Antiretroviral adherence, elevated viral load, and drug resistance mutations in human immunodeficiency virus - infected women initiating treatment in pregnancy: a nested case-control study

Background Elevated viral load (VL) early after antiretroviral therapy (ART) initiation appears frequently in pregnant and postpartum women living with human immunodeficiency virus; however the relative contributions of pre-ART drug resistance mutations (DRMs) vs nonadherence in the etiology of elevated VL are unknown. Methods Within a cohort of women initiating ART during pregnancy in Cape Town, South Africa, we compared women with elevated VL after initial suppression (cases, n = 80) incidence-density matched to women who maintained suppression over time (controls, n = 87). Groups were compared on pre-ART DRMs and detection of antiretrovirals in stored plasma. Results The prevalence of pre-ART DRMs was 10% in cases and 5% in controls (adjusted odds ratio [aOR], 1.53 [95% confidence interval {CI}, .4­5.9]); all mutations were to nonnucleoside reverse transcriptase inhibitors. At the time of elevated VL, 19% of cases had antiretrovirals detected in plasma, compared with 87% of controls who were suppressed at a matched time point (aOR, 131.43 [95% CI, 32.8­527.4]). Based on these findings, we estimate that <10% of all elevated VL in the cohort may be attributable to pre-ART DRMs vs >90% attributable to ART nonadherence...

Resistência genotípica para inibidores da integrase do HIV-1

A Integrase participa de uma das etapas fundamentais para a replicação do HIV, a inserção do DNA retrotranscrito no genoma humano.Atualmente já foram licenciados três inibidores da integrase (INIs) para o usode pacientes naïve à terapia antirretroviral ou multi-experimentados, raltegravir (RAL), elvitgeravir (EVG) e dolutegravir (DTG). Embora esses medicamentos sejam eficientes e bem tolerados, a falha terapêutica pode estar associada a seleção de mutações em pelo menos quatro vias distintas(E92Q, Q148H/R/K, N155H e menos frequente a Y143R/H/C) associadas ou não à mutações secundárias. Este estudo teve por objetivo avaliar o gene da integra-se em pacientes vivendo com HIV/AIDS. Foram incluídas 265amostras de pacientes com perfis diferentes de exposições à terapia antirretroviral (TARV): naïve de TARV (n=34), naïve para INIs (n=59), em terapia com TARV+RAL com carga viral suprimida (n=35) e em terapia com TARV+RAL com falha virológica (n=137). As amostras dos pacientes com exposição a INIs foram coletadas no período entre julho de 2009 e maio de2015...

The integrase part of one of the key steps for HIV replication, insertionof DNA retrotranscribed in the human genome. Currently they were alreadylicensed three integrase inhibitors (INIs) for the use of antiretroviral therapy naïve patients or multi-experienced, raltegravir, elvitegravir and dolutegravir. Although these drugs are effective and well tolerated, therapy failure may beassociated with selection of mutations in at least four distinct pathways(E92Q, Q148H/R/K N155H and less frequent Y143R/ F/C) or not associatedwith secondary mutations. This study aims to evaluate the integrase gene inpatients living with HIV/Aids. We included 265 samples from patients withdifferent profiles of exposure to antiretroviral therapy (ART): naïve to antiretroviral therapy (n=34), naïve to INIS (n=59), in therapy with TARV+RAL with suppressed viral load (n=35) and therapy with TARV+RAL withvirologic failure (n=137). Samples from patients exposed to INIs were collected between July 2009 and May 2015...

Resistência genotípica para inibidores da integrase do HIV-1 / Genotypic resistance to HIV-1 integrase inhibitors

A Integrase participa de uma das etapas fundamentais para a replicação do HIV, a inserção do DNA retrotranscrito no genoma humano. Atualmente já foram licenciados três inibidores da integrase (INIs) para o uso de pacientes naïve à terapia antirretroviral ou multi-experimentados, raltegravir (RAL), elvitgeravir (EVG) e dolutegravir (DTG). Embora esses medicamentos sejam eficientes e bem tolerados, a falha terapêutica pode estar associada a seleção de mutações em pelo menos quatro vias distintas(E92Q, Q148H/R/K, N155H e menos frequente a Y143R/H/C) associadas ou não à mutações secundárias. Este estudo teve por objetivo avaliar o gene da integrase em pacientes vivendo com HIV/AIDS. Foram incluídas 265 amostras de pacientes com perfis diferentes de exposições à terapia antirretroviral (TARV): naïve de TARV (n=34), naïve para INIs (n=59), em terapia com TARV+RAL com carga viral suprimida (n=35) e em terapia com TARV+RAL com falha virológica (n=137). As amostras dos pacientes com exposição a INIs foram coletadas no período entre julho de 2009 e maio de 2015. Sequências genéticas foram submetidas à websites e ferramentas de bioinformática para a análise de resistência aos antirretrovirais e determinação de subtipos virais. Nenhuma mutação principal foi observada em amostras de pacientes naïve para INIs, porém alguns polimorfismos observados parecem estar associados a certos subtipos do HIV-1. Entre os pacientes expostos as TARV+RAL, a maioria tinham poucos antirretrovirais ativos compondo a terapia. A adesão e a viremia nas semanas 12-24 após aTARV+RAL (p<0,01) apresentaram associação à supressão viral. Mutações principais para o INIs foram observadas em 62% dos pacientes em uso de TARV+RAL. Em um paciente houve a seleção da mutação F121Y, com evolução subsequente para Y143R. Entre os pacientes com falha virológica ao TARV+RAL, 35% apresentaram resistência intermediaria ou alta ao DTG,com associação das mutações G140S/A e E138A/K (p<0,001)...

Transmitted Drug Resistance Among Recently Diagnosed Adults and Children in São Paulo, Brazil.

Transmitted drug resistance mutations (TDRM) have been a constant threat to treatment efficacy. We evaluated TDRM in plasma RNA of 217 antiretroviral therapy-naive patients from sites in the São Paulo metropolitan area, collected from 2012 to 2014. The partial HIV-1 polymerase region was sequenced using Big Dye terminators at an ABI 3130 Genetic Analyzer. TDRM was defined according to the Stanford database calibrated population resistance (CPR v.6.0), but other drug resistance mutations (DRM) considered at the IAS list (IAS, 2014) and at the Stanford HIV Database Genotyping Resistance Interpretation (GRI-HIVdb) were also described. Out of 78% (170/217) of patients with information on the time of diagnosis, most (83%, 141/170) had been recently diagnosed, with the first positive HIV serology at a median of 58 days (IQR 18-184). Subtype B predominated (70%), followed by subtype F (10%), BF (7.5%), C (7.5%), and BC (5%). TDRMs were observed in 9.2% (20/217, CI 95% 5.9% to 13.6%), mostly (5.2%) to nonnucleoside reverse transcriptase inhibitor (NNRTI) antiretroviral class. Among children and adolescents, only a single patient showed TDRMs. Additional non-CPR mutations were observed: 11.5% (25/217) according to IAS or 4.6% (10/217) according to GRI-HIVdb. Overall, 23.5% (51/217) of the cases had one or more DRM identified. TDRM prevalence differed significantly among some sites. These trends deserve continuous and systematic surveillance, especially with the new policies of treatment as prevention being implemented in the country.

High frequency of dolutegravir resistance in patients failing a raltegravir-containing salvage regimen.

OBJECTIVES: Dolutegravir is a second-generation integrase strand transfer inhibitor (InSTI) that has been recently approved by the FDA to treat antiretroviral therapy-naive as well as treatment-experienced HIV-infected individuals, including those already exposed to the first-generation InSTI. Despite having a different mutational profile, some cross-resistance mutations may influence its susceptibility. The aim of this study was to evaluate the impact of a raltegravir-containing salvage regimen on dolutegravir activity. PATIENTS AND METHODS: Blood samples of 92 HIV-infected individuals with virological failure (two or more viral loads >50 copies/mL after 6 months of treatment) using raltegravir with optimized background therapy were sequenced and evaluated according to the Stanford University HIV Drug Resistance Database algorithm. RESULTS: Among the 92 patients analysed, 32 (35%) showed resistance to dolutegravir, in most cases associated with the combination of Q148H/R/K with G140S/A mutations. At genotyping, patients with resistance to dolutegravir had viral load values closer to the highest previously documented viral load. CONCLUSIONS: Changes in viraemia during virological failure may indicate the evolution of raltegravir resistance and may predict the emergence of secondary mutations that are associated with a decrease in dolutegravir susceptibility. Early discontinuation of raltegravir from failing regimens might favour subsequent salvage with dolutegravir, but further studies are necessary to evaluate this issue.

Transmitted drug resistance among recently diagnosed adults and children in São Paulo, Brazil

Transmitted drug resistance mutations (TDRM) have been a constant threat to treatment efficacy. We evaluated TDRM in plasma RNA of 217 antiretroviral therapy-naive patients from sites in the São Paulo metropolitan area, collected from 2012 to 2014. The partial HIV-1 polymerase region was sequenced using Big Dye terminators at an ABI 3130 Genetic Analyzer. TDRM was defined according to the Stanford database calibrated population resistance (CPR v.6.0), but other drug resistance mutations (DRM) considered at the IAS list (IAS, 2014) and at the Stanford HIV Database Genotyping Resistance Interpretation (GRI-HIVdb) were also described. Out of 78% (170/217) of patients with information on the time of diagnosis, most (83%, 141/170) had been recently diagnosed, with the first positive HIV serology at a median of 58 days (IQR 18-184). Subtype B predominated (70%), followed by subtype F (10%), BF (7.5%), C (7.5%), and BC (5%). TDRMs were observed in 9.2% (20/217, CI 95% 5.9% to 13.6%), mostly (5.2%) to nonnucleoside reverse transcriptase inhibitor (NNRTI) antiretroviral class. Among children and adolescents, only a single patient showed TDRMs. Additional non-CPR mutations were observed: 11.5% (25/217) according to IAS or 4.6% (10/217) according to GRI-HIVdb. Overall, 23.5% (51/217) of the cases had one or more DRM identified. TDRM prevalence differed significantly among some sites. These trends deserve continuous and systematic surveillance, especially with the new policies of treatment as prevention being implemented in the country.

Association of X4 tropism with disease progression in antiretroviral-treated children and adolescents living with HIV/AIDS in São Paulo, Brazil

Management of children with HIV/AIDS is specially challenging. Age-related issues do not allow for direct transposition of adult observations to this population. CXCR4 tropism has been associated with disease progression in adults. The geno2pheno web-base is a friendly tool to predict viral tropism on envelope V3 sequences, generating a false positive rate for a CXCR4 prediction. We evaluated the association of HIV-1 tropism prediction with clinical and laboratory outcome of 73 children with HIV/AIDS in São Paulo, Brazil. The CXCR4 tropism was strongly associated with a lower (nadir) CD4 documented during follow-up (p < 0.0001) and with disease severity (clinical event and/or CD4 below 200 cells/mm3) at the last observation, using commonly applied clinical cutoffs, such as10%FPRclonal (p = 0.001). When variables obtained during follow-up are included, both treatment adherence and viral tropism show a significant association with disease severity. As for viremia suppression, 30% (22/73) were undetectable at the last observation, with only adherence strongly associated with suppression after adjustment. The study brings further support to the notion that antiretroviral treatment adherence is pivotal to management of HIV disease, but suggests that tropism prediction may provide an additional prognostic marker to monitor HIV disease in children.

Association of X4 tropism with disease progression in antiretroviral-treated children and adolescents living with HIV/AIDS in São Paulo, Brazil.

Management of children with HIV/AIDS is specially challenging. Age-related issues do not allow for direct transposition of adult observations to this population. CXCR4 tropism has been associated with disease progression in adults. The geno2pheno web-base is a friendly tool to predict viral tropism on envelope V3 sequences, generating a false positive rate for a CXCR4 prediction. We evaluated the association of HIV-1 tropism prediction with clinical and laboratory outcome of 73 children with HIV/AIDS in São Paulo, Brazil. The CXCR4 tropism was strongly associated with a lower (nadir) CD4 documented during follow-up (p<0.0001) and with disease severity (clinical event and/or CD4 below 200cells/mm(3)) at the last observation, using commonly applied clinical cutoffs, such as (10%)FPRclonal (p=0.001). When variables obtained during follow-up are included, both treatment adherence and viral tropism show a significant association with disease severity. As for viremia suppression, 30% (22/73) were undetectable at the last observation, with only adherence strongly associated with suppression after adjustment. The study brings further support to the notion that antiretroviral treatment adherence is pivotal to management of HIV disease, but suggests that tropism prediction may provide an additional prognostic marker to monitor HIV disease in children.

Evaluation of genotypic prediction of HIV-1 tropism using population sequencing of replicates.

Determination of human immunodeficiency virus tropism has contributed to the understanding of the pathogenesis of HIV and is necessary prior to the use of CCR5 antagonists. Replicate V3 sequences may generate different sequences and improve viral tropism prediction. The diversity of HIV was evaluated to access its influence on prediction. Plasma RNA was retro-transcribed and amplified using a one-step protocol, followed by nested PCR and sequencing using an ABI3130XL. Eighty-one patients, 74% male and 26% female, with a median age of 44 years had either a single sequence (n=50) or 2-4 replicates (n=31) evaluated. Most patients (92%) had used multiple anti-retroviral regimens. Tropism prediction was performed using the Geno2pheno clonal option. The number of ambiguous nucleotides, the deduced non-synonymous amino acids at V3 and the genetic distance were quantified. Using a 20% false positive rate (FPR) cut-off, 41/81 (50.6%) was predicted as X4. TCD4 was lower, 226 cells/mm(3) (IQR 82-378), in patients infected with X4; TCD4 for R5 was 324 cells/mm(3) (IQR 200-538, p<0.05). The number of ambiguous nucleotides correlated with a lower FPR value (p<0.0027). Although different sequences may be generated, the number of replicates was not associated to a lower FPR or X4 assignment, and may allow a better prediction of this biological characteristic. Ambiguous nucleotides correlate inversely to a lower FPR.