TY - JOUR AU - Artesi, Maria AU - Hahaut, Vincent AU - Cole, Basiel AU - Lambrechts, Laurens AU - Ashrafi, Fereshteh AU - Marçais, Ambroise AU - Hermine, Olivier AU - Griebel, Philip AU - Arsic, Natasa AU - van der Meer, Frank AU - Burny, Arsène AU - Bron, Dominique AU - Bianchi, Elettra AU - Delvenne, Philippe AU - Bours, Vincent AU - Charlier, Carole AU - Georges, Michel AU - Vandekerckhove, Linos AU - Van den Broeke, Anne AU - Durkin, Keith PY - 2021 DA - 2021/04/06 TI - PCIP-seq: simultaneous sequencing of integrated viral genomes and their insertion sites with long reads JO - Genome Biology SP - 97 VL - 22 IS - 1 AB - 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. SN - 1474-760X UR - https://doi.org/10.1186/s13059-021-02307-0 DO - 10.1186/s13059-021-02307-0 ID - Artesi2021 ER -