Archived HIV-1 minority variants detected by ultra-deep pyrosequencing in provirus may be fully replication competent

HIV-1 dual/mixed tropic isolates show different genetic and phenotypic characteristics and response to maraviroc in vitro

“…Second, the methodology used to generate viral isolates (based on CD8 + -depleted PBMC co-culture) could have posed a selective pressure towards the use of a specific co-receptor. However, our results are similar to those obtained in other studies where viral tropism and quasispecies-variability within each subject were investigated at both plasmatic and cellular level (Rozera et al, 2009;Swenson et al, 2010a,b). Third, we assessed viral tropism by using a phenotypic assay based on multiple cycles of replication.…”

Detection of quasispecies variants predicted to use CXCR4 by ultra-deep pyrosequencing during early HIV infection

“…The recently available high-throughput sequencing methods, on the whole referred to as UDPS, provided an enormous increase of the resolution power of the quasispecies analysis, and allowed to highlight and to count the relative frequency of even rare variants with different coreceptors usage as compared with the dominant virus population [19][20][21][22]29].…”

Low-Abundance Resistant Mutations in HIV-1 Subtype C Antiretroviral Therapy-Naive Individuals as Revealed by Pyrosequencing

“…While proviral DNA provides a good account of archived resistance mutations it may not represent those variants involved in active replication. However, previous studies using UDPS have revealed that proviral DNA may hide segregated variants [38, 39] that represent a minor subpopulation of the viral quasispecies and may be a source of replication competent virus. Although it is not possible to evaluate the level of proviral variants being expressed we can assume that some of them will generate viral progeny or even recombine with replicating virus as previously shown [38].…”

“…However, previous studies using UDPS have revealed that proviral DNA may hide segregated variants [38, 39] that represent a minor subpopulation of the viral quasispecies and may be a source of replication competent virus. Although it is not possible to evaluate the level of proviral variants being expressed we can assume that some of them will generate viral progeny or even recombine with replicating virus as previously shown [38]. As a result archived provirus variants may preferential replicate at a given time point and undergo selective expansion in the presence of ART, possibly affecting the therapeutic response.…”