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Manyana S, Gounder L, Pillay M, Manasa J, Naidoo K, Chimukangara B. HIV-1 Drug Resistance Genotyping in Resource Limited Settings: Current and Future Perspectives in Sequencing Technologies. Viruses 2021; 13:1125. [PMID: 34208165 PMCID: PMC8230827 DOI: 10.3390/v13061125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/27/2021] [Accepted: 05/31/2021] [Indexed: 12/14/2022] Open
Abstract
Affordable, sensitive, and scalable technologies are needed for monitoring antiretroviral treatment (ART) success with the goal of eradicating HIV-1 infection. This review discusses use of Sanger sequencing and next generation sequencing (NGS) methods for HIV-1 drug resistance (HIVDR) genotyping, focusing on their use in resource limited settings (RLS). Sanger sequencing remains the gold-standard method for detecting HIVDR mutations of clinical relevance but is mainly limited by high sequencing costs and low-throughput. NGS is becoming a more common sequencing method, with the ability to detect low-abundance drug-resistant variants and reduce per sample costs through sample pooling and massive parallel sequencing. However, use of NGS in RLS is mainly limited by infrastructure costs. Given these shortcomings, our review discusses sequencing technologies for HIVDR genotyping, focusing on common in-house and commercial assays, challenges with Sanger sequencing in keeping up with changes in HIV-1 treatment programs, as well as challenges with NGS that limit its implementation in RLS and in clinical diagnostics. We further discuss knowledge gaps and offer recommendations on how to overcome existing barriers for implementing HIVDR genotyping in RLS, to make informed clinical decisions that improve quality of life for people living with HIV.
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Affiliation(s)
- Sontaga Manyana
- National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4058, South Africa; (L.G.); (M.P.); (B.C.)
| | - Lilishia Gounder
- National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4058, South Africa; (L.G.); (M.P.); (B.C.)
| | - Melendhran Pillay
- National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4058, South Africa; (L.G.); (M.P.); (B.C.)
| | - Justen Manasa
- Department of Laboratory Medicine and Investigative Sciences, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe;
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa;
- South African Medical Research Council (SAMRC), CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban 4013, South Africa
| | - Benjamin Chimukangara
- National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4058, South Africa; (L.G.); (M.P.); (B.C.)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa;
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Patil S, Rao A, Pathak P, Kurle S, Mane A, Nirmalkar A, Singhal AK, Verma V, Singh MK, Reddy DCS, Shete A, Singh M, Gangakhedkar R, Panda S. Unsterile injection equipment associated with HIV outbreak and an extremely high prevalence of HCV-A case-control investigation from Unnao, India. PLoS One 2020; 15:e0243534. [PMID: 33275646 PMCID: PMC7717531 DOI: 10.1371/journal.pone.0243534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 11/23/2020] [Indexed: 01/30/2023] Open
Abstract
The integrated counseling and testing center (ICTC) located in the district hospital, Unnao in the northern state of Uttar Pradesh (UP), India witnessed an increased detection of HIV among its attendees in July 2017. Subsequently, health camps were organized by the UP State AIDS Control Society in the villages and townships contributing to such detection. We conducted a case-control study to identify factors associated with this increased detection; 33 cases and 125 controls were enrolled. Cases were individuals, detected HIV sero-reactive during November 2017-April 2018 from three locations namely Premganj, Karimuddinpur and Chakmeerapur in the Bangarmau block of the district of Unnao. Controls hailed from the same geographical setting and tested HIV sero-nonreactive either in health camps or at ICTC centers from where the cases were detected. Misclassification bias was avoided by confirming HIV sero-status of both cases as well as controls prior to final analysis. Study participants were interviewed on various risk practices and invasive treatment procedures. They were also tested for HIV and other bio-markers reflecting unsafe injecting and sexual exposures such as hepatitis B surface antigen (HBsAg), anti-HCV antibody (HCV Ab), anti-herpes simplex-2 Immunoglobulin G (HSV-2 IgG) and rapid plasma regain (RPR) test for syphilis. Secondary data analysis on three time points during 2015 through 2018 revealed a rising trend of HIV among attendees of the ICTCs (ICTC-Hasanganj, ICTC-Unnao district hospital and ICTC- Nawabganj) catering to the entire district of Unnao. While there was a seven fold rise of HIV among ICTC attendees of Hasanganj (χ2 value for trend 23.83; p < 0.001), the rise in Unnao district hospital was twofold (χ2 value for trend 4.37; p < 0.05) and was tenfold at ICTC-Nawabganj (χ2 value for trend 5.23; p < 0.05) indicating risk of infection prevailing throughout the district. Primary data was generated through interviews and laboratory investigations as mentioned above. The median age of cases and controls was 50 year (minimum 18 –maximum 68; IQR 31–57) and 38 year (minimum 18 –maximum 78; IQR 29–50) respectively. Thirty six percent of the cases and 47% of controls were male. A significantly higher proportion of cases (85%) had HCV Ab compared to controls (56%; OR 4.4, 95% CI 1.5–12.1); none reported injection drug use. However, cases and controls did not differ significantly regarding presence of HSV-2 IgG (6% versus 8% respectively). Neither any significant difference existed between cases and controls in terms of receiving blood transfusion, undergoing invasive surgical procedures, tattooing, tonsuring of head or skin piercing. In multivariate logistic regression model, ‘unsafe injection exposure during treatment-seeking’(AOR 6.61, 95% CI 1.80–24.18) and ‘receipt of intramuscular injection in last five years’ (AOR 7.20, 95% CI 1.48–34.88) were independently associated with HIV sero-reactive status. The monophyletic clustering of HIV sequences from 14 cases (HIV-1 pol gene amplified) indicated a common ancestry. Availability of auto-disabled syringes and needles, empowerment of the local communities and effective regulatory practices across care settings would serve as important intervention measures in this context.
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Affiliation(s)
- Sandip Patil
- Indian Council of Medical Research-National AIDS Research Institute, Pune, Maharashtra, India
| | - Amrita Rao
- Indian Council of Medical Research-National AIDS Research Institute, Pune, Maharashtra, India
| | - Preety Pathak
- Uttar Pradesh State AIDS Control Society, Lucknow, Uttar Pradesh, India
| | - Swarali Kurle
- Indian Council of Medical Research-National AIDS Research Institute, Pune, Maharashtra, India
| | - Arati Mane
- Indian Council of Medical Research-National AIDS Research Institute, Pune, Maharashtra, India
| | - Amit Nirmalkar
- Indian Council of Medical Research-National AIDS Research Institute, Pune, Maharashtra, India
| | - A. K. Singhal
- Community Health Centre, Department of Medical & Health, Government of Uttar Pradesh, Bangarmau, India
| | - Vinita Verma
- National AIDS Control Organization, New Delhi, India
| | - Mukesh Kumar Singh
- Community Health Centre, Department of Medical & Health, Government of Uttar Pradesh, Bangarmau, India
| | - D. C. S. Reddy
- Technical Resource Group, National AIDS Control Organization, New Delhi, India
| | - Ashwini Shete
- Indian Council of Medical Research-National AIDS Research Institute, Pune, Maharashtra, India
| | - Manjula Singh
- Indian Council of Medical Research Headquarter, New Delhi, India
| | | | - Samiran Panda
- Indian Council of Medical Research-National AIDS Research Institute, Pune, Maharashtra, India
- Indian Council of Medical Research Headquarter, New Delhi, India
- * E-mail: , ,
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Deng X, Liu J, Li J, Yang B, Shu Y, Zhang M, Dong X. Prevalence of HIV-1 Drug-Resistance Genotypes Among Unique Recombinant Forms from Yunnan Province, China in 2016-2017. AIDS Res Hum Retroviruses 2020; 36:389-398. [PMID: 31914782 DOI: 10.1089/aid.2019.0041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
To investigate the prevalence and characteristics of drug-resistance genotypes among unique recombinant forms (URFs) in HIV-1 infected people under long-term antiretroviral treatment failure from Yunnan Province. The plasma samples were collected from antiretroviral therapy (ART)-failure experienced individuals from 2016 to 2017 in Yunnan Province, China. The genotyping drug resistance of HIV-1 pol gene fragments was implemented using in-house assay. According to the analysis of RIP and MEGA 7.0, the HIV-1 strains related to URFs were screened for recombinant identification and drug resistance analysis. A total of 130 pol sequences of HIV-1 URF strains were obtained from 1,121 samples. The proportion of HIV-1 URF strains was 11.6% among the ART-failure individuals from 2016 to 2017 in Yunnan. The overall drug-resistance rate of HIV-1 URF strains was 56.9%. Meanwhile, the percentage of protease inhibitors, nucleoside reverse transcriptase inhibitors (NRTIs), and non-nucleoside reverse transcriptase inhibitors (NNRTIs) resistance was 3.8% (5/130), 36.2% (47/130), and 53.8% (70/130), respectively. Mutations such as M184V/I (35.4%) in NRTIs and K103N/R/S/T (25.4%), V179D/E/T/Y (18.9%), G190A/E/R/S (13.8%), and Y181C (9.2%) in NNRTIs were common among the HIV-1 URF strains relative to other mutations. Factors such as male, sexual transmission pathway, and source of the year 2017 were significantly correlated with the development of HIV-1 URF drug resistance. The emergence of the multiple recombinant forms identified in Yunnan indicates active transmission networks of HIV-1 of different HIV-1 subtype/circulating recombinant forms cross-infection in this region. Therefore, it is necessary to further monitor the molecular epidemiology and drug resistance of HIV-1 in Yunnan.
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Affiliation(s)
- Xuemei Deng
- Yunnan Provincial Infectious Disease Hospital, Yunnan AIDS Care Center (YNACC), Kunming, Yunnan, China
| | - Jiafa Liu
- Yunnan Provincial Infectious Disease Hospital, Yunnan AIDS Care Center (YNACC), Kunming, Yunnan, China
| | - Jianjian Li
- Yunnan Provincial Infectious Disease Hospital, Yunnan AIDS Care Center (YNACC), Kunming, Yunnan, China
| | - Bihui Yang
- Yunnan Provincial Infectious Disease Hospital, Yunnan AIDS Care Center (YNACC), Kunming, Yunnan, China
| | - Yuanlu Shu
- Yunnan Provincial Infectious Disease Hospital, Yunnan AIDS Care Center (YNACC), Kunming, Yunnan, China
| | - Mi Zhang
- Yunnan Provincial Infectious Disease Hospital, Yunnan AIDS Care Center (YNACC), Kunming, Yunnan, China
| | - Xingqi Dong
- Yunnan Provincial Infectious Disease Hospital, Yunnan AIDS Care Center (YNACC), Kunming, Yunnan, China
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Magomere EO, Nyangahu DD, Kimoloi S, Webala BA, Ondigo BN. Performance characteristics of a modified HIV-1 drug resistance genotyping method for use in resource-limited settings. F1000Res 2019; 8:1518. [PMID: 31656591 PMCID: PMC6798314 DOI: 10.12688/f1000research.20083.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/14/2019] [Indexed: 11/20/2022] Open
Abstract
Background: HIV-1 drug resistance (HIVDR) assays are critical components of HIV clinical management programs in the face of emerging drug resistance. However, the high costs associated with existing commercial HIVDR assays prohibit their routine usage in resource-limited settings. We present the performance characteristics of a modified commercial HIVDR testing assay. Methods: A total of 26 plasma samples were used to validate and assess the accuracy, precision, reproducibility and amplification sensitivity of a modified HIVDR assay by HIV genotyping. In addition, a cost comparison between the original and the modified assay was performed using the ingredient costing approach. Results: The performance characteristics of the modified assay were in agreement with the original assay. Accuracy, precision and reproducibility showed nucleotide sequence identity of 98.5% (confidence interval (CI), 97.9-99.1%), 98.67% (CI, 98.1-99.23) and 98.7% (CI, 98.1-99.3), respectively. There was no difference in the type of mutations detected by the two assays (χ 2 = 2.36, p = 0.26). Precision and reproducibility showed significant mutation agreement between replicates (kappa = 0.79 and 0.78), respectively ( p < 0.05). The amplification sensitivity of the modified assay was 100% and 62.5% for viremia ≥1000 copies/ml and <1000 copies/ml respectively. Our assay modification translates to a 39.2% reduction in the cost of reagents. Conclusions: Our findings underscore the potential of modifying commercially available HIVDR testing assays into cost-effective, yet accurate assays for use in resource-limited settings.
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Affiliation(s)
- Edwin O. Magomere
- Department of Biochemistry and Molecular Biology, Egerton University, Nakuru, Nakuru, 20115, Kenya
| | - Donald D. Nyangahu
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Seattle, Washington, USA
| | - Sammy Kimoloi
- Department of Medical Laboratory Sciences, Masinde Muliro University of Science and Technology, Kakamega, Kakamega, Kenya
| | - Brenda A. Webala
- Faculty of Health Sciences, Egerton University, Nakuru, Nakuru, Kenya
| | - Bartholomew N. Ondigo
- Department of Biochemistry and Molecular Biology, Egerton University, Nakuru, Nakuru, 20115, Kenya
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kisumu, Kenya
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, NIH, USA, Bethesda, Maryland, USA
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Karade SK, Kulkarni SS, Ghate MV, Patil AA, Londhe R, Salvi SP, Kadam DB, Joshi RK, Rewari BB, Gangakhedkar RR. Antiretroviral resistance following immunological monitoring in a resource-limited setting of western India: A cross-sectional study. PLoS One 2017; 12:e0181889. [PMID: 28763465 PMCID: PMC5538665 DOI: 10.1371/journal.pone.0181889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 07/07/2017] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The 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 FINDINGS This 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). CONCLUSION The 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.
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Affiliation(s)
- Santosh K. Karade
- HIV Drug Resistance Laboratory, National AIDS Research Institute (ICMR), Pune, India
- Department of Microbiology, Armed Forces Medical College, Pune, India
| | - Smita S. Kulkarni
- Department of Virology, National AIDS Research Institute (ICMR), Pune, India
| | - Manisha V. Ghate
- Department of Clinical Sciences, National AIDS Research Institute (ICMR), Pune, India
| | - Ajit A. Patil
- HIV Drug Resistance Laboratory, National AIDS Research Institute (ICMR), Pune, India
| | - Rajkumar Londhe
- Department of Virology, National AIDS Research Institute (ICMR), Pune, India
| | - Sonali P. Salvi
- Department of Medicine, BJ Medical College and Sasoon General Hospital, Pune, India
| | - Dileep B. Kadam
- Department of Medicine, BJ Medical College and Sasoon General Hospital, Pune, India
| | - Rajneesh K. Joshi
- Department of Epidemiology and Biostatistics, National AIDS Research Institute (ICMR), Pune, India
- Department of Community Medicine, Armed Forces Medical college, Pune, India
| | - Bharat B. Rewari
- Department of AIDS Control, National AIDS Control Organization, New Delhi, India
| | - Raman R. Gangakhedkar
- Department of Clinical Sciences, National AIDS Research Institute (ICMR), Pune, India
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Chimukangara B, Varyani B, Shamu T, Mutsvangwa J, Manasa J, White E, Chimbetete C, Luethy R, Katzenstein D. HIV drug resistance testing among patients failing second line antiretroviral therapy. Comparison of in-house and commercial sequencing. J Virol Methods 2017; 243:151-157. [PMID: 27894862 PMCID: PMC5393912 DOI: 10.1016/j.jviromet.2016.11.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 11/07/2016] [Accepted: 11/23/2016] [Indexed: 01/05/2023]
Abstract
INTRODUCTION HIV genotyping is often unavailable in low and middle-income countries due to infrastructure requirements and cost. We compared genotype resistance testing in patients with virologic failure, by amplification of HIV pol gene, followed by "in-house" sequencing and commercial sequencing. METHODS Remnant plasma samples from adults and children failing second-line ART were amplified and sequenced using in-house and commercial di-deoxysequencing, and analyzed in Harare, Zimbabwe and at Stanford, U.S.A, respectively. HIV drug resistance mutations were determined using the Stanford HIV drug resistance database. RESULTS Twenty-six of 28 samples were amplified and 25 were successfully genotyped. Comparison of average percent nucleotide and amino acid identities between 23 pairs sequenced in both laboratories were 99.51 (±0.56) and 99.11 (±0.95), respectively. All pairs clustered together in phylogenetic analysis. Sequencing analysis identified 6/23 pairs with mutation discordances resulting in differences in phenotype, but these did not impact future regimens. CONCLUSIONS The results demonstrate our ability to produce good quality drug resistance data in-house. Despite discordant mutations in some sequence pairs, the phenotypic predictions were not clinically significant.
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Affiliation(s)
- Benjamin Chimukangara
- Department of Molecular Biology, Biomedical Research and Training Institute, Harare, Zimbabwe; Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, Durban, South Africa.
| | - Bhavini Varyani
- Department of Molecular Biology, Biomedical Research and Training Institute, Harare, Zimbabwe.
| | - Tinei Shamu
- Newlands Clinic, Newlands, Harare, Zimbabwe.
| | - Junior Mutsvangwa
- Department of Molecular Biology, Biomedical Research and Training Institute, Harare, Zimbabwe.
| | - Justen Manasa
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
| | - Elizabeth White
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
| | - Cleophas Chimbetete
- Newlands Clinic, Newlands, Harare, Zimbabwe; Institute of Social and Preventive Medicine, University of Bern, Switzerland.
| | | | - David Katzenstein
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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Suryawanshi R, Jadhav S, Makwana N, Desai D, Chaturbhuj D, Sonawani A, Idicula-Thomas S, Murugesan V, Katti SB, Tripathy S, Paranjape R, Kulkarni S. Evaluation of 4-thiazolidinone derivatives as potential reverse transcriptase inhibitors against HIV-1 drug resistant strains. Bioorg Chem 2017; 71:211-218. [PMID: 28236450 DOI: 10.1016/j.bioorg.2017.02.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 02/10/2017] [Accepted: 02/13/2017] [Indexed: 02/03/2023]
Abstract
Rapid emergence of drug resistance is crucial in management of HIV infection limiting implementation of efficacious drugs in the ART regimen. Designing new molecules against HIV drug resistant strains is utmost essential. Based on the anti-HIV-1 activity, we selected four 4-thiazolidinone derivatives (S009-1908, S009-1909, S009-1911, S009-1912) and studied their interaction with reverse transcriptase (RT) from a panel of 10 clinical isolates (8 nevirapine resistant and two susceptible) using in silico methods, and inhibition pattern using in vitro cell based assays. On the basis of binding affinity observed in in silico analysis, 2-(2-chloro-6-nitrophenyl)-3-(4, 6-dimethylpyridin-2-yl) thiazolidin-4-one (S009-1912) was identified as the lead molecule followed by S009-1908, S009-1909 and S009-1911. The in vitro activity against the same panel was assessed using TZM-bl assay (IC50: 0.4-11.44µg/ml, TI: 4-126) and subsequently in PBMC assay against a nevirapine resistant clinical isolate (IC50: 0.8-6.65µg/ml, TI: 8.31-11.43) and standard strain from NIH ARRRP (IC50: 0.95-3.6µg/ml, TI: 9-26). The study shows analogue with pyrimidin-2-yl amino substitution at N-3 position of thiazolidin-4-one ring (S009-1908, S009-1909, S009-1911) exhibited enhanced activity as compared to pyridin-2-yl substituted derivatives (S009-1912), suggesting the use 4-thiazolidinones for developing potent inhibitors against HIV-1 drug resistant strains.
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Affiliation(s)
| | | | | | - Dipen Desai
- National AIDS Research Institute, Pune, India
| | | | - Archana Sonawani
- National Institute for Research in Reproductive Health, Mumbai, India
| | | | - Vanangamudi Murugesan
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute (CDRI), Jankipuram Extension, Sector-10, Lucknow 226031, Uttar Pradesh, India
| | - Seturam B Katti
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute (CDRI), Jankipuram Extension, Sector-10, Lucknow 226031, Uttar Pradesh, India
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Karade SK, Ghate MV, Chaturbhuj DN, Kadam DB, Shankar S, Gaikwad N, Gurav S, Joshi R, Sane SS, Kulkarni SS, Kurle SN, Paranjape RS, Rewari BB, Gangakhedkar RR. Cross-sectional study of virological failure and multinucleoside reverse transcriptase inhibitor resistance at 12 months of antiretroviral therapy in Western India. Medicine (Baltimore) 2016; 95:e4886. [PMID: 27631260 PMCID: PMC5402603 DOI: 10.1097/md.0000000000004886] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The free antiretroviral therapy (ART) program in India has scaled up to register second largest number of people living with HIV/AIDS across the globe. To assess the effectiveness of current first-line regimen we estimated virological suppression on completion of 1 year of ART. The study describes the correlates of virological failure (VF) and multinucleoside reverse transcriptase inhibitor (NRTI) drug resistance mutations (DRMs).In this cross-sectional study conducted between June and August 2014, consecutive adults from 4 State sponsored ART clinics of western India were recruited for plasma viral load screening at 12 ± 2 months of ART initiation. Individuals with plasma viral load >1000 copies/mL were selected for HIV drug resistance (HIVDR) genotyping. Logistic regression analyses were performed to assess factors associated with VF and multi-NRTI resistance mutations. Criteria adopted for multi-NRTI resistance mutation were either presence of K65R or 3 or more thymidine analog mutations (TAMs) or presence of M184V along with 2 TAMs.Of the 844 study participants, virological suppression at 1 year was achieved in 87.7% of individuals. Factors significantly associated with VF (P < 0.005) were 12 months CD4 count of ≤100 cells/μL (adjusted OR -7.11), low reported adherence (adjusted OR -4.44), and those living without any partner (adjusted OR -1.98). In patients with VF, the prevalence of non-nucleoside reverse transcriptase inhibitor (NNRTI) DRM (78.75%) were higher as compared to NRTI (58.75%). Multi-NRTI DRMs were present in 32.5% of sequences and were significantly associated with CD4 count of ≤100 cells/μL at baseline (adjusted OR -13.00) and TDF-based failing regimen (adjusted OR -20.43). Additionally, low reported adherence was negatively associated with multi-NRTI resistance (adjusted OR -0.11, P = 0.015). K65R mutation was significantly associated with tenofovir (TDF)-based failing regimen (P < 0.001).The study supports early linkage of HIV-infected individuals to the program for ART initiation, adherence improvement, and introduction of viral load monitoring. With recent introduction of TDF-based regimen, the emergence of K65R needs to be monitored closely among HIV-1 subtype C-infected Indian population.
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Affiliation(s)
| | - Manisha V. Ghate
- Department of Clinical Sciences, National AIDS Research Institute
| | | | - Dileep B. Kadam
- Department of Medicine, BJ Medical College and Sasoon General Hospital, Pune
| | | | - Nitin Gaikwad
- Department of Tuberculosis and Chest Diseases, YCM Hospital
| | | | | | | | | | | | | | - Bharat B. Rewari
- Department of AIDS Control, National AIDS Control Organization, New Delhi, India
| | - Raman R. Gangakhedkar
- Department of Clinical Sciences, National AIDS Research Institute
- Correspondence: Raman R. Gangakhedkar, National AIDS Research Institute (ICMR), 73 G Block, MIDC Bhosari, Pune 411026, India (e-mail: )
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Karade S, Patil AA, Ghate M, Kulkarni SS, Kurle SN, Risbud AR, Rewari BB, Gangakhedkar RR. Short Communication: Limited HIV Pretreatment Drug Resistance Among Adults Attending Free Antiretroviral Therapy Clinic of Pune, India. AIDS Res Hum Retroviruses 2016; 32:377-80. [PMID: 26573132 DOI: 10.1089/aid.2015.0277] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In India, the roll out of the free antiretroviral therapy (ART) program completed a decade of its initiation in 2014. The success of first-line ART is influenced by prevalence of HIV pretreatment drug resistance (PDR) in the population. In this cross-sectional study, we sought to determine the prevalence of PDR among adults attending the state-sponsored free ART clinic in Pune in western India. Fifty-two individuals eligible for ART as per national guidelines with median CD4 cell count of 253 cells/mm(3) (inter quartile range: 149-326) were recruited between January 2014 and April 2015. Population-based sequencing of partial pol gene sequences from plasma specimen revealed predominant HIV-1 subtype C infection (96.15%) and presence of single-drug resistance mutations against non-nucleoside reverse transcriptase inhibitor in two sequences. The study supports the need for periodic surveillance, when offering PDR testing at individual level is not feasible.
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Affiliation(s)
- Santosh Karade
- HIV Drug Resistance Laboratory, National AIDS Research Institute, Pune, India
- Maharashtra University of Health Sciences, Nashik, India
| | - Ajit A. Patil
- HIV Drug Resistance Laboratory, National AIDS Research Institute, Pune, India
| | - Manisha Ghate
- Department of Clinical Sciences, National AIDS Research Institute, Pune, India
| | - Smita S. Kulkarni
- Department of Molecular Virology, National AIDS Research Institute, Pune, India
| | - Swarali N. Kurle
- HIV Drug Resistance Laboratory, National AIDS Research Institute, Pune, India
| | - Arun R. Risbud
- Department of Microbiology, National AIDS Research Institute, Pune, India
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Chakravarty J, Sundar S, Chourasia A, Singh PN, Kurle S, Tripathy SP, Chaturbhuj DN, Rai M, Agarwal AK, Mishra RN, Paranjape RS. Outcome of patients on second line antiretroviral therapy under programmatic condition in India. BMC Infect Dis 2015; 15:517. [PMID: 26572102 PMCID: PMC4647630 DOI: 10.1186/s12879-015-1270-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 11/06/2015] [Indexed: 11/10/2022] Open
Abstract
Background The National AIDS Control Organization of India has been providing free second line antiretroviral therapy (ART) since 2008. This observational study reports the survival and virologic suppression of patients on second-line ART under programmatic condition and type of mutations acquired by those failing therapy. Methods 170 patients initiated on second-line therapy between 2008 and 2012 were followed up till 2013. Viral Load (VL) was repeated at 6 months for all patients and at 12 months for those with VL >400 copies/ml at 6 months. Adequate virological response was defined as plasma HIV-1 VL <400 copies/ml and virological failure was defined as VL >1000 copies/ml. Genotyping was done in 16 patients with virological failure. Results Out of 170 patients, 110 (64.7 %) were alive and on therapy and 35 (20.5 %) expired. In the first year the occurrence of death was 13.7 /100 person years while between1 and 5 year it was 3.88 /100 person years. In the first year, duration of immunological failure >12 months, weight <45 kg, WHO clinical stage 3 and 4 and WHO criteria CD4 count less than pretherapy baseline [hazard ratio HR 4.2. 15.8, 11.9 & 4.1 respectively] and beyond first year poor first and second line adherence and first line CD4 count < 200/μL [HR 5.2,15.8, 3.3 respectively] had high risk of death. 119/152 (78.2 %) had adequate virological response and 27/152 (17.7 %) had virological failure. High viral load at baseline and poor second line adherence (Odds Ratio 3.4 & 2.8 respectively) had increased risk of virological failure. Among those genotyped, 50 % had major Protease Inhibitor mutation (M46I commonest) however 87.5 % were still susceptible to darunavir. Conclusions Second line therapy has shown high early mortality but good virological suppression under programmatic conditions.
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Affiliation(s)
- Jaya Chakravarty
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India.
| | - Shyam Sundar
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India.
| | - Ankita Chourasia
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India.
| | - Pallav Narayan Singh
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India.
| | - Swarali Kurle
- Indian Council of Medical Research, National AIDS Research Institute, Bhosari, Pune, India.
| | - Srikanth P Tripathy
- Indian Council of Medical Research, National JALMA Institute of Leprosy and Other Mycobacterial Diseases, Agra, India.
| | - Devidas N Chaturbhuj
- Indian Council of Medical Research, National AIDS Research Institute, Bhosari, Pune, India.
| | - Madhukar Rai
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India.
| | - Amit Kumar Agarwal
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India.
| | - Rabindra Nath Mishra
- Department of Community Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India.
| | - Ramesh S Paranjape
- Indian Council of Medical Research, National AIDS Research Institute, Bhosari, Pune, India.
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Subtype-independent near full-length HIV-1 genome sequencing and assembly to be used in large molecular epidemiological studies and clinical management. J Int AIDS Soc 2015; 18:20035. [PMID: 26115688 PMCID: PMC4482814 DOI: 10.7448/ias.18.1.20035] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 05/08/2015] [Accepted: 06/01/2015] [Indexed: 11/30/2022] Open
Abstract
Introduction HIV-1 near full-length genome (HIV-NFLG) sequencing from plasma is an attractive multidimensional tool to apply in large-scale population-based molecular epidemiological studies. It also enables genotypic resistance testing (GRT) for all drug target sites allowing effective intervention strategies for control and prevention in high-risk population groups. Thus, the main objective of this study was to develop a simplified subtype-independent, cost- and labour-efficient HIV-NFLG protocol that can be used in clinical management as well as in molecular epidemiological studies. Methods Plasma samples (n=30) were obtained from HIV-1B (n=10), HIV-1C (n=10), CRF01_AE (n=5) and CRF01_AG (n=5) infected individuals with minimum viral load >1120 copies/ml. The amplification was performed with two large amplicons of 5.5 kb and 3.7 kb, sequenced with 17 primers to obtain HIV-NFLG. GRT was validated against ViroSeq™ HIV-1 Genotyping System. Results After excluding four plasma samples with low-quality RNA, a total of 26 samples were attempted. Among them, NFLG was obtained from 24 (92%) samples with the lowest viral load being 3000 copies/ml. High (>99%) concordance was observed between HIV-NFLG and ViroSeq™ when determining the drug resistance mutations (DRMs). The N384I connection mutation was additionally detected by NFLG in two samples. Conclusions Our high efficiency subtype-independent HIV-NFLG is a simple and promising approach to be used in large-scale molecular epidemiological studies. It will facilitate the understanding of the HIV-1 pandemic population dynamics and outline effective intervention strategies. Furthermore, it can potentially be applicable in clinical management of drug resistance by evaluating DRMs against all available antiretrovirals in a single assay.
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Alemán Y, Vinken L, Kourí V, Pérez L, Álvarez A, Abrahantes Y, Fonseca C, Pérez J, Correa C, Soto Y, Schrooten Y, Vandamme AM, Van Laethem K. Performance of an in-house human immunodeficiency virus type 1 genotyping system for assessment of drug resistance in Cuba. PLoS One 2015; 10:e0117176. [PMID: 25671421 PMCID: PMC4324769 DOI: 10.1371/journal.pone.0117176] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 12/19/2014] [Indexed: 11/20/2022] Open
Abstract
As commercial human immunodeficiency virus type 1 drug resistance assays are expensive, they are not commonly used in resource-limited settings. Hence, a more affordable in-house procedure was set up taking into account the specific epidemiological and economic circumstances of Cuba. The performance characteristics of the in-house assay were evaluated using clinical samples with various subtypes and resistance patterns. The lower limit of amplification was determined on dilutions series of 20 clinical isolates and ranged from 84 to 529 RNA copies/mL. For the assessment of trueness, 14 clinical samples were analyzed and the ViroSeq HIV-1 Genotyping System v2.0 was used as the reference standard. The mean nucleotide sequence identity between the two assays was 98.7% ± 1.0. Additionally, 99.0% of the amino acids at drug resistance positions were identical. The sensitivity and specificity in detecting drug resistance mutations was respectively 94.1% and 99.5%. Only few discordances in drug resistance interpretation patterns were observed. The repeatability and reproducibility were evaluated using 10 clinical samples with 3 replicates per sample. The in-house test was very precise as nucleotide sequence identity among paired nucleotide sequences ranged from 98.7% to 99.9%. The acceptance criteria were met by the in-house test for all performance characteristics, demonstrating a high degree of accuracy. Subsequently, the applicability in routine clinical practice was evaluated on 380 plasma samples. The amplification success rate was 91% and good quality consensus sequences encoding the entire protease and the first 335 codons in reverse transcriptase could be obtained for 99% of the successful amplicons. The reagent cost per sample using the in-house procedure was around € 80 per genotyping attempt. Overall, the in-house assay provided good results, was feasible with equipment and reagents available in Cuba and was half as expensive as commercial assays.
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Affiliation(s)
- Yoan Alemán
- Virology Department, Institute of Tropical Medicine “Pedro Kourí”, Havana City, Cuba
| | - Lore Vinken
- Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Vivian Kourí
- Virology Department, Institute of Tropical Medicine “Pedro Kourí”, Havana City, Cuba
| | - Lissette Pérez
- Virology Department, Institute of Tropical Medicine “Pedro Kourí”, Havana City, Cuba
| | - Alina Álvarez
- Virology Department, Institute of Tropical Medicine “Pedro Kourí”, Havana City, Cuba
| | - Yeissel Abrahantes
- Hospital at Institute of Tropical Medicine “Pedro Kourí”, Havana City, Cuba
| | - Carlos Fonseca
- Hospital at Institute of Tropical Medicine “Pedro Kourí”, Havana City, Cuba
| | - Jorge Pérez
- Hospital at Institute of Tropical Medicine “Pedro Kourí”, Havana City, Cuba
| | - Consuelo Correa
- Virology Department, Institute of Tropical Medicine “Pedro Kourí”, Havana City, Cuba
| | - Yudira Soto
- Virology Department, Institute of Tropical Medicine “Pedro Kourí”, Havana City, Cuba
| | - Yoeri Schrooten
- Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Anne-Mieke Vandamme
- Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
- Centro de Malária e outras Doenças Tropicais and Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universida de Nova de Lisboa, Lisboa, Portugal
| | - Kristel Van Laethem
- Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
- * E-mail:
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Acharya A, Vaniawala S, Shah P, Misra RN, Wani M, Mukhopadhyaya PN. Development, validation and clinical evaluation of a low cost in-house HIV-1 drug resistance genotyping assay for Indian patients. PLoS One 2014; 9:e105790. [PMID: 25157501 PMCID: PMC4144911 DOI: 10.1371/journal.pone.0105790] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 07/24/2014] [Indexed: 01/08/2023] Open
Abstract
Human Immunodeficiency Virus-1 (HIV-1) drug resistance genotyping assay is a part of clinical management of HIV-1 positive individuals under treatment with highly active antiretroviral therapy (HAART). Routine monitoring of drug resistance mutations in resource limited settings like India is not possible due to high cost of commercial drug resistance assays. In this study we developed an in-house, cost effective HIV-1 drug resistance genotyping assay for Indian patients and validated it against the US-FDA-approved ViroSeq HIV-1 drug resistance testing system. A reference panel of 20 clinical samples was used to develop and validate the assay against ViroSeq HIV-1 drug resistance testing system which was subsequently used to genotype a clinical panel of 225 samples. The Stanford HIV database was used to identify drug resistant mutations. The analytical sensitivity of the assay was 1000 HIV-1 RNA copies/ml of plasma sample while precision and reproducibility was 99.68±0.16% and 99.76±0.18% respectively. One hundred and one drug resistant mutations were detected by the in-house assay compared to 104 by ViroSeq system in the reference panel. The assay had 91.55% success rate in genotyping the clinical panel samples and was able to detect drug resistant mutations related to nucleoside reverse transcriptase inhibitor (NRTI), non-nucleoside reverse-transcriptase inhibitor (NNRTI) as well as protease inhibitor (PI) classes of antiretroviral drugs. It was found to be around 71.9% more cost effective compared to ViroSeq genotyping system. This evaluation of the assay on the clinical panel demonstrates its potential for monitoring clinical HIV-1 drug resistance mutations and population-based surveillance in resource limited settings like India.
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Affiliation(s)
- Arpan Acharya
- Department of Molecular Biology, Dr. D. Y. Patil Biotechnology & Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, Maharashtra, India
| | - Salil Vaniawala
- Department of Molecular Diagnostics, SN Genelab, Surat, Gujarat, India
| | - Parth Shah
- Department of Molecular Diagnostics, Supratech Micropath Laboratory & Research Institute, Ahmedabad, Gujarat, India
| | - Rabindra Nath Misra
- Department of Microbiology, Padmashree Dr. D. Y. Patil Medical College & Research Centre, Dr. D. Y. Patil Vidyapeeth, Pune, Maharashtra, India
| | - Minal Wani
- Department of Molecular Biology, Dr. D. Y. Patil Biotechnology & Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, Maharashtra, India
| | - Pratap N. Mukhopadhyaya
- Department of Microbiology, Interdisciplinary Science, Technology and Research Academy, AISC, Pune, Maharashtra, India
- * E-mail:
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