HIV-1 Disease Progression and Drug Resistance Mutations among Children on First-Line Antiretroviral Therapy in Ethiopia.

At the end of 2005 an estimated 650 000 people in China were infected with HIV among whom 75 000 were in need of ART. The Division of Treatment and Care at the National Center for AIDS/STD Control and Prevention (NCAIDS) Chinese Center for Disease Control (CCDC) has been responsible for the overall scale up of the National Free ART Program. As of December 2005 a total of 20 453 patients in 28 provinces autonomous regions and special municipalities had benefited from this national program and received free ART. The increase in access to ART however is accompanied by the risk of drug resistance development. A small body of literature already documents HIV drug resistance in China in these treated populations. These preliminary findings are consistent with the development of drug resistance observed in developed countries soon after the initiation of wide-scale HIV treatment. Therefore it is imperative that clinicians understand the causes and implications of HIV resistance in both patientcare and in the public health perspective. (excerpt)

The aim of this study was to evaluate HIV-1 drug resistance among patients failing first-line antiretroviral therapy in Ethiopia. A total of 699 adults infected with HIV (aged ≥15 years) who failed first-line Antiretroviral Therapy (ART) were recruited between 2017 and 2019 from 63 ART-providing sites in Ethiopia. Treatment failure was defined as patients with two consecutive viral loads (VLs) ≥1000 copies/mL within six months of follow-up. The pol gene region of HIV-1 was amplified and sequenced using an in-house assay of the Chinese Center for Disease Prevention and Control. The Stanford HIVDB v9.0 algorithm was used for identification of resistance mutations. Resistance mutations were characterized according to the 2019 International AIDS Society-USA mutation list. P values of <0.05 were considered statistically significant during multivariate analysis, which was done using SPSS v26.0 (SPSS Inc., Chicago, IL). Overall, HIV drug resistance (HIVDR) among patients failing first-line therapy in Ethiopia was 77.8%. Non-nucleoside/tide reverse transcriptase inhibitors (NNRTI) and NRTI resistance were 75.7% and 71.2%, respectively. Neverapine (NVP) and Efavirenz (EFV) accounted for 74.2% and 60.8% of HIVDR, respectively. About half (48.1%) of NRTI-associated mutations were responsible for Abacavir resistance, while 34% were responsible for multi-NRTI resistance. Mutations responsible for resistance to the commonly used EFV and NVP accounted for 62.9%, while resistance to Etravirine, Doravirine, and Rilivirine, which were not part of the country's ART program, were 37.1%, and can be explained by cross-resistance within the drug class. Protease Inhebitor(PI)associated resistance was detected in only 1.6% of the study's participants. The most common mutations identified were M184V (30.1%), K103N (18.7%), Y181C (13.6%), and K65R (12.1%). In a multivariate logistic regression analysis, predictors of HIVDR were prior ART exposure (adjusted odds ratio [AOR]=2.3; 95% confidence interval [CI]=1.8, 3.6), absence of HIV status disclosure (AOR=2.05; 95%CI=1.26, 3.35), CD4 count of ≤200 cells/mm3 (AOR=1.94; 95%CI=1.21, 3.12), and bedridden status (AOR=4.16; 95% CI=3.21, 5.16). The high-levels of HIVDR among patients with failure of first-line ART in Ethiopia calls for individualized HIVDR testing. Mutations associated with multi-NRTI and NNRTI cross-resistance may alert the program for considering drugs of higher genetic barrier targeting protease and other regions. Patients with low CD4 count and those who are bedridden should be given special attention for the potential development of HIVDR during clinical management.

The emergence of HIV-1 drug resistance mutations has mainly been linked to the duration and composition of antiretroviral treatment (ART), as well as the level of adherence. This study reports the incidence and pattern of acquired antiretroviral drug resistance mutations and long-term outcomes of ART in a prospective cohort from Northwest Ethiopia. Two hundred and twenty HIV-1C infected treatment naïve patients were enrolled and 127 were followed-up for up to 38 months on ART. ART initiation and patients’ monitoring was based on the WHO clinical and immunological parameters. HIV viral RNA measurement and drug resistance genotyping were done at baseline (N = 160) and after a median time of 30 (IQR, 27–38) months on ART (N = 127). Viral suppression rate (HIV RNA levels ≤ 400 copies/ml) after a median time of 30 months on ART was found to be 88.2% (112/127), which is in the range for HIV drug resistance prevention suggested by WHO. Of those 15 patients with viral load >400 copies/ml, six harboured one or more drug resistant associated mutations in the reverse transcriptase (RT) region. Observed NRTIs resistance associated mutations were the lamivudine-induced mutation M184V (n = 4) and tenofovir associated mutation K65R (n = 1). The NNRTIs resistance associated mutations were K103N (n = 2), V106M, Y181S, Y188L, V90I, K101E and G190A (n = 1 each). Thymidine analogue mutations and major drug resistance mutations in the protease (PR) region were not detected. Most of the patients (13/15) with virologic failure and accumulated drug resistance mutations had not met the WHO clinical and/or immunological failure criteria and continued the failing regimen. The incidence and pattern of acquired antiretroviral drug resistance mutations is lower and less complex than previous reports from sub Saharan Africa countries. Nevertheless, the data suggest the need for virological monitoring and resistance testing for early detection of failure. Moreover, adherence reinforcement will contribute to improving overall treatment outcomes.

BackgroundThe ongoing scale-up of antiretroviral therapy (ART) in sub-Saharan Africa has prompted the interest in surveillance of transmitted and acquired HIV drug resistance. Resistance data on virological failure and mutations in HIV infected populations initiating treatment in sub-Saharan Africa is sparse.MethodsHIV viral load (VL) and resistance mutations pre-ART and after 6 months were determined in a prospective cohort study of ART-naïve HIV patients initiating first-line therapy in Jimma, Ethiopia. VL measurements were done at baseline and after 3 and 6 months. Genotypic HIV drug resistance (HIVDR) was performed on patients exhibiting virological failure (>1000 copies/mL at 6 months) or slow virological response (>5000 copies/mL at 3 months and <1000 copies/mL at 6 months).ResultsTwo hundred sixty five patients had VL data available at baseline and at 6 months. Virological failure was observed among 14 (5.3%) participants out of 265 patients. Twelve samples were genotyped and six had HIV drug resistance (HIVDR) mutations at baseline. Among virological failures, 9/11 (81.8%) harbored one or more HIVDR mutations at 6 months. The most frequent mutations were K103N and M184VI.ConclusionsOur data confirm that the currently recommended first-line ART regimen is efficient in the vast majority of individuals initiating therapy in Jimma, Ethiopia eight years after the introduction of ART. However, the documented occurrence of transmitted resistance and accumulation of acquired HIVDR mutations among failing patients justify increased vigilance by improving the availability and systematic use of VL testing to monitor ART response, and underlines the need for rapid, inexpensive tests to identify the most common drug resistance mutations.

Introduction of HIV drug-resistance testing in clinical practice.

Introduction of pediatric-friendly dolutegravir (DTG) formulations to treat children living with HIV (CLHIV) has presented new opportunities to improve viral suppression; however, there are limited data on emerging patterns of HIV drug resistance (HIVDR) in this population. We identified CLHIV aged 0-15 years experiencing virologic failure on first-line antiretroviral therapy in Uganda between January 2021 and November 2021 from the Central Public Health Laboratory database. Remnant viral load samples were tested for HIVDR using Sanger sequencing. Drug resistance mutations (DRMs) were identified, and antiretroviral susceptibility was interpreted using the Stanford University HIVDR Database algorithms. The prevalence of DRMs and HIVDR is summarized using descriptive statistics, and associations with demographic and clinical factors were determined using χ 2 tests. Among 333 successfully genotyped patient samples, 122 (36.6%) CLHIV were on a DTG-based regimen and 136 (40.8%) on a lopinavir-based regimen. Among all CLHIV, 271 (81.4%) had DRMs and 262 (78.7%) had any intermediate-to-high level HIVDR [including DTG (1.8%), lopinavir (9.6%), abacavir (ABC) (25.5%), and zidovudine (19.2%)]. Among CLHIV on a DTG-based regimen, 6.6% had any integrase inhibitor DRMs and 4.1% had intermediate-to-high resistance to DTG. Children on DTG-based regimens were less likely to have DRMs ( P = 0.007) or HIVDR ( P = 0.02) compared with all other regimens. CLHIV on DTG-based regimens with an ABC backbone were no more likely to have DRMs ( P = 0.9) or HIVDR ( P = 0.5) compared with those with a backbone not containing ABC. Low rates of DTG resistance among Ugandan CLHIV failing first-line DTG-based antiretroviral therapy regimens underscore the durability of DTG. Lack of difference in ABC resistance across all regimens supports maintaining an ABC backbone for CLHIV <30 kg when transitioning to a DTG-based regimen despite virologic failure.

Viral reservoirs, residual viremia, and the potential of highly active antiretroviral therapy to eradicate HIV infection

Time to overcome pretreatment HIV drug resistance

BackgroundVirological treatment failure is a problem that a Human Immune Virus patient faces after starting treatment due to different factors. However, there were few studies done on the predictors of virological treatment failure among adult patients on first-line antiretroviral therapy in Ethiopia in general, and no study was done in the study area in particular. Therefore, the aim of the study was to identify predictors of virological treatment failure among adult patients on first-line antiretroviral therapy in Woldiya and Dessie Hospitals, Northeast Ethiopia.MethodHospital based case–control study was conducted in Woldia and Dessie Hospitals from from 12 August 2016–28 February 2018 on 154 cases and 154 controls among adult patients on first-line antiretroviral treatment. All cases were included and comparable controls were selected using stratified random sampling technique. Data were collected by document review using checklists and entered into Epidata version 3.1 and analyzed by SPSS version 21.Multivariable logistic regression analysis was done to identify the independent predictors of virological treatment failure.ResultsIn this study, statistically higher odds of virological failure was observed among patients who had current CD4 T-cell count of < 200 mm3 (AOR = 2.4, 95% CI: 1.35, 4, 18) compared withCD4 T-cell count of > 200 mm3, current body mass index(BMI) < 16 kg/m2 (AOR = 4.2, 95% CI:1.85, 9.51) compared with BMI > 18.5 kg/m2, BMI between 16 and 18.5 kg/m2 (AOR = 3.72, 95% CI: 1.75, 7.92) versus BMI > 18.5 kg/m2, poor adherence to antiretroviral therapy (AOR = 5.4, 95% CI: 2.95, 9.97) compared with good adherence.ConclusionThis study showed that low current CD4 T-cell count and body mass index, as well as poor adherence for ART treatment predicts virological failure. Therefore, deliberate efforts are urgently needed in HIV care through improving their nutritional status by enhancing nutritional education and support, and by strengthening enhanced adherence counseling.

There has been significant reduction in the scale of the global HIV pandemic over the last decade due to increased awareness and the effectiveness of Highly Active antiretroviral therapy (HAART). However, new challenges have emerged which when not effectively addressed may hinder the progress made so far. One important area of difficulty in the management of HIV infection is the emergence and transmission of drug resistant mutations (DRM), which threatens the long-term use of current HAART. Also, there is a growing need for more effective and relatively cheaper markers for monitoring HIV especially in resource-limited areas. One of such potential markers is HIV-l intracellular (IC) DNA load. We analyzed plasma and buffy coat samples as well as clinical data of 86 HIV-1 infected drug naive patients and eight follow-up patients with persistently high viral loads after 24 weeks of HAART from Nouna in Burkina Faso. The participants were predominantly females. Among drug naive patients, paired RNA and DNA templates were polymerase chain reaction (PCR) amplified and Sanger sequenced for the detection of DRMs. Templates encompassed 1461 base pairs sequenced from the protease and reverse transcriptase region of HIV-1 pol. A total of eight patients harboured transmitted drug resistance mutations (TDRMs). Six had TDRMs to non-nucleoside reverse transcriptase inhibitors (NNRTIs), one to nucleoside reverse transcriptase inhibitors (NRTIs), and one to protease inhibitors (PIs). Given that interest is growing in the use of viral DNA sequencing to complement or replace RNA for DRM monitoring, we compared sequences from RNA and DNA templates, for similarities and differences in regions with DRMs and for nucleotide differences. A high level of concordance 78 (94%) was observed in regions with DRMs. Also, nucleotide sequences of paired templates were highly similar (84%). Furthermore, observed nucleotide differences greater than 10 within viral sequence pairs were resolved with deep sequencing using the so-called “Nextera tagmentation” approach. Deep sequencing of thirteen RNA and DNA template pairs revealed predominantly major reverse transcriptase (RT) mutations M230I and M184I within the minority viral population. It also confirmed differences in DRMs observed in Sanger sequencing and showed that patterns of synonymous and non-synonymous nucleotide changes were similar to those seen in Sanger sequencing. Predominant HIV-1 subtypes found in patients were CRF02_AG and CRF06_cpx. With the eight follow-up patients, DRMs and HIV-1 subtyping were determined from RNA templates only. Drug resistance mutations contributing to virological failure after HAART were assessed. Major DRMs to RTIs mainly K103N, E138Q, G190A and M230L were detected. Finally we assessed the utility of HIV-1 IC DNA load as a tool for disease monitoring and found that HIV-1 IC DNA levels did not correlate with traditional HIV-1 disease monitoring markers such as CD4+ T-cell counts (r2=0.017; p=0.23) and plasma viral loads (r2=0.003; p=0.60), as well as other markers of disease progression. Also, there was no association (p=0.26) found between HIV-1 IC DNA levels of drug resistant (median 2.96 log10 copies/106 cells, IQR 2.30-3.52) and drug susceptible (median 2.62 log10 copies/106 cells, IQR 2.23-3.06) strains of HIV-1, signifying that the presence of TDRMs does not affect HIV-1 IC DNA levels. However, a significantly higher baseline HIV-1 IC DNA level (p=0.045) was found in patients failing HAART after 24 weeks of therapy (median 3.16 log10 copies/106 cells, IQR 2.75-3.62) as opposed to those who did not (median 2.63 log10 copies/106 cells, IQR, 2.12-3.04). Our findings show that the prevalence of TDRMs is high and new DRMs develop over time making it necessary to institute resistance testing for more effective clinical management. Also the high concordance in DRMs between viral RNA and DNA templates suggests that DNA could be used for resistance monitoring, as it is cheaper and relatively easy to handle. HIV-1 IC DNA load is an independent marker that could be used alone or together with plasma viral load, CD4+ T-cell counts and other markers to monitor disease progression. A larger follow-up study is recommended to confirm these findings.

Human Immunodeficiency Virus-1 (HIV-1) drug resistance genotyping assay is a part of clinical management of HIV-1 positive individuals under treatment with highly active antiretroviral therapy (HAART). Routine monitoring of drug resistance mutations in resource limited settings like India is not possible due to high cost of commercial drug resistance assays. In this study we developed an in-house, cost effective HIV-1 drug resistance genotyping assay for Indian patients and validated it against the US-FDA-approved ViroSeq HIV-1 drug resistance testing system. A reference panel of 20 clinical samples was used to develop and validate the assay against ViroSeq HIV-1 drug resistance testing system which was subsequently used to genotype a clinical panel of 225 samples. The Stanford HIV database was used to identify drug resistant mutations. The analytical sensitivity of the assay was 1000 HIV-1 RNA copies/ml of plasma sample while precision and reproducibility was 99.68±0.16% and 99.76±0.18% respectively. One hundred and one drug resistant mutations were detected by the in-house assay compared to 104 by ViroSeq system in the reference panel. The assay had 91.55% success rate in genotyping the clinical panel samples and was able to detect drug resistant mutations related to nucleoside reverse transcriptase inhibitor (NRTI), non-nucleoside reverse-transcriptase inhibitor (NNRTI) as well as protease inhibitor (PI) classes of antiretroviral drugs. It was found to be around 71.9% more cost effective compared to ViroSeq genotyping system. This evaluation of the assay on the clinical panel demonstrates its potential for monitoring clinical HIV-1 drug resistance mutations and population-based surveillance in resource limited settings like India.

ObjectiveThis study aimed to pool the prevalence of virological failure and associated factors.DesignSystematic review and meta-analysis.Primary outcome measurePrevalence of virological failure.Secondary outcome measureFactors affecting virological failure.AnalysisThe extracted data were exported...

BackgroundThe national antiretroviral therapy in the Republic of Chad provides free of charge antiretroviral regimens and therapeutic monitoring for patients receiving antiretroviral therapy nationwide. For a successful programmatic uptake, these efforts merit to be supported by thorough assessments of antiretroviral therapy response and HIV-1 drug resistance surveillance, especially with risks of cross-resistance due to the gradual stavudine phasing out in such national settings. We therefore evaluated the virological response to antiretroviral therapy, HIV-1 drug resistance emergence and circulating HIV-1 clades in a Chad context. A cross-sectional and prospective study was conducted among 116 patients (41 [δ ± 6.87] years, 59% female) receiving first-line antiretroviral therapy for ≥ 6 months in Ndjamena, Chad, in 2011–2012, enrolled consecutively. To ensure accuracy, plasma viral load was concomitantly measured using Abbott Real-Time and Cobas AmpliPrep/TaqMan (v2.0), and virological failure defined as ≥ 1000 HIV-1 RNA copies/ml. Plasma from patients experiencing virological failure were processed for sequencing of HIV-1 protease-reverse transcriptase using the ANRS-AC.11 resistance testing protocol; drug resistant mutations were interpreted using the ANRS-AC11 algorithm; and phylogenetic analysis was performed using MEGA.v.6.ResultsMajority of patients was receiving zidovudine plus lamivudine plus nevirapine (46%), stavudine plus lamivudine plus nevirapine (41%) and tenofovir plus emtricitabine plus efavirenz (11%), for a median time-on-treatment of 5 [IQR 4–7] years. The rate of virological failure was 43% (50/116), with 86% (43/50) sequencing performance. Overall, 32% (37/116) patients presented ≥ one major drug resistant mutation(s), with 29% (34/116) to nucleos(t)ide reverse transcriptase inhibitors (67% [29/43] M184V/I, 30% [13/43] T215Y/F, 19% [8/43] V75A/F/I/L/M, 9% [4/43] K70P/R/W, 9% [4/43] K219E/N/Q and 5% [2/43] A62V); 86% (37/43) to non-nulceos(t)ide reverse transcriptase inhibitors (30% [13/43] K103N/S/E, 26% [11/43] Y181C/V/F/L, 2% [1/43] L100I, 2% [1/43] F227L, 2% [1/43] P225H); and 2% (1/43) to protease inhibitors (M46I, I54V, V82S). Six HIV-1 subtypes were found: 30% circulating recombinant form (CRF02_AG), 30% J, 16% G, 9% A, 9% D, 5% F.ConclusionsIn Chad, almost half of patients are failing first-line antiretroviral therapy after 5 years, with considerable drug resistant mutations at failure. Absence of K65R supports the use of tenofovir-containing regimens as preferred first-line and as suitable drug for second-line combinations, in this setting with significant HIV-1 genetic diversity.

The effect of dolutegravir (DTG)-based regimens on reducing attrition from care among women enrolled in the prevention of mother-to-child transmission (PMTCT) care program is unknown. Therefore, this study aimed to compare the incidence of attrition among women exposed to DTG-based with those exposed to efavirenz (EFV)-based first-line antiretroviral therapy (ART) in Ethiopia. An uncontrolled before-and-after study was conducted involving 932 women (with 466 on EFV-based and 466 on DTG-based regimens) who were enrolled in the PMTCT care program from September 2015 to February 2023. The outcome variable was attrition (i.e., maternal death or loss to follow-up before their infants' final HIV status was determined). A Kaplan-Meier estimator was employed to estimate the probability of attrition. The Cox proportional hazards regression model was fitted to identify predictor variables. The adjusted hazard ratio (aHR) with the corresponding 95% confidence interval (CI) was calculated to examine the risk difference in the comparison groups. The cumulative incidence of attrition among women was 5.2% (3.0% for those placed in the DTG-based regimen arm and 7.3% for those placed in the EFV-based regimen arm). Women on DTG-based regimens had a 57% (aHR: 0.43; 95% CI: 0.23-0.80) lower risk of attrition from care compared to those on EFV-based regimens. Women who delivered their infants at home (aHR: 2.35; 95% CI: 1.14-4.85), had poor/fair adherence (aHR: 3.23; 95% CI: 1.62-6.45), had unsuppressed/unknown viral load status (aHR: 2.61; 95% CI: 1.42-4.79), and did not disclose their status to partners (aHR: 2.56; 95% CI: 1.34-4.92) had a higher risk of attrition from PMTCT care compared to their counterparts. The cumulative incidence of attrition among women receiving PMTCT care is optimal. In addition, the risk of attrition among women receiving DTG-based regimens is lower than that among women receiving EFV-based regimens. Thus, DTG-based first-line ART regimen supplementation should be sustained to achieve a national retention target of 95% and above.

Emerging HIV drug resistance (HIVDR) poses a growing threat to the long-term success and durability of highly active antiretroviral therapy (HAART). To understand the incidence of HIVDR and estimate the proportion of potential HIVDR and its associated risk factors among the patients on HAART for one year. Antiretroviral-naïve patients ≥ 18 years old were invited to participate in this one-year prospective study from seven clinics in Yunnan, Guangxi, and Xinjiang provinces. A questionnaire and blood draw were collected at baseline and 12 month follow-up. The protocol used was modified slightly from the WHO Protocol for Surveys of HIV Drug Resistance Emerging During Treatment and Related Program Factors in Sentinel ART Sites in Resource-limited Settings. 435 subjects were included in the final analysis, with median baseline CD4 cell count 139 cells/mm3. Of the total 417 patients who fall under WHO guidelines for 'Classification of outcomes based on endpoints' (on ART at 12 months, switch, lost to follow-up, and stop), 90 (21.6%) did not have any drug resistant mutations (potential HIVDR) and 17 (4.1%) did (HIVDR, Table 2). The remaining 310 (75.3%) had a viral load <1000 copies/ml (HIVDR prevention). Among 351 patients retained at 12 months, 41 (11.7%) had a viral load >1000 copies/ml.Patients who self-reported missing doses in the previous month were 6.2 fold (95% CI 2.5-15.7) more likely to fail than those who did not. and those from Xinjiang were 12.1 fold (95% CI 5.2-28.1) more likely to fail compared to those from Yunnan and Guangxi. Why Xinjiang was associated with virologic failure was not clear but may be related to the demographics of the participants from Xinjiang, being significantly more IDUs, poorer, and less adherent than those from Yunnan and Guangxi. Although successful virologic outcomes were seen in the vast majority (75.3%) of those treated at one year, virologic failure continues to be a problem particularly among those less adherent and from Xinjiang. Additional data are needed to understand the generalizability of these results, particularly those related to Xinjiang. For IDUs, enhancing adherence to HAART and considering the treatment of drug addiction as an integral part of the treatment for HIV infection should be considered. As China's National Free Antiretroviral Treament Program continues to mature and improve, ramping up treatment in these settings may be important considerations to the long-term success of the program.