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Barik SK, Bansal AK, Mohanty PS, Tripathy SP, Hanna LE, Karunaianantham R, Pattabiraman S, Singh TP, Tandon R, Tomar S, Jena S, Patil SA, Mohanty KK. Detection of Drug Resistance Mutations in the Reverse Transcriptase Gene of HIV-1-Infected North Indian Population Failing First-Line Antiretroviral Therapy "A Follow-Up Cohort Study". AIDS Res Hum Retroviruses 2021; 37:796-805. [PMID: 33390085 DOI: 10.1089/aid.2020.0132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
We aim to characterize the drug resistance mutations in reverse transcriptase gene of HIV-1 subtype C-infected North Indian population in those who are failing first-line antiretroviral therapy (ART) and if these mutations are associated with mortality. We also attempted the assessment of switch over to second-line antiretroviral therapy in these patients. Based on the immunological marker CD4 count (<350 cubic/mm), 192 HIV/AIDS patients were selected and viral load was estimated in those who were enrolled from December 2009 to November 2016. Based on viral load, genotyping was carried out in 57 HIV-1 isolates (VL ≥1,000 copies/mL) by sequencing and drug resistance mutations were examined through the Stanford HIV Drug Resistance Database, USA. Among them, 21 (36.84%) first-line ART failure patients were shifted to second-line ART. These patients were followed for a period wide ranging from 10 months to 11 years. Drug resistance mutation M184V (ATG to GTA) (63.15%) associated with lamivudine and abacavir and K103N (AAG or AAA to AAU) (36.84%) associated with efavirenz and nevirapine were predominantly identified in first-line ART failure patients. During follow-up, it was observed that 3 out of 21 who were in second-line ART died, whereas 9 out of 36 died who were in the first-line ART. No mutation could be associated with mortality although TAM-2 mutations were absent in patients who died. This study indorses the need for a facility for viral load estimation and resistance monitoring in each treatment failure patient and availability of appropriate antiretroviral therapies.
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Affiliation(s)
- Sushanta Kumar Barik
- National JALMA Institute for Leprosy and Other Mycobacterial Diseases (Indian Council of Medical Research), Agra, India
| | - Avi Kumar Bansal
- National JALMA Institute for Leprosy and Other Mycobacterial Diseases (Indian Council of Medical Research), Agra, India
| | - Partha Sarathi Mohanty
- National JALMA Institute for Leprosy and Other Mycobacterial Diseases (Indian Council of Medical Research), Agra, India
| | - Srikanth Prasad Tripathy
- National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Luke Elizabeth Hanna
- National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Ramesh Karunaianantham
- National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | | | | | | | | | - Srikanta Jena
- Zoology Department, Ravenshaw University, Cuttack, India
| | - Shripad A. Patil
- National JALMA Institute for Leprosy and Other Mycobacterial Diseases (Indian Council of Medical Research), Agra, India
| | - Keshar Kunja Mohanty
- National JALMA Institute for Leprosy and Other Mycobacterial Diseases (Indian Council of Medical Research), Agra, India
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Tuberculosis research conducted over the years at the ICMR-National Institute for Research in Tuberculosis (ICMR-NIRT). Indian J Tuberc 2020; 67:S7-S15. [PMID: 33308675 DOI: 10.1016/j.ijtb.2020.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This review article highlights some of the key research conducted at the ICMR-National Institute for Research in Tuberculosis (ICMR-NIRT) over the years since its inception in 1956 till the present. The research carried out in the field of tuberculosis at ICMR-NIRT has been a joint effort between the ICMR, NIRT, the TB control program in India with assistance from World Health Organization (WHO) and the National Institutes of Health (NIH), USA. The research carried out at ICMR-NIRT has helped to formulate the national guidelines for the control and the management of tuberculosis in India. The major highlights of the research carried out at ICMR-NIRT are provided in this manuscript.
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Wang X, Cerrone M, Ferretti F, Castrillo N, Maartens G, McClure M, Boffito M. Pharmacokinetics of dolutegravir 100 mg once daily with rifampicin. Int J Antimicrob Agents 2019; 54:202-206. [DOI: 10.1016/j.ijantimicag.2019.04.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 01/14/2019] [Accepted: 04/09/2019] [Indexed: 12/12/2022]
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Nesakumar M, Haribabu H, Cheedarla N, Karunaianantham R, Kailasam N, Sathyamurthi P, Selvachithiram M, Tripathy SP, Hanna LE. Transmitted HIV-1 Drug Resistance in a Treatment-Naive Cohort of Recently Infected Individuals from Chennai, India. AIDS Res Hum Retroviruses 2019; 35:775-779. [PMID: 31001987 DOI: 10.1089/aid.2019.0022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A cross-sectional study was undertaken to examine the prevalence and pattern of HIV drug resistance mutations (DRMs) among recently HIV-1-infected and antiretroviral therapy (ART)-naive individuals from Chennai, South India. The HIV-1 pol gene encompassing the protease and reverse transcriptase (RT) regions were analyzed from 53 ART-naive HIV-1-infected individuals using an in-house method for identifying DRMs by genotyping. The overall prevalence of transmitted drug resistance (TDR) was found to be 11.3% (6/53), which is categorized as moderate level (5.0%-15.0%) of TDR according to the World Health Organization (WHO) survey guidelines. Surveillance drug resistance mutations to non-nucleoside reverse transcriptase inhibitors (NNRTI) were observed in 8.3% (n = 4) of the 48 RT sequences analyzed. No major DRMs related to the protease and nucleoside reverse transcriptase inhibitor (NRTIs) class of drugs were identified.
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Affiliation(s)
- Manohar Nesakumar
- Department of HIV/AIDS, National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Hemalatha Haribabu
- Department of HIV/AIDS, National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Narayanaiah Cheedarla
- Department of HIV/AIDS, National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Ramesh Karunaianantham
- Department of HIV/AIDS, National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | | | - Pattabiraman Sathyamurthi
- Department of HIV/AIDS, National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Murugesan Selvachithiram
- Department of HIV/AIDS, National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Srikanth Prasad Tripathy
- Department of HIV/AIDS, National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
| | - Luke Elizabeth Hanna
- Department of HIV/AIDS, National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai, India
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Sinha S, Gupta K, Khan NH, Mandal D, Kohli M, Das BK, Pandey RM. Higher Frequency of HIV-1 Drug Resistance and Increased Nucleoside Reverse Transcriptase Inhibitor Mutations among the HIV-1 Positive Antiretroviral Therapy-Naïve patients Coinfected With Mycobacterium tuberculosis Compared With Only HIV Infection in India. Infect Dis (Lond) 2018; 11:1178633718788870. [PMID: 30046244 PMCID: PMC6056791 DOI: 10.1177/1178633718788870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 06/24/2018] [Indexed: 11/16/2022] Open
Abstract
Background: Emergence of human immunodeficiency virus (HIV) drug resistance mutations
prior to highly active antiretroviral therapy is a serious problem in
clinical management of HIV/AIDS. Risk factors for appearance of drug
resistance mutations are not known. We hypothesize that
Mycobacterium tuberculosis infection may contribute to
rapid emergence of such mutations in antiretroviral therapy–naïve
patients. Methods: A total of 115 patients were recruited in this study of which 75 were HIV+TB+
coinfected (group 1) and 40 were HIV+TB− (group 2). Blood samples from all
the patients were collected and CD4+ cell counts; HIV-1 plasma viral load
and sequencing of protease and two-third region of reverse transcriptase of
HIV-1 was performed and analyzed for drug resistance pattern. Results: For patients with HIV+TB+, 10.6% (8/75) had mutations to non-nucleoside
reverse transcriptase inhibitors (NNRTIs), 4% (3/75) to nucleoside reverse
transcriptase inhibitors, and only 2.6% (2/75) patients had mutations to
protease inhibitors. Interestingly, for group 2 (HIV+TB−), there were only
NNRTI mutations found among these patients, and only 3 patients (7.5%) had
these drug-resistant mutations. Clade typing and phylogenetic tree analysis
showed HIV-1 subtype C predominance in these patients. Conclusions: Our study showed that higher percentage of HIV drug resistance mutations was
found among HIV+TB+ individuals compared with tuberculosis-uninfected
patients. Tuberculosis coinfection may be a risk factor for emergence of
high frequency of drug resistance mutations. Studies with a larger sample
size will help to confirm these findings from the Indian population.
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Affiliation(s)
- Sanjeev Sinha
- Department of Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, New Delhi, India
| | - Kartik Gupta
- Department of Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, New Delhi, India
| | - Nawaid Hussain Khan
- Department of Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, New Delhi, India
| | - Dibyakanti Mandal
- Department of Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, New Delhi, India
| | - Mikashmi Kohli
- Department of Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, New Delhi, India
| | - B K Das
- Department of Microbiology, All India Institute of Medical Sciences (AIIMS), New Delhi, New Delhi, India
| | - R M Pandey
- Department of Biostatistics, All India Institute of Medical Sciences (AIIMS), New Delhi, New Delhi, India
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Karade S, Chaturbhuj DN, Sen S, Joshi RK, Kulkarni SS, Shankar S, Gangakhedkar RR. HIV drug resistance following a decade of the free antiretroviral therapy programme in India: A review. Int J Infect Dis 2017; 66:33-41. [PMID: 29128646 DOI: 10.1016/j.ijid.2017.10.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/12/2017] [Accepted: 10/27/2017] [Indexed: 02/08/2023] Open
Abstract
OBJECTIVE The objective of this review was to assess the burden of HIV drug resistance mutations (DRM) in Indian adults exposed to first-line antiretroviral therapy (ART) as per national guidelines. METHODS An advanced search of the published literature on HIV drug resistance in India was performed in the PubMed and Scopus databases. Data pertaining to age, sex, CD4 count, viral load, and prevalence of nucleoside reverse transcriptase inhibitor (NRTI)/non-nucleoside reverse transcriptase inhibitor (NNRTI) DRM were extracted from each publication. Year-wise Indian HIV-1 reverse transcriptase (RT) sequences were retrieved from the Los Alamos HIV database and mutation analyses were performed. A time trend analysis of the proportion of sequences showing NRTI resistance mutations among individuals exposed to first-line ART was conducted. RESULTS Overall, 23 studies (1046 unique RT sequences) were identified indicating a prevalence of drug resistance to NRTI and NNRTI. The proportion of RT sequences with any DRM, any NRTI DRM, and any NNRTI DRM was 78.39%, 68.83%, and 73.13%, respectively. The temporal trend analysis of individual DRM from sequences retrieved during 2004-2014 indicated a rising trend in K65R mutations (p=0.013). CONCLUSIONS Although the overall burden of resistance against first-line ART agents remained steady over the study decade, periodic monitoring is essential. There is the need to develop an HIV-1 subtype C-specific resistance database in India.
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Affiliation(s)
- Santosh Karade
- HIV Drug Resistance Laboratory, National AIDS Research Institute (ICMR), Pune, India; Department of Microbiology, Armed Forces Medical College, Pune, India
| | - Devidas N Chaturbhuj
- HIV Drug Resistance Laboratory, National AIDS Research Institute (ICMR), Pune, India; Symbiosis International University, Lavale, Pune, India
| | - Sourav Sen
- Department of Microbiology, Armed Forces Medical College, Pune, India
| | - Rajneesh K Joshi
- Department of Epidemiology and Biostatistics, National AIDS Research Institute, Pune, India; Department of Community Medicine, Armed Forces Medical College, Pune, India
| | - Smita S Kulkarni
- Department of Molecular Virology, National AIDS Research Institute, Pune, India
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von Braun A, Sekaggya-Wiltshire C, Scherrer AU, Magambo B, Kambugu A, Fehr J, Castelnuovo B. Early virological failure and HIV drug resistance in Ugandan adults co-infected with tuberculosis. AIDS Res Ther 2017; 14:1. [PMID: 28086929 PMCID: PMC5237283 DOI: 10.1186/s12981-016-0128-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 12/07/2016] [Indexed: 11/30/2022] Open
Abstract
Purpose This cross-sectional study took place in the integrated tuberculosis (TB) clinic of a large outpatient clinic for HIV-infected patients in Kampala, Uganda. The purpose of this study was to describe the proportion of TB/HIV co-infected adults with virological failure, type and frequency of HIV drug resistance-associated mutations, and the proportion of patients with suboptimal efavirenz levels. Methods HIV-1 plasma viral loads, CD4 cell count measurements, and efavirenz serum concentrations were done in TB/HIV co-infected adults. Genotypic resistance testing was performed in case of confirmed virological failure. Results After a median time on ART of 6 months, virological failure was found in 22/152 patients (14.5%). Of 147 participants with available efavirenz serum concentration, 26 (17.6%) had at least one value below the reference range, including 20/21 (95.2%) patients with confirmed virological failure. Genotypic resistance testing was available for 16/22 (72.7%) patients, of which 15 (93.8%) had at least one major mutation, most commonly M184V (81.2%) and K103NS (68.8%). Conclusion We found a high proportion of TB/HIV co-infected patients with virological failure, the majority of which had developed relevant resistance-mutations after a median time on anti-retroviral treatment (ART) of 6 months. Virological monitoring should be prioritized in TB/HIV co-infected patients in resource-limited settings.
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Pandey SS, Cherian S, Thakar M, Paranjape RS. Short Communication: Phylogenetic and Molecular Characterization of Six Full-Length HIV-1 Genomes from India Reveals a Monophyletic Lineage of Indian Sub-Subtype A1. AIDS Res Hum Retroviruses 2016; 32:489-502. [PMID: 26756665 DOI: 10.1089/aid.2015.0207] [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
Although HIV-1 epidemic in India is mainly driven by subtype C, subtype A has been reported for over two decades. This is the first comprehensive analysis of sequences of HIV-1 subtype A from India, based on the near full-length genome sequences of six different HIV-1 subtype A Indian isolates along with available partial gene sequences from India and global sequences. The phylogenetic analyses revealed the convergence of all Indian whole-genome sequences and majority of the partial gene sequences to a single node with the sequences most closely related to African sub-subtype A1. The presence of the signature motifs consistent with those observed in subtype A and CTL epitopes characterized specifically for subtype A1 were observed among the study sequences. Deletion of LY amino acid of LYPXnL motif of p6gag and one amino acid in V3 loop have been observed among the study isolates, which have also been observed in a few sequences from East Africa. Overall, the results are indicative of a monophyletic lineage or founder effect of the Indian epidemic due to sub-subtype A1 and supportive of a possible migration of subtype A1 into India from East Africa.
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Affiliation(s)
| | - Sarah Cherian
- Bioinformatics Group, National Institute of Virology (ICMR), Pune, India
| | - Madhuri Thakar
- Department of Immunology, National AIDS Research Institute (ICMR), Pune, India
| | - Ramesh S. Paranjape
- Department of Immunology, National AIDS Research Institute (ICMR), Pune, India
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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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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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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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Patil RT, Gupta RM, Sen S, Tripathy SP, Chaturbhuj DN, Hingankar NK, Paranjape RS. Emergence of drug resistance in human immunodeficiency virus type 1 infected patients from pune, India, at the end of 12 months of first line antiretroviral therapy initiation. ISRN AIDS 2014; 2014:674906. [PMID: 25006528 PMCID: PMC4003797 DOI: 10.1155/2014/674906] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 03/16/2014] [Indexed: 02/05/2023]
Abstract
Introduction. In India, 4,86,173 HIV infected patients are on first line antiretroviral therapy (ART) as of January 2012. HIV drug resistance (HIVDR) is drug and regimen-specific and should be balanced against the benefits of providing a given ART regimen. Material & Methods. The emergence of HIVDR mutations in a cohort of 100 consecutive HIV-1 infected individuals attending ART centre, on first line ART for 12 months, was studied. CD4(+) T-cell counts and plasma HIV-1 RNA level were determined. Result. Out of the 100 HIV-1 infected individuals, 81 showed HIVDR prevention (HIV-1 RNA level < 1000/mL), while the remaining 19 had HIV-1 viral RNA level > 1000/mL. HIVDR genotyping was carried out for individuals with evidence of virologic failure (HIV-1 RNA level > 1000/mL). The most frequent NRTI-associated mutation observed was M184V, while K103N/S was the commonest mutation at NNRTI resistance position. Conclusion. Our study has revealed the emergence of HIVDR in HIV-1 infected patients at the end of 12 months of first line ART initiation. For NRTIs, the prevalence of HIVDR mutations was 9% and 10% for NNRTIs. Our findings will contribute information in evidence-based decision making with reference to first and second line ART delivery and prevention of HIVDR emergence.
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Affiliation(s)
- Rajesh T. Patil
- Department of Microbiology, Azeezia Institute of Medical Sciences & Research, Kollam, Kerala, India
| | - Rajiv M. Gupta
- DDGMS (IT) Office of Directorate General of Medical Services (Army) Integrated HQ of MoDAG's Branch, L Block, New Delhi, India
| | - Sourav Sen
- Department of Microbiology, Army Hospital (Research & Referral), Delhi, India
| | - Srikanth P. Tripathy
- National JALMA Institute of Leprosy and other Mycobacterial Diseases (Indian Council of Medical Research), Agra, India
| | | | - Nitin K. Hingankar
- National AIDS Research Institute (Indian Council of Medical Research), Pune, India
| | - Ramesh S. Paranjape
- National AIDS Research Institute (Indian Council of Medical Research), Pune, India
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Neogi U, Gupta S, Palchaudhuri R, Rao SD, Shastri S, Diwan V, Laishram RS, De Costa A, Shet A. Limited evolution but increasing trends of primary non-nucleoside reverse transcriptase inhibitor resistance mutations in therapy-naive HIV-1-infected individuals in India. Antivir Ther 2014; 19:813-8. [DOI: 10.3851/imp2769] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2014] [Indexed: 10/25/2022]
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Neogi U, Sahoo PN, De Costa A, Shet A. High viremia and low level of transmitted drug resistance in anti-retroviral therapy-naïve perinatally-infected children and adolescents with HIV-1 subtype C infection. BMC Infect Dis 2012; 12:317. [PMID: 23171203 PMCID: PMC3537751 DOI: 10.1186/1471-2334-12-317] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 11/20/2012] [Indexed: 12/28/2022] Open
Abstract
Background High plasma viremia in HIV-1 infection is associated with rapid CD4 cell decline and faster disease progression. Children with HIV infection have high viral loads, particularly in early childhood. In this study we sought to understand the relationship between duration of HIV-1 infection and viral dynamics among perinatally-infected children and adolescents in India along with transmitted drug resistance in this population. Methods During 2007–2011, cross-sectional samples were collected from ART-naïve children (n = 105) with perinatally-acquired HIV infection, aged 2–16 years from Bangalore, India. CD4 counts, viral load and in-house genotyping were performed and transmitted drug resistance mutations were identified using the World Health Organization recommendations for Surveillance of Drug Resistance Mutations (SDRM_2009) list. Results Among 105 children studied, 73.3% (77/105) were asymptomatic, but had a median viral load of 5.24 log copies/mL (IQR 4.62-5.66). In the adolescent age group, 54% (21/39) had high levels of viremia (median 5.14 log copies/mL) but were asymptomatic. HIV-1 subtyping identified 98% strains (103/105) as subtype C; one A1 and one unique recombinant form (URF). Transmitted NRTI resistance was 1.9% (2/105); NNRTI resistance was 4.8% (5/105) and overall prevalence of transmitted drug resistance was 5.7% (6/105). Conclusions The high burden of plasma viremia found among untreated asymptomatic adolescents needs to be addressed both from an individual angle to halt disease progression, and from a public health perspective to arrest horizontal transmission. The low level of transmitted drug resistance among perinatally-infected children is reassuring; however with improving ART access globally, regular genotyping surveillance is indicated.
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Affiliation(s)
- Ujjwal Neogi
- Division of Infectious Disease, Department of Medicine, Huddinge,Karolinska Institutet, Stockholm, Sweden
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The Impact of HIV Genetic Polymorphisms and Subtype Differences on the Occurrence of Resistance to Antiretroviral Drugs. Mol Biol Int 2012; 2012:256982. [PMID: 22792462 PMCID: PMC3390109 DOI: 10.1155/2012/256982] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Accepted: 04/12/2012] [Indexed: 12/20/2022] Open
Abstract
The vast majority of reports on drug resistance deal with subtype B infections in developed countries, and this is largely due to historical delays in access to antiretroviral therapy (ART) on a worldwide basis. This notwithstanding the concept that naturally occurring polymorphisms among different non-B subtypes can affect HIV-1 susceptibility to antiretroviral drugs (ARVs) is supported by both enzymatic and virological data. These findings suggest that such polymorphisms can affect both the magnitude of resistance conferred by some major mutations as well as the propensity to acquire certain resistance mutations, even though such differences are sometimes difficult to demonstrate in phenotypic assays. It is mandatory that tools are optimized to assure accurate measurements of drug susceptibility in non-B subtypes and to recognize that each subtype may have a distinct resistance profile and that differences in resistance pathways may also impact on cross-resistance and the choice of regimens to be used in second-line therapy. Although responsiveness to first-line therapy should not theoretically be affected by considerations of viral subtype and drug resistance, well-designed long-term longitudinal studies involving patients infected by viruses of different subtypes should be carried out.
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Saravanan S, Vidya M, Balakrishnan P, Kantor R, Solomon SS, Katzenstein D, Kumarasamy N, Yeptomi T, Sivamalar S, Rifkin S, Mayer KH, Solomon S. Viremia and HIV-1 drug resistance mutations among patients receiving second-line highly active antiretroviral therapy in Chennai, Southern India. Clin Infect Dis 2012; 54:995-1000. [PMID: 22323567 DOI: 10.1093/cid/cir967] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND A cross-sectional study among individuals receiving second-line antiretroviral treatment was conducted to report on the level of detectable viremia and the types of drug resistance mutations among those with detectable human immunodeficiency virus (HIV) type 1 plasma viral loads (PVLs). METHODS PVLs were measured using Abbott m2000rt real-time polymerase chain reaction, and genotyping was performed with the ViroSeq genotyping system, version 2.0, and ViroSeq analysis software, version 2.8. RESULTS Of 107 patient plasma specimens consecutively analyzed, 30 (28%) had undetectable PVLs (<150 copies/mL), and 77 (72%) were viremic with a median PVL of 5450 copies/mL (interquartile range, 169-1 997 967). Sequencing was done for 107 samples with PVLs >2000 copies/mL: 33 patients (73%) had 1 of the protease (PR) inhibitor mutations; 41 (91%) had nucleoside reverse-transcriptase inhibitor (NRTI) mutations; 33 (73%) had non-NRTI (NNRTI) mutations; and 30 (66.7%) had both NRTI and NNRTI mutations. Triple-class resistance to NRTIs, NNRTIs, and PR inhibitors was observed in 24 (53%) patients. Based on the mutational profiles observed, all 45 sequences were susceptible to darunavir and tipranavir, whereas 47% showed resistance to lopinavir, 58% showed resistance to atazanavir, and >60% showed resistance to saquinavir, indinavir, nelfinavir, and fosamprenavir. CONCLUSIONS The results of the study showed that the majority of patients receiving second-line antiretroviral therapy started to accumulate PR resistance mutations, and the mutation profiles suggest that darunavir might be the drug of choice for third-line regimens in India.
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Swaminathan S, Padmapriyadarsini C, Venkatesan P, Narendran G, Ramesh Kumar S, Iliayas S, Menon PA, Selvaraju S, Pooranagangadevi NP, Bhavani PK, Ponnuraja C, Dilip M, Ramachandran R. Efficacy and safety of once-daily nevirapine- or efavirenz-based antiretroviral therapy in HIV-associated tuberculosis: a randomized clinical trial. Clin Infect Dis 2011; 53:716-24. [PMID: 21890776 DOI: 10.1093/cid/cir447] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Nevirapine (NVP) can be safely and effectively administered once-daily but has not been assessed in human immunodeficiency virus (HIV)-infected patients with tuberculosis (TB). We studied the safety and efficacy of once-daily NVP, compared with efavirenz (EFV; standard therapy); both drugs were administered in combination with 2 nucleoside reverse-transcriptase inhibitors. METHODS An open-label, noninferiority, randomized controlled clinical trial was conducted at 3 sites in southern India. HIV-infected patients with TB were treated with a standard short-course anti-TB regimen (2EHRZ(3)/4RH(3); [2 months of Ethambutol, Isoniazid, Rifampicin, Pyrazinamide / 4 months of Isoniazid and Rifampicin] thrice weekly) and randomized to receive once-daily EFV at a dose of 600 mg or NVP at a dose of 400 mg (after 14 days of 200 mg administered once daily) with didanosine 250/400 mg and lamivudine 300 mg after 2 months. Sputum smears and mycobacterial cultures were performed every month. CD4+ cell count, viral load, and liver function test results were monitored periodically. Primary outcome was a composite of death, virological failure, default, or serious adverse event (SAE) at 24 weeks. Both intent-to-treat and per protocol analyses were done, and planned interim analyses were performed. RESULTS A total of 116 patients (75% [87 patients] of whom had pulmonary TB), with a mean age of 36 years, a median CD4+ cell count of 84 cells/mm(3), and a median viral load of 310 000 copies/mL, were randomized. At 24 weeks, 50 of 59 patients in the EFV group and 37 of 57 patients in the NVP group had virological suppression (P = .024). There were no deaths, 1 SAE, and 5 treatment failures in the EFV arm, compared with 5 deaths, 2 SAEs, and 10 treatment failures in the NVP arm. The trial was halted by the data and safety monitoring board at the second interim analysis. Favorable TB treatment outcomes were observed in 93% of the patients in the EFV arm and 84% of the patients in the NVP arm (P = .058). CONCLUSIONS Compared with a regimen of didanosine, lamivudine, and EFV, a regimen of once-daily didanosine, lamivudine, and NVP was inferior and was associated with more frequent virologic failure and death. Clinical Trials Registration. NCT00332306.
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Affiliation(s)
- Soumya Swaminathan
- Department of Clinical Research, Tuberculosis Research Centre, Indian Council of Medical Research, Chennai, India.
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Prediction of drug-resistance in HIV-1 subtype C based on protease sequences from ART naive and first-line treatment failures in North India using genotypic and docking analysis. Antiviral Res 2011; 92:213-8. [PMID: 21875619 DOI: 10.1016/j.antiviral.2011.08.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Revised: 08/01/2011] [Accepted: 08/08/2011] [Indexed: 11/22/2022]
Abstract
Genotyping reveal emergence of drug resistance (DR)-related mutations in HIV-1 protease (PR) gene in the first-line treatment failure patients as per Stanford DR database. In order to have a subtype C specific prediction model, a three dimensional structure of local wild type C variant is created and the identified mutations were introduced to assess the mutational effects on protease inhibitors (PI) in a homology model. We estimated viral load, CD4 count and conducted DR genotyping in HIV isolates from 129 therapy naive and 20 first-line treatment failure individuals. Several genotypic variations, as compared to subtype B sequence in the Stanford gene database were detected in HIV-1 subtype C isolates from treatment naive individuals. Among these, nine mutations (12S, 15V, 19I, 36I, 41K, 63P, 69K, 89M, 93L) occurred in more than 60% of the isolates and were considered as local wild type for molecular modelling studies. No major mutations were seen in the PR sequences in isolates from treatment-naive individuals, although isolates from two patients had T74S mutation, known to be associated with reduced susceptibility to nelfinavir (NFV) and a combination of M36I, H69K and L89M mutations found in isolates from 77 patients (59.7%), considered to be conferring resistance to tipranavir (TPV) according to ANRS algorithm. Among the first-line treatment failures, an isolate from one patient showed L33F, I47T, M46G, and G48E mutations conferring intermediate resistance to saquinavir (SQV) and lopinavir (LPV). Though the docking energy scores are in agreement with this interpretation for SQV, it, however, indicated these mutations to be causing intermediate to high level resistance to atazanavir (ATV) and tipranavir (TPV) but making it susceptible to LPV. The patient finally responded to a second-line regimen containing 3TC, AZT and LPV with significant viral suppression. All the DR genotyping studies analyse the results using available databases which are all based on subtype B specific sequences. The proposed homology model in this study is unique, as it may predict subtype C specific susceptibility criteria for the available PIs.
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Affiliation(s)
- Mark A Wainberg
- McGill University AIDS Centre, Lady Davis Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada.
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Selection of nonnucleoside reverse transcriptase inhibitor-associated mutations in HIV-1 subtype C: evidence of etravirine cross-resistance. AIDS 2011; 25:1123-6. [PMID: 21505320 DOI: 10.1097/qad.0b013e328346269f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Prevalence of etravirine genotypic resistance was assessed among 92 HIV-1C-infected patients failing nevirapine and efavirenz-based regimens from a cohort of 552 Indian patients. Overall, prevalence of etravirine cross-resistance identified using the Tibotec Weighted Score was 41% (31.5% intermediately-resistant and 9.8% fully-resistant). The most frequently described nonnucleoside reverse transcriptase inhibitor-associated mutations included Y181 (35.9%), K101 (20.7%), G190 (17.4%), and V108 (15.2%). The resistant group demonstrated higher viral load (P = 0.01) and longer duration of antiretroviral treatment (P = 0.03) compared with the susceptible group.
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Wainberg MA, Brenner BG. Role of HIV Subtype Diversity in the Development of Resistance to Antiviral Drugs. Viruses 2010; 2:2493-508. [PMID: 21994627 PMCID: PMC3185584 DOI: 10.3390/v2112493] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 10/26/2010] [Accepted: 10/28/2010] [Indexed: 12/13/2022] Open
Abstract
Despite the fact that over 90% of HIV-1 infected people worldwide harbor non-subtype B variants of HIV-1, knowledge of resistance mutations in non-B HIV-1 and their clinical relevance is limited. Due to historical delays in access to antiretroviral therapy (ART) on a worldwide basis, the vast majority of reports on drug resistance deal with subtype B infections in developed countries. However, both enzymatic and virological data support the concept that naturally occurring polymorphisms among different nonB subtypes can affect HIV-1 susceptibility to antiretroviral drugs (ARVs), the magnitude of resistance conferred by major mutations, and the propensity to acquire some resistance mutations. Tools need to be optimized to assure accurate measurements of drug susceptibility of non-B subtypes. Furthermore, there is a need to recognize that each subtype may have a distinct resistance profile and that differences in resistance pathways may also impact on cross-resistance and the selection of second-line regimens. It will be essential to pay attention to newer drug combinations in well designed long-term longitudinal studies involving patients infected by viruses of different subtypes.
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Affiliation(s)
- Mark A Wainberg
- McGill University AIDS Centre, Jewish General Hospital, 3755 Cote-Ste-Catherine Road, Montreal, Quebec, H3T 1E2, Canada; E-Mail:
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