Increasing trends in primary NNRTI resistance 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 characterized by high antiretroviral (ARV) coverage over the diagnosed population and also by an important proportion of undiagnosed individuals, in order to determine whether any change in primary resistance occurred in the past five years. Design: We carried out a multi-site resistance surveillance study according to WHO HIV resistance guidelines, using a weighted sampling technique based on annual HIV case reports per site. Methods: Blood samples were collected from 197 drug-naive HIV-1-infected individuals diagnosed between March 2010 and August 2011 at 20 HIV voluntary counselling and testing centres in Buenos Aires. Clinical records of enrolled patients at the time of diagnosis were compiled. Viral load and CD4 counts were performed on all samples. The pol gene was sequenced and the resistance profile determined. Phylogenetic analysis was performed by neighbour-joining (NJ) trees and bootscanning analysis. Results: We found that 12 (7.9%) of the 152 successfully sequenced samples harboured primary resistance mutations, of which K103N and G190A were the most prevalent. Non-nucleoside reverse transcriptase inhibitors (NNRTI) resistance mutations were largely the most prevalent (5.9%), accounting for 75% of all primary resistance and exhibiting a significant increase (p =0.0072) in prevalence during the past 10 years as compared to our previous study performed in 1997-2000 and in 2003-2005. Nucleoside reverse transcriptase inhibitor (NRTI) and protease inhibitor primary resistance were low and similar to the one previously reported. Conclusions: Levels of primary NNRTI resistance in Buenos Aires appear to be increasing in the context of a sustained ARV coverage and a high proportion of undiagnosed HIV-positive individuals. © 2013 Rodriguez-Rodrigues N et al; licensee International AIDS Society.Fil: Rodriguez Rodrigues, Nahuel Emiliano. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas en Retrovirus y Sida; ArgentinaFil: Duran, Adriana. Ministerio de Salud de la Nación; ArgentinaFil: Bouzas, Maria Belen. Gobierno de la Ciudad de Buenos Aires. Hospital de Infecciosas F. J. Muñiz; ArgentinaFil: Zapiola, Ines. Gobierno de la Ciudad de Buenos Aires. Hospital de Infecciosas F. J. Muñiz; ArgentinaFil: Vila, Marcelo. Organizacion Mundial de la Salud; ArgentinaFil: Indyk, Debbie. Icahn School of Medicine at Mount Sinai; Estados UnidosFil: Bissio, Emiliano. Ministerio de Salud de la Nación; ArgentinaFil: Salomon, Horacio Eduardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas en Retrovirus y Sida; Argentina. Universidad de Buenos Aires. Facultad de Medicina. Departamento de Microbiología; ArgentinaFil: Dilernia, Dario Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas en Retrovirus y Sida; Argentin

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-naive 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

CD8 T cells targeting adapted epitopes in chronic HIV infection promote dendritic cell maturation and CD4 T cell trans-infection.

HIV-1 frequently escapes from CD8 T cell responses via HLA-I restricted adaptation, leading to the accumulation of adapted epitopes (AE). We previously demonstrated that AE compromise CD8 T cell responses during acute infection and are associated with poor clinical outcomes. Here, we examined the impact of AE on CD8 T cell responses and their biological relevance in chronic HIV infection (CHI). In contrast to acute infection, the majority of AE are immunogenic in CHI. Longitudinal analyses from acute to CHI showed an increased frequency and magnitude of AE-specific IFNγ responses compared to NAE-specific ones. These AE-specific CD8 T cells also were more cytotoxic to CD4 T cells. In addition, AE-specific CD8 T cells expressed lower levels of PD1 and CD57, as well as higher levels of CD28, suggesting a more activated and less exhausted phenotype. During CHI, viral sequencing identified AE-encoding strains as the dominant quasispecies. Despite increased CD4 T cell cytotoxicity, CD8 T cells responding to AE promoted dendritic cell (DC) maturation and CD4 T cell trans-infection perhaps explaining why AE are predominant in CHI. Taken together, our data suggests that the emergence of AE-specific CD8 T cell responses in CHI confers a selective advantage to the virus by promoting DC-mediated CD4 T cell trans-infection

Detail of the INPUTS for the model.

<p>Detail of the INPUTS for the model.</p

Interferon-α resistance of TF and NT viruses.

<p>(A) Spearman correlation of the replication measured by area under the curve (AUC) (y-axis) of each tested variant (black dots) and the replication (AUC) in the presence of interferon alpha (x-axis) (Non-parametric Spearman p < .0001, r = 0.8844). (B) Virus growth over 10 days in culture as measured by reverse transcriptase (RT) activity (DLU = digital light units) of the TF (blue), and NT variants (red) in the presence of IFN-α (dotted) and absence of IFN-α (solid lines) in an example pair 331. (C) RC scores in the presence of IFN-α were divided by the RC score in the absence of IFN-α for TF (blue) and selected NT (red) viruses with similar replication kinetics (Wilcoxon matched-pairs signed rank test, two tailed, p = 0.219). Subtype B TF (blue) and 6-month consensus (red) viruses are shown as controls on the right.</p

Mortality rate in the first year of HAART for each of the analytical settings.

<p>For the present analysis, the percentage of newly treated patients that die during the first year of initiation of the first HAART regimen was estimated. In this case, data recovered across the whole simulation was analyzed by identifying patients that have initiated HAART and whose date of death occurred within the 12 simulation cycles after initiation of HAART, over the total individuals that have initiated HAART during the model run. *Significantly different with a <i>p</i>-value<0.05.</p

Analysis of the impact of detection rate on diagnosis delay.

<p>The data was obtained from simulations where the diagnosis delay was relaxed. Then testing rate was modified and distribution of year of infection in the undiagnosed population was analyzed. In the figure, each curve corresponds to a different percentile of that distribution. In dark blue is shown the curve for the median.</p

Proportion of HIV positive individuals unaware of their infection status having CD4 counts below 250 (dark bars) or 350 cells/µl (light bars), for each of the analytical settings.

<p>In this case, model’s outputs were further analyzed to determine the proportion of HIV positive individuals unaware of their infection whose CD4 count have drop below critical levels (250 and 350 cells/µl).</p

Comparison of average age at death of HIV positive individuals according to the capacity of detecting infection by symptomatology and the access to treatment.

<p>Age at death for the population living with HIV are compared with those individuals who have achieved diagnosis. Predictions show the impact of early diagnoses on extending life of individuals living with HIV, as well as show that improvements in efficiency of detecting HIV infections through symptomatology can significantly extend life expectancy in cases where the diagnosis is achieved later than 8 years post-infection. Predictions show the major impact that access to therapy can have on extending life expectancy even for patients diagnosed in advanced stages of infection.</p