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Caniels TG, Bontjer I, van der Straten K, Poniman M, Burger JA, Appelman B, Lavell HAA, Oomen M, Godeke GJ, Valle C, Mögling R, van Willigen HDG, Wynberg E, Schinkel M, van Vught LA, Guerra D, Snitselaar JL, Chaturbhuj DN, Cuella Martin I, Moore JP, de Jong MD, Reusken C, Sikkens JJ, Bomers MK, de Bree GJ, van Gils MJ, Eggink D, Sanders RW. Emerging SARS-CoV-2 variants of concern evade humoral immune responses from infection and vaccination. Sci Adv 2021; 7:eabj5365. [PMID: 34516917 PMCID: PMC8442901 DOI: 10.1126/sciadv.abj5365] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/13/2021] [Indexed: 05/21/2023]
Abstract
Emerging SARS-CoV-2 variants of concern (VOCs) pose a threat to human immunity induced by natural infection and vaccination. We assessed the recognition of three VOCs (B.1.1.7, B.1.351, and P.1) in cohorts of COVID-19 convalescent patients (n = 69) and Pfizer-BioNTech vaccine recipients (n = 50). Spike binding and neutralization against all three VOCs were substantially reduced in most individuals, with the largest four- to sevenfold reduction in neutralization being observed against B.1.351. While hospitalized patients with COVID-19 and vaccinees maintained sufficient neutralizing titers against all three VOCs, 39% of nonhospitalized patients exhibited no detectable neutralization against B.1.351. Moreover, monoclonal neutralizing antibodies show sharp reductions in their binding kinetics and neutralizing potential to B.1.351 and P.1 but not to B.1.1.7. These data have implications for the degree to which pre-existing immunity can protect against subsequent infection with VOCs and informs policy makers of susceptibility to globally circulating SARS-CoV-2 VOCs.
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Affiliation(s)
- Tom G. Caniels
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Ilja Bontjer
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Karlijn van der Straten
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
- Department of Internal Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Meliawati Poniman
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Judith A. Burger
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Brent Appelman
- Center for Experimental and Molecular Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - H. A. Ayesha Lavell
- Department of Internal Medicine, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Melissa Oomen
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Gert-Jan Godeke
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Coralie Valle
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Ramona Mögling
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Hugo D. G. van Willigen
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Elke Wynberg
- Department of Infectious Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
- Public Health Service of Amsterdam, Amsterdam, Netherlands
| | - Michiel Schinkel
- Center for Experimental and Molecular Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Lonneke A. van Vught
- Center for Experimental and Molecular Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Denise Guerra
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Jonne L. Snitselaar
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Devidas N. Chaturbhuj
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Isabel Cuella Martin
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Amsterdam UMC COVID-19 S3/HCW study group
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
- Department of Internal Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
- Center for Experimental and Molecular Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
- Department of Internal Medicine, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
- Department of Infectious Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
- Public Health Service of Amsterdam, Amsterdam, Netherlands
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - John P. Moore
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Menno D. de Jong
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Chantal Reusken
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Jonne J. Sikkens
- Department of Internal Medicine, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Marije K. Bomers
- Department of Internal Medicine, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Godelieve J. de Bree
- Department of Internal Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Marit J. van Gils
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Dirk Eggink
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Rogier W. Sanders
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
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Caniels TG, Bontjer I, van der Straten K, Poniman M, Burger JA, Appelman B, Lavell AHA, Oomen M, Godeke GJ, Valle C, Mögling R, van Willigen HDG, Wynberg E, Schinkel M, van Vught LA, Guerra D, Snitselaar JL, Chaturbhuj DN, Martin IC, Moore JP, de Jong MD, Reusken C, Sikkens JJ, Bomers MK, de Bree GJ, van Gils MJ, Eggink D, Sanders RW. Emerging SARS-CoV-2 variants of concern evade humoral immune responses from infection and vaccination. medRxiv 2021. [PMID: 34100023 DOI: 10.1101/2021.05.26.21257441] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Emerging SARS-CoV-2 variants pose a threat to human immunity induced by natural infection and vaccination. We assessed the recognition of three variants of concern (B.1.1.7, B.1.351 and P.1) in cohorts of COVID-19 patients ranging in disease severity (n = 69) and recipients of the Pfizer/BioNTech vaccine (n = 50). Spike binding and neutralization against all three VOC was substantially reduced in the majority of samples, with the largest 4-7-fold reduction in neutralization being observed against B.1.351. While hospitalized COVID-19 patients and vaccinees maintained sufficient neutralizing titers against all three VOC, 39% of non-hospitalized patients did not neutralize B.1.351. Moreover, monoclonal neutralizing antibodies (NAbs) show sharp reductions in their binding kinetics and neutralizing potential to B.1.351 and P.1, but not to B.1.1.7. These data have implications for the degree to which pre-existing immunity can protect against subsequent infection with VOC and informs policy makers of susceptibility to globally circulating SARS-CoV-2 VOC.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Chaturbhuj DN, Nirmalkar AP, Paranjape RS, Tripathy SP. Evaluation of a cost effective in-house method for HIV-1 drug resistance genotyping using plasma samples. PLoS One 2014; 9:e87441. [PMID: 24533056 PMCID: PMC3922725 DOI: 10.1371/journal.pone.0087441] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 12/25/2013] [Indexed: 11/18/2022] Open
Abstract
Objectives Validation of a cost effective in-house method for HIV-1 drug resistance genotyping using plasma samples. Design The validation includes the establishment of analytical performance characteristics such as accuracy, reproducibility, precision and sensitivity. Methods The accuracy was assessed by comparing 26 paired Virological Quality Assessment (VQA) proficiency testing panel sequences generated by in-house and ViroSeq Genotyping System 2.0 (Celera Diagnostics, US) as a gold standard. The reproducibility and precision were carried out on five samples with five replicates representing multiple HIV-1 subtypes (A, B, C) and resistance patterns. The amplification sensitivity was evaluated on HIV-1 positive plasma samples (n = 88) with known viral loads ranges from 1000–1.8 million RNA copies/ml. Results Comparison of the nucleotide sequences generated by ViroSeq and in-house method showed 99.41±0.46 and 99.68±0.35% mean nucleotide and amino acid identity respectively. Out of 135 Stanford HIVdb listed HIV-1 drug resistance mutations, partial discordance was observed at 15 positions and complete discordance was absent. The reproducibility and precision study showed high nucleotide sequence identities i.e. 99.88±0.10 and 99.82±0.20 respectively. The in-house method showed 100% analytical sensitivity on the samples with HIV-1 viral load >1000 RNA copies/ml. The cost of running the in-house method is only 50% of that for ViroSeq method (112$ vs 300$), thus making it cost effective. Conclusions The validated cost effective in-house method may be used to collect surveillance data on the emergence and transmission of HIV-1 drug resistance in resource limited countries. Moreover, the wide applications of a cost effective and validated in-house method for HIV-1 drug resistance testing will facilitate the decision making for the appropriate management of HIV infected patients.
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Affiliation(s)
- Devidas N. Chaturbhuj
- Drug Resistance Lab, National AIDS Research Institute, Indian Council of Medical Research, Bhosari, Pune, India
| | - Amit P. Nirmalkar
- Department of Epidemiology & Biostatistics, National AIDS Research Institute, Indian Council of Medical Research, Bhosari, Pune, India
| | - Ramesh S. Paranjape
- National AIDS Research Institute, Indian Council of Medical Research, Bhosari, Pune, India
| | - Srikanth P. Tripathy
- National JALMA Institute Of Leprosy And Other Mycobacterial Diseases, Indian Council of Medical Research, Bhosari, Agra, India
- * E-mail:
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Chaturbhuj DN, Deshmukh PS, Hingankar NK, Siddhaarth K, Deshpande SN, Sen S, Kabra S, Paranjape RS, Tripathy SP. Evaluations of an in-house drug resistance method for HIV-1 drug resistance using ViroSeq™ 2.0 genotyping system as a gold standard. J Virol Methods 2013; 189:87-92. [PMID: 23353551 DOI: 10.1016/j.jviromet.2013.01.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 12/14/2012] [Accepted: 01/02/2013] [Indexed: 02/08/2023]
Abstract
An in-house method was evaluated for its efficiency to detect the HIV-1 drug resistance mutations. This method was compared with the ViroSeq™ Genotyping System 2.0 (Celera Diagnostics, US) a gold standard. Sixty-five stored plasma samples, previously tested for HIV-1 drug resistance using the ViroSeq™ method were used to evaluate the in-house method. Out of the sixty five plasma samples, sixty were HIV-1 positive clinical samples; four samples from the Virology Quality Assessment (VQA) program and one positive control from the ViroSeq™ kit were used in this study. The sequences generated by the ViroSeq™ and an in-house method showed 99.5±0.5% and 99.7±0.4% (mean±SD) nucleotide and amino acid identity, respectively. Out of 214 Stanford HIVdb listed HIV-1 drug resistance mutations in the protease and reverse transcriptase regions, concordance was observed in 203 (94.9%), partial discordance in 11 (5.1%) and complete discordance was absent. The in-house primers are broadly sensitive in genotyping multiple HIV-1 group M subtypes. The amplification sensitivity of the in-house method was 1000 copies/ml. The evaluation of the in-house method provides results comparable with that of ViroSeq™ method thus, making the in-house method suitable for HIV-1 drug resistance testing in the developing countries.
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Affiliation(s)
- Devidas N Chaturbhuj
- National AIDS Research Institute, Plot 73, 'G' Block, M.I.D.C., Bhosari, Pune 411 026, India.
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Hingankar NK, Thorat SR, Deshpande A, Rajasekaran S, Chandrasekar C, Kumar S, Srikantiah P, Chaturbhuj DN, Datkar SR, Deshmukh PS, Kulkarni SS, Sane S, Reddy DCS, Garg R, Jordan MR, Kabra S, Tripathy SP, Paranjape RS. Initial virologic response and HIV drug resistance among HIV-infected individuals initiating first-line antiretroviral therapy at 2 clinics in Chennai and Mumbai, India. Clin Infect Dis 2012; 54 Suppl 4:S348-54. [PMID: 22544202 DOI: 10.1093/cid/cis005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Human immunodeficiency virus drug resistance (HIVDR) in cohorts of patients initiating antiretroviral therapy (ART) at clinics in Chennai and Mumbai, India, was assessed following World Health Organization (WHO) guidelines. Twelve months after ART initiation, 75% and 64.6% of participants at the Chennai and Mumbai clinics, respectively, achieved viral load suppression of <1000 copies/mL (HIVDR prevention). HIVDR at initiation of ART (P <.05) and 12-month CD4 cell counts <200 cells/μL (P <.05) were associated with HIVDR at 12 months. HIVDR prevention exceeded WHO guidelines (≥ 70%) at the Chennai clinic but was below the target in Mumbai due to high rates of loss to follow-up. Findings highlight the need for defaulter tracing and scale-up of routine viral load testing to identify patients failing first-line ART.
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Thorat SR, Chaturbhuj DN, Hingankar NK, Chandrasekhar V, Koppada R, Datkar SR, Srikantiah P, Garg R, Kabra S, Haldar P, Reddy DC, Bachani D, Tripathy SP, Paranjape RS. Surveillance of transmitted HIV type 1 drug resistance among HIV type 1-positive women attending an antenatal clinic in Kakinada, India. AIDS Res Hum Retroviruses 2011; 27:1291-7. [PMID: 21568760 DOI: 10.1089/aid.2011.0036] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The World Health Organizations HIV Drug Resistance (WHO HIVDR) Threshold survey method was used to assess transmitted HIVDR in newly diagnosed HIV-1-infected primigravida women attending the Prevention of Parent to Child Transmission (PPTCT) centers in Kakinada, in whom it is likely that the infection had recently occurred. Out of the 56 consecutively collected eligible specimens, 51 were tested using the ViroSeq RT-PCR method (Abbott Germany) to obtain 47 consecutive sequences for the HIV-1 protease (PR) and reverse transcriptase (RT) region. As per the 2009 WHO list of mutations for surveillance of transmitted HIVDR, only one nonnucleoside reverse transcriptase inhibitor (NNRTI) mutation was detected at K101E from all specimens tested, suggesting a low prevalence (<5%) of resistance to NNRTIs and no mutations were detected at other sites, suggesting a low prevalence (<5%) of resistance to nucleoside reverse transcriptase inhibitors (NRTI) and protease inhibitors (PI) drug classes as well. Phylogenetic analysis showed all sequences belonged to HIV-1 subtype C. In the wake of antiretroviral treatment (ART) scale-up, future evaluation of transmitted HIVDR is essential in Kakinada as well as in other regions of India.
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Affiliation(s)
| | | | | | | | | | | | - Padmini Srikantiah
- World Health Organization, South East Asia Regional Office, New Delhi, India
| | - Renu Garg
- World Health Organization, South East Asia Regional Office, New Delhi, India
| | - Sandhya Kabra
- National AIDS Control Organization, Ministry of Health and Family Welfare, New Delhi, India
| | - Partha Haldar
- World Health Organization, India Country Office at New Delhi, New Delhi, India
| | - Dandu C.S. Reddy
- World Health Organization, India Country Office at New Delhi, New Delhi, India
| | - Damodar Bachani
- National AIDS Control Organization, Ministry of Health and Family Welfare, New Delhi, India
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Chaturbhuj DN, Hingankar NK, Srikantiah P, Garg R, Kabra S, Deshmukh PS, Jadhav SD, Thorat SR, Datkar SR, Mehta P, Ingole N, Mathur M, Ramachandran A, Haldar P, Reddy D, Bachani D, Rao S, Tripathy SP, Paranjape RS. Transmitted HIV drug resistance among HIV-infected voluntary counseling and testing centers (VCTC) clients in Mumbai, India. AIDS Res Hum Retroviruses 2010; 26:927-32. [PMID: 20704495 DOI: 10.1089/aid.2010.0032] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A survey for transmitted HIV drug resistance (HIVDR) was conducted according to WHO guidelines among clients newly diagnosed with HIV-1 infection at two voluntary counseling and testing centers (VCTC) in Mumbai. HIVDR testing was performed using the ViroSeq RT-PCR method (Abbott). Out of 50 successfully amplified and sequenced specimens, analysis of the first 34 consecutively collected specimens revealed no nucleoside reverse transcriptase inhibitor, nonnucleoside reverse transcriptase inhibitor, or protease inhibitor mutations from the 2007 WHO list of mutations for surveillance of transmitted HIVDR, indicating that the prevalence of transmitted HIVDR to all three drug classes was <5% among recently infected VCTC clients in Mumbai. The phylogenetic analysis revealed that all samples belonged to HIV-1 subtype C. Continued ART program monitoring and further evaluation of transmitted HIV drug resistance in coming years are essential in Mumbai as well as in other regions of the country in which ART is being scaled up rapidly.
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Affiliation(s)
| | | | - Padmini Srikantiah
- World Health Organization, South East Asia Regional Office, New Delhi, India
| | - Renu Garg
- World Health Organization, South East Asia Regional Office, New Delhi, India
| | - Sandhya Kabra
- Formerly at National AIDS Control Organization, Ministry of Health and Family Welfare, New Delhi, India
| | | | | | | | | | | | | | | | | | - Partha Haldar
- World Health Organization, South East Asia Regional Office, New Delhi, India
| | - D.C.S. Reddy
- World Health Organization, South East Asia Regional Office, New Delhi, India
| | - Damodar Bachani
- Formerly at National AIDS Control Organization, Ministry of Health and Family Welfare, New Delhi, India
| | - Sujatha Rao
- Formerly at National AIDS Control Organization, Ministry of Health and Family Welfare, New Delhi, India
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