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 (1, 2) , Olivier Hermine (1, 2) , 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

1 Hôpital Necker - Enfants Malades [AP-HP]
2 UPCité - Université Paris Cité

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.

Domaines: Sciences du Vivant [q-bio]

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⟩