A Subset of Extreme Human Immunodeficiency Virus (HIV) Controllers Is Characterized by a Small HIV Blood Reservoir and a Weak T-Cell Activation Level

International audienceBACKGROUND:Human immunodeficiency virus controllers (HICs) form a heterogeneous group of patients with regard to formal definitions, immunologic characteristics, and changes over time in viral load.PATIENTS AND METHODS:The HICs with undetectable viral load ([uHICs] ie, for whom a viral load had never been detected with routine assays; n = 52) were compared with 178 HICs with blips during the follow up (bHICs). Clinical characteristics, ultrasensitive HIV-ribonucleic acid (RNA) and HIV-deoxyribonucleic acid (DNA) loads, HIV1-Western blot profiles, and immune parameters were analyzed.RESULTS:Relative to bHICs, uHICs had significantly lower ultrasensitive plasma HIV-RNA loads (P < .0001) and HIV-DNA levels in peripheral blood mononuclear cells (P = .0004), higher CD4+ T-cell count (P = .04) at enrollment, and lower T-cell activation levels. Between diagnosis and inclusion in the cohort, the CD4+ T-cell count had not changed in uHICs but had significantly decreased in bHICs. Twenty-one percent of the uHICs lacked specific anti-HIV immunoglobulin G antibodies, and these individuals also had very low levels of HIV-DNA. Half of the uHICs had a protective human leukocyte antigen (HLA) allele (-B57/58/B27), a weak CD8+ T-cell response, and very small HIV-DNA reservoir.CONCLUSIONS:We suggest that an interesting HIC phenotype combines protective HLA alleles, low level of HIV blood reservoirs, and reduced immune activation. Prospective studies aimed at evaluating the benefit of combined antiretroviral therapy in HICs might take into account the identification of uHICs and bHICs

Sexually-Transmitted/Founder HIV-1 Cannot Be Directly Predicted from Plasma or PBMC-Derived Viral Quasispecies in the Transmitting Partner

International audienceObjectiveCharacterization of HIV-1 sequences in newly infected individuals is important for elucidating the mechanisms of viral sexual transmission. We report the identification of transmitted/founder viruses in eight pairs of HIV-1 sexually-infected patients enrolled at the time of primary infection (“recipients”) and their transmitting partners (“donors”).MethodsUsing a single genome-amplification approach, we compared quasispecies in donors and recipients on the basis of 316 and 376 C2V5 env sequences amplified from plasma viral RNA and PBMC-associated DNA, respectively.ResultsBoth DNA and RNA sequences indicated very homogeneous viral populations in all recipients, suggesting transmission of a single variant, even in cases of recent sexually transmitted infections (STIs) in donors (n = 2) or recipients (n = 3). In all pairs, the transmitted/founder virus was derived from an infrequent variant population within the blood of the donor. The donor variant sequences most closely related to the recipient sequences were found in plasma samples in 3/8 cases and/or in PBMC samples in 6/8 cases. Although donors were exclusively (n = 4) or predominantly (n = 4) infected by CCR5-tropic (R5) strains, two recipients were infected with highly homogeneous CXCR4/dual-mixed-tropic (X4/DM) viral populations, identified in both DNA and RNA. The proportion of X4/DM quasispecies in donors was higher in cases of X4/DM than R5 HIV transmission (16.7–22.0% versus 0–2.6%), suggesting that X4/DM transmission may be associated with a threshold population of X4/DM circulating quasispecies in donors.ConclusionsThese suggest that a severe genetic bottleneck occurs during subtype B HIV-1 heterosexual and homosexual transmission. Sexually-transmitted/founder virus cannot be directly predicted by analysis of the donor’s quasispecies in plasma and/or PBMC. Additional studies are required to fully understand the traits that confer the capacity to transmit and establish infection, and determine the role of concomitant STIs in mitigating the genetic bottleneck in mucosal HIV transmission

Increasing contribution of integrated forms to total HIV DNA in blood during HIV disease progression from primary infection

International audienceBACKGROUND:In the current context of research on HIV reservoirs, offering new insights into the persistence of HIV DNA in infected cells, which prevents viral eradication, may aid in identifying cure strategies. This study aimed to describe the establishment of stable integrated forms among total HIV DNA during primary infection (PHI) and their dynamics during the natural history of infection.METHODS:Total and integrated HIV DNA were quantified in blood from 74 PHI patients and 97 recent seroconverters (<12 months following infection, "progression cohort"). The evolution of both markers over six years was modelled (mixed-effect linear models). Their predictive values for disease progression were studied (Cox models).FINDINGS:For most patients during PHI, stable integrated forms were a minority among total HIV DNA (median: 12%) and became predominant thereafter (median at AIDS stage: 100%). Both total and integrated HIV DNA increased over a six-year period. Patients from the progression cohort who reached clinical AIDS during follow-up (n = 34) exhibited higher total and integrated HIV DNA levels at seroconversion and a higher percentage of integrated forms than did slower progressors (n = 63) (median: 100% vs 44%). The integrated HIV DNA load was strongly associated with the risk of developing AIDS (aRR = 2.63, p = 0.002).INTERPRETATION:The profile of "rapid" or "slower" progression in the natural history of HIV infection appears to be determined early in the course of HIV infection. The strong predominance of unstable unintegrated forms in PHI may explain the great benefit of this early treatment, which induces a sharp decrease in total HIV DNA. FUND: French National Agency for Research on AIDS and Viral Hepatitis

In-Depth Characterization of Full-Length Archived Viral Genomes after Nine Years of Posttreatment HIV Control

International audienceIn the search for control of human immunodeficiency virus type 1 (HIV-1) infection without antiretroviral therapy, posttreatment controllers (PTCs) are models of HIV remission. To better understand their mechanisms of control, we characterized the HIV blood reservoirs of 8 PTCs (median of 9.4 years after treatment interruption) in comparison with those of 13 natural HIV infection controllers (HICs) (median of 18 years of infection) and with those of individuals receiving efficient antiretroviral therapy initiated during either primary HIV infection (PHIs; n = 8) or chronic HIV infection (CHIs; n = 6). This characterization was performed with single-genome amplification and deep sequencing. The proviral diversity, which reflects the history of past viral replication, was lower in the PTCs, PHIs, and aviremic HICs than in the blipper HICs and CHIs. The proportions of intact and defective proviruses among the proviral pool in PTCs were not significantly different from those of other groups. When looking at the quantities of proviruses per million peripheral blood mononuclear cells (PBMCs), they had similar amounts of intact proviruses as other groups but smaller amounts of defective proviruses than CHIs, suggesting a role of these forms in HIV pathogenesis. Two HICs but none of the PTCs harbored only proviruses with deletion in nef; these attenuated strains could contribute to viral control in these participants. We show, for the first time, the presence of intact proviruses and low viral diversity in PTCs long after treatment interruption, as well as the absence of evolution of the proviral quasispecies in subsequent samples. This reflects low residual replication over time. Further data are necessary to confirm these results.IMPORTANCE Most people living with HIV need antiretroviral therapy to control their infection and experience viral relapse in case of treatment interruption, because of viral reservoir (proviruses) persistence. Knowing that proviruses are very diverse and most of them are defective in treated individuals, we aimed to characterize the HIV blood reservoirs of posttreatment controllers (PTCs), rare models of drug-free remission, in comparison with spontaneous controllers and treated individuals. At a median time of 9 years after treatment interruption, which is unprecedented in the literature, we showed that the proportions and quantities of intact proviruses were similar between PTCs and other individuals. Unlike 2/7 spontaneous controllers who harbored only nef-deleted proviruses, which are attenuated strains, which could contribute to their control, no such case was observed in PTCs. Furthermore, PTCs displayed low viral genetic diversity and no evolution of their reservoirs, indicating very low residual replication, despite the presence of intact proviruses

Comparative <i>Highlighter</i> analyses of <i>env</i> diversity in a donor-recipient HIV-1 transmission pair.

<p>(A) Recipient#1 shows evidence of infection with a single virus. (B) Donor#1 was the chronically infected partner of recipient#1. The same reference amplicon, a V3 RNA sequence from recipient plasma, was used to depict the viral diversity in both individuals.</p

Characteritics of the 8 donors.

¶<p>Results based on the declaration of the recipient.</p><p>EIA-RI test = enzyme-linked immunosorbent assay for recent infection <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069144#pone.0069144-Barin1" target="_blank">[29]</a>, PBMC = peripheral blood mononuclear cells; Het = heterosexual; MSM = man having sex with men; HBV = hepatits B virus; HBsAg = HBV surface antigen; HBsAb = HBV surface antibodies; HBcAb = HBV core antibodies; HCV = hepatitis C virus; n.d. = not done; n.a. = data not available; und = undetectable.</p

Evolutionary relationships between the HIV-1 <i>env</i> genes in the eight donor/recipient pairs.

<p>The evolutionary history was inferred using the Neighbor-Joining method <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069144#pone.0069144-Boeras1" target="_blank">[38]</a>. The optimal tree with the sum of branch length = 2.01912678 is shown. The tree is drawn to scale, with branch length in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Maximum Composite Likelihood method <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069144#pone.0069144-Whitney1" target="_blank">[39]</a> and the unit is the number of base substitutions per site. Codon positions included were 1^st+2^nd+3^rd+noncoding. All positions containing gaps and missing data were eliminated from the dataset. There were a total of 230 positions in the final dataset. Phylogenetic analyses were conducted in MEGA4 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069144#pone.0069144-Redd1" target="_blank">[40]</a>. For each recipient, viruses isolated from PBMC-derived DNA (•) and plasma RNA (○) are represented, with a different color for each donor/recipient pair. Asterisks indicate branches with bootstrap values greater than 98%.</p

Characteritics of the 8 recipients.

*<p>In the 6 months preceding PHI diagnosis.</p>§<p>Urethritis, rectitis, genital herpes infection, vulvo-vaginal candidosis, condyloma and/or syphilis.</p><p>PBMC = peripheral blood mononuclear cells; Het = heterosexual; MSM = man having sex with men; HBV = hepatits B virus; HBsAg = HBV surface antigen; HBsAb = HBV surface antibodies; HBcAb = HBV core antibodies; HCV = hepatitis C virus; n.d. = not done; und = undetectable.</p