HIV-1 continues to replicate and evolve in patients with natural control of HIV infection

Abstract

Elucidating mechanisms leading to the natural control of HIV-1 infection is of great importance for vaccine design and for understanding viral pathogenesis. Rare HIV-1-infected individuals, termed HIV-1 controllers, have plasma HIV-1 RNA levels below the limit of detection by standard clinical assays (<50 to 75 copies/ml) without antiretroviral therapy. Although several recent studies have documented persistent low-grade viremia in HIV-1 controllers at a level not significantly different from that in HIV-1-infected individuals undergoing treatment with combination antiretroviral therapy (cART), it is unclear if plasma viruses are undergoing full cycles of replication in vivo or if the infection of new cells is completely blocked by host immune mechanisms. We studied a cohort of 21 HIV-1 controllers with a median level of viremia below 1 copy/ml, followed for a median of 11 years. Less than half of the cohort carried known protective HLA types (B*57/27). By isolating HIV-1 RNA from large volumes of plasma, we amplified single genome sequences of both pro-rt and env longitudinally. This study is the first to document that HIV-1 pro-rt and env evolve in this patient group, albeit at rates somewhat lower than in HIV-1 noncontrollers, in HLA B*57/27-positive, as well as HLA B*57/27-negative, individuals. Viral diversity and adaptive events associated with immune escape were found to be restricted in HIV-1 controllers, suggesting that replication occurs in the face of less overall immune selection.

FIG. 1.

Viremia in HIV-1 controllers measured by SCA. (A) HIV-1 RNA levels in 18 controllers. The open symbols indicate undetectable values plotted at the limit of detection; the closed symbols indicate measurable HIV-1 RNA values. The detection limit of SCA varied with the volume of plasma assayed. The minimum median was 0.3 copies/ml, and the maximum median was 0.8 copies/ml, shown with dashed lines. (B) Longitudinal HIV-1 RNA values from 3 controllers.

FIG. 2.

Sequence trees from two HIV-1 controllers. (A and B) Rooted maximum-likelihood phylogenetic trees of pro-rt (A) and env (B) from HIV-1 controller C23. The trees were rooted using HXB2 as an outgroup. (C and D) Root-to-tip distances plotted against sampling time.

FIG. 3.

Diversity in HIV-1 controllers and noncontrollers. (A to C) Comparison of diversity, length (measured in amino acids), and numbers of PNLGS of the V1/V2 region of env between controllers (white circles) and noncontrollers during early infection (black circles) and chronic infection (black diamonds). (D to F) Diversity of pro-rt during chronic infection in controllers (white circles) and noncontrollers (black diamonds), with linear regression lines. AA, amino acids.

FIG. 4.

Synonymous and nonsynonymous divergence in HIV-1 controllers and noncontrollers. The accumulation of synonymous (syn.) (dS) (A and C) and nonsynonymous (non-syn.) substitutions (subst.) (dN) (B and D) in controllers (blue) and noncontrollers (red) in pro-rt (A and B) and env (C and D) relative to the earliest sample time is plotted for each patient. Absolute values of dS and dN were estimated using maximum-likelihood codon models under the assumption of a relaxed molecular clock.