PCIP-seq: simultaneous sequencing of integrated viral genomes and their insertion sites with long reads - Université Paris Cité Access content directly
Journal Articles Genome Biology Year : 2021

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

Maria Artesi
  • Function : Author
Vincent Hahaut
  • Function : Author
Basiel Cole
  • Function : Author
Laurens Lambrechts
  • Function : Author
Fereshteh Ashrafi
  • Function : Author
Philip Griebel
  • Function : Author
Natasa Arsic
  • Function : Author
Frank van Der Meer
  • Function : Author
Arsène Burny
  • Function : Author
Dominique Bron
  • Function : Author
Elettra Bianchi
  • Function : Author
Philippe Delvenne
  • Function : Author
Vincent Bours
  • Function : Author
Carole Charlier
  • Function : Author
Michel Georges
  • Function : Author
Linos Vandekerckhove
  • Function : Author
Anne van den Broeke
  • Function : Author
Keith Durkin
  • Function : Author

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.

Dates and versions

hal-03244131 , version 1 (01-06-2021)

Identifiers

Cite

Maria Artesi, Vincent Hahaut, Basiel Cole, Laurens Lambrechts, Fereshteh Ashrafi, et al.. PCIP-seq: simultaneous sequencing of integrated viral genomes and their insertion sites with long reads. Genome Biology, 2021, 22 (1), ⟨10.1186/s13059-021-02307-0⟩. ⟨hal-03244131⟩
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