Chemistry and Bioinformatics Considerations in Using Next-Generation Sequencing Technologies to Inferring HIV Proviral DNA Genome-Intactness
Year: 2021
Type: article
Abstract: HIV persists via integration of the viral DNA into the human genome. The HIV DNA pool within an infected individual is a complex population that comprises both intact and defective viral genomes, each with a distinct integration site, in addition to a unique repertoire of viral quasi-species. Obtaining an accurate profile of the viral DNA pool is critical to understanding viral persistence and resolving interhost differences. Recent advances in next-generation deep sequencing (NGS) technologies have enabled the development of two sequencing assays to capture viral near-full- genome sequences at single molecule resolution (FLIP-seq) or to co-capture full-length viral genome sequences in conjunction with its associated viral integration site (MIP-seq). This commentary aims to provide an overview on both FLIP-seq and MIP-seq, discuss their strengths and limitations, and outline specific chemistry and bioinformatics concerns when using these assays to study HIV persistence.
Source: Viruses
DOI: 10.3390/v13091874
Author: Guinevere Lee
Institution: Weill Cornell Medicine
Language: English
Topic: HIV Research and Treatment
Subfield: Virology
Field: Immunology and Microbiology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $2,376
Awards: BELIEVE: Bench to Bed Enhanced Lymphocyte Infusions to Engineer Viral Eradication, Insights into the dynamics of clonal expansion of genome-intact proviruses by examining longitudinal evolution of HIV proviral DNA compositions, Characterization of Non-subtype B HIV-1 Reservoirs and its Association with Longitudinal Clinical Outcomes
OpenAlex ID: W3199102521