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Digban TO, Iweriebor BC, Obi LC, Nwodo U, Okoh AI. Molecular Genetics and the Incidence of Transmitted Drug Resistance Among Pre-Treatment HIV-1 Infected Patients in the Eastern Cape, South Africa. Curr HIV Res 2020; 17:335-342. [PMID: 31584370 DOI: 10.2174/1570162x17666191004093433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 09/17/2019] [Accepted: 09/20/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Transmitted drug resistance (TDR) remains a significant threat to Human immunodeficiency virus (HIV) infected patients that are not exposed to antiretroviral treatment. Although, combined antiretroviral therapy (cART) has reduced deaths among infected individuals, emergence of drug resistance is gradually on rise. OBJECTIVE To determine the drug resistance mutations and subtypes of HIV-1 among pre-treatment patients in the Eastern Cape of South Africa. METHODS Viral RNA was extracted from blood samples of 70 pre-treatment HIV-1 patients while partial pol gene fragment amplification was achieved with specific primers by RT-PCR followed by nested PCR and positive amplicons were sequenced utilizing ABI Prism 316 genetic sequencer. Drug resistance mutations (DRMs) analysis was performed by submitting the generated sequences to Stanford HIV drug resistance database. RESULTS Viral DNA was successful for 66 (94.3%) samples of which 52 edited sequences were obtained from the protease and 44 reverse transcriptase sequences were also fully edited. Four major protease inhibitor (PI) related mutations (I54V, V82A/L, L76V and L90M) were observed in seven patients while several other minor and accessory PIs were also identified. A total of 11(25.0%) patients had NRTIs related mutations while NNRTIs were observed among 14(31.8%) patients. K103N/S, V106M and M184V were the most common mutations identified among the viral sequences. Phylogenetic analysis of the partial pol gene indicated all sequences clustered with subtype C. CONCLUSION This study indicates that HIV-1 subtype C still predominates and responsible for driving the epidemic in the Eastern Cape of South Africa with slow rise in the occurrence of transmitted drug resistance.
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Affiliation(s)
- Tennison Onoriode Digban
- Applied Environmental and Microbiology Research Group, University of Fort Hare, Private Mail Bag X1314, Alice 5700, Eastern Cape, South Africa.,Department of Microbiology and Biochemistry, University of Fort Hare, Private mail bag X1314, Alice 5700, Eastern Cape, South Africa
| | - Benson Chucks Iweriebor
- Applied Environmental and Microbiology Research Group, University of Fort Hare, Private Mail Bag X1314, Alice 5700, Eastern Cape, South Africa
| | - Larry Chikwelu Obi
- Department of Microbiology and Biochemistry, University of Fort Hare, Private mail bag X1314, Alice 5700, Eastern Cape, South Africa
| | - Uchechuwku Nwodo
- Applied Environmental and Microbiology Research Group, University of Fort Hare, Private Mail Bag X1314, Alice 5700, Eastern Cape, South Africa.,Department of Microbiology and Biochemistry, University of Fort Hare, Private mail bag X1314, Alice 5700, Eastern Cape, South Africa
| | - Anthony Ifeanyi Okoh
- Applied Environmental and Microbiology Research Group, University of Fort Hare, Private Mail Bag X1314, Alice 5700, Eastern Cape, South Africa.,Department of Microbiology and Biochemistry, University of Fort Hare, Private mail bag X1314, Alice 5700, Eastern Cape, South Africa
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2
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Hunt GM, Ledwaba J, Kalimashe M, Salimo A, Cibane S, Singh B, Puren A, Dean NE, Morris L, Jordan MR. Provincial and national prevalence estimates of transmitted HIV-1 drug resistance in South Africa measured using two WHO-recommended methods. Antivir Ther 2020; 24:203-210. [PMID: 30741163 DOI: 10.3851/imp3294] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND Sentinel surveillance of transmitted HIV drug resistance (TDR) among recently infected populations within a country was recommended by the World Health Organization from 2004 to 2015. METHODS Serum specimens collected as part of the 2010, 2011 and 2012 National Antenatal Sentinel HIV Prevalence Surveys were used to estimate provincial and national TDR prevalence in South Africa. RESULTS Moderate (5-15%) levels of transmitted non-nucleoside reverse transcriptase inhibitor (NNRTI) drug class resistance were detected in three of five provinces surveyed in 2010 and 2011 (Eastern Cape, Free State and KwaZulu-Natal). Inclusion of all nine of South Africa's provinces in the 2012 survey enabled calculation of a national TDR point prevalence estimate: TDR to the NNRTI drug class was 5.4% (95% CI 3.7, 7.8%), with K103N and V106M being the most frequently detected mutations. TDR estimates for the nucleoside reverse transcriptase inhibitor (NRTI) drug class were 1.1% (95% CI 0.5, 2.4%) and 0.6% (95% CI 0.1, 1.6%) for protease inhibitors (PI). CONCLUSIONS These data provide national TDR estimates for South Africa in 2012 and indicate that levels of TDR were low to moderate for the NNRTI drug class and low for NRTIs and PIs in the population surveyed.
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Affiliation(s)
- Gillian M Hunt
- Centre for HIV and STIs, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa.,Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Johanna Ledwaba
- Centre for HIV and STIs, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Monalisa Kalimashe
- Centre for HIV and STIs, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Anna Salimo
- Centre for HIV and STIs, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Siyabonga Cibane
- Centre for HIV and STIs, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Beverly Singh
- Centre for HIV and STIs, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Adrian Puren
- Centre for HIV and STIs, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Natalie Exner Dean
- Department of Biostatistics, College of Public Health & Health Professions, University of Florida, Gainesville, FL, USA
| | - Lynn Morris
- Centre for HIV and STIs, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa.,Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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3
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Hauser A, Kusejko K, Johnson LF, Wandeler G, Riou J, Goldstein F, Egger M, Kouyos RD. Bridging the gap between HIV epidemiology and antiretroviral resistance evolution: Modelling the spread of resistance in South Africa. PLoS Comput Biol 2019; 15:e1007083. [PMID: 31233494 PMCID: PMC6611642 DOI: 10.1371/journal.pcbi.1007083] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 07/05/2019] [Accepted: 05/06/2019] [Indexed: 11/19/2022] Open
Abstract
The scale-up of antiretroviral therapy (ART) in South Africa substantially reduced AIDS-related deaths and new HIV infections. However, its success is threatened by the emergence of resistance to non-nucleoside reverse-transcriptase inhibitors (NNRTI). The MARISA (Modelling Antiretroviral drug Resistance In South Africa) model presented here aims at investigating the time trends and factors driving NNRTI resistance in South Africa. MARISA is a compartmental model that includes the key aspects of the local HIV epidemic: continuum of care, disease progression, and gender. The dynamics of NNRTI resistance emergence and transmission are then added to this framework. Model parameters are informed using data from HIV cohorts participating in the International epidemiology Databases to Evaluate AIDS (IeDEA) and literature estimates, or fitted to UNAIDS estimates. Using this novel approach of triangulating clinical and resistance data from various sources, MARISA reproduces the time trends of HIV in South Africa in 2005–2016, with a decrease in new infections, undiagnosed individuals, and AIDS-related deaths. MARISA captures the dynamics of the spread of NNRTI resistance: high levels of acquired drug resistance (ADR, in 83% of first-line treatment failures in 2016), and increasing transmitted drug resistance (TDR, in 8.1% of ART initiators in 2016). Simulation of counter-factual scenarios reflecting alternative public health policies shows that increasing treatment coverage would have resulted in fewer new infections and deaths, at the cost of higher TDR (11.6% in 2016 for doubling the treatment rate). Conversely, improving switching to second-line treatment would have led to lower TDR (6.5% in 2016 for doubling the switching rate) and fewer new infections and deaths. Implementing drug resistance testing would have had little impact. The rapid ART scale-up and inadequate switching to second-line treatment were the key drivers of the spread of NNRTI resistance in South Africa. However, even though some interventions could have substantially reduced the level of NNRTI resistance, no policy including NNRTI-based first line regimens could have prevented this spread. Thus, by combining epidemiological data on HIV in South Africa with biological data on resistance evolution, our modelling approach identified key factors driving NNRTI resistance, highlighting the need of alternative first-line regimens. Resistance to non-nucleoside reverse transcriptase inhibitors (NNRTI) threatens the long-term success of antiretroviral therapy (ART) roll-out in South Africa. We developed a compartmental model integrating the local HIV epidemiology with biological mechanisms of drug resistance. A first dimension of the model accounts for the continuum of care: infection, diagnosis, first-line treatment with suppression or failure, and second-line treatment. Other dimensions include: disease progression (CD4 counts), gender, and acquisition and transmission of NNRTI resistance. Whenever possible, we informed the parameters using the data available from local cohorts. Other parameters were informed using literature or UNAIDS estimates. The model captured the rise of NNRTI resistance during the period. We assessed the impact of counter-factual scenarios reflecting alternative countrywide policies during the period 2005 to 2016, considering either increasing ART coverage, improving management of treatment failure, broadening ART eligibility, or implementing drug resistance testing before ART initiation. We identified key drivers of the NNRTI resistance epidemic: large-scale ART roll-out and insufficient monitoring of first-line treatment failure. The model also suggested that no policy including NNRTI-based first line regimens could have prevented the spread of NNRTI resistance.
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Affiliation(s)
- Anthony Hauser
- Institute of Social and Preventive Medicine, University of Bern, Switzerland
| | - Katharina Kusejko
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Leigh F. Johnson
- Centre for Infectious Disease Epidemiology and Research, University of Cape Town, South Africa
| | - Gilles Wandeler
- Institute of Social and Preventive Medicine, University of Bern, Switzerland
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Julien Riou
- Institute of Social and Preventive Medicine, University of Bern, Switzerland
| | - Fardo Goldstein
- Institute of Social and Preventive Medicine, University of Bern, Switzerland
| | - Matthias Egger
- Institute of Social and Preventive Medicine, University of Bern, Switzerland
- Centre for Infectious Disease Epidemiology and Research, University of Cape Town, South Africa
| | - Roger D. Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
- * E-mail:
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4
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Wallis CL, Godfrey C, Fitzgibbon JE, Mellors JW. Key Factors Influencing the Emergence of Human Immunodeficiency Virus Drug Resistance in Low- and Middle-Income Countries. J Infect Dis 2017; 216:S851-S856. [PMID: 29207000 PMCID: PMC5853971 DOI: 10.1093/infdis/jix409] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The emergence and spread of human immunodeficiency virus (HIV) drug resistance from antiretroviral roll-out programs remain a threat to long-term control of the HIV-AIDS epidemic in low- and middle-income countries (LMICs). The patterns of drug resistance and factors driving emergence of resistance are complex and multifactorial. The key drivers of drug resistance in LMICs are reviewed here, and recommendations are made to limit their influence on antiretroviral therapy efficacy.
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Affiliation(s)
- Carole L Wallis
- Bio Analytical Research Corporation-South Africa and Lancet Laboratories, Johannesburg, South Africa
| | - Catherine Godfrey
- HIV Research Branch, Therapeutics Research Program, Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health
| | - Joseph E Fitzgibbon
- Drug Development and Clinical Sciences Branch, Therapeutics Research Program, Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health
| | - John W Mellors
- HIV Research Branch, Therapeutics Research Program, Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pennsylvania
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5
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Etta EM, Mavhandu L, Manhaeve C, McGonigle K, Jackson P, Rekosh D, Hammarskjold ML, Bessong PO, Tebit DM. High level of HIV-1 drug resistance mutations in patients with unsuppressed viral loads in rural northern South Africa. AIDS Res Ther 2017; 14:36. [PMID: 28750647 PMCID: PMC5531022 DOI: 10.1186/s12981-017-0161-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 07/19/2017] [Indexed: 02/07/2023] Open
Abstract
Background Combination antiretroviral therapy (cART) has significantly reduced HIV morbidity and mortality in both developed and developing countries. However, the sustainability of cART may be compromised by the emergence of viral drug resistance mutations (DRM) and the cellular persistence of proviruses carrying these DRM. This is potentially a more serious problem in resource limited settings. Methods DRM were evaluated in individuals with unsuppressed viral loads after first or multiple lines of cART at two sites in rural Limpopo, South Africa. Seventy-two patients with viral loads of >1000 copies/ml were recruited between March 2014 and December 2015. Complete protease (PR) and partial Reverse Transcriptase (RT) sequences were amplified from both plasma RNA and paired proviral DNA from 35 of these subjects. Amplicons were directly sequenced to determine subtype and DRM using the Stanford HIV Drug Resistance Interpretation algorithm. Results Among the 72 samples, 69 could be PCR amplified from RNA and 35 from both RNA and DNA. Sixty-five (94.2%) viruses were subtype C, while one was subtype B (1.4%), one recombinant K/C, one recombinant C/B and one unclassified. Fifty-eight (84%) sequences carried at least one DRM, while 11 (15.9%) displayed no DRM. DRM prevalence according to drug class was: NRTI 60.8% NNRTI 65.2%, and PI 5.8%. The most common DRMs were; M184V (51.7%), K103N (50%), V106M (20.6%), D67N (13.3%), K65R (12%). The frequency of the DRM tracked well with the frequency of use of medications to which the mutations were predicted to confer resistance. Interestingly, a significant number of subjects showed predicted resistance to the newer NNRTIs, etravirine (33%) and rilpivirine (42%), both of which are not yet available in this setting. The proportion of DRM in RNA and DNA were mostly similar with the exception of the thymidine analogue mutations (TAMs) D67N, K70R, K219QE; and K103N which were slightly more prevalent in DNA than RNA. Subjects who had received cART for at least 5 years were more likely to harbour >2 DRM (p < 0.05) compared to those treated for a shorter period. DRM were more prevalent in this rural setting compared to a neighbouring urban setting. Conclusion We found a very high prevalence of NRTI and NNRTI DRM in patients from rural Limpopo settings with different durations of treatment. The prevalence was significantly higher than those reported in urban settings in South Africa. The dominance of NNRTI based mutations late in treatment supports the use of PI based regimens for second line treatment in this setting. The slight dominance of TAMs in DNA from infected PBMCs compared to plasma virus requires further studies that should include cART subjects with suppressed virus. Such studies will improve our understanding of the pattern of drug resistance and dynamics of viral persistence in these rural settings.
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6
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HIV Drug Resistance Mutations in Non-B Subtypes After Prolonged Virological Failure on NNRTI-Based First-Line Regimens in Sub-Saharan Africa. J Acquir Immune Defic Syndr 2017; 75:e45-e54. [PMID: 28129253 PMCID: PMC5427983 DOI: 10.1097/qai.0000000000001285] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
OBJECTIVE To determine drug resistance mutation (DRM) patterns in a large cohort of patients failing nonnucleoside reverse transcriptase inhibitor (NNRTI)-based first-line antiretroviral therapy regimens in programs without routine viral load (VL) monitoring and to examine intersubtype differences in DRMs. DESIGN Sequences from 787 adults/adolescents who failed an NNRTI-based first-line regimen in 13 clinics in Uganda, Kenya, Zimbabwe, and Malawi were analyzed. Multivariable logistic regression was used to determine the association between specific DRMs and Stanford intermediate-/high-level resistance and factors including REGA subtype, first-line antiretroviral therapy drugs, CD4, and VL at failure. RESULTS The median first-line treatment duration was 4 years (interquartile range 30-43 months); 42% of participants had VL ≥100,000 copies/mL and 63% participants had CD4 <100 cells/mm. Viral subtype distribution was A1 (40%; Uganda and Kenya), C (31%; Zimbabwe and Malawi), and D (25%; Uganda and Kenya), and recombinant/unclassified (5%). In general, DRMs were more common in subtype-C than in subtype-A and/or subtype-D (nucleoside reverse transcriptase inhibitor mutations K65R and Q151M; NNRTI mutations E138A, V106M, Y181C, K101E, and H221Y). The presence of tenofovir resistance was similar between subtypes [P (adjusted) = 0.32], but resistance to zidovudine, abacavir, etravirine, or rilpivirine was more common in subtype-C than in subtype-D/subtype-A [P (adjusted) < 0.02]. CONCLUSIONS Non-B subtypes differ in DRMs at first-line failure, which impacts on residual nucleoside reverse transcriptase inhibitor and NNRTI susceptibility. In particular, higher rates of etravirine and rilpivirine resistance in subtype-C may limit their potential utility in salvage regimens.
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7
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Rapid Detection of Common HIV-1 Drug Resistance Mutations by Use of High-Resolution Melting Analysis and Unlabeled Probes. J Clin Microbiol 2016; 55:122-133. [PMID: 27795333 DOI: 10.1128/jcm.01291-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 10/05/2016] [Indexed: 01/08/2023] Open
Abstract
HIV rapidly accumulates resistance mutations following exposure to subtherapeutic concentrations of antiretroviral drugs that reduces treatment efficacy. High-resolution melting analysis (HRMA) has been used to successfully identify single nucleotide polymorphisms (SNPs) and to genotype viral and bacterial species. Here, we tested the ability of HRMA incorporating short unlabeled probes to accurately assign drug susceptibilities at the 103, 181, and 184 codons of the HIV-1 reverse transcriptase gene. The analytical sensitivities of the HRMA assays were 5% of mixed species for K103N and Y181C and 20% for M184V. When applied to 153 HIV-1 patient specimens previously genotyped by Sanger population sequencing, HRMA correctly assigned drug sensitivity or resistance profiles to 80% of the samples at codon 103 (K103K/N) (Cohen's kappa coefficient [κ] > 0.6; P < 0.05), 90% at 181 (Y181Y/C) (κ > 0.74, P < 0.05), and 80% at 184 (M184M/V) (κ > 0.62; P < 0.05). The frequency of incorrect genotypes was very low (≤1 to 2%) for each assay, which in most cases was due to the higher sensitivity of the HRMA assay. Specimens for which drug resistance profiles could not be assigned (9 to 20%) often had polymorphisms in probe binding regions. Thus, HRMA is a rapid, inexpensive, and sensitive method for the determination of drug sensitivities caused by major HIV-1 drug resistance mutations and, after further development to minimize the melting effects of nontargeted polymorphisms, may be suitable for surveillance purposes.
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8
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Steegen K, Carmona S, Bronze M, Papathanasopoulos MA, van Zyl G, Goedhals D, MacLeod W, Sanne I, Stevens WS. Moderate Levels of Pre-Treatment HIV-1 Antiretroviral Drug Resistance Detected in the First South African National Survey. PLoS One 2016; 11:e0166305. [PMID: 27907009 PMCID: PMC5132262 DOI: 10.1371/journal.pone.0166305] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 10/26/2016] [Indexed: 11/29/2022] Open
Abstract
Background In order to assess the level of transmitted and/or pre-treatment antiretroviral drug resistance to HIV-1, the World Health Organization (WHO) recommends that regular surveys are conducted. This study’s objective was to assess the frequency of HIV-1 antiretroviral drug resistance in patients initiating antiretroviral treatment (ART) in the public sector throughout South Africa. Methods A prospective cross-sectional survey was conducted using probability proportional to size sampling. This method ensured that samples from each province were proportionally collected, based on the number of patients receiving ART in each region. Samples were collected between March 2013 and October 2014. Pol sequences were obtained using RT-PCR and Sanger sequencing and submitted to the Stanford Calibrated Population Resistance tool v6.0. Results A total of 277 sequences were available for analysis. Most participants were female (58.8%) and the median age was 34 years (IQR: 29–42). The median baseline CD4-count was 149 cells/mm3 (IQR: 62–249) and, based on self-reporting, participants had been diagnosed as HIV-positive approximately 44 days prior to sample collection (IQR: 23–179). Subtyping revealed that 98.2% were infected with HIV-1 subtype C. Overall, 25 out of 277 patients presented with ≥1 surveillance drug resistance mutation (SDRM, 9.0%, 95% CI: 6.1–13.0%). Non-nucleoside reverse transcriptase inhibitor (NNRTI) mutations were the most numerous mutations detected (n = 23). Only two patients presented with a protease inhibitor (PI) mutation. In four patients ≥4 SDRMs were detected, which might indicate that these patients were not truly ART-naïve or were infected with a multi-resistant virus. Conclusions These results show that the level of antiretroviral drug resistance in ART-naïve South Africans has reached moderate levels, as per the WHO classification. Therefore, regular surveys of pre-treatment drug resistance levels in all regions of South Africa is highly recommended to monitor the changing levels of pre-treatment antiretroviral drug resistance.
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Affiliation(s)
- Kim Steegen
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
- * E-mail:
| | - Sergio Carmona
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
- National Health Laboratory Services, Johannesburg, South Africa
| | - Michelle Bronze
- National Health Laboratory Services, Johannesburg, South Africa
| | - Maria A. Papathanasopoulos
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - Gert van Zyl
- National Health Laboratory Services, Johannesburg, South Africa
- Division of Medical Virology, Stellenbosch University, Stellenbosch, South Africa
| | - Dominique Goedhals
- National Health Laboratory Services, Johannesburg, South Africa
- Department of Medical Microbiology and Virology, University of the Free State, Bloemfontein, South Africa
| | - William MacLeod
- Center for Global Health and Development, Boston University School of Public Health, Boston, Massachusetts, United States of America
- Health Economics and Epidemiology Research Office, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ian Sanne
- Right to Care, Johannesburg, South Africa
| | - Wendy S. Stevens
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
- National Health Laboratory Services, Johannesburg, South Africa
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Steegen K, Bronze M, Papathanasopoulos MA, van Zyl G, Goedhals D, Variava E, MacLeod W, Sanne I, Stevens WS, Carmona S. HIV-1 antiretroviral drug resistance patterns in patients failing NNRTI-based treatment: results from a national survey in South Africa. J Antimicrob Chemother 2016; 72:210-219. [PMID: 27659733 DOI: 10.1093/jac/dkw358] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/29/2016] [Accepted: 07/31/2016] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Routine HIV-1 antiretroviral drug resistance testing for patients failing NNRTI-based regimens is not recommended in resource-limited settings. Therefore, surveys are required to monitor resistance profiles in patients failing ART. METHODS A cross-sectional survey was conducted amongst patients failing NNRTI-based regimens in the public sector throughout South Africa. Virological failure was defined as two consecutive HIV-1 viral load results >1000 RNA copies/mL. Pol sequences were obtained using RT-PCR and Sanger sequencing and submitted to Stanford HIVdb v7.0.1. RESULTS A total of 788 sequences were available for analysis. Most patients failed a tenofovir-based NRTI backbone (74.4%) in combination with efavirenz (82.1%) after median treatment duration of 36 months. K103N (48.9%) and V106M (34.9%) were the most common NNRTI mutations. Only one-third of patients retained full susceptibility to second-generation NNRTIs such as etravirine (36.5%) and rilpivirine (27.3%). After M184V/I (82.7%), K65R was the most common NRTI mutation (45.8%). The prevalence of K65R increased to 57.5% in patients failing a tenofovir regimen without prior stavudine exposure. Cross-resistance to NRTIs was often observed, but did not seem to affect the predicted activity of zidovudine as 82.9% of patients remained fully susceptible to this drug. CONCLUSIONS The introduction of tenofovir-based first-line regimens has dramatically increased the prevalence of K65R mutations in the HIV-1-infected South African population. However, most patients failing tenofovir-based regimens remained fully susceptible to zidovudine. Based on these data, there is currently no need to change either the recommended first- or second-line ART regimens in South Africa.
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Affiliation(s)
- K Steegen
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - M Bronze
- National Health Laboratory Service, Johannesburg, South Africa
| | - M A Papathanasopoulos
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - G van Zyl
- National Health Laboratory Service, Johannesburg, South Africa.,Division of Medical Virology, Stellenbosch University, Stellenbosch, South Africa
| | - D Goedhals
- National Health Laboratory Service, Johannesburg, South Africa.,Department of Medical Microbiology and Virology, University of the Free State, Bloemfontein, South Africa
| | - E Variava
- Department of Internal Medicine, Klerksdorp Tshepong Hospital Complex, Klerksdorp, South Africa.,Department of Internal Medicine, University of the Witwatersrand, Johannesburg, South Africa.,Perinatal HIV Research Unit, Johannesburg, South Africa
| | - W MacLeod
- Center for Global Health and Development, Boston University School of Public Health, Boston, MA, USA.,Health Economics and Epidemiology Research Office, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - I Sanne
- Right to Care, Johannesburg, South Africa
| | - W S Stevens
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa.,National Health Laboratory Service, Johannesburg, South Africa
| | - S Carmona
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa.,National Health Laboratory Service, Johannesburg, South Africa
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Lam EP, Moore CL, Gotuzzo E, Nwizu C, Kamarulzaman A, Chetchotisakd P, van Wyk J, Teppler H, Kumarasamy N, Molina JM, Emery S, Cooper DA, Boyd MA. Antiretroviral Resistance After First-Line Antiretroviral Therapy Failure in Diverse HIV-1 Subtypes in the SECOND-LINE Study. AIDS Res Hum Retroviruses 2016; 32:841-50. [PMID: 27346600 DOI: 10.1089/aid.2015.0331] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We investigate mutations and correlates according to HIV-1 subtype after virological failure (VF) of standard first-line antiretroviral therapy (ART) (non-nucleoside/nucleotide reverse transcriptase inhibitor [NNRTI] +2 nucleoside/nucleotide reverse transcriptase inhibitor [N(t)RTI]). SECOND-LINE study participants were assessed at baseline for HIV-1 subtype, demographics, HIV-1 history, ART exposure, viral load (VL), CD4(+) count, and genotypic ART resistance. We used backward stepwise multivariate regression (MVR) to assess associations between baseline variables and presence of ≥3 N(t)RTI mutations, ≥1 NNRTI mutation, ≥3 thymidine analog-N(t)RTI [ta-N(t)RTI] mutations (TAMs), the K65/K70 mutation, and predicted etravirine (ETV)/rilpivirine (RPV) activity. The inclusion p-value for MVR was p < .2. The exclusion p-value from stepwise elimination was p > .05. Of 541 participants, 491 (91%) had successfully characterized baseline viral isolates. Subtype distribution: B (n = 123, 25%), C (n = 202, 41%), CRF01_AE (n = 109, 22%), G (n = 25, 5%), and CRF02_AG (n = 27, 5%). Baseline CD4(+) 200-394 cells/mm(3) were associated with <3 N(t)RTI mutations (OR = 0.47; 95% CI 0.29-0.77; p = .003), absence of the K65/K70 mutation (OR = 0.43; 95% CI 0.26-0.73; p = .002), and higher ETV sensitivity (OR = 0.52; 95% CI 0.35-0.78; p = .002). Recent tenofovir (TDF) use was associated with K65/K70 mutations (OR = 8.91; 95% CI 5.00-15.85; p < .001). Subtype CRF01_AE was associated with ≥3 N(t)RTI mutations (OR = 2.34; 95% CI 1.31-4.17; p = .004) and higher RPV resistance (OR = 2.13; 95% CI 1.30-3.49; p = .003), and subtype C was associated with <3 TAMs (OR = 0.45; 95% CI 0.21-0.99; p = .015). Subtypes CRF01_AE (OR = 2.46; 95% CI 1.26-4.78; p = .008) and G (OR = 4.77; 95% CI 1.44-15.76; p = .01) were associated with K65/K70 mutations. Higher VL at confirmed first-line VF was associated with ≥3 N(t)RTI mutations (OR = 1.39; 95% CI 1.07-1.78; p = .013) and ≥3 TAMs (OR = 1.62; 95% CI 1.15-2.29; p = .006). The associations of first-line resistance mutations across the HIV-1 subtypes in this study are consistent with knowledge derived from subtype B, with some exceptions. Patterns of resistance after failure of a first-line ta-N(t)RTI regimen support using TDF in N(t)RTI-containing second-line regimens, or using N(t)RTI-sparing regimens.
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Affiliation(s)
- Edward P. Lam
- The Kirby Institute UNSW Australia, Sydney, Australia
| | | | - Eduardo Gotuzzo
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano, Heredia, Lima, Peru
| | - Chidi Nwizu
- Center for Clinical Care and Clinical Research in Nigeria, Abuja, Nigeria
| | - Adeeba Kamarulzaman
- Clinical Investigations Centre, University of Malaya, Kuala Lumpur, Malaysia
| | | | | | | | | | - Jean-Michel Molina
- Department of Clinical Infectious Diseases, Hôpital Saint-Louis, Paris, France
| | - Sean Emery
- The Kirby Institute UNSW Australia, Sydney, Australia
| | | | - Mark A. Boyd
- The Kirby Institute UNSW Australia, Sydney, Australia
- University of Adelaide, Lyell McEwin Hospital, Adelaide, South Australia, Australia
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11
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Rossouw TM, Nieuwoudt M, Manasa J, Malherbe G, Lessells RJ, Pillay S, Danaviah S, Mahasha P, van Dyk G, de Oliveira T. HIV drug resistance levels in adults failing first-line antiretroviral therapy in an urban and a rural setting in South Africa. HIV Med 2016; 18:104-114. [PMID: 27353262 DOI: 10.1111/hiv.12400] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2016] [Indexed: 11/28/2022]
Abstract
OBJECTIVES Urban and rural HIV treatment programmes face different challenges in the long-term management of patients. There are few studies comparing drug resistance profiles in patients accessing treatment through these programmes. The aim of this study was to perform such a comparison. METHODS HIV drug resistance data and associated treatment and monitoring information for adult patients failing first-line therapy in an urban and a rural programme were collected. Data were curated and managed in SATuRN RegaDB before statistical analysis using Microsoft Excel 2013 and stata Ver14, in which clinical parameters, resistance profiles and predicted treatment responses were compared. RESULTS Data for 595 patients were analysed: 492 patients from a rural setting and 103 patients from an urban setting. The urban group had lower CD4 counts at treatment initiation than the rural group (98 vs. 126 cells/μL, respectively; P = 0.05), had more viral load measurements performed per year (median 3 vs. 1.4, respectively; P < 0.01) and were more likely to have no drug resistance mutations detected (35.9% vs. 11.2%, respectively; P < 0.01). Patients in the rural group were more likely to have been on first-line treatment for a longer period, to have failed for longer, and to have thymidine analogue mutations. Notwithstanding these differences, the two groups had comparable predicted responses to the standard second-line regimen, based on the genotypic susceptibility score. Mutations accumulated in a sigmoidal fashion over failure duration. CONCLUSIONS The frequency and patterns of drug resistance, as well the intensity of virological monitoring, in adults with first-line therapy failure differed between the urban and rural sites. Despite these differences, based on the genotypic susceptibility scores, the majority of patients across the two sites would be expected to respond well to the standard second-line regimen.
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Affiliation(s)
- T M Rossouw
- Department of Immunology, Institute for Cellular and Molecular Medicine, University of Pretoria, Pretoria, South Africa
| | - M Nieuwoudt
- South African Department of Science and Technology/National Research Foundation Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | - J Manasa
- Department of Infectious Diseases, Stanford University, Stanford, CA, USA.,Africa Centre Population Health, University of KwaZulu-Natal, South Africa
| | - G Malherbe
- Department of Immunology, Institute for Cellular and Molecular Medicine, University of Pretoria, Pretoria, South Africa
| | - R J Lessells
- Africa Centre Population Health, University of KwaZulu-Natal, South Africa.,Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK
| | - S Pillay
- Africa Centre Population Health, University of KwaZulu-Natal, South Africa
| | - S Danaviah
- Africa Centre Population Health, University of KwaZulu-Natal, South Africa
| | - P Mahasha
- Department of Immunology, Institute for Cellular and Molecular Medicine, University of Pretoria, Pretoria, South Africa
| | - G van Dyk
- Department of Immunology, Institute for Cellular and Molecular Medicine, University of Pretoria, Pretoria, South Africa
| | - T de Oliveira
- Africa Centre Population Health, University of KwaZulu-Natal, South Africa.,Research Department of Infection, University College London, London, UK.,School of Laboratory Medicine and Medical Sciences, Nelson R. Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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12
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Hoffmann CJ, Cohn S, Mashabela F, Hoffmann JD, McIlleron H, Denti P, Haas D, Dooley KE, Martinson NA, Chaisson RE. Treatment Failure, Drug Resistance, and CD4 T-Cell Count Decline Among Postpartum Women on Antiretroviral Therapy in South Africa. J Acquir Immune Defic Syndr 2016; 71:31-7. [PMID: 26334739 PMCID: PMC4713347 DOI: 10.1097/qai.0000000000000811] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND We assessed HIV RNA suppression, resistance, and CD4 T-cell count 12 months postpartum among pregnant women retained in care in an observational cohort study. METHODS We prospectively followed two groups of HIV-infected pregnant women--with or without tuberculosis--recruited from prenatal clinics in South Africa. Women who received antiretroviral therapy during pregnancy and reported being on therapy 12 months postpartum were included. Serum samples from women with HIV viremia 12 months postpartum were tested for drug resistance. RESULTS Of 103 women in the study, median age and CD4 T-cell count at enrollment were 29 years [interquartile range (IQR): 26-32] and 317 cells per cubic millimeter (IQR: 218-385), respectively; 43 (42%) had tuberculosis at baseline. During pregnancy, 87% of the women achieved an HIV RNA <400 copies per milliliter compared with 71% at 12 months postpartum (P < 0.001). Factors independently associated with an HIV RNA <400 copies per milliliter at 12 months were age ≥ 30 years, detectable plasma efavirenz concentration, and HIV RNA <400 copies per milliliter while pregnant; there was a trend toward both a detectable viral load and peripartum depression. HIV drug resistance results were available from 25 women, and 12 (48%) had major drug resistance mutations. CD4 T-cell count declined a median of 13 cells per cubic millimeter (IQR: -66 to 140) from delivery to 12 months in women with viremia at 12 months. CONCLUSIONS Success with maintaining virologic control declined postpartum among HIV-infected women who remained in care and on antiretroviral therapy, and CD4 T-cell count decline and drug resistance were common.
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Affiliation(s)
| | - Silvia Cohn
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fildah Mashabela
- Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Soweto, South Africa
| | | | - Helen McIlleron
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Paolo Denti
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - David Haas
- Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Kelly E Dooley
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Neil A Martinson
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Soweto, South Africa
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13
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Witten JA, Thomas KGF, Westgarth-Taylor J, Joska JA. Executive Dyscontrol of Learning and Memory: Findings from a Clade C HIV-positive South African Sample. Clin Neuropsychol 2015; 29:956-84. [PMID: 26552492 DOI: 10.1080/13854046.2015.1108455] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
OBJECTIVE Although pre-clinical work suggests there might be differences in neurovirulence across HIV-1 clades, few studies investigate neuropsychological deficits in the globally predominant clade C infection. The purpose of this study was to investigate verbal learning and memory performance in HIV-positive individuals in Cape Town, South Africa, where clade C is the most prevalent subtype of the virus. METHOD Using a case-control design, we recruited 53 isiXhosa-speaking, cART-naïve HIV-positive adults and 53 demographically matched HIV-negative controls. Participants were administered a comprehensive neuropsychological test battery. The test of interest was the Hopkins Verbal Learning Test-Revised (HVLT-R); previous studies have used that instrument to identify executive dyscontrol of verbal learning and memory processes in clade B HIV-positive participants. RESULTS HIV-positive participants showed only partial impairment on the HVLT-R's learning/memory components (e.g., they recalled significantly fewer words across learning trials, but displayed relatively intact performance on delayed recall trials). They also displayed little executive dyscontrol over encoding and retrieval processes (e.g., there were no significant between-group differences on measures of semantic or serial clustering). CONCLUSIONS Post-cART era studies suggest that verbal learning and memory performance is impaired in clade B samples, at least partially due to executive dyscontrol over encoding and retrieval processes. We found few such impairments in the current clade C sample. These preliminary findings suggest different CNS vulnerability across clades that would have implications for delineating clade-specific neuropathological and neurocognitive clinical features.
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Affiliation(s)
- Jade A Witten
- a ACSENT Laboratory, Department of Psychology , University of Cape Town , Cape Town , South Africa
| | - Kevin G F Thomas
- a ACSENT Laboratory, Department of Psychology , University of Cape Town , Cape Town , South Africa
| | | | - John A Joska
- b Department of Psychiatry and Mental Health , University of Cape Town , Cape Town , South Africa
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14
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Bila DCA, Boullosa LT, Vubil AS, Mabunda NJ, Abreu CM, Ismael N, Jani IV, Tanuri A. Trends in Prevalence of HIV-1 Drug Resistance in a Public Clinic in Maputo, Mozambique. PLoS One 2015; 10:e0130580. [PMID: 26151752 PMCID: PMC4494809 DOI: 10.1371/journal.pone.0130580] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 05/22/2015] [Indexed: 11/30/2022] Open
Abstract
Background An observational study was conducted in Maputo, Mozambique, to investigate trends in prevalence of HIV drug resistance (HIVDR) in antiretroviral (ART) naïve subjects initiating highly active antiretroviral treatment (HAART). Methodology/Principal Findings To evaluate the pattern of drug resistance mutations (DRMs) found in adults on ART failing first-line HAART [patients with detectable viral load (VL)]. Untreated subjects [Group 1 (G1; n=99)] and 274 treated subjects with variable length of exposure to ARV´s [6–12 months, Group 2 (G2;n=93); 12-24 months, Group 3 (G3;n=81); >24 months (G4;n=100)] were enrolled. Virological and immunological failure (VF and IF) were measured based on viral load (VL) and T lymphocyte CD4+ cells (TCD4+) count and genotypic resistance was also performed. Major subtype found was C (untreated: n=66, 97,06%; treated: n=36, 91.7%). Maximum virological suppression was observed in G3, and significant differences intragroup were observed between VF and IF in G4 (p=0.022). Intergroup differences were observed between G3 and G4 for VF (p=0.023) and IF between G2 and G4 (p=0.0018). Viral suppression (<50 copies/ml) ranged from 84.9% to 90.1%, and concordant VL and DRM ranged from 25% to 57%. WHO cut-off for determining VF as given by 2010 guidelines (>5000 copies/ml) identified 50% of subjects carrying DRM compared to 100% when lower VL cut-off was used (<50 copies/ml). Length of exposure to ARVs was directly proportional to the complexity of DRM patterns. In Mozambique, VL suppression was achieved in 76% of individuals after 24 months on HAART. This is in agreement with WHO target for HIVDR prevention target (70%). Conclusions We demonstrated that the best way to determine therapeutic failure is VL compared to CD4 counts. The rationalized use of VL testing is needed to ensure timely detection of treatment failures preventing the occurrence of TDR and new infections.
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Affiliation(s)
- Dulce Celina Adolfo Bila
- National Institute of Health of Mozambique, Maputo, Mozambique
- Department of Genetic, Molecular Virology Laboratory, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Department of Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lídia Teodoro Boullosa
- Department of Genetic, Molecular Virology Laboratory, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Celina Monteiro Abreu
- Department of Genetic, Molecular Virology Laboratory, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Nalia Ismael
- National Institute of Health of Mozambique, Maputo, Mozambique
| | | | - Amilcar Tanuri
- Department of Genetic, Molecular Virology Laboratory, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- * E-mail:
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15
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Orrell C, Kaplan R. Limited use for dual treatment with boosted protease inhibitors plus lamivudine in first-line antiretroviral therapy. THE LANCET. INFECTIOUS DISEASES 2015; 15:748-9. [PMID: 26062879 DOI: 10.1016/s1473-3099(15)00098-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 04/14/2015] [Indexed: 10/23/2022]
Affiliation(s)
- Catherine Orrell
- Desmond Tutu HIV Foundation, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa.
| | - Richard Kaplan
- Desmond Tutu HIV Foundation, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
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16
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Cardoso SW, Luz PM, Velasque L, Torres TS, Tavares IC, Ribeiro SR, Moreira RI, Veloso VG, Moore RD, Grinsztejn B. Outcomes of second-line combination antiretroviral therapy for HIV-infected patients: a cohort study from Rio de Janeiro, Brazil. BMC Infect Dis 2014; 14:699. [PMID: 25523385 PMCID: PMC4297410 DOI: 10.1186/s12879-014-0699-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 12/11/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND World-wide, the notable expansion of HIV/AIDS treatment programs in resource-limited settings has lead to an increasing number of patients in need of second-line cART. To adequately address and prepare for this scenario, critical assessments of the outcomes of second-line cART are particularly relevant in settings where monitoring strategies may be inadequate. We evaluated virologic outcomes of second-line combination antiretroviral therapy (cART) among HIV-infected individuals from Brazil. METHODS This study was conducted at the Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, at Rio de Janeiro, Brazio. For this study we included all patients who started first-line and second-line cART between 2000 and 2013. Second-line cART required a switch in the anchor drug of first-line cART. We evaluated time from second-line start to virologic failure and factors associated with increased risk of failure using multivariable Cox proportional hazards regression models. RESULTS Among the 1,311 patients who started first-line cART a total of 386 patients (29.5%) initiated second-line cART, out of which 35.0% and 60.6% switched from their first-line to their second-line cART when their HIV RNA was undetectable and after documented virologic failure, respectively. At second line cART initiation, median age was 38 years [interquartile range (IQR): 31-45years]. Median CD4 count was significantly different for patients starting second-line cART undetectable [412 cells/mm3 (IQR: 240-617)] compared to those starting second-line cART after documented virologic failure [230 cells/mm3 (IQR: 118-322.5)] (p < 0.01). Median time from second-line cART initiation to failure was also significantly different for patients starting second-line cART undetectable compared to those who with documented virologic failure (log-rank test p < 0.01). Multivariable Cox models showed that younger age, lower education, and HIV RNA level were independently associated with an increased hazard of second-line failure among those with documented virologic failure at start of second-line cART. CONCLUSIONS We have shown that in a middle-income country with universal access to cART, having a detectable HIV RNA at the start of second-line cART as well as younger age and lower education negatively impact second-line outcomes. Our findings could guide HIV treatment efforts as to which strategies would help maximize the durability of these regimens.
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17
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Impact of drug resistance-associated amino acid changes in HIV-1 subtype C on susceptibility to newer nonnucleoside reverse transcriptase inhibitors. Antimicrob Agents Chemother 2014; 59:960-71. [PMID: 25421485 DOI: 10.1128/aac.04215-14] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The objective of this study was to assess the phenotypic susceptibility of HIV-1 subtype C isolates, with nonnucleoside reverse transcriptase inhibitor (NNRTI) resistance-associated amino acid changes, to newer NNRTIs. A panel of 52 site-directed mutants and 38 clinically derived HIV-1 subtype C clones was created, and the isolates were assessed for phenotypic susceptibility to etravirine (ETR), rilpivirine (RPV), efavirenz (EFV), and nevirapine (NVP) in an in vitro single-cycle phenotypic assay. The amino acid substitutions E138Q/R, Y181I/V, and M230L conferred high-level resistance to ETR, while K101P and Y181I/V conferred high-level resistance to RPV. Y181C, a major NNRTI resistance-associated amino acid substitution, caused decreased susceptibility to ETR and, to a lesser extent, RPV when combined with other mutations. These included N348I and T369I, amino acid changes in the connection domain that are not generally assessed during resistance testing. However, the prevalence of these genotypes among subtype C sequences was, in most cases, <1%. The more common EFV/NVP resistance-associated substitutions, such as K103N, V106M, and G190A, had no major impact on ETR or RPV susceptibility. The low-level resistance to RPV and ETR conferred by E138K was not significantly enhanced in the presence of M184V/I, unlike for EFV and NVP. Among patient samples, 97% were resistant to EFV and/or NVP, while only 24% and 16% were resistant to ETR and RPV, respectively. Overall, only a few, relatively rare NNRTI resistance-associated amino acid substitutions caused resistance to ETR and/or RPV in an HIV-1 subtype C background, suggesting that these newer NNRTIs would be effective in NVP/EFV-experienced HIV-1 subtype C-infected patients.
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18
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Singh K, Flores JA, Kirby KA, Neogi U, Sonnerborg A, Hachiya A, Das K, Arnold E, McArthur C, Parniak M, Sarafianos SG. Drug resistance in non-B subtype HIV-1: impact of HIV-1 reverse transcriptase inhibitors. Viruses 2014; 6:3535-62. [PMID: 25254383 PMCID: PMC4189038 DOI: 10.3390/v6093535] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 09/09/2014] [Accepted: 09/09/2014] [Indexed: 01/20/2023] Open
Abstract
Human immunodeficiency virus (HIV) causes approximately 2.5 million new infections every year, and nearly 1.6 million patients succumb to HIV each year. Several factors, including cross-species transmission and error-prone replication have resulted in extraordinary genetic diversity of HIV groups. One of these groups, known as group M (main) contains nine subtypes (A-D, F-H and J-K) and causes ~95% of all HIV infections. Most reported data on susceptibility and resistance to anti-HIV therapies are from subtype B HIV infections, which are prevalent in developed countries but account for only ~12% of all global HIV infections, whereas non-B subtype HIV infections that account for ~88% of all HIV infections are prevalent primarily in low and middle-income countries. Although the treatments for subtype B infections are generally effective against non-B subtype infections, there are differences in response to therapies. Here, we review how polymorphisms, transmission efficiency of drug-resistant strains, and differences in genetic barrier for drug resistance can differentially alter the response to reverse transcriptase-targeting therapies in various subtypes.
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Affiliation(s)
- Kamalendra Singh
- Christopher Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
| | - Jacqueline A Flores
- Christopher Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
| | - Karen A Kirby
- Christopher Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm 141 86, Sweden.
| | - Anders Sonnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm 141 86, Sweden.
| | - Atsuko Hachiya
- Clinical Research Center, Department of Infectious Diseases and Immunology, National Hospital Organization, Nagoya Medical Center, Nagoya 460-0001, Japan.
| | - Kalyan Das
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854, USA.
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854, USA.
| | - Carole McArthur
- Department of Oral and Craniofacial Science , School of Dentistry, University of Missouri, Kansas City, MO 64108, USA.
| | - Michael Parniak
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
| | - Stefan G Sarafianos
- Christopher Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
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