Table 3.

Combined genome amplification and integration site analysis.

Technique	Description	Advantages	Limitations
Matched integration site and proviral sequencing (MIP-Seq) [115]	Genomic DNA is isolated from CD4+ T cells, quantified using ddPCR for viral gag, and diluted to single proviral genomes based on ddPCR and Poisson distribution. This is followed by multiple displacement amplification (MDA) and whole genome amplification (WGA), generating 1,000-10,000 copies of gDNA. Amplified gDNA is divided such that some is used for NFL sequencing [14] and some for integration site analysis (ISLA; Table 1; Figure 5) or other methods.	Allows for the determination of both the provirus sequence and the integration site from the same cell Integration site analysis is flexible depending on the user-preferred technique Combines techniques already published in the literature for both integration site and genome sequencing	Involves many steps in order to determine the integration site and genome sequence Relies on ddPCR for initial quantification of DNA Must copy the entire human genome, which can lead to errors Sequencing techniques introduce errors that can be mistaken for real mutations
Multiple-displacement amplification with single-genome sequencing (MDA-SGS) [131]	Genomic DNA is extracted from PBMCs or other primary cells and diluted across a 96-well plate. Whole-gDNA is amplified in-well using MDA. MDA wells are screened for proviruses of interest using SGS (subgenomic fragments) from P6 through part of RT. Then integration sites are determined using modified TC-Seq (Table 1) followed by NFL amplification using Sanger sequencing or PacBio sequencing.	Allows for the determination of both the provirus sequence and the integration site from the same cell Combines techniques already published in the literature	Involves many steps in order to determine the integration site and genome sequence Must copy the entire human genome, which can lead to errors Sequencing techniques introduce errors that can be mistaken for real mutations Custom pipeline needed to determine intactness of HIV genome