Nucleoside Reverse Transcriptase Inhibitor Resistance Mutations Research Articles

Resistance rates among antiretroviral regimens in pregnant people living with HIV.

To update nucleoside reverse transcriptase inhibitor (NRTI), nonnucleoside reverse transcriptase inhibitor (NNRTI) and protease inhibitor (PI) resistance rates and describe the frequency of HIV subtypes in a cohort of pregnant people living with HIV (PPLH) at a national Prevention of Mother-To-Child HIV Transmission (PMTCT) centre. We evaluated genotypic resistance among PPLH during prenatal care who were antiretroviral therapy-naïve or experienced. We determined mutations by the Surveillance of Drug Resistance Mutations (SDRM) dataset and also focused on studying participants with intermediate or high resistance defined through the Stanford score. From 2018 to 2021, 1170 PPLH received prenatal care at the centre and 550 were genotyped. Among the 295 SDRMs, with respect to NRTI resistance mutations, there were 27/295 (9.2%) M184V/I, 14/295 (4.7%) T215Y/C/D/E/F/V/I/S and 12/295 (4.1%) M41L. For NNRTI, there were 75/295 (25.4%) K103N, 18/295 (6.1%) M230L and 14/295 (4.7%) G190A/E/S mutations. For PI, the most frequent mutations were 13/295 (4.4%) V82A/S/F/T, 12/295 (4.1%) M46I/L and 10/295 (3.4%) D30N. Based on the Stanford score, 36/224 (16%) naïve participants had one or more antiretroviral resistance mutations, 81% of whom had NNRTI resistance. In the treatment-experience group, 108/326 (33%) had one or more mutations, 91% of whom had NNRTI resistance. The most frequent HIV subtype was B (82.5%). Our findings suggest that continuous surveys of HIV genotype appear to be important tools to map the distribution and evolution of HIV subtypes and resistance to provide information to support treatment policies. Furthermore, concerns about the use of rilpivirine-containing regimens underscore the importance of resistance surveillance.

AntiRetroviral Therapy In Second-line: investigating Tenofovir-lamivudine-dolutegravir (ARTIST): protocol for a randomised controlled trial

Background: Dolutegravir has superior efficacy and tolerability than lopinavir-ritonavir in second-line antiretroviral therapy after failure of a first-line non-nucleoside reverse transcriptase inhibitors-based regimen, when dolutegravir is accompanied by at least one fully active nucleoside reverse transcriptase inhibitor (NRTI). Resistance testing to select NRTIs is not feasible in low- and middle-income countries due to cost and limited laboratory capacity. Evidence suggests that recycling tenofovir plus lamivudine or emtricitabine backbone with dolutegravir could provide an effective second-line option. This study aims to determine the virologic efficacy of tenofovir-lamivudine-dolutegravir (TLD) with and without a lead-in supplementary dose of dolutegravir (to counteract the inducing effect of efavirenz) in patients failing a first-line regimen of tenofovir-emtricitabine-efavirenz (TEE). Methods: We will perform a parallel group, randomised (1:1), double blind, placebo-controlled, Phase II trial, comparing TLD fixed dose combination daily with a lead-in supplementary 50 mg dolutegravir dose versus matching placebo taken 12 hours later for the first 14 days, in patients failing a first-line TEE regimen. The trial will be set in two primary care clinics in Khayelitsha; a large, peri-urban informal settlement in Cape Town, South Africa. We will enrol 130 participants, with follow-up to 48 weeks. The primary endpoint is proportion achieving viral load <50 copies/mL at week 24 using a modified intention-to-treat analysis and the U.S. Food and Drug Administration snapshot algorithm. Secondary endpoints include virologic suppression at weeks 12 and 48, time to suppression, emergence of dolutegravir and new NRTI resistance mutations, safety, and tolerability. Discussion: Impaired viral fitness due to NRTI resistance mutations and dolutegravir’s high barrier to resistance provide rationale for switching patients from a failing TEE regimen to TLD; however, clinical evidence regarding virologic efficacy is lacking. This study provides estimates of such a strategy’s early virologic efficacy with and without a supplementary dolutegravir dosing. Registration: ClinicalTrials.gov NCT03991013 (19/06/2019).

AntiRetroviral Therapy In Second-line: investigating Tenofovir-lamivudine-dolutegravir (ARTIST): protocol for a randomised controlled trial.

Background: Dolutegravir has superior efficacy and tolerability than lopinavir-ritonavir in second-line antiretroviral therapy after failure of a first-line non-nucleoside reverse transcriptase inhibitors-based regimen, when dolutegravir is accompanied by at least one fully active nucleoside reverse transcriptase inhibitor (NRTI). Resistance testing to select NRTIs is not feasible in low- and middle-income countries due to cost and limited laboratory capacity. Evidence suggests that recycling tenofovir plus lamivudine or emtricitabine backbone with dolutegravir could provide an effective second-line option. This study aims to determine the virologic efficacy of tenofovir-lamivudine-dolutegravir (TLD) with and without a lead-in supplementary dose of dolutegravir (to counteract the inducing effect of efavirenz) in patients failing a first-line regimen of tenofovir-emtricitabine-efavirenz (TEE). Methods: We will perform a parallel group, randomised (1:1), double blind, placebo-controlled, Phase II trial, comparing TLD fixed dose combination daily with a lead-in supplementary 50 mg dolutegravir dose versus matching placebo taken 12 hours later for the first 14 days, in patients failing a first-line TEE regimen. The trial will be set in two primary care clinics in Khayelitsha; a large, peri-urban informal settlement in Cape Town, South Africa. We will enrol 130 participants, with follow-up to 48 weeks. The primary endpoint is proportion achieving viral load <50 copies/mL at week 24 using a modified intention-to-treat analysis and the U.S. Food and Drug Administration snapshot algorithm. Secondary endpoints include virologic suppression at weeks 12 and 48, time to suppression, emergence of dolutegravir and new NRTI resistance mutations, safety, and tolerability. Discussion: Impaired viral fitness due to NRTI resistance mutations and dolutegravir's high barrier to resistance provide rationale for switching patients from a failing TEE regimen to TLD; however, clinical evidence regarding virologic efficacy is lacking. This study provides estimates of such a strategy's early virologic efficacy with and without a supplementary dolutegravir dosing. Registration: ClinicalTrials.gov NCT03991013 (19/06/2019).

HSV-2 Infection as a Potential Cofactor for HIV Disease Progression and Selection of Drug Resistance Mutations in Adults under WHO-Recommended First-Line Antiretroviral Therapy: A Multicentric, Cross-Sectional Study in Cameroon, Central African Republic, Chad, and Gabon.

Although herpes simplex virus-2 (HSV-2) infection is a known cofactor for HIV transmission in Central Africa, its role in HIV disease progression is unclear. The aim of this study was to examine the potential link between HSV-2 infection and HIV disease progression, in addition to identifying the presence of genes conferring HIV antiretroviral resistance mutations. This was a cross-sectional study involving 302 HIV-infected adults in Central Africa with virological failure (viral load >1000 copies/mL) on first-line antiretroviral therapy from four different countries. The seroprevalence of HSV-2 was 32% (96/302). Amongst the HIV-infected individuals who were HSV-2 seropositive, the mean HIV viral load and CD4 count were 4.82 ± 0.83 log copies/mL and 243 ± 144 cells/microliter, respectively. Among the HIV-infected individuals who were HSV-2-seronegative, the mean HIV viral load and CD4 count were 3.48 ± 0.44 log copies/mL and 646 ± 212 cells/microliter, respectively (p < 0.001). There was a statistically significant relationship (p < 0.001) between HSV-2 seropositivity and the presence of resistance mutations to antiretrovirals (ARV), non-nucleoside reverse transcriptase inhibitors (NNRTI), and nucleoside reverse transcriptase inhibitors (NRTI) with odds ratios of 9.7, 10, and 11.9, respectively. There was no link between HSV-2 serostatus and protease inhibitor (PI) resistance mutations. There was a substantial accumulation of resistance mutations in HSV-2-seropositive compared to -seronegative patients. These findings support the link between HIV disease progression and HSV-2 infection. An association was observed between the presence of NNRTI and NRTI resistance mutations and HSV-2 seropositivity.

Drug resistance mutations and its associated factors among 579 HIV/AIDS patients experiencing failure of antiretroviral therapy in Jiangsu Province, China

Objective: To understand the incidence and related factors of HIV-1 drug resistance among HIV/AIDS patients experiencing treatment failure in Jiangsu province, China. Methods: The HIV/AIDS integrated prevention and control data information management system of China were used to collect the basic data of patients, blood specimens were collected from patients who had antiretroviral therapy (ART) failure with ≥12 months and older than 18 years in 2016 in Jiangsu, excluding cases with missing information, 713 cases were enrolled in this study. HIV-1 RNA was extracted, and then pol gene region was amplified and sequenced. The obtain sequences were submitted to Stanford University HIV Drug Resistance Database to interpret and analyse HIV-1 drug resistance and sub-types. Multivariate logistic regression model was used to explore the related factors of drug resistance. Results: A total of 579 subjects were amplified successfully, male accounted for 85.66% (496 cases), and the median age was 39 years old. The main route of infection was sexual transmission (553 cases, 95.51%). A total of 331 patients with drug resistance gene mutation were detected, drug resistance mutation rate was 57.18%. Compared with patients with baseline CD4(+)T cell count >500 cells/μl, patients with CD4(+)T cell count in 201-500 cells/mm(3) and ≤200 cells/μl had a higher incidence of genetic drug resistance, the odds ratio was 3.33 and 6.87, respectively. Compared with patients with treatment less than 24 months, patients treated for 25-48 months had a higher incidence of drug resistance, the odds ratio was 1.88. Compared with patients infected by CRF07_BC strains, patients infected by CRF01_AE strains were associated with higher incidence of drug resistance, the odds ratio was 2.22 and 3.32, respectively. Protease inhibitor (PI) resistance mutations, nucleoside reverse transcriptase inhibitor (NRTI) and non-nucleoside reverse transcriptase inhibitor (NNRTI) were found in 3.80%, 33.16% and 53.37% of patients, respectively. 31.95% of patients harbored NRTI and NNRTI resistance mutations simultaneously. M184V/I and K103N/Q were the highest frequency of NRTI and NNRTI resistance mutation, the prevalence of M184V/I and K103N/Q were 28.15% and 22.28%, respectively. Conclusion: The status of HIV-1 drug resistance mutations are complex and diverse among patients experiencing failure of ART in Jiangsu. Patients with lower baseline CD4(+)T cell count, longer treatment time and HIV-1 CRF01_AE and B strains infection were associated with higher incidence of drug resistance mutation.

Antiretroviral resistance following immunological monitoring in a resource-limited setting of western India: A cross-sectional study.

BackgroundThe free antiretroviral therapy (ART) program in India still relies on the clinico-immunological monitoring for diagnosis of treatment failure. As the nucleoside reverse transcriptase inhibitor (NRTI) backbone is shared in first- and second-line regimens, accumulation of drug resistant mutations (DRMs) can compromise the efficacy of NRTI. This study was undertaken to describe the pattern of HIV DRMs following immunological monitoring and investigate its impact on the cycling of NRTI between first- and second-line ART.Methods and findingsThis cross-sectional study was performed at a state-sponsored ART clinic of Pune city in western India between January and June 2016. Consecutive adults receiving first-line ART with immunological failure (IF) were recruited for plasma viral load (PVL) estimation. Randomly selected 80 participants with PVL >1000 copies/mL underwent HIV drug resistance genotyping. Of these, 75 plasma sample were successfully genotyped. The median CD4 count and duration of ART at the time of failure were 98 (IQR: 61.60–153.50) cells/μL and 4.62 (IQR: 3.17–6.15) years, respectively. The prevalence of NRTI, non-NRTI, and major protease inhibitor resistance mutations were 89.30%, 96%, and 1.33%, respectively. Following first-line failure, sequences from 56.67% of individuals indicated low- to high-level resistance to all available NRTI. The proportion of sequences with ≥2 thymidine analogue mutations (TAMs) and ≥3 TAMs were 62.12% and 39.39%, respectively. An average of 1.98 TAMs per sequence were observed following IF as compared to 0.37 TAMs per sequence following targeted PVL monitoring at 12 months of ART from a prior study; this difference was significant (p<0.001).ConclusionThe option of cycling of NRTI analogues between first- and second-line regimens would no longer be effective if individuals are followed-up by immunological monitoring due to accumulation of mutations. Introduction of routine PVL monitoring is a priority for the long-term sustainability of free ART program in India.

The prevalence of primary HIV-1 drug resistance in newly reported HIV infections in Henan

To study the prevalence of primary HIV-1 drug resistance in newly reported HIV infected individuals receiving no antiviral treatment in Henan. Network direct reporting information of newly reported HIV infection cases in six cities of Henan during January to June, 2013 and January to June, 2014 were collected, and blood samples were collected from the cases to conduct genotypic drug resistance test and sequence analysis. Primary HIV-1 drug resistance was detected in 45 of 624 newly reported HIV infection cases, the prevalence of primary HIV-1 drug resistance was 7.21%, which was classified as moderate. Univariate analysis revealed that the prevalence of primary HIV-1 drug resistance was higher in females(χ(2)=11.463, P = 0.001), in age group <20 years(χ(2)=8.969, P=0.011), in illiterates(χ(2)=18.072, P=0.001)and in cases of HIV subtype B infection(χ(2)=9.897, P=0.019). Multi-univariate analysis revealed that the risk of primary HIV-1 drug resistance was high in females(OR=2.194, 95%CI: 1.111-4.331). Non-nucleoside reverse transcriptase inhibitor(NNRTI), Nucleoside reverse transcriptase inhibitor(NRTI)and Protease inhibitor(PI)resistance mutations were found in 4.97%, 3.53% and 1.12% of the cases, respectively. M184V/I(2.08%)and K103N/S(2.88%)were the most commonly emerged NRTI and NNRTI resistance mutation. Multiple NRTI resistance mutation was found in four cases. HIV subtype B infections accounted for largest proportion(51.76%, 323/624), followed by CRF07_BC cases(23.72%, 148/624)and CRF01_AE cases(19.71%, 123/624). The prevalence of primary HIV-1 drug resistance was moderate in the newly reported HIV infected individuals in Henan. The surveillance for HIV-1 drug resistance transmission should be strengthened and drug resistance test before the antiviral treatment should be given.

Transmitted HIV-1 Drug resistance and the Role of Herpes Simplex Virus -2 Coinfection among Fishermen along the Shores of Lake Victoria, Kisumu, Kenya

Introduction: Herpes simplex virus type 2 (HSV-2) infection has been associated with a 3-fold risk of HIV-1 acquisition. The prevalence of HIV-1 and HSV-2 in the fishing communities along the shores of Lake Victoria in Kisumu have been reported to be high. This may contribute to the growing HIV epidemic in Kenya including the spread of transmitted drug resistance (TDR). We report data on the association of HSV2/HIV-1 co-infection and TDR in this antiretroviral (ARV)-naïve population. Methods: Blood samples were obtained from 249 consenting fishermen from 5 beaches and a detailed sociodemographic questionnaire was administered. Blood samples were analyzed for HIV-1/HSV2 co-infection. The HSV-2 serology was performed using Kalon HSV type 2 enzyme-linked immunosorbent assay (ELISA). The HIV-1 counselling and serology were carried out according to local standards of practice in Kenya, using two parallel rapid assays (Alere Determine HIV-1/2 and Trinity Biotech Uni- Gold), with a third ELISA-Vironostika HIV Uni-Form II Ag/Ab for resolving discrepancies. All HIV positive samples were tested for TDR using an in house HIV-1 pol-RT genotyping protocol. Results: Of the 249 recruited fishermen (mean age 35.1 years), 134 (53.8%) were positive for HSV-2, 59 (23.7%) were HIV positive while 48 (19.3%) were HIV/HSV-2 coinfected. Twenty-three of 59 (38.9%) HIV positive men had TDR, with the majority (19/23, 82.6%) in HIV/HSV-2 coinfected fishermen. Among the 48 HIV/HSV-2 co-infected fishermen, 9 had nucleoside reverse-transcriptase inhibitor (NRTI) resistance mutations with NRTI- associated mutations [NAMS], M184V (77.8%) and K65R (11.1%) being the highest. Nineteen (19) fishermen had Non-NRTI (NNRTIs) mutations including; four (21.1%) each of K103N, Y181C and G190A. Three (15.7%) V179T, two V901V and single A98G and Y188L mutations. Among the 11 fishermen who had HIV-1 mono-infection, four (36.4%) had drug resistant mutations. One fisherman had NRTI resistance mutation M184V. In addition, three men (3/4) had NNRTI resistance; K103N, G190A and Y181C mutations each. In the regression model, HIV/HSV-2 co-infection was independently associated with TDR [OR 4.1 (95% CI 1.4 to 11.9)]. Conclusion: The level of TDR to NNRTIs in these ARV-naive fishermen was significantly high especially among those coinfected with HSV-2. HSV-2 infection may increase the risk of TDR in this population.

HIV CRF08_BC AND X4 STRAIN ARE ASSOCIATED WITH POSING MAJOR NUCLEOSIDE AND NON-NUCLEOSIDE REVERSE TRANSCRIPTASE INHIBITORS RESISTANCE MUTATIONS

In HIV treatment, surveillance of mutations inducing resistance to NRTIs (Nucleoside Reverse Transcriptase Inhibitors) and NNRTIs (Non-Nucleoside Reverse Transcriptase Inhibitors) is important. This study analyzed 2,071 HIV-1 genomic sequences directed to detection of major NRTIs and NNRTIs resistance mutations and viral tropism. CRF08_BC and X4 strain more likely had major NRTIs (adjusted odds ratio (aOR) 3.0, 95% CI 1.182-7.820, p=0.021 and aOR 1.7, 95% CI 1.233-2.368, p=0.001; respectively) and NNRTIs (aOR 3.3, 95% CI 1.281-8.365, p=0.013 and aOR 1.4, 95% CI 1.037-1.977, p=0.029, respectively) resistance mutations. Subtype A1 (aOR 0.2, 95% CI 0.069-0.702, p=0.011) and C (aOR 0.4, 95% CI 0.241-0.648, p&lt;0.001) were associated with major NRTIs resistance mutations. The occurrence of major NRTIs and NNRTIs resistance mutations in HIV subtype A1, C, CRF08_BC, and X4 viruses should be a particular concern.

Analysis of HIV-1 drug resistance among 1 922 individuals experiencing virological failure of first-line antiretroviral therapy in Henan province

To study the condition of HIV-1 drug resistance mutation among failures of first-line antiretroviral therapy in Henan province. The sub platform of China's legal infectious disease monitoring information reporting system-HIV/AIDS integrated prevention and control data information management system was used to collect the information of patients experiencing first-line antiretroviral treatment failure (virus load ≥ 1 000 copies/ml) more than one year among nine cities of Henan in 2011. A total of 40 cases with no information and 212 cases with incomplete drug resistance results were deleted, and 1 922 cases were included in this study and genotype resistance testing was carried out. Non-conditional logistic regression analysis was used to analyse the influencing factors of drug resistance mutation. A total of 1 922 cases were included in the analysis. 1 039 cases were males, 833 cases were females, the age was (45.7 ± 12.1) years, 82.73% (1 590) were married, and 87.93% (1 690) were transmitted by blood. 64.20% (1 234) patients acquired drug resistance. Nucleoside reverse transcriptase inhibitor (NRTI), non-nucleoside reverse transcriptase inhibitor (NNRTI) and protease inhibitor (PI) resistance mutations were found in 62.59% (1 203), 49.74% (956) and 0.94% (18) of subjects, respectively. 42.09% (809) of patients harbored NRTI and NNRTI resistance mutations synchronously. ≥ 1TAM was the most commonly emerged NRTI resistance mutation (41.94% (806)), the prevalences of TAM-1 and TAM-2 were 8.48% (163) and 4.24% (81), respectively. K65R/N and Q151M complex existed in 23 and 4 patients, respectively. K103N/S was the most commonly emerged NNRTI resistance mutation (34.32% (659)). Non-conditional logistic regression analysis showed that, factors associated with high drug resistance were the following: transmitted by mother to child (OR = 9.05, 95% CI: 1.14-72.12), clinical stage was IV (OR = 1.70, 95% CI: 1.09-2.66) and 5-year-treated (OR = 1.59, 95% CI: 1.03-2.47). Factors associated with low drug resistance were the following: 1-year-treated (OR = 0.19, 95% CI: 0.13-0.27). Complex patterns of HIV-1 drug resistance mutations were identified among individuals experiencing failure of first-line antiretroviral therapy in Henan province. Factors associated with high drug resistance were lived in Luohe, Shangqiu, Nanyang, Xinyang, transmitted by mother to child, clinical stage was IV, and 5-year-treated.

96-week resistance analyses of the STaR study: rilpivirine/emtricitabine/tenofovir DF versus efavirenz/emtricitabine/tenofovir DF in antiretroviral-naive, HIV-1-infected subjects

Background:STaR (GS-US-264-0110) was a 96-week phase 3b study evaluating the safety and efficacy of two single-tablet regimens, rilpivirine/emtricitabine/tenofovir DF (RPV/FTC/TDF) and efavirenz/emtricitabine/tenofovir DF (EFV/FTC/TDF) in treatment-naive, HIV-1-infected subjects.Methods:Genotypic analyses (population sequencing) of HIV-1 protease (PR) and reverse transcriptase (RT) were performed at screening; subjects with pre-existing resistance to study drugs were excluded. The protocol-defined resistance analysis population had genotypic/phenotypic analyses at failure and baseline for PR and RT.Results:Through week 96, the resistance analysis population included 24/394 subjects (6.1%) receiving RPV/FTC/TDF and 9/392 subjects (2.3%) receiving EFV/FTC/TDF. In the RPV/FTC/TDF arm, HIV-1 isolates from 21/394 subjects (5.3%) developed non-nucleoside reverse transcriptase inhibitor (NNRTI) and/or nucleoside reverse transcriptase inhibitor (NRTI) resistance mutations and 20/21 isolates had both NNRTI and NRTI genotypic and/or phenotypic resistance. In the EFV/FTC/TDF arm, isolates from 4/392 subjects (1.0%) developed NNRTI and/or NRTI resistance mutations. Resistance development after week 48 was infrequent (1.0% RPV/FTC/TDF; 0.3% EFV/FTC/TDF). When stratified by baseline HIV-1 RNA ≤ or >100 000 copies/ml, 9/260 (3.5%) versus 12/134 (9.0%) RPV/FTC/TDF-treated subjects and 3/250 (1.2%) versus 1/142 (0.7%) EFV/FTC/TDF-treated subjects developed resistant isolates, respectively. Pre-existing NRTI- and NNRTI-associated resistance mutations (not related to study drugs) did not impact treatment response to either regimen.Conclusions:Resistance development to RPV/FTC/TDF consisted of NNRTI and NRTI mutations and was more frequent than resistance development to EFV/FTC/TDF through week 96. Emergent resistance after week 48 was infrequent in both arms. Within the RPV/FTC/TDF arm, resistance development was more frequent in subjects with baseline HIV-1 RNA >100 000 copies/ml compared to baseline HIV-1 RNA ≤ 100 000 copies/ml.

Short communication: Prevalence of HIV-1 transmitted drug resistance in Liberia.

No data on HIV-transmitted drug resistance (TDR) are available in Liberia in which the HIV prevalence in the general population is estimated at 1.5%. The aim of the study was to assess the prevalence of TDR in HIV-1 from recently diagnosed and untreated patients living in Monrovia, Liberia. The study was performed in the John F. Kennedy Medical Center and in the Redemption Hospital, both located in Monrovia. All newly HIV-1 diagnosed patients attending voluntary counseling testing centers and antiretroviral therapy naive were consecutively included. Protease and reverse transcriptase (RT) regions sequencing was performed using the ANRS procedures (www.hivfrenchresistance.org). Drug resistance mutations (DRM) were identified according to the 2009 updated WHO surveillance DRM list. Among the 116 HIV-1-infected patients enrolled in the study, 85 (73%) were women. Protease and RT sequencing was successful in 109 (94%) and 102 (88%) samples, respectively. Seventy-five (66%) patients were infected with CRF02_AG. One DRM was observed in six samples, leading to a TDR prevalence of 5.9% (CI 95%=1.7-10.1). DRM were observed in two patients (2.0%; CI 95%=0.0-4.7), four patients (3.9%; CI 95%=0.1-7.7), and one patient (0.9%; CI 95%=0.0-2.7) for nucleoside RT inhibitors (NRTI), non-NRTI (NNRTI), and protease inhibitors, respectively. Overall, one patient exhibited dual class-resistant viruses, harboring NRTI and NNRTI resistance mutations (1.0%; CI 95%=0.0-2.9). This first survey study in Liberia reported a TDR prevalence of 5.9%, classified as moderate according to the WHO criteria, indicating that further surveillance is warranted to follow the level and evolution of TDR prevalence in recently HIV-1 diagnosed patients.

Clinical and virological response to antiretroviral drugs among HIV patients on first-line treatment in Dar-es-Salaam, Tanzania.

In Tanzania, the follow-up on antiretroviral therapy (ART) response is based on clinical outcomes. We investigated virological response and ARV resistance mutations in relation to clinical response in ARV-treated patients. A cross-sectional study of a cohort of 150 patients taking first-line ART in Dar-es-Salaam was conducted. Data were collected using standardized questionnaires and patients' blood samples. HIV viral load testing and genotyping was performed on all viremic samples. Statistical analyses compared clinical responders and non-responders. The median time on ART was 20 months; 71 (47%) patients were ART clinical responders. Clinical non-responders were more likely to have started ART with advanced disease with significantly lower median percentage weight gain (6% versus 20%) with respect to pre-treatment levels. Sixty-one (86%) and 64 (81%) of clinical responders and non-responders, respectively, had undetectable viral loads. Genotyping was successful in 24 (96%) virologically failing patients, among whom 83% had resistance mutations; 67% had dual nucleoside reverse transcriptase inhibitor (NRTI)/non-NRTI (NNRTI) resistance mutations. Seventeen (71%) and 19 (79%) patients had NRTI and NNRTI resistance mutations, respectively, which were related to the ART in use, with no difference between clinical responders and non-responders. The most prevalent subtypes were A and C, found in 9 (38%) and 7 (29%) patients, respectively. The observed virological response was high and did not correlate with clinical response. The prevalence of ARV resistance mutations was high in viraemic patients and was related to the ARV prescribed. We recommend use of viral load monitoring during ART in Tanzania.

Characterization of HIV-1 Drug Resistance Development Through Week 48 in Antiretroviral Naive Subjects on Rilpivirine/Emtricitabine/Tenofovir DF or Efavirenz/Emtricitabine/Tenofovir DF in the STaR Study (GS-US-264-0110)

The Single-Tablet Regimen (STaR) study (GS-US-264-0110) is a 96-week phase 3b study evaluating the safety and efficacy of 2 single-tablet regimens, rilpivirine/emtricitabine/tenofovir DF (RPV/FTC/TDF), and efavirenz/emtricitabine/tenofovir DF (EFV/FTC/TDF) in treatment-naive HIV-1-infected subjects. Genotypic analyses (population sequencing) of HIV-1 protease and reverse transcriptase were performed at screening; subjects with pre-existing resistance to study drugs were excluded. The primary protocol-defined resistance analysis population (RAP) had genotypic/phenotypic analyses at failure and baseline for protease and reverse transcriptase. At week 48, the primary RAP included 20/394 subjects (5.1%) receiving RPV/FTC/TDF and 7/392 subjects (1.8%) receiving EFV/FTC/TDF. In the RPV/FTC/TDF arm, isolates from 17/394 subjects (4.3%) developed nonnucleoside reverse transcriptase inhibitor (NNRTI) and/or nucleoside reverse transcriptase inhibitor (NRTI) resistance mutations, and 16/17 isolates had both NNRTI and NRTI resistance mutations. In the EFV/FTC/TDF arm, isolates from 3/392 subjects (0.8%) developed NNRTI and/or NRTI resistance mutations. When stratified by baseline viral load of either ≤ 100,000 or >100,000 copies/mL, 5/260 (1.9%) versus 12/134 (9.0%) RPV/FTC/TDF-treated subjects and 2/250 (0.8%) versus 1/142 (0.7%) EFV/FTC/TDF-treated subjects developed resistant isolates, respectively. The presence of pre-existing NRTI- and NNRTI-associated resistance mutations not excluded at screening (not related to study drugs) did not impact treatment response to either regimen. Among subjects in the primary RAP, resistance development to RPV/FTC/TDF consisted of NNRTI and NRTI mutations and was more frequent than resistance development to EFV/FTC/TDF. In subjects with baseline viral load ≤ 100,000 copies/mL, resistance development was low (<2%) for both RPV/FTC/TDF and EFV/FTC/TDF arms and less frequent compared with subjects with baseline viral load >100,000 copies/mL, for RPV/FTC/TDF.

In vitro cross-resistance profile of nucleoside reverse transcriptase inhibitor (NRTI) BMS-986001 against known NRTI resistance mutations.

BMS-986001 is a novel HIV nucleoside reverse transcriptase inhibitor (NRTI). To date, little is known about its resistance profile. In order to examine the cross-resistance profile of BMS-986001 to NRTI mutations, a replicating virus system was used to examine specific amino acid mutations known to confer resistance to various NRTIs. In addition, reverse transcriptases from 19 clinical isolates with various NRTI mutations were examined in the Monogram PhenoSense HIV assay. In the site-directed mutagenesis studies, a virus containing a K65R substitution exhibited a 0.4-fold change in 50% effective concentration (EC50) versus the wild type, while the majority of viruses with the Q151M constellation (without M184V) exhibited changes in EC50 versus wild type of 0.23- to 0.48-fold. Susceptibility to BMS-986001 was also maintained in an L74V-containing virus (0.7-fold change), while an M184V-only-containing virus induced a 2- to 3-fold decrease in susceptibility. Increasing numbers of thymidine analog mutation pattern 1 (TAM-1) pathway mutations correlated with decreases in susceptibility to BMS-986001, while viruses with TAM-2 pathway mutations exhibited a 5- to 8-fold decrease in susceptibility, regardless of the number of TAMs. A 22-fold decrease in susceptibility to BMS-986001 was observed in a site-directed mutant containing the T69 insertion complex. Common non-NRTI (NNRTI) mutations had little impact on susceptibility to BMS-986001. The results from the site-directed mutants correlated well with the more complicated genotypes found in NRTI-resistant clinical isolates. Data from clinical studies are needed to determine the clinically relevant resistance cutoff values for BMS-986001.

Resistance-Associated Mutations after Initial Antiretroviral Treatment Failure in a Large Cohort of Patients Infected with HIV-1 Subtype CRF01_AE

The nucleoside reverse transcriptase inhibitors (NRTIs), zidovudine (AZT) and stavudine (d4T) are thymidine analog drugs recommended as first-line antiretroviral therapy in HIV-1-naive patients. Two thymidine analog mutation (TAM) pathways, TAM-1 and TAM-2, confer high levels of resistance with mutations in the viral RT. The relative prevalence of TAM pathways and their associations with other NRTI resistance mutations acquired under the pressure of drug treatment in a large cohort of 1,876 patients infected with HIV-1 CRF01_AE attending the Infectious Disease Clinic, Chiang Mai University Hospital, Chiang Mai, Thailand, were studied. From 117 patients infected with HIV-1 CRF01_AE who had plasma HIV-1 RNA of ≥500 copies/mL, 69 patients had at least one TAM. The most common mutation associated with NRTI resistance was M184V/I (89.9%). The TAM-2 (89.9%) pathway occurred approximately two times more frequently than the TAM-1 (43.5%) pathway. The presence of TAM and the TAM-1 pathway was significantly more frequent in the AZT- than the d4T-receiving group ((OR, 2.89; 95% CI, 1.12-7.46; P< 0.05) and (OR, 3.33; 95% CI, 1.19-9.37; P< 0.05), respectively). In conclusion, the TAM-2 pathway was selected more frequently than the TAM-1 pathway by thymidine analog drugs in HIV-1 CRF01_AE-infected patients, while the TAM-1 pathway occurred more frequently than the TAM-2 pathway in such patients with AZT-based treatment. Routine monitoring of plasma HIV-1 RNA may result in less exposure to failing regimens and reduce the opportunity for TAMs to accumulate. However, the low frequency of the TAM-1 pathway in our cohort data suggests that these patients should respond well to second-line regimens containing a ritonavir-boosted protease inhibitor.

Comparing Peripheral Blood Mononuclear Cell DNA and Circulating Plasma viral RNA pol Genotypes of Subtype C HIV-1

INTRODUCTION: Drug resistance mutations (DRM) in viral RNA are important in defining to provide effective antiretroviral therapy (ART) in HIV-1 infected patients. Detection of DRM in peripheral blood mononuclear cell (PBMC) DNA is another source of information, although the clinical significance of DRMs in proviral DNA is less clear. MATERIALS AND METHODS: From 25 patients receiving ART at a center in Zimbabwe, 32 blood samples were collected. Dideoxy-sequencing of gag-pol identified subtype and resistance mutations from plasma viral RNA and proviral DNA. Drug resistance was estimated using the calibrated population resistance tool on www.hivdb.stanford.edu database. Numerical resistance scores were calculated for all antiretroviral drugs and for the subjects' reported regimen. Phylogenetic analysis as maximum likelihood was performed to determine the evolutionary distance between sequences. RESULTS: Of the 25 patients, 4 patients (2 of which had given 2 blood samples) were not known to be on ART (NA) and had exclusively wild-type virus, 17 had received Protease inhibitors (PI), 18, non-nucleoside reverse transcriptase inhibitors (NNRTI) and 19, two or more nucleoside reverse transcriptase inhibitors (NRTI). Of the 17 with history of PI, 10 had PI mutations, 5 had minor differences between mutations in RNA and DNA. Eighteen samples had NNRTI mutations, six of which demonstrated some discordance between DNA and RNA mutations. Although NRTI resistance mutations were frequently different between analyses, mutations resulted in very similar estimated phenotypes as measured by resistance scores. The numerical resistance scores from RNA and DNA for PIs differed between 2/10, for NNRTIs between 8/18, and for NRTIs between 17/32 pairs. When calculated resistance scores were collapsed, 3 pairs showed discordance between RNA and DNA for at least one PI, 6 were discordant for at least one NNRTI and 11 for at least one NRTI. Regarding phylogenetic evolutionary analysis, all RNA and DNA sequence pairs clustered closely in a maximum likelihood tree. CONCLUSION: PBMC DNA could be useful for testing drug resistance in conjunction with plasma RNA where the results of each yielded complementary information about drug resistance. Identification of DRM, archived in proviral DNA, could be used to provide for sustainable public health surveillance among subtype C infected patients.

Drug Resistance Mutations in HIVpolSequences from Argentinean Patients Under Antiretroviral Treatment: Subtype, Gender, and Age Issues

We studied drug resistance mutations (DRMs) in 2623 pol sequences. Out of 94,828 amino acid substitutions that were detected, 8749 corresponded to nucleoside reverse transcriptase inhibitor (NRTI), 3765 to nonnucleoside reverse transcriptase inhibitor (NNRTI), and 7141 to protease inhibitor (PI) resistance-associated mutations. The most common DRMs were L10I, I54V, L90M, V82A, A71V, L10V, M46I, M184V, M41L, T215Y, D67N, L210W, K70R, N348I, V118I, K103N, Y181C, G190A, K101E, V108I, L100I, V90I, K101Q, and A98G. As expected, DRMs frequencies depended on viral genotype. The amounts of NRTI and PI resistance mutations among B and BF sequences from children were higher than among sequences from adults. The frequencies of PI and NRTI resistance mutations among B and BF sequences from adult men were higher than among sequences from women. Some of these observations can be explained in light of the available epidemiological information, but some cannot, indicating that further studies are needed to understand the antiretroviral resistance epidemics in Argentina.

Resistance-Associated Mutations in HIV-1 among Patients Failing First-Line Antiretroviral Therapy

Thirty-five HIV-1 infected patients showing clinical and/or immunological failure to first line antiretroviral therapy (ART) according to WHO criteria were recruited from the ART center of Lok Nayak Hospital, New Delhi to detect the presence of resistance-mutations in reverse transcriptase (RT) and protease (PR) region of pol gene of HIV-1. Plasma viral load (PVL) was estimated. HIV-1 pol gene region encoding complete protease and reverse transcriptase (codons; 1-232 to 1-242) was reverse transcribed, followed by nested PCR. The PCR product was sequenced and analyzed. Plasma samples from 94.3% of patients with PVL >log(10) 3.0 c/mL could be amplified and analyzed. Virologic failure was detected in 65.7% of patients according to WHO criteria (PVL >log(10) 4.0). All patients were found to be infected with subtype C. One or more resistance-mutations were observed among 90.9% of study sequences. Nucleoside reverse transcriptase inhibitor (NRTI) resistance mutations were seen among all patients, with M184V and thymidine analogue mutations (TAM) being most frequently detected (75.6% and 72.7%, respectively). Nonnucleoside reverse transcriptase inhibitor (NNRTI) resistance-mutations were detected in 63.6% of sequences, of which Y181C/I (47.6%), K103N (33.3%) and G190S (28.6%) are the most common. None of the sequences showed major protease inhibitors (PIs) resistance mutation. High prevalence of NRTI and NNRTI drug resistance mutations among the study participants warrants the use of genotypic resistance testing to prevent accumulation of resistance mutations, which would limit future treatment options.

No selection of nucleoside reverse transcriptase inhibitor resistance associated mutations by acyclovir suppressive therapy in herpes simplex virus-2/HIV-1 dually infected persons

Genital herpes simplex virus type 2 (HSV-2) shedding has been associated with increased concentrations of HIV-1 in the genital tract and plasma [1,2]. Recent data from randomized controlled trials suggest that daily HSV-2 suppressive therapy with acyclovir (ACV) or valacyclovir over periods of up to 3 months may reduce plasma and genital HIV RNA load by 0.3–0.5 log10 copies/ml among HIV/HSV-2 coinfected individuals not receiving antiretroviral therapy (ART) [3–7]. However, a recent trial of suppressive therapy [ACV 400 mg twice daily (b.i.d.)] delivered to the HIV/HSV-2 seropositive partner in HIV discordant couples found no decrease in the rate of HIV transmission to the HIV negative partner [8]. ACV is an acyclic guanosine analog that inhibits HSV DNA polymerase after conversion to its triphosphate form. As the first phosphorylation is synthesized selectively by HSV thymidine kinase [9], ACV is mainly active in HSV-infected cells and was therefore thought to have no or poor antiretroviral activity. The postulated mechanism of impact on HIV is that herpes suppressive therapy is able to prevent HIV replication by disrupting direct HSV-2/HIV-1 interaction and, indirectly, by reducing the systemic and local immune activation induced by HSV-2 [10]. However, recent in-vitro experiments have suggested that ACV may directly inhibit HIV replication and induce the selection of mutations in the HIV reverse transcriptase known to confer resistance to nucleoside reverse transcriptase inhibitors (NRTIs) [11,12]. ACV has been shown to select the mutation V75I, associated with the reverse transcriptase multidrug resistance complex, and also, to a lesser extent, T69N and M184I, which typically precedes the emergence of the M184V mutation that confers a high level of resistance to lamivudine/emtricitabine. These results suggest that the use of ACV may select HIV variants harboring mutations associated with resistance to NRTI. If confirmed in vivo, this may impact the choice and efficacy of antiretroviral regimens among HIV patients who have previously been treated with ACV, and would suggest that the use of ACV in ART-naïve HIV-positive patients should be carefully considered. To determine the impact of ACV suppressive therapy on the selection of mutations in the HIV reverse transcriptase gene in vivo, we analyzed plasma samples from dually HIV/HSV-2-infected women receiving ACV suppressive therapy who were enrolled in a randomized placebo-controlled trial of ACV 400 mg b.i.d. for HSV suppression in Tanzania [13,14]. The detection of mutations was performed by HIV reverse transcriptase gene sequence analysis on plasma samples selected from women with a reported high-ACV adherence (defined as taking >90% tablets by tablet counts) and HIV RNA load more than 3 log10 copies/ml after 12 months of ACV suppressive therapy, and who were not on ART. Among 21 selected samples, none of the mutations V75I, T69N and M184I were detected. No other mutations known to confer resistance to NRTI were detected in the reverse transcriptase gene. In four samples, mutations at the codon 69 (69A n = 2, 69P n = 1, T69S n = 1) were detected. T69A and T69P are not known to be associated with NRTI resistance, but T69S in combination with other mutations may be associated with tenofovir resistance. This mutation may have been selected owing to ACV exposure or owing to natural polymorphism. These results suggest that b.i.d. HSV-2 suppressive therapy with a standard dose of 400 mg of ACV for 12 months did not induce the selection of NRTI resistance mutations in HIV-infected women not receiving ART. Because the threshold of resistant variant detection with sequence analysis is above 20%, we cannot completely rule out the presence of minor populations containing NRTI resistance mutations. However, we selected samples from women with high-ACV adherence to guarantee the highest selective pressure of ACV, and restricted the laboratory analyses to those who had been on ACV therapy for 12 months in order to be able to detect late emergence of ACV-associated NRTI resistance mutations. Thus, the selection of mutations in the reverse transcriptase gene by ACV exposure seems unlikely in our population. Considering the bioavailability of oral ACV, plasma concentrations after 400 mg b.i.d. should not exceed 1 μmol/l, five-fold lower than the half maximal inhibitory concentration for HIV [12] and such concentrations might not be sufficient to achieve antiretroviral activity. Our results do not confirm the in-vitro data obtained studies using high-dose ACV [12], but corroborate results recently presented on patients receiving ACV or valacyclovir for periods of 8–24 months [15]. These reassuring results for the use of 400 mg b.i.d. ACV in HSV-2/HIV coinfected patients deserve further confirmation especially if higher dosage of ACV is used in HIV-infected individuals.