Public Health, Calgary, AB, Canada , Calgary (Canada)
  • 10 University Hospital (CHU), University of Liège, Liège, Belgium , Liège (Belgium)
Published Article
Publication Date
Apr 06, 2021
DOI: 10.1186/s13059-021-02307-0
Springer Nature


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.

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