Chimeric antigen receptor T Cells and stem cells control and protect against SHIV replication in non-human primates
Journal of virus eradication
To increase analytical resolution of the viral dynamics underlying establishment and persistence of the rebound competent reservoir (RCR), we used a barcoded virus (SIVmac239M) to assess the reactivation of individual viral lineages during successive analytic treatment interruptions (ATIs). Methods: Four rhesus macaques infected intravenously with 10,000IU of SIVmac239M received combination antiretroviral therapy (cART) initiated at 10 days post infection (dpi). Three ATIs of 21 days or less
... 21 days or less were initiated at 313, 444 and 682 dpi in each animal, with the second and third ATI preceded by antibody-mediated, CD8+ lymphocyte depletion 3 days prior to cessation of treatment. Plasma viremia was suppressed to below 15 copies/mL for at least 3 months between ATIs, and cART was resumed after peak viremia was reached during viral recrudescence. Next generation sequencing was used to assess the distribution of barcodes in plasma during primary infection and during each viral rebound. Results: Infection with many distinct barcodes was established in each animal, with a mean of 599 (557 to 650) barcodes observed pre-cART (10 dpi). The magnitude and diversity of viral recrudescence was the highest during the second ATI in each animal, with a mean of 109 (89 to 133) detectable lineages, vs 22 (8 to 34) and 27 (8 to 37) barcodes during the first and third ATIs, respectively. The probability of detection of individual barcodes during each ATI increased proportionately to their frequencies at 10 dpi, demonstrating the establishment of a large RCR representative of pre-cART viral lineages. However, in three out of four animals, the proportion of barcodes shared between consecutive ATIs was significantly higher than expected based on their relative frequency before cART, indicating enrichment of reactivated barcodes in the RCR following ATI. Conclusions: The barcoded virus allowed assessment of the contribution of individual viral lineages to the RCR, and changes in composition of the reservoir over time. Evaluating barcode dynamics by sequencing viral DNA during suppressive cART may help define the roles of clonal expansion and reservoir re-seeding during ATIs in the observed enrichment of certain barcodes.