HLA-driven convergence of HIV-1 viral subtypes B and F toward the adaptation to immune responses in human populations.

BACKGROUND: Cytotoxic T-Lymphocyte (CTL) response drives the evolution of HIV-1 at a host-level by selecting HLA-restricted escape mutations. Dissecting the dynamics of these escape mutations at a population-level would help to understand how HLA-mediated selection drives the evolution of HIV-1. METHODOLOGY/PRINCIPAL FINDINGS: We undertook a study of the dynamics of HIV-1 CTL-escape mutations by analyzing through statistical approaches and phylogenetic methods the viral gene gag sequenced in plasma samples collected between the years 1987 and 2006 from 302 drug-naïve HIV-positive patients. By applying logistic regression models and after performing correction for multiple test, we identified 22 potential CTL-escape mutations (p-value<0.05; q-value<0.2); 10 of these associations were confirmed in samples biologically independent by a Bayesian Markov Chain Monte-Carlo method. Analyzing their prevalence back in time we found that escape mutations that are the consensus residue in samples collected after 2003 have actually significantly increased in time in one of either B or F subtype until becoming the most frequent residue, while dominating the other viral subtype. Their estimated prevalence in the viral subtype they did not dominate was lower than 30% for the majority of samples collected at the end of the 80's. In addition, when screening the entire viral region, we found that the 75% of positions significantly changing in time (p<0.05) were located within known CTL epitopes. CONCLUSIONS: Across HIV Gag protein, the rise of polymorphisms from independent origin during the last twenty years of epidemic in our setting was related to an association with an HLA allele. The fact that these mutations accumulated in one of either B or F subtypes have also dominated the other subtype shows how this selection might be causing a convergence of viral subtypes to variants which are more likely to evade the immune response of the population where they circulate.

HIV type 1 genetic diversity surveillance among newly diagnosed individuals from 2003 to 2005 in Buenos Aires, Argentina.

To perform a diversity surveillance study we characterized viral subtypes among newly diagnosed individuals in Buenos Aires city. Plasma samples were collected from 322 drug-naive newly diagnosed HIV-1 individuals attending two voluntary counseling and testing centers. Sequences of pol and vpu genes were obtained from 283 samples and viral subtype was characterized by Neighbor-joining trees and Bootscanning analysis. BF recombinants were found in 56.9% followed by subtype B strains (39.2%). CRF12_BF structure was found in 27% of BF while another 27% had that structure only in one of both genes analyzed. Unusual non-B-non-BF strains were found in 3.9% (11/283). They were further analyzed by database searching and maximum likelihood trees in order to track their origin. Two subtype C sequences were found to be related to South American isolates while another two subtype C sequences and the subtype C segment of a BC recombinant were found to be related to isolates from Senegal. We also identified the CRF16_A2D previously found in Argentina and the CRF06_cpx commonly prevalent in Africa. The B segment of a BD recombinant was also found to be related to the Argentinean Bs suggesting a recombination between an African and a local strain. We also found a BK and two BA recombinants. In conclusion, CRF16_A2D and a new line of subtype C (of Senegalese origin) seem to be successfully established and are now spreading in Buenos Aires. BF recombinants keep recombining with local strains losing the CRF12_BF structure. Altogether they are changing the diversity of HIV in Argentina.

Risk of cancers during interrupted antiretroviral therapy in the SMART study.

OBJECTIVE: To compare rates of AIDS-defining and non-AIDS-defining malignancies between patients on a CD4 T-cell-guided antiretroviral therapy (ART) strategy and continuous ART. DESIGN: A randomized clinical trial. METHODS: Malignancy rates were compared between the drug conservation arm in which ART was stopped if the CD4 T-cell count exceeded 350 cells/microl and (re)started if it fell to less than 250 cells/microl and the viral suppression arm utilizing continuous ART. Cox models were used to examine baseline characteristics including age, sex, race, cigarette use, previous malignancies, CD4 T-cell and HIV-RNA levels, hepatitis B or C, and ART duration. RESULTS: A total of 5472 participants were randomly assigned to treatment groups, of whom 70 developed cancer: 13 AIDS-defining malignancies and 58 non-AIDS-defining malignancies (one patient had both). The AIDS-defining malignancy rate per 1000 person-years was higher in the drug conservation arm (3.0 versus 0.5). Proximal CD4 T-cell and HIV RNA levels mediated much of this increased risk. The drug conservation arm also had higher rates of Kaposi's sarcoma (1.9 versus 0.3) and lymphoma (Hodgkin's and non-Hodgkin's; 1.1 versus 0.3). The non-AIDS-defining malignancy rate was similar between the drug conservation and viral suppression arms (8.8 versus 7.1). The most common non-AIDS-defining malignancies were skin (n = 16), lung (n = 8) and prostate (n = 6) cancers. CONCLUSION: Non-AIDS-defining malignancies were more common in this cohort than AIDS-defining malignancies. This analysis provides further evidence against the use of CD4 T-cell-guided ART because of a higher risk of AIDS-defining malignancies in addition to opportunistic infections and deaths.

Drug-resistance surveillance among newly HIV-1 diagnosed individuals in Buenos Aires, Argentina.

OBJECTIVE: Our objective was to estimate primary resistance in an urban setting in a developing country with a long history of antiretroviral delivery and high coverage levels. DESIGN: We carried out a resistance surveillance study according to WHO HIV-Resistance Guidelines. METHODS: Blood samples were collected from 323 drug-naive HIV-1 infected individuals diagnosed at two HIV voluntary counselling and testing centers in Buenos Aires. Viral-load, CD4 cell counts and detuned assays were performed on all samples. The pol gene was sequenced and the resistance profile determined. Phylogenetic analysis was performed by neighbor-joining trees and bootscanning analysis. RESULTS: We found that 12 (4.2%) of the 284 samples sequenced harbored primary resistance mutations, of which K103N, M41L and V108I were most prevalent. Phylogenetic analysis revealed evidence for the transmission of the K103N mutation among the drug-naive population. The proportion of recent infections identified by the detuned assay was 10.1%. CONCLUSIONS: Levels of primary resistance in Buenos Aires are still low, despite a long history of ARV delivery and high coverage levels.

Prevalencia de infección por VIH en la experiencia del CePAD del Hospital Ramos Mejía / Infection prevalence by VIH in the experience of the CePAD of the Ramos Mejía Hospital

Como resultado de un estudio observacional retrospectivo se describen características demográficas de la población que concurrió al Centro de Prevención, Asesoramiento y Diagnóstico (CePAD) del Hospital Ramos Mejía de la Ciudad de Buenos Aires, y que funciona desde Noviembre de 2001. Los datos relevados son prevalencia de infección por VIH y de otras enfermedades de transmisión sexual, fuente de conocimiento del CePAD, y utilización del recurso