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.
Highlights
HIV-1 infection leads to lifelong viral persistence
This implies that PCR and sequencing errors should be strictly monitored for any viralsequence-based clonal expansion analyses that are not supported by viral integration site data
MIP-seq has been applied to compare viral integration sites of intact versus defective genomes [32], reveal unique patterns of genomeintact viral integration sites in HIV elite controllers [24], and has been further developed by another group of researchers to include co-capturing of T-cell receptor sequences for antigen specificity inferences of the infected cells [73]
Summary
HIV-1 infection leads to lifelong viral persistence. Upon infection, the viral RNA genome is reverse transcribed the into viral cDNA, which is followed by an irreversible integration into the human genome [1]. The HIV reservoir population structure within a single infected individual is complex, changes over time, and contains viral genomes that are either intact or defective, while each viral genome is associated with unique viral integration sites that may impact their likelihoods of transcription activation. To study viral persistence and its longitudinal dynamics and to identify future targets for HIV cure research, it is crucial to accurately characterize “genome-intact” HIV-DNA genomes. In this commentary, the author will discuss technical considerations and limitations of two assays, FLIP-seq and MIP-seq, both of which are single-copy, next-generation deep sequencing techniques for the study of HIV DNA genomes and reservoirs
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