Browsing by Author "Dilernia, Dario"
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Item Bioinformatic analysis of post-transmission viral readaptation in Argentine patients with acute HIV-1 infection(2020-07) Damilano, G; Sued, Omar; Satorres, S; Ruiz, Maria; Ghiglione, Y; Guzman, F; Turk, Gabriela ; Quiroga, F; Cahn, Pedro; Salomon, Horacio; Dilernia, DarioDuring the acute phase of HIV-1 infection, a strong readaptation occurs in the viral population. Our objective was to analyze the post-transmission mutations associated with escape to the cytotoxic immune response and its relationship with the progression of the infection. In this study, a total of 17 patients were enrolled during acute/early primary HIV infection and 8 subjects that were the HIV positive partner resulting in 8 transmission pairs. Genotyping of the genetic polymorphisms of HLA class I A and B was performed using PCR-SSOP. Viral RNA extraction was from plasma. 570 single Gag-gene amplifications were obtained by limiting-dilution RT-PCR. Epitope prediction was performed with NetMHC CBS prediction server for the 19 HLA-A and single bondB alleles. Cytotoxic response prediction was performed by using the IEDB Analysis Resource. From our results, we deduce that the transmitted CTL / gag escape frequency in the founder virus was at least double compared to the post-transmission events. Additionally, by means of an algorithm that combines these frequencies, we observed that the founder viruses better adapted to the HLA A / B alleles of the recipient could contribute to a greater progression of the infection. Our results suggest that there is a large adaptation of HIV-1 to the HLA A / B alleles prevalent in our population. However, despite this adaptive advantage, the virus needs to make “readjustments” through new escape and compensatory mutations. Interestingly, according to our results, this readaptation could have a role in the progression of the infection.Item Computational comparison of availability in CTL/gag epitopes among patients with acute and chronic HIV-1 infection(2016) Damilano, Gabriel Dario; Sued, Omar; Ruiz, Maria; Ghiglione, Yanina; Canitano, Flavia; Pando, Maria; Turk, Gabriela; Cahn, Pedro; Salomon, Horacio; Dilernia, DarioBackground Recent studies indicate that there is selection bias for transmission of viral polymorphisms associated with higher viral fitness. Furthermore, after transmission and before a specific immune response is mounted in the recipient, the virus undergoes a number of reversions which allow an increase in their replicative capacity. These aspects, and others, affect the viral population characteristic of early acute infection. Methods 160 single gag-gene amplifications were obtained by limiting-dilution RT-PCR from plasma samples of 8 ARV-naïve patients with early acute infection (<30 days, 22 days average) and 8 ARV-naive patients with approximately a year of infection (10 amplicons per patient). Sanger sequencing and NGS SMRT technology (Pacific Biosciences) were implemented to sequence the amplicons. Phylogenetic analysis was performed by using MEGA 6.06. HLA-I (A and B) typing was performed by SSOP-PCR method. The chromatograms were analyzed with Sequencher 4.10. Epitopes and immune-proteosomal cleavages prediction was performed with CBS prediction server for the 30 HLA-A and -B alleles most prevalent in our population with peptide lengths from 8 to 14 mer. Cytotoxic response prediction was performed by using IEDB Analysis Resource. Results After implementing epitope prediction analysis, we identified a total number of 325 possible viral epitopes present in two or more acute or chronic patients. 60.3% (n = 196) of them were present only in acute infection (prevalent acute epitopes) while 39.7% (n = 129) were present only in chronic infection (prevalent chronic epitopes). Within p24, the difference was equally dramatic with 59.4% (79/133) being acute epitopes (p < 0.05). This is consistent with progressive viral adaptation to immune response in time and further supported by the fact that cytotoxic responses prediction showed that acute epitopes are more likely to generate immune response than chronic epitopes. Interestingly, only 27.5% of acute epitopes match the population-level consensus sequence of the virus. Conclusions Our results indicate that certain non-consensus viral residues might be transmitted more frequently than consensus-residues when located in immunological relevant positions (epitopes). This observation might be relevant to the rationale behind development of an effective vaccine to reduce viral reservoir and induce functional cure of HIV infection based in prevalent acute epitopes. Introduction Following transmission, Cytotoxic CD8+T lymphocytes (CTLs) mount a powerful response to transmitted HIV in the acute phase of infection [1]. However, the vast majority of cases is an inefficient response and directed to a limited number of epitopes [2]. This response is manifested producing a viral set point generally after first month of infection [3], [4], [5] with great specificity on the gag protein, which is strongly associated with control of viral replication [6], [7], [8], [9]. At this point, just after the peak of viremia, the first viral populations with HLA/CTL escape mutations are generated [2], which will increase over time and will have an impact on viral diversity during the chronic phase [10], [11], [12]. Therefore, it is interesting to investigate if these HLA-dependent reversions that occur during the acute phase are associated with a greater availability of epitopes in this stage. Reversions are another important aspect to be considered among viral factors shaping the viral diversity during the acute stage of infection [13], [14]. While their impact on viral fitness on transmitted/founder virus has not yet been elucidated, it is believes reversal mutations make the virus more fit [13], [15], [16].These post-transmission reversions may range from those associated with HLA alleles present on the donor [17], to the CD8 T-cell TCR receptor [13], [18], [19], to the proteasome [20], [21], or reversions that arise at random and increase the viral fitness that end up being established in the major viral population [22], [24]. Also, these reversions could occur prior to transmission, in a process of viral compartmentalization in mucosal associated tissues [25], [26], [27]. In this research, our objective was to determine, in patients under study, whether the viral sequences approach phylogenetically in acute patients compared with chronic patients. In turn, we evaluated whether possible reversions in acute viral sequences could significantly influence to decrease viral phylogenetic distance in these patients. Also, using computational prediction analysis, we evaluated the relationship of phylogenetically relevant amino acid positions (possibly reversions), with epitopes associated with cytotoxic immune response mediated by HLA I. Finally, we evaluated the distribution and characteristics of CTL epitopes, in conserved viral segments. We did an availability and frequency analysis of possible CTL epitopes found in the early acute phase compared to those found in the chronic phase.Item Correction: HLA-Driven Convergence of HIV-1 Viral Subtypes B and F Toward the Adaptation to Immune Responses in Human Populations(2008-11-04) Dilernia, Dario; Jones, Leandro; Rodriguez, Sabrina; Turk, Gabriela; Rubio, Andrea E; Pampuro, Sandra; Gomez-Carrillo, Manuel; Bautista, Christian T; Deluchi, Gabriel; Benetucci, Jorge; Lasala, María Beatriz; Lourtau, Leonardo; Losso, Marcelo Horacio; Perez, Héctor; Cahn, Pedro; Salomon, HoracioThe eighth author's name was displayed incorrectly. It should be: Christian T. Bautista.Item HLA-Driven Convergence of HIV-1 Viral Subtypes B and F Toward the Adaptation to Immune Responses in Human Populations(2008-10-21) Dilernia, Dario; Jones, Leandro; Rodriguez, Sabrina; Turk, Gabriela; Rubio, Andrea E; Pampuro, Sandra; Gomez-Carrillo, Manuel; Bautista, Christian; Deluchi, Gabriel; Benetucci, Jorge; Lasala, María Beatriz; Lourtau, Leonardo; Losso, Marcelo Horacio; Perez, Héctor; Cahn, Pedro; Salomon, HoracioFil: Cahn P. Fundación Huésped, Buenos Aires; ArgentinaItem Host Genetic Factors Associated with Symptomatic Primary HIV Infection and Disease Progression among Argentinean Seroconverters(2014) Coloccini, Romina; Dilernia, Dario; Ghiglione, Yanina; Turk, Gabriela; Laufer, Natalia; Rubio, Andrea; Socias, Maria E.; Figueroa, Maria Ines; Sued, Omar; Cahn, Pedro; Salomon, Horacio; Mangano, Andrea; Pando, María AngelesBackground Variants in HIV-coreceptor C-C chemokine receptor type 5 (CCR5) and Human leukocyte antigen (HLA) genes are the most important host genetic factors associated with HIV infection and disease progression. Our aim was to analyze the association of these genetic factors in the presence of clinical symptoms during Primary HIV Infection (PHI) and disease progression within the first year. Methods Seventy subjects diagnosed during PHI were studied (55 symptomatic and 15 asymptomatic). Viral load (VL) and CD4 T-cell count were evaluated. HIV progression was defined by presence of B or C events and/or CD4 T-cell counts <350 cell/mm3. CCR5 haplotypes were characterized by polymerase chain reaction and SDM-PCR-RFLP. HLA-I characterization was performed by Sequencing. Results Symptoms during PHI were significantly associated with lower frequency of CCR5-CF1 (1.8% vs. 26.7%, p = 0.006). Rapid progression was significantly associated with higher frequency of CCR5-CF2 (16.7% vs. 0%, p = 0.024) and HLA-A*11 (16.7% vs. 1.2%, p = 0.003) and lower frequency of HLA-C*3 (2.8% vs. 17.5%, p = 0.035). Higher baseline VL was significantly associated with presence of HLA-A*11, HLA-A*24, and absence of HLA-A*31 and HLA-B*57. Higher 6-month VL was significantly associated with presence of CCR5-HHE, HLA-A*24, HLA-B*53, and absence of HLA-A*31 and CCR5-CF1. Lower baseline CD4 T-cell count was significantly associated with presence of HLA-A*24/*33, HLA-B*53, CCR5-CF2 and absence of HLA-A*01/*23 and CCR5-HHA. Lower 6-month CD4 T-cell count was associated with presence of HLA-A*24 and HLA-B*53, and absence of HLA-A*01 and HLA-B*07/*39. Moreover, lower 12-month CD4 T-cell count was significantly associated with presence of HLA-A*33, HLA-B*14, HLA-C*08, CCR5-CF2, and absence of HLA-B*07 and HLA-C*07. Conclusion Several host factors were significantly associated with disease progression in PHI subjects. Most results agree with previous studies performed in other groups. However, some genetic factor associations are being described for the first time, highlighting the importance of genetic studies at a local level.Item La importancia del diagnóstico temprano en la supervivencia de los pacientes HIV positivos(2010) Dilernia, Dario; Monaco, Carolina; Krolewiecki, Alejandro J.; Cesar, Carina; Cahn, Pedro; Salomon, HoracioEn la Argentina, el diagnóstico del HIV se realiza por solicitud voluntaria de los individuos o a través de la detección de sintomatología asociada a la infección. Sin embargo, debido a la elevada proporción de sujetos portadores que desconocen su estado serológico son necesarias nuevas estrategias. En el presente artículo mostramos cómo un modelo matemático predice el impacto de la expansión de la prueba diagnóstica del HIV en la Argentina. El modelo se basa en matrices de Markov y utiliza probabilidades de transición dependientes de parámetros obtenidos de estudios de cohortes nacionales e internacionales. Las predicciones incluyen tiempo en estadios clínicos y tratamiento, conteo de CD4, carga viral, estadío de infección, edad, tasas de mortalidad y proporción de infección desconocida a nivel poblacional. Las simulaciones se desarrollaron para la situación actual y para un escenario hipotético con diagnóstico más temprano. Mostramos predicciones que sugieren que el diagnóstico realizado antes de la progresión a sida incrementaría la expectativa de vida en unos 10.7 años. También, mostramos cómo la reducción del tiempo al diagnóstico hasta 5 años o menos desde la infección reduciría la tasa de mortalidad en el primer año de HAART de 7.6% a 2.1%, la proporción de infección no reconocida de 43.2% a 23.8% y la proporción de individuos con infección desconocida y que requieren tratamiento de 12% a 0.2%. Basados en estas predicciones resaltamos la importancia de implementar políticas de salud destinadas a detectar la infección por HIV en estadios tempranos en la Argentina.Item Lack of viral selection in human immunodeficiency virus type 1 mother-to-child transmission with primary infection during late pregnancy and/or breastfeeding(2008) Ceballos, Ana; Andreani, Guadalupe; Ripamonti, Chiara; Dilernia, Dario; Mendez, Ramiro; Rabinovich, Roberto D.; Cardenas, Patricia; Zala, Carlos; Cahn, Pedro; Scarlatti, Gabriella; Martínez Peralta, LilianaMother-to-child transmission (MTCT) of human immunodeficiency virus type 1 (HIV-1) as described for women with an established infection is, in most cases, associated with the transmission of few maternal variants. This study analysed virus variability in four cases of maternal primary infection occurring during pregnancy and/or breastfeeding. Estimated time of seroconversion was at 4 months of pregnancy for one woman (early seroconversion) and during the last months of pregnancy and/or breastfeeding for the remaining three (late seroconversion). The C2V3 envelope region was analysed in samples of mother-child pairs by molecular cloning and sequencing. Comparisons of nucleotide and amino acid sequences as well as phylogenetic analysis were performed. The results showed low variability in the virus population of both mother and child. Maximum-likelihood analysis showed that, in the early pregnancy seroconversion case, a minor viral variant with further evolution in the child was transmitted, which could indicate a selection event in MTCT or a stochastic event, whereas in the late seroconversion cases, the mother's and child's sequences were intermingled, which is compatible with the transmission of multiple viral variants from the mother's major population. These results could be explained by the less pronounced selective pressure exerted by the immune system in the early stages of the mother's infection, which could play a role in MTCT of HIV-1.