An analytical pipeline for identifying and mapping the integration sites of HIV and other retroviruses.

ABSTRACT:

Background

All retroviruses, including human immunodeficiency virus (HIV), must integrate a DNA copy of their genomes into the genome of the infected host cell to replicate. Although integrated retroviral DNA, known as a provirus, can be found at many sites in the host genome, integration is not random. The adaption of linker-mediated PCR (LM-PCR) protocols for high-throughput integration site mapping, using randomly-sheared genomic DNA and Illumina paired-end sequencing, has dramatically increased the number of mapped integration sites. Analysis of samples from human donors has shown that there is clonal expansion of HIV infected cells and that clonal expansion makes an important contribution to HIV persistence. However, analysis of HIV integration sites in samples taken from pati

SUBMITTER: Wells DW 

PROVIDER: S-EPMC7063773 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature