Impact of genotypic diversity on selection of subtype-specific drug resistance profiles during raltegravir-based therapy in individuals infected with B and BF recombinant HIV-1 strains.

BACKGROUND: Current knowledge on HIV-1 resistance to integrase inhibitors (INIs) is based mostly on subtype B strains. This contrasts with the increasing use of INIs in low- and middle-income countries, where non-B subtypes predominate. MATERIALS AND METHODS: HIV-1 drug resistance genotyping was performed in 30 HIV-1-infected individuals undergoing virological failure to raltegravir. Drug resistance mutations (DRMs) and HIV-1 subtype were characterized using Stanford HIVdb and phylogenetic analyses. RESULTS: Of the 30 integrase (IN) sequences, 14 were characterized as subtype F (47%), 8 as subtype B (27%), 7 as BF recombinants (23%) and 1 as a putative CRF05_DF (3%). In 25 cases (83%), protease and reverse transcriptase (PR-RT) sequences from the same individuals confirmed the presence of different BF recombinants. Stanford HIVdb genotyping was concordant with phylogenetic inference in 70% of IN and 60% of PR-RT sequences. INI DRMs differed between B and F IN subtypes, with Q148K/R/H, G140S and E138K/A being more prevalent in subtype B (63% versus 0%, P = 0.0021; 50% versus 0%, P = 0.0096; and 50% versus 0%, P = 0.0096, respectively). These differences were independent of the time on raltegravir therapy or viral load at the time of genotyping. INI DRMs in subtype F IN genomes predicted a lower level of resistance to raltegravir and no cross-resistance to second-generation INIs. CONCLUSIONS: Alternative resistance pathways to raltegravir develop in subtypes B and F IN genomes, with implications for clinical practice. Evaluating the role of HIV-1 subtype in development and persistence of mutations that confer resistance to INIs will be important to improve algorithms for resistance testing and optimize the use of INIs.

Pre-treatment drug resistance and HIV-1 subtypes in infants from Argentina with and without exposure to antiretroviral drugs for prevention of mother-to-child transmission.

OBJECTIVES: To assess the prevalence and patterns of pre-treatment HIV drug resistance (PDR) and HIV-1 subtype in infants from Argentina with exposure to different antiretroviral drugs (ARVs) for the prevention of mother-to-child transmission (PMTCT). PATIENTS AND METHODS: HIV-1 genotyping was performed in 115 infants (median age = 2.3 months) born between 2007 and 2014 to screen for drug resistance mutations (DRMs) before starting first-line ART. HIV-1 subtype was characterized by phylogenetic and recombination analysis. RESULTS: Overall, DRMs were found in 34 of 115 infants (PDR level 30% to any ARV, 3.5% to PIs, 12% to NRTIs and 22% to NNRTIs). Of the 115 infants, 22 (19.1%) were ARV-unexposed. Another 93 were ARV-exposed: 28 (24.3%) to short-course zidovudine monotherapy ARV prophylaxis; 25 (21.7%) to nevirapine-based ARV prophylaxis; 12 (10.4%) to perinatal infant zidovudine prophylaxis + maternal combination ART with NNRTIs; and 28 (24.3%) to perinatal infant zidovudine prophylaxis+maternal combination ART with PIs. Transmitted drug resistance among ARV-unexposed infants was 32% (5% to PIs, 9% to NRTIs and 18% to NNRTIs). ART-exposed infants showed multi-class ARV resistance. Importantly, vertical transmission of a triple-class-resistant virus was confirmed in one case. Patterns of DRMs predicted high-level resistance to NNRTIs in a similar and high proportion (>50%) of infants with at least one DRM independently of ARV exposure. BF recombinants were found in 74%, subtype B in 20%, subtype C in 3% and novel AG and AB recombinants in 3%. CONCLUSIONS: PDR in HIV-1-infected children from Argentina is among the highest reported, jeopardizing successful lifelong suppressive ART as well as the efficacy of current PMTCT regimens.

[HIV-1 resistance to antiretroviral drugs in pregnant women from Buenos Aires metropolitan area]. / Resistencia de HIV-1 a drogas antirretrovirales en gestantes del área Metropolitana de Buenos Aires.

The study aimed to determine the prevalence of antiretroviral resistance associated mutations in HIV-1 infected pregnant woman treated in Buenos Aires metropolitan area (period 2008-2014). A total of 136 women with viral load = 500 copies/ml were included: 77 (56.6%) were treatment-naïve and 59 (43.4%) were antiretroviral-experienced patients either with current (n: 24) or previous (n = 35) antiretroviral therapy. Genotypic baseline resistance was investigated in plasma of antiretroviral-naïve patients and antiretroviral-experienced patients. The resistance mutations were identified according to the lists of the World Health Organization and the International Antiviral Society, respectively. Frequencies of resistance associated mutations detected in 2008-2011 and 2012-2014 were compared. A total of 37 (27.2%) women presented at least one resistance associated mutation: 25/94 (26.5%) in 2008-2011 and 12/42 (28.5%) in 2012-2014 (p > 0.05). Among naïves, 15 (19.5%) had at least one mutation: 10/49 (20.4%) in the period 2008-2011 and 5/28 (17.8%) in 2012-2014 (p > 0.05). The resistance mutations detected in naïves were associated with non nucleoside reverse transcriptase inhibitors, being K103N the most common mutation in both periods. In antiretroviral experienced patients, 22/59 (37.3%) had at least one resistance mutation. This study demonstrates a high frequency of resistance associated mutations which remained stable in the period analyzed. These levels suggest an increased circulation of HIV-1 antiretroviral resistant strains in our setting compared to previous reports from Argentina.

Pretreatment HIV-1 Resistance in Argentina: Results from the Second Surveillance Study Following World Health Organization Guidelines (2019).

More than 62,000 individuals are currently on antiretroviral treatment within the public health system in Argentina. In 2019, more than 50% of people on ART received non-nucleoside reverse transcriptase inhibitors (NNRTIs). In this context, the second nationwide HIV-1 pretreatment drug resistance surveillance study was carried out between April and December 2019 to assess the prevalence of HIV-1 drug resistance in Argentina using the World Health Organization guidelines. This was a nationwide cross-sectional study enrolling consecutive 18-year-old and older individuals starting ARVs at 19 ART-dispensing centers. This allowed us to estimate a point prevalence rate of resistance-associated mutations (RAMs) with a confidence interval (CI) of 5% (for the total population and for those without antiretroviral exposure). Four-hundred forty-seven individuals were included in the study. The prevalence of mutations associated with resistance was detected in 27.7% (95% CI 25.6-34.9%) of the population. For NNRTI, it was 19.6% (95% CI 16.3-24.5%), for integrase strand transfer inhibitor (INSTI) 6.1% (95% CI 6.1-11.9%), for nucleoside/nucleotide reverse transcriptase inhibitor (NRTI) 3% (95% CI 1.9-5.9%), and for protease inhibitors 1.5% (95% CI 0.7-3.6%). Naive individuals had variants of resistance to NRTIs in 16.8% (95% CI 12.8-21.4) and 5.7% (95% CI 2.9-15.9) to INSTI. For experienced individuals, the prevalence of variants associated with resistance was 30.38% (95% CI 20.8-42.2) for NRTIs and 7.7% (95% CI 2.9-15.9) for INSTI. This study shows an increase in the frequency of nonpolymorphic RAMs associated with resistance to NNRTI. This study generates the framework of evidence that supports the use of schemes based on high genetic barrier integrase inhibitors as the first line of treatment and the need for the use of resistance test before prescribing schemes based on NNRTI. We report for the first time the presence of a natural polymorphism associated with the most prevalent recombinant viral form in Argentina and the presence of a mutation linked to first-line integrase inhibitors such as raltegravir.

Prevalence of rilpivirine resistance in people starting antiretroviral treatment in Argentina.

BACKGROUND: Rilpivirine-based regimens are now preferred or alternative first-line regimens according to many HIV treatment guidelines. Recently, a surveillance study conducted in Argentina determined that prevalence of pretreatment resistance to first-generation non-nucleoside reverse transcriptase inhibitors (NNRTIs) was 10%. The aim of this study was to analyse the prevalence of resistance mutations to newer generation NNRTIs in the population starting ART in Argentina. METHODS: We analysed the prevalence of resistance mutations to rilpivirine and etravirine (according to the IAS list), obtained through a nationally representative pretreatment HIV-drug resistance (PDR) surveillance study performed in Argentina in 2014-2015. Briefly, 25 ART-dispensing sites throughout the country were randomly chosen to enrol 330 adults starting ART. Samples were processed with Trugene (Siemens)® and analysed using the Stanford algorithm. RESULTS: All 270 samples corresponding to participants with no prior exposure to antiretroviral drugs were included in this analysis. Median (IQR) age was 35 years (28-43); 66.7% were male; median (IQR) CD4+ T-cell count was 284 cells/mm3 (112-489). The prevalence of resistance to any antiretroviral was 16% (±5%) and prevalence of NNRTI RAMs was 13% (±4%). The prevalence of resistance to rilpivirine was 8% (±3%). Prevalence of resistance to etravirine was 4% (±3%). The most frequent mutations conferring resistance to rilpivirine were: E138A (n=6) and G190A (n=4). CONCLUSIONS: This PDR surveillance study showed concerning levels of HIV drug resistance (HIVDR) in Argentina, not only for first-generation NNRTIs but also to rilpivirine. In our setting, performing resistance testing would be necessary before prescription of ART even if a second-generation NNRTI-based regimen was used as first-line therapy.

Transmitted drug resistance in women with intrapartum HIV-1 diagnosis: a pilot epidemiological survey in Buenos Aires, Argentina.

INTRODUCTION: Surveillance of primary resistance to antiretroviral drugs is particularly important in pregnant population, in which infection by drug-resistant HIV has not only implications for maternal treatment, but could also jeopardize the efficacy of neonatal prophylaxis. We aim to describe the prevalence of resistance associated mutations (RAMs) in pregnant women with intrapartum HIV diagnosis in a public hospital of Buenos Aires, Argentina. MATERIALS AND METHODS: Prospective pilot study (period from 2008 to October 2013). Plasma samples were tested for viral load by Versant HIV-1 RNA 3.0 (bDNA) and sequenced using HIV-1 TRUGENE™Genotyping Kit (Siemens). The prevalence of RAMs was analyzed according to World Health Organization (WHO) criteria. RESULTS: Of 231 HIV-infected pregnant women assisted, 6% (n=14) had intrapartum diagnosis of HIV infection. 12 patients (85.7%) had previous pregnancies, 10 (71.4%) had inadequate prenatal care and 3 (23.1%) seroconverted during pregnancy. Maternal characteristics (expressed medians and ranges) were: age 25.5 (16-35) years; gestational age at birth: 39 (30-42) weeks; CD4 count: 500 (132-925) cells/µL; viral load: 9418 (1800-55299) copies/mL. No one had hepatitis B virus (HBV) or hepatitis C virus (HCV) coinfection; four (33.3%) had syphilis. Eight patients (57.1%) had vaginal delivery and six emergency C-section (42.9%). In six cases (46.2%), membrane rupture was spontaneous; four patients (28.6%) failed to receive intrapartum zidovudine (ZDV) infusion. In 12 patients a genotypic resistance test was performed: two (16.7%) had WHO RAMs corresponding to K103N mutation in both cases, conferring high-level resistance to nevirapine (NVP) and efavirenz. Two newborns (14.3%) were preterm. All received neonatal prophylaxis: ZDV in 1 case and combined prophylaxis (ZDV/3TC/NVP) in the remaining 13 (92.9%). All newborns were formula-fed. Two (14.3%) had congenital syphilis, one of whom died. One newborn was HIV-infected (positive proviral DNA at 24 hours of life, wild-type HIV). CONCLUSIONS: This pilot study suggests that levels of transmitted resistance in this high-risk population of pregnant women could be moderate to high. We preliminarily observed high-level resistance to NVP: if this finding is confirmed with a larger sample, it could potentially jeopardize the utility of this drug in the combined neonatal prophylaxis recommended in the absence of maternal antiretroviral therapy.

Resistencia de HIV-1 a drogas antirretrovirales en gestantes del área metropolitana de Buenos Aires / HIV-1 resistance to antiretroviral drugs in pregnant women from Buenos Aires metropolitan area

Se determinó la frecuencia de mutaciones asociadas a resistencia de HIV-1 a antirretrovirales en embarazadas del área metropolitana de Buenos Aires, 2008-2014. Se incluyeron 136 mujeres con carga viral ≥ 500 copias/ml: 77 (56.6%) eran naïve; las otras 59 (43.4%) eran expuestas, ya sea con tratamiento en curso (n: 24) o previo (n: 35). Se realizó análisis de resistencia genotípica basal en plasma de pacientes naïve y con experiencia de tratamiento antirretroviral. Las mutaciones se identificaron según las listas de la Organización Mundial de la Salud y la International Antiviral Society, respectivamente. Se comparó la frecuencia de mutaciones detectadas en los subperíodos 2008-2011 vs. 2012-2014. Un total de 37 (27.2%) mujeres presentaron ≥ 1 mutación asociada a resistencia: 25/94 (26.5%) en 2008-2011 y 12/42 (28.5%) en 2012-2014 (p > 0.05). Entre las naïve, 15 (19.5%) tenían ≥ 1 mutación: 10/49 (20.4%) en el subperíodo 2008-2011 y 5/28 (17.8%) en 2012-2014 (p > 0.05). Las mutaciones encontradas en pacientes naïve estuvieron asociadas a inhibidores no nucleosídicos de la transcriptasa reversa, y, como en estudios anteriores, K103N fue la más frecuente a lo largo de todo el período. Entre las pacientes expuestas, 22/59 (37.3%) presentaron ≥ 1 mutación asociada a resistencia. Este estudio demuestra una alta frecuencia de mutaciones asociadas a resistencia que se mantuvo estable a lo largo del período. Los niveles detectados sugieren una mayor circulación en nuestro medio de cepas de HIV-1 resistentes a antirretrovirales con respecto a los niveles previamente observados en Argentina.

The study aimed to determine the prevalence of antiretroviral resistance associated mutations in HIV-1 infected pregnant woman treated in Buenos Aires metropolitan area (period 2008-2014). A total of 136 women with viral load ≥ 500 copies/ml were included: 77 (56.6%) were treatment-naïve and 59 (43.4%) were antiretroviral-experienced patients either with current (n: 24) or previous (n = 35) antiretroviral therapy. Genotypic baseline resistance was investigated in plasma of antiretroviral-naïve patients and antiretroviral-experienced patients. The resistance mutations were identified according to the lists of the World Health Organization and the International Antiviral Society, respectively. Frequencies of resistance associated mutations detected in 2008-2011 and 2012-2014 were compared. A total of 37 (27.2%) women presented at least one resistance associated mutation: 25/94 (26.5%) in 2008-2011 and 12/42 (28.5%) in 2012-2014 (p > 0.05). Among naïves, 15 (19.5%) had at least one mutation: 10/49 (20.4%) in the period 2008-2011 and 5/28 (17.8%) in 2012-2014 (p > 0.05). The resistance mutations detected in naïves were associated with non nucleoside reverse transcriptase inhibitors, being K103N the most common mutation in both periods. In antiretroviral experienced patients, 22/59 (37.3%) had at least one resistance mutation. This study demonstrates a high frequency of resistance associated mutations which remained stable in the period analyzed. These levels suggest an increased circulation of HIV-1 antiretroviral resistant strains in our setting compared to previous reports from Argentina.

Characterization of the basal core promoter and precore regions in anti-HBe-positive inactive carriers of hepatitis B virus.

BACKGROUND: The study of hepatitis B virus (HBV) genomic heterogeneity has become a major issue in investigations aimed at understanding the relationship between HBV mutants and the wide spectrum of clinical and pathological conditions associated with HBV infection. Although most chronically infected HBV patients are inactive carriers, several virological aspects of this state remain unclear. METHODS: In order to determine the prevalence and clinical significance of mutations in the basal core promoter (BCP) and precore (pC) regions among inactive carriers, the nucleotide sequences from 41 inactive carriers were analyzed and compared with those from 29 individuals with chronic active hepatitis. RESULTS: Genotypes A (24.3%), D (37.1%), F1b (12.9%), and F4 (18.6%) were the most prevalent. Mutations in the BCP/pC regions were observed in most of the inactive carriers (92.7%) and in most of the patients with chronic active hepatitis (93.1%). The prevalence of mutation 1764(A) was significantly higher in patients with chronic active hepatitis (65.5%) than in inactive carriers (36.6%) (p=0.038), whereas the prevalences of mutations at the other positions analyzed were not significantly different. Older patients (>50 years) showed BCP/pC patterns with a higher number of substitutions. Mutations were found to be biased by genotype: the 1896(A) mutation was highly prevalent in genotypes D and F4, while alternative substitutions in the pC region were more prevalent in genotypes A and F1b. CONCLUSIONS: Mutations in the BCP/pC regions are the hallmark of chronic anti-HBe-positive individuals; nevertheless, the even distribution of mutations in active and inactive carriers suggests that BCP/pC mutations may occur during HBV infection not strictly related to the HBV infection activity.

Score de sensibilidad genotípico de tratamientos antirretrovirales en embarazadas naïve infectadas por VIH-1 / Genotypic sensitivity score of antiretroviral therapies in naïve HIV-1 infected pregnant women

Introducción: el score de sensibilidad genotípica (GSS) es una herramienta para predecir el resultado virológico del TARV. El objetivo de este estudio es comparar el GSS de tres tratamientos an-tirretrovirales (TARVs) en una población de embarazadas infectadas por VIH (EIV) naïve en Buenos Aires, Argentina. Materiales y Métodos: se analizaron las pruebas de resistencia de 47 EIV naïve en la ciudad de Buenos Aires (período 2008-2011), utilizan-do el algoritmo de la Universidad de Stanford-HIVdb program (pre-valencia de resistencia primaria del 21,2 %). La eficacia predicha de cada fármaco se computó como 1,00-0,75-0,50-0,25 y 0,00 para las cinco categorías HIVdb: desde susceptible a resistencia de alto nivel. El GSS se obtuvo con la suma de las puntuaciones de los fármacos individuales incluidos (GSS = 3, significa tres medicamentos total-mente activos). Tres TARVs se compararon: zidovudina+lamivudina más nevirapina (ART1), nelfinavir (ART2) o lopinavir/ritonavir (ART3). Resultados: se obtuvo un GSS de 3 en el 80,9 % con ART1 y el 91,5 % con ART2 y ART3. No hubo diferencia estadísticamente significati-va en la posibilidad de lograr un GSS de 3 entre los TARVs evaluados. Conclusiones: no hubo diferencia estadística en la probabilidad de proporcionar un régimen comple-tamente activo con un inhibidor de la proteasa o nevirapina. En nuestra opinión, un TARV con una alta barrera genética sería preferible en el contex-to de la alta prevalencia de resistencia primaria ob-servada

Background: The genotypic sensitivity score (GSS) is a tool to predict virological treatment outcome. The objective of this study is to compare the GSS of three antiretroviral treatment (ART) strategies in a population of naive pregnant women (NPW) in Buenos Aires city, Argentina. Methods: Resistance tests from 47 NPW were analyzed in the context of a sentinel resistance surveillance study in Buenos Aires city (period 2008-2011), considering the genotype interpretation system of the Stanford HIVdb program (prevalence of primary drug resistance of 21.2%). The predicted efficacy of each drug was scored either as 1.00-0.75-0.50-0.25 and 0.00 for the five HIVdb categories: from susceptible to high-level resistance. GSS was obtained with the sum of the scores for the individual drugs included in a regimen (GSS of 3 means three fully active drugs). GSS of three ARTs were compared: zidovudine+lamivudine plus either nevirapine (ART1), nelfinavir (ART2) or lopinavir/ritonavir (ART3). Results: A GSS of 3 was achieved in 80.9% with ART1 and 91.5% with both ART2 and ART3. There was no statistical difference in the possibility of achieving a GSS of 3 between the three ARTs evaluated. Conclusions: There was no statistical difference in the probability of providing a fully active regimen with either a protease inhibitor or nevirapine. In our opinion, an ART with a high genetic barrier backbone may be preferred in the context of the high prevalence of primary resistance observed

Utilización del ensayo Cobas Amplicor Monitor HIV-1 en el diagnóstico temprano de la infección por HIV en pediatría / Utility of the Cobas Amplicor Monitor HIV-1 assay in the early diagnosis of HIV pediatric infection

Dado que en Argentina el ensayo de HIV RNA cualitativo (QL) ha sido discontinuado, el objetivo del presente trabajo fue evaluar el ensayo de RNA cuantitativo (CV) COBAS AMPLICOR Monitor HIV-1 para su posible incorporación en el diagnóstico pediátrico de infección por HIV en niños expuestos perinatalmente y estimar la concordancia con QL. Fueron incluidas 214 muestras (134 pacientes), 174 muestras de 113 pacientes negativos y 40 correspondientes a 21 pacientes positivos con diagnóstico definitivo. Todas las muestras fueron estudiadas para CV usando el procedimiento estándar (ST, rango 400-750.000 copias/ml) y aquellas por debajo del rango lineal se procesaron por el método ultrasensible (US, rango 50-100.000 copias/ml). El ensayo de CV fue comparado con el de QL en un subgrupo de 93 muestras (78 negativas y 15 positivas). Las 174 muestras pertenecientes a niños HIV negativos tuvieron CV indetectables y entre las 40 muestras pertenecientes a niños HIV positivos, 37 evidenciaron CV detectables (2-5,88 log 10). En 4/37 muestras se detectaron CV entre 165-575 copias/ml, que en muestras posteriores evidenciaron altos valores de CV. El 83,7 % de las muestras resultaron con CV> a 4 log 10. La sensibilidad de la CV según grupo etario fue de 77,7 % < 15 días, 93,3 % entre 15-45 días y la especificidad general del 100 %. La concordancia global entre QL y CV fue del 97,8 %, siendo el ensayo de CV más sensible. Nuestros resultados sugieren la inclusión del ensayo COBAS AMPLICOR en el algoritmo diagnóstico, no presentando resultados falsos positivos.

Since in Argentina qualitative dHIV RNA (QL) test, has been discontinued, the objective of this study was to evaluate the quantitative RNA (VL) COBAS AMPLICOR monitor HIV-1, for its possible inclusion in the paediatric diagnosis of HIV infection and to evaluate the concordance between both assays. In this study 214 samples corresponding to 134 patients were included, 174 and 40 specimens from 113 HIV-negative and 21 HIV-positive patients respectively. All samples were studied for VL using the standard procedure (ST, range 400-750.000 copies/mal), and those below the linear range were further tested by the ultrasensitive method (US, range 50-100.000 copies/ml) QL and VL assays were compared among a subgroup of 93 samples (78 negative and 15 positive). All 174 samples from HIV negative children had undetectable VL. 37/40 samples from HIV-positive had detectable VL (2-5,88 log 10) 4/37 specimens had VL between 165-575 copies/ml, later samples from the corresponding patients showed high VL. 83,7 % of the samples had VL> 4 log 10. The sensitivities found were 77,7 % and 93,3 % among infants < 15 days and between 15-45 days of aged respectively. The general specificity of the COBAS AMPLICOR was 100 %. The concordance between QL and VL eas 97,8 %, showing the later one better sensitivity. Our results support the inclusion of COBAS AMPLICOR in the diagnosis algorithm, not showing false positive results.

Evaluación comparativa de COBAS TaqMan HIV-1 y COBAS AMPLICOR HIV-1 para la cuantificación de carga viral plasmática de HIV-1 / Comparative evaluation of the COBAS TaqMan HIV-1 assay and the COBAS AMPLICOR HIV-1 for the quantitation of HIV-1 viral load

La determinación de carga viral plasmática es utilizada para el seguimiento y monitoreo de pacientes infectados por el HIV-1. El objetivo del trabajo es evaluar la performance de PCR en tiempo real COBAS TaqMan 48 HIV-1 RNA en comparación con COBAS AMPLICOR HIV-1 MONITOR versión 1.5 para la cuantificación de RNA viral.

The quantification of HIV-1 viral load in plasma is a useful tool for the manafement of infected patients. Objective: to evaluate the performance of the COBAS TaquMan 48 HIV-1 real-time PCR in comparasion with the COBAS AMPLICOR HIV-1 MONITOR version 1.5 assay for quantification of viral load.