Reduced and highly diverse peripheral HIV-1 reservoir in virally suppressed patients infected with non-B HIV-1 strains in Uganda

Abstract

Background Our understanding of the peripheral human immunodeficiency virus type 1 (HIV-1) reservoir is strongly biased towards subtype B HIV-1 strains, with only limited information available from patients infected with non-B HIV-1 subtypes, which are the predominant viruses seen in low- and middle-income countries (LMIC) in Africa and Asia. Results In this study, blood samples were obtained from well-suppressed ART-experienced HIV-1 patients monitored in Uganda (n = 62) or the U.S. (n = 50), with plasma HIV-1 loads < 50 copies/ml and CD4+ T-cell counts > 300 cells/ml. The peripheral HIV-1 reservoir, i.e., cell-associated HIV-1 RNA and proviral DNA, was characterized using our novel deep sequencing-based EDITS assay. Ugandan patients were slightly younger (median age 43 vs 49 years) and had slightly lower CD4+ counts (508 vs 772 cells/ml) than U.S. individuals. All Ugandan patients were infected with non-B HIV-1 subtypes (31% A1, 64% D, or 5% C), while all U.S. individuals were infected with subtype B viruses. Unexpectedly, we observed a significantly larger peripheral inducible HIV-1 reservoir in U.S. patients compared to Ugandan individuals (48 vs. 11 cell equivalents/million cells, p < 0.0001). This divergence in reservoir size was verified measuring proviral DNA (206 vs. 88 cell equivalents/million cells, p < 0.0001). However, the peripheral HIV-1 reservoir was more diverse in Ugandan than in U.S. individuals (8.6 vs. 4.7 p-distance, p < 0.0001). Conclusions The smaller, but more diverse, peripheral HIV-1 reservoir in Ugandan patients might be associated with viral (e.g., non-B subtype with higher cytopathicity) and/or host (e.g., higher incidence of co-infections or co-morbidities leading to less clonal expansion) factors. This highlights the need to understand reservoir dynamics in diverse populations as part of ongoing efforts to find a functional cure for HIV-1 infection in LMICs.

The cell biology of HIV-1 latency and rebound

“…Analogously to the IPDA, this requires pairs of primers located before the major 5ʹ splice donor and within the env gene that are widely dispersed along the genome as well as the expression of Tat and Rev. The estimates of the size of the inducible intact proviral reservoir (~ 10-60 HIV-1 RNA + cells/10 6 CD4 + T cells) by EDITS corresponds closely to the estimates obtained by the IPDA assay [73,74].…”

“…Although these assays are limited by the inefficiency of proviral reactivation ex vivo and cytotoxic effects, like the proviral DNA assays, they allow for strong enrichment of replication-competent genomes. For example, sequence analysis of a library of HIV genomes obtained from patients has shown that EDITS, which measures the production of multiply spliced envelope mRNA in patient-derived cells, can provide a 97% enrichment of viral RNA originating from full-length HIV-1 genomes [74]. Analogously to the IPDA, this requires pairs of primers located before the major 5ʹ splice donor and within the env gene that are widely dispersed along the genome as well as the expression of Tat and Rev.…”

HIV-1 subtypes and latent reservoirs

“…The paucity of a universal assay to quantify the latent reservoir across subtypes could be one of the reasons why only a handful of studies examined the latent reservoir characteristics among the viral subtypes. These assays primarily quantify the reservoir in the proviral DNA Compartment [45,46 ▪ ,47,48]. Despite the low number of such studies on non-B viral reservoirs, interesting observations have been reported, especially when the differences are semi-qualitative.…”

“…Another interesting observation is the demonstration that the total latent reservoir size in HIV-1B infections is relatively larger than those of non-B infections [45,46 ▪ ,47,48] or comparable [53,54]. Surprisingly, no study demonstrated that the latent reservoir size of HIV-1B is smaller than other subtypes; therefore, caution must be applied while interpreting these results.…”

Differences in HIV-1 reservoir size, landscape characteristics and decay dynamics in acute and chronic treated HIV-1 Clade C infection

“…HIV-1 reservoir studies in African populations are limited, particularly in subtype C HIV-1 infection, which is the most prevalent form of HIV-1 globally and predominates in southern Africa. The epidemic in Africa is characterized by extensive viral diversity with multiple subtypes, human genetic heterogeneity which influences immunological and disease outcomes; and unique co-morbidities that modulate HIV reservoirs and immune responses [43–46]. The design of a globally applicable HIV cure strategies and interventions to target the viral reservoir depend on a deeper understanding of the variability in the size, composition and characteristics of the genetic landscapes of persisting reservoir genomes in African populations with non-subtype B HIV infections.…”