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Nationwide Study of Drug Resistance Mutations in HIV-1 Infected Individuals under Antiretroviral Therapy in Brazil. Int J Mol Sci 2021; 22:ijms22105304. [PMID: 34069929 PMCID: PMC8157590 DOI: 10.3390/ijms22105304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/02/2022] Open
Abstract
The success of antiretroviral treatment (ART) is threatened by the emergence of drug resistance mutations (DRM). Since Brazil presents the largest number of people living with HIV (PLWH) in South America we aimed at understanding the dynamics of DRM in this country. We analyzed a total of 20,226 HIV-1 sequences collected from PLWH undergoing ART between 2008–2017. Results show a mild decline of DRM over the years but an increase of the K65R reverse transcriptase mutation from 2.23% to 12.11%. This increase gradually occurred following alterations in the ART regimens replacing zidovudine (AZT) with tenofovir (TDF). PLWH harboring the K65R had significantly higher viral loads than those without this mutation (p < 0.001). Among the two most prevalent HIV-1 subtypes (B and C) there was a significant (p < 0.001) association of K65R with subtype C (11.26%) when compared with subtype B (9.27%). Nonetheless, evidence for K65R transmission in Brazil was found both for C and B subtypes. Additionally, artificial neural network-based immunoinformatic predictions suggest that K65R could enhance viral recognition by HLA-B27 that has relatively low prevalence in the Brazilian population. Overall, the results suggest that tenofovir-based regimens need to be carefully monitored particularly in settings with subtype C and specific HLA profiles.
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HIV Drug Resistance in Adults Receiving Early vs. Delayed Antiretroviral Therapy: HPTN 052. J Acquir Immune Defic Syndr 2019; 77:484-491. [PMID: 29293156 DOI: 10.1097/qai.0000000000001623] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
INTRODUCTION We evaluated HIV drug resistance in adults who received early vs. delayed antiretroviral therapy (ART) in a multinational trial [HIV Prevention Trials Network (HPTN) 052, enrollment 2005-2010]. In HPTN 052, 1763 index participants were randomized to start ART at a CD4 cell count of 350-550 cells/mm (early ART arm) or <250 cells/mm (delayed ART arm). In May 2011, interim study results showed benefit of early ART, and all participants were offered ART regardless of CD4 cell count; the study ended in 2015. METHODS Virologic failure was defined as 2 consecutive viral loads >1000 copies/mL >24 weeks after ART initiation. Drug resistance testing was performed for pretreatment (baseline) and failure samples from participants with virologic failure. RESULTS HIV genotyping results were obtained for 211/249 participants (128 early ART arm and 83 delayed ART arm) with virologic failure. Drug resistance was detected in 4.7% of participants at baseline; 35.5% had new resistance at failure. In univariate analysis, the frequency of new resistance at failure was lower among participants in the early ART arm (compared with delayed ART arm, P = 0.06; compared with delayed ART arm with ART initiation before May 2011, P = 0.032). In multivariate analysis, higher baseline viral load (P = 0.0008) and ART regimen (efavirenz/lamivudine/zidovudine compared with other regimens, P = 0.024) were independently associated with higher risk of new resistance at failure. CONCLUSIONS In HPTN 052, the frequency of new drug resistance at virologic failure was lower in adults with early ART initiation. The main factor associated with reduced drug resistance with early ART was lower baseline viral load.
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Cantão NM, Fogaça de Almeida L, Rodrigo Wolf I, Oliveira Almeida R, Alves de Almeida Cruz A, Nunes C, Barbosa AN, Valente GT, de Moura Campos Pardini MI, Grotto RMT. HIV Reverse Transcriptase and Protease Genes Variability Can Be a Biomarker Associated with HIV and Hepatitis B or C Coinfection. Sci Rep 2018; 8:8280. [PMID: 29844604 PMCID: PMC5974300 DOI: 10.1038/s41598-018-26675-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 05/10/2018] [Indexed: 11/09/2022] Open
Abstract
Variability of the HIV reverse transcriptase (RT) and protease (PR) genes has been used as indicators of drug resistance and as a mean to evaluate phylogenetic relationships among circulating virus. However, these studies have been carried in HIV mono-infected populations. The goal of this study was to evaluate, for the first time, the HIV PR and RT sequences from HIV/HBV and HIV/HCV co-infected patients. HIV PR and RT genes were amplificated and sequenced to resistance analysis. The bioinformatics analysis was performed to infer about sequences clustering and molecular evolution. The results showed that the most frequent amino acid substitutions in RT were L214F (67.6%), I135T (55.9%), and in PR was V15I (41.2%). The molecular clock analysis showed that the HIV circulating in co-infected patients were separated in two clusters in the years 1999-2000. Some patients included as HIV mono-infected according patients' medical records and inside the co-infected cluster were, in fact, co-infected by PCR analysis. Analysis of the decision trees showed susceptibility to lamivudine and emtricitabine were important attribute to characterize co-infected patients. In conclusion, the results obtained in this study suggest, for the first time, that HIV RT and PR genes variability could be a genetic biomarker to coinfection.
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Affiliation(s)
- Natália Mirele Cantão
- São Paulo State University (Unesp), Medical School, Botucatu, Sao Paulo State, Brazil
| | - Lauana Fogaça de Almeida
- São Paulo State University (Unesp), School of Agriculture (FCA), Department of Bioprocess and Biotechnology, Botucatu, Sao Paulo State, Brazil
| | - Ivan Rodrigo Wolf
- São Paulo State University (Unesp), School of Agriculture (FCA), Department of Bioprocess and Biotechnology, Botucatu, Sao Paulo State, Brazil
| | - Rodrigo Oliveira Almeida
- São Paulo State University (Unesp), School of Agriculture (FCA), Department of Bioprocess and Biotechnology, Botucatu, Sao Paulo State, Brazil
| | | | - Caroline Nunes
- São Paulo State University (Unesp), Medical School, Botucatu, Sao Paulo State, Brazil
| | | | - Guilherme Targino Valente
- São Paulo State University (Unesp), School of Agriculture (FCA), Department of Bioprocess and Biotechnology, Botucatu, Sao Paulo State, Brazil
| | | | - Rejane Maria Tommasini Grotto
- São Paulo State University (Unesp), Medical School, Botucatu, Sao Paulo State, Brazil.
- São Paulo State University (Unesp), School of Agriculture (FCA), Department of Bioprocess and Biotechnology, Botucatu, Sao Paulo State, Brazil.
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Corado ADLG, Bello G, Leão RAC, Granja F, Naveca FG. HIV-1 genetic diversity and antiretroviral drug resistance among individuals from Roraima state, northern Brazil. PLoS One 2017; 12:e0173894. [PMID: 28301548 PMCID: PMC5354385 DOI: 10.1371/journal.pone.0173894] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 02/28/2017] [Indexed: 11/18/2022] Open
Abstract
The HIV-1 epidemic in Brazil has spread towards the Northern country region, but little is known about HIV-1 subtypes and prevalence of HIV strains with resistance mutations to antiretrovirals in some of the Northern states. HIV-1 protease (PR) and reverse transcriptase (RT) sequences were obtained from 73 treatment-naive and -experienced subjects followed between 2013 and 2014 at a public health reference unit from Roraima, the northernmost Brazilian state. The most prevalent HIV-1 clade observed in the study population was the subtype B (91%), followed by subtype C (9%). Among 12 HIV-1 strains from treatment-naïve patients, only one had a transmitted drug resistance mutation for NNRTI. Among 59 treatment-experienced patients, 12 (20%) harbored HIV-1 strains with acquired drug resistance mutations (ADRM) that reduce the susceptibility to two classes of antiretroviral drugs (NRTI and NNRTI or NRTI and PI), and five (8%) harbored HIV-1 strains with ADRM that reduced susceptibility to only one class of antiretroviral drugs (NNRTI or PI). No patients harboring HIV strains with reduced susceptibility to all three classes of antiretroviral drugs were detected. A substantial fraction of treatment-experienced patients with (63%) and without (70%) ADRM had undetectable plasma viral loads (<40 copies/ml) at the time of sampling. Among treatment-experienced with plasma viral loads above 2,000 copies/ml, 44% displayed no ADRM. This data showed that the HIV-1 epidemic in Roraima displayed a much lower level of genetic diversity and a lower prevalence of ADRM than that described in other Brazilian states.
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Affiliation(s)
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | | | - Fabiana Granja
- Laboratório de Biologia Molecular, Universidade Federal de Roraima (UFRR), Boa Vista, Roraima, Brazil
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Brites C, Pinto-Neto L, Medeiros M, Nunes E, Sprinz E, Carvalho M. Extensive variation in drug-resistance mutational profile of Brazilian patients failing antiretroviral therapy in five large Brazilian cities. Braz J Infect Dis 2016; 20:323-9. [PMID: 27291892 PMCID: PMC9427579 DOI: 10.1016/j.bjid.2016.03.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 12/21/2015] [Accepted: 03/30/2016] [Indexed: 02/06/2023] Open
Abstract
Background Development of drug-resistance mutations is the main cause of failure in antiretroviral therapy. In Brazil, there is scarce information on resistance pattern for patients failing antiretroviral therapy. Objectives To define the HIV mutational profile associated with drug resistance in Brazilian patients from 5 large cities, after first, second or further failures to antiretroviral therapy. Methods We reviewed genotyping results of 1520 patients failing therapy in five Brazilian cities. Frequency of mutations, mean number of active drugs, viral susceptibility to each antiretrovirals drug, and regional differences were assessed. Results Mean time of antiretrovirals use was 22.7 ± 41.1 months. Mean pre-genotyping viral load was 4.2 ± 0.8 log (2.1 ± 2.0 after switching antiretrovirals). Mean number of remaining active drugs was 9.4, 9.0, and 7.9 after 1st, 2nd, and 3rd failure, respectively. We detected regional variations in drug susceptibility: while BA and RS showed the highest (∼40%) resistance level to ATV/r, FPV/r and LPV/r, in the remaining cities it was around half of this rate. We detected 90% efavirenz/nevirapine resistance in SP, only 45% in RS, and levels between 25% and 30% in the other cities. Regarding NRTI, we found a similar pattern, with RJ presenting the highest, and CE the lowest susceptibility rates for all NRTI. Zidovudine resistance was detected in only 3% of patients in RJ, against 45–65% in the other cities. RJ and RS showed 3% resistance to tenofovir, while in CE it reached 55%. DRV/r (89–97%) and etravirine (61–85%) were the most active drugs, but again, with a wide variation across cities. Conclusions The resistance mutational profile of Brazilian patients failing antiretroviral therapy is quite variable, depending on the city where patients were tested. This variation likely reflects distinctive choice of antiretrovirals drugs to initiate therapy, adherence to specific drugs, or circulating HIV-1 strains. Overall, etravirine and DRV/r remain as the most active drugs.
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Affiliation(s)
- Carlos Brites
- Fundação Bahiana de Infectologia (FBaI), Salvador, BA, Brazil; Universidade Federal da Bahia (UFBA), Laboratório de Pesquisa em Infectologia (LAPI), Salvador, BA, Brazil.
| | - Lauro Pinto-Neto
- Escola de Ciências da Saúde da Santa Casa de Vitoria, Vitória, ES, Brazil
| | | | - Estevão Nunes
- Fundação Oswaldo Cruz (FIOCRUZ), Instituto de Infectologia Evandro Chagas, Rio de Janeiro, RJ, Brazil
| | - Eduardo Sprinz
- Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
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The Evolving Genotypic Profile of HIV-1 Mutations Related to Antiretroviral Treatment in the North Region of Brazil. BIOMED RESEARCH INTERNATIONAL 2015; 2015:738528. [PMID: 26543866 PMCID: PMC4620255 DOI: 10.1155/2015/738528] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 09/05/2015] [Accepted: 09/20/2015] [Indexed: 01/08/2023]
Abstract
HIV related mutations can be associated with decreased susceptibility to antiretrovirals and treatment failures. There is scarce information about HIV mutations in persons failing HIV treatment in North of Brazil. Our aim was to evaluate evolution of HIV subtypes and mutations patterns related to antiretroviral therapy in this region. We investigated HIV resistance profile in adults failing antiretroviral regimen in Northern Brazil from January, 2004, through December, 2013. Genotype data was evaluated through Stanford University algorithm. There were 377 genotypes from different individuals to evaluate. Resistance mutations were similar to worldwide reports and related to antiretroviral exposure. Most prevalent mutations in the reverse transcriptase gene were M184V (80.1%) and K130N (40.6%). Thymidine associated mutations were more frequent in multiexperienced patients. Most common protease mutations were M46I, V82A, I54V, L90M, I84V, M46L, and L76V. Subtype B was the most prevalent (90.7%). There were differences between subtypes B and non-B mutations. We documented for the first time subtypes and patterns of HIV associated mutations in Northern Brazil. A1 subtype was identified for the first time in this area. Depending on drug regimen and how experienced the patient is, an empirical switch of a failing antiretroviral treatment could be a reasonable option.
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Thirunavukarasu D, Udhaya V, Iqbal HS, Umaarasu T. Patterns of HIV-1 Drug-Resistance Mutations among Patients Failing First-Line Antiretroviral Treatment in South India. J Int Assoc Provid AIDS Care 2015; 15:261-8. [PMID: 26385878 DOI: 10.1177/2325957415603508] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Although highly active antiretroviral therapy has improved the quality of life among HIV-infected people in India, the emergence of drug resistance along with the limited access and affordability to routine monitoring continues to be a challenge worldwide. METHODS The frequency and patterns of HIV-1 drug-resistance mutations among the first-line failing HIV-infected patients attending a hospital in Salem, Tamil Nadu, India, were genotypically analyzed using the online Stanford HIV Database. RESULTS Of the study patients followed up for 6 months, 23 patients failed first-line therapy and the mutation of I135R/T/V/X, L178 I/M, M184V/I, D67N, K70R, and K103N was most common. Phylogenetic analysis revealed that most of these patients belonged to HIV subtype C. CONCLUSION The study documents the frequency of nucleoside reverse transcriptase inhibitor and nonnucleoside reverse transcriptase inhibitor mutations that are prevalent in the first-line failing HIV-infected patients of South Indian region and adds up to the data for developing future algorithms to study the drug-resistance mutations of HIV subtype C. Thus, the results of the study call for the need for rational approach for selecting and for frequent viral monitoring to be performed to detect failure, followed by genotyping.
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Affiliation(s)
| | - Visvanathan Udhaya
- Department of Microbiology, Faculty of Medicine, Annamalai University, Chidambaram, Tamil Nadu, India
| | | | - Thirunavukarasu Umaarasu
- Department of Microbiology, Vivekanandha Dental College for Women, Tiruchengode, Tamil Nadu, India
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Koigi P, Ngayo MO, Khamadi S, Ngugi C, Nyamache AK. HIV type 1 drug resistance patterns among patients failing first and second line antiretroviral therapy in Nairobi, Kenya. BMC Res Notes 2014; 7:890. [PMID: 25487529 PMCID: PMC4295353 DOI: 10.1186/1756-0500-7-890] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 11/21/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The ever-expanding rollout of antiretroviral therapy in poor resource settings without routine virological monitoring has been accompanied with development of drug resistance that has resulted in limited treatment success. METHODS A cross-sectional study with one time viral load was conducted during the period between 2012 and 2013 to determine treatment failure and drug resistance mutations among adults receiving first-line (44) (3TC_d4T/AZT_NVP/EFV) and second-line (20) (3TC/AZT/LPV/r) in Nairobi, Kenya. HIV-1 pol-RT genotyping for drug resistance was performed using an in-house protocol. RESULTS A total of 64 patients were recruited (mean age 36.9 yrs.) during the period between 2012 and 2013 of the 44 adult patients failing first-line 24 (40.9%) had drug resistance mutations. Eight (8) patients had NRTI resistance mutations with NAMS M184V (54.2%) and K65R (8.4%) mutations being the highest followed by TAMs T215Y and K70R (12.5%). In addition, among patients failing second-line (20), six patients (30%) had NNRTI resistance; two patients on K103N and G190A mutations while V106A, Y184V, A98G, Y181C mutations per patient were also detected. However, for NRTI two patients had TAM T215Y. M184V mutation occurred in one patient. CONCLUSIONS The study findings showed that HIV-1 drug resistance was significantly high in the study population. The detected accumulated resistance strains show that emergence of HIV drug resistance will continue to be a big challenge and should be given more attention as the scale up of treatment in the country continues.
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Affiliation(s)
- Peter Koigi
- />Department of Medical Laboratory Sciences, Kenyatta University, Nairobi, Kenya
| | - Musa Otieno Ngayo
- />Center for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Samoel Khamadi
- />Centre for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Caroline Ngugi
- />Department of Medical Microbiology, Jomo Kenyatta University of Agriculture & Technology, Nairobi, Kenya
| | - Anthony Kebira Nyamache
- />Centre for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
- />Department of Microbiology, Kenyatta University, Nairobi, Kenya
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Yang J, Geng W, Zhang M, Han X, Shang H. Discordance between genotypic resistance and pseudovirus phenotypic resistance in AIDS patients after long-term antiretroviral therapy and virological failure. J Basic Microbiol 2013; 54:1120-5. [PMID: 24338739 DOI: 10.1002/jobm.201300415] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Accepted: 10/11/2013] [Indexed: 11/06/2022]
Abstract
Sixteen original recombinant pseudoviruses were generated by cloning the reverse transcriptase and protease genes of human immunodeficiency virus (HIV)-1 from patients into a plasmid vector (pNL4-3-ΔE-EGFP). By site-directed mutagenesis two restriction endonuclease sites, ApaI and AgeI, were inserted into pNL4-3-ΔE-EGFP. Phenotypic susceptibility of recombinant pseudoviruses to five different classes of antiretroviral drugs was determined using a luciferase reporter assay system. The results were subjected to comparative analyses to detect genotype-phenotype associations. Among 16 strains tested, 12 strains had a discordant genotype-phenotype resistance pattern to at least one drug. In five strains resistance to two, in two strains to three, and in one strain resistance to four drugs was detected. HIV resistance genotyping could predict the phenotype for nevirapine and azidothymidine. For lamivudine, 2'-3'-didehydro-2'-3'dideoxythymidine and didanosine, phenotypic resistance testing was necessary. The study showed that in patients who experienced long-term highly active antiretroviral therapy and virological failure, there is some discordance between genotypic and phenotypic HIV drug resistance. To address the issue of limited resources in China, genotypic and phenotypic resistance testing should be done for different drugs in order to guide clinical therapy more effectively.
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Affiliation(s)
- Jing Yang
- Key Laboratory of AIDS Immunology of Ministry of Health, Department of Laboratory Medicine, the First Affiliated Hospital of China Medical University, Shenyang, China; Infection Control Department, General Hospital of Shenyang military Area Command, Shenyang, China
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