【Publications】HIV-1 DNA-capture-seq is a useful tool for the comprehensive characterization of HIV-1 provirus

September 3 2019

Saori C. Iwase

Paper information

Saori C. Iwase, Paola Miyazato, Hiroo Katsuya, Saiful Islam, Benjy Tan Jek Yang, Jumpei Ito, Misaki Matsuo, Hiroaki Takeuchi, Takaomi Ishida, Kouki Matsuda, Kenji Maeda & Yorifumi Satou

HIV-1 DNA-capture-seq is a useful tool for the comprehensive characterization of HIV-1 provirus

Sci Rep. 2019 Aug 23;9(1):12326. doi: 10.1038/s41598-019-48681-5.

 
Highlights

• HIV-1 DNA-probes hybridize not only viral fragments but also virus-host chimeric ones, which contain viral integration site information.
• HIV-1 DNA-capture-seq is a powerful tool to obtain the entire proviral sequence, its structure, the viral integration site, and information related to clonal abundance comprehensively.
• This cost-effective protocol is useful for various experiments for HIV-1 cure research.

Abstract

Human immunodeficiency virus type 1 (HIV-1) is the causative agent for AIDS. Despite reductions in mortality with anti-retroviral drugs, it is still extremely difficult to eradicate HIV-1 from infected individuals. The characterization of the HIV-1 provirus with a high resolution is key to HIV-1 cure research. We use biotinylated DNA probes targeting the entire HIV-1 sequence to capture fragments containing HIV-1 sequences from DNA-seq libraries prepared for high throughput sequencing. This approach provides not only the complete proviral sequence, but also the viral integration site information in a cost-effective manner. By using commonly used HIV-1 infected cell lines and newly established ones, we demonstrate that this HIV-1 DNA-capture-seq is a powerful tool to characterize the HIV-1 provirus at a single nucleotide resolution and therefore might be useful for various experiments aiming for an HIV-1 cure.