Background:
In the randomized-controlled eCLEAR study focusing on the administration of the broadly neutralizing antibody 3BNC117 at the time of ART initiation, one post-treatment controller was identified. He initiated ART and 3BNC117 during primary HIV-1 infection (plasma viral load of 188,945 copies/mL and CD4 counts of 470 cells/mm3) and has had sustained virologic control for 5.3 years following ART interruption (ATI). However, immunological and virological mechanisms in this post-treatment controller are poorly understood.
Methods:
Viral reservoir cells were evaluated using quantitative in vitro viral outgrowth assays, duplex ddPCR (3dPCR), near full-genome proviral sequencing (FLIP-Seq) and matched integration site and proviral sequencing (MIP-Seq). Single cell transcriptome, surface protein and T-cell receptor profiling of 14,230 CD4 T cells were performed with the 10x platform. HIV-1-specific CD8 T cells were analyzed using the activation-induced marker (AIM) assay.
Results:
The person did not have any known protective HLA alleles and plasma samples repeatedly tested negative for antiretroviral drugs. Replication-competent proviruses were detected during ATI at a frequency of 0.2-0.5 infectious units/ million CD4 T cells. Intact proviruses/million CD4 T cells declined during ATI. PreART intact proviruses were predominantly (85%) located in ordinary genic locations, although 2 clones of intact proviruses in ZNF genes on chromosome 19 were already observed at this time. During the ATI stage, two large clones of intact proviruses were observed, one integrated in the centromere region of chromosome 4, and one in the peri centromere region of chromosome Y; one single provirus integrated in the centromere region of chromosome 9 was also noted. A strong HIV-1-specific CD8 T response towards Gag was maintained during the ATI, whereas responses towards Pol, Nef and Env decreased. Single cell analysis showed widespread CD4 T cell activation during ATI compared to pre-ATI and upregulation of cytotoxic and antiviral markers (GZMA, CX3CR1, APOBEC3G) by a subset of highly clonally expanded Th1 CD4 T cells.
Conclusions:
Post-treatment control in this individual was associated with persistence of genome-intact HIV-1 proviruses that grew out under in vitro tissue culture assays but not under physiological in vivo conditions. This is possibly due to a strong immune-mediated selection of intact proviruses in heterochromatin locations that may have a weaker ability to drive rebound in vivo.