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

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.

SUBMITTER: Artesi M

PROVIDER: S-EPMC8025556 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature

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

Artesi Maria M Hahaut Vincent V Cole Basiel B Lambrechts Laurens L Ashrafi Fereshteh F Marçais Ambroise A Hermine Olivier O Griebel Philip P Arsic Natasa N van der Meer Frank F Burny Arsène A Bron Dominique D Bianchi Elettra E Delvenne Philippe P Bours Vincent V Charlier Carole C Georges Michel M Vandekerckhove Linos L Van den Broeke Anne A Durkin Keith K

Genome biology 20210406 1

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 as ...[more]

PMID: 33823910

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