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Mbuagbaw L, Garcia C, Brenner B, Cecchini D, Chakroun M, Djiadeu P, Holguin A, Mor O, Parkin N, Santoro MM, Ávila-Ríos S, Fokam J, Phillips A, Shafer RW, Jordan MR. Checklist for studies of HIV drug resistance prevalence or incidence: rationale and recommended use. Lancet HIV 2023; 10:e684-e689. [PMID: 37716367 PMCID: PMC11060097 DOI: 10.1016/s2352-3018(23)00173-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 05/24/2023] [Accepted: 07/05/2023] [Indexed: 09/18/2023]
Abstract
HIV drug resistance (HIVDR) is a major challenge to the effectiveness of antiretroviral therapy. Global efforts in addressing HIVDR require clear, transparent, and replicable reporting in HIVDR studies. We describe the rationale and recommended use of a checklist that should be included in reports of HIVDR incidence and prevalence. After preliminary consultations with experts on HIVDR and establishing the need for guidance on HIVDR reporting, we used a sequential, explanatory, mixed methods approach to create the checklist; together with the accompanying articles, the checklist was reviewed by the authors and validated externally. The checklist for studies on HIVDR prevalence or incidence (CEDRIC-HIV) includes 15 recommended items that would enhance transparency and facilitate interpretation, comparability, and replicability of HIVDR studies. CEDRIC-HIV will help authors of HIVDR studies prepare research reports and assist reviewers and editors in assessments of completeness of reporting. The checklist will also facilitate statistical pooling and interpretation of HIVDR data.
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Affiliation(s)
- Lawrence Mbuagbaw
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, ON, Canada; Department of Anesthesia, McMaster University, Hamilton, ON, Canada; Department of Pediatrics, McMaster University, Hamilton, ON, Canada; Biostatistics Unit, Father Sean O'Sullivan Research Centre, St Joseph's Healthcare, Hamilton, ON, Canada; Centre for Development of Best Practices in Health, Yaoundé Central Hospital, Yaoundé, Cameroon; Department of Global Health, Stellenbosch University, Cape Town, South Africa.
| | - Cristian Garcia
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, ON, Canada
| | - Bluma Brenner
- McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research, Montréal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada; Department of Medicine, Surgery, and Infectious Disease, McGill University, Montréal, QC, Canada
| | - Diego Cecchini
- Hospital General de Agudos Dr. Cosme Argerich, Buenos Aires, Argentina; Helios Salud, Buenos Aires, Argentina
| | - Mohamed Chakroun
- Infectious Diseases Department, Fatouma Bourguiba University Hospital, Monastir, Tunisia
| | - Pascal Djiadeu
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, ON, Canada; Yale University School of Nursing, Yale University, West Haven, CT, USA; Centre for Urban Health Solutions, St Michael's Hospital, Toronto, ON, Canada
| | - Africa Holguin
- HIV-1 Molecular Epidemiology Laboratory, Microbiology and Parasitology Department, Hospital Ramón y Cajal-IRYCIS and CIBEREsp-RITIP, Madrid, Spain
| | - Orna Mor
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel; Central Virology Laboratory, Ministry of Health and Sheba Medical Centre, Tel-Hashomer, Israel
| | | | - Maria M Santoro
- Department of Experimental Medicine, University of Rome 'Tor Vergata', Rome, Italy
| | - Santiago Ávila-Ríos
- Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico; Centro de Investigaciones en Enfermedades Infecciosas, Mexico City, Mexico
| | - Joseph Fokam
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon; Faculty of Health Science, University of Buea, Buea, Cameroon; National HIV Drug Resistance Working Group, Ministry of Public Health, Yaoundé, Cameroon
| | - Andrew Phillips
- Institute for Global Health, University College London, London, UK
| | - Robert W Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Michael R Jordan
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, MA, USA; Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA, USA; Tufts Center for Integrated Management of Antimicrobial Resistance, Tufts University School of Medicine, Boston, MA, USA
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Next Generation Sequencing for HIV-1 Drug Resistance Testing-A Special Issue Walkthrough. Viruses 2021; 13:v13020340. [PMID: 33671700 PMCID: PMC7926934 DOI: 10.3390/v13020340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 12/18/2022] Open
Abstract
Drug resistance remains a global challenge in the fight against the HIV pandemic [...].
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Application of a Sanger-Based External Quality Assurance Strategy for the Transition of HIV-1 Drug Resistance Assays to Next Generation Sequencing. Viruses 2020; 12:v12121456. [PMID: 33348705 PMCID: PMC7766986 DOI: 10.3390/v12121456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 12/15/2020] [Indexed: 01/05/2023] Open
Abstract
The National Institute of Allergy and Infectious Diseases (NIAID) Virology Quality Assurance (VQA) established a robust proficiency testing program for Sanger sequencing (SS)-based HIV-1 drug resistance (HIVDR) testing in 2001. While many of the lessons learned during the development of such programs may also apply to next generation sequencing (NGS)-based HIVDR assays, challenges remain for the ongoing evaluation of NGS-based testing. These challenges include a proper assessment of assay accuracy and the reproducibility of low abundance variant detection, intra- and inter-assay performance comparisons among laboratories using lab-defined tests, and different data analysis pipelines designed for NGS. In collaboration with the World Health Organization (WHO) Global HIVDR Laboratory Network and the Public Health Agency of Canada, the Rush VQA program distributed archived proficiency testing panels to ten laboratories to evaluate internally developed NGS assays. Consensus FASTA files were submitted using 5%, 10%, and 20% variant detection thresholds, and scored based on the same criteria used for SS. This small study showed that the SS External Quality Assurance (EQA) approach can be used as a transitional strategy for using NGS to generate SS-like data and for ongoing performance while using NGS data from the same quality control materials to further evaluate NGS assay performance.
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Noguera-Julian M, Lee ER, Shafer RW, Kantor R, Ji H. Dry Panels Supporting External Quality Assessment Programs for Next Generation Sequencing-Based HIV Drug Resistance Testing. Viruses 2020; 12:v12060666. [PMID: 32575676 PMCID: PMC7354622 DOI: 10.3390/v12060666] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/18/2020] [Accepted: 06/18/2020] [Indexed: 12/18/2022] Open
Abstract
External quality assessment (EQA) is a keystone element in the validation and implementation of next generation sequencing (NGS)-based HIV drug resistance testing (DRT). Software validation and evaluation is a critical element in NGS EQA programs. While the development, sharing, and adoption of wet lab protocols is coupled with the increasing access to NGS technology worldwide, rendering it easy to produce NGS data for HIV-DRT, bioinformatic data analysis remains a bottleneck for most of the diagnostic laboratories. Several computational tools have been made available, via free or commercial sources, to automate the conversion of raw NGS data into an actionable clinical report. Although different software platforms yield equivalent results when identical raw NGS datasets are analyzed for variations at higher abundance, discrepancies arise when variations at lower frequencies are considered. This implies that validation and performance assessment of the bioinformatics tools applied in NGS HIV-DRT is critical, and the origins of the observed discrepancies should be determined. Well-characterized reference NGS datasets with ground truth on the genotype composition at all examined loci and the exact frequencies of HIV variations they may harbor, so-called dry panels, would be essential in such cases. The strategic design and construction of such panels are challenging but imperative tasks in support of EQA programs for NGS-based HIV-DRT and the validation of relevant bioinformatics tools. Here, we present criteria that can guide the design of such dry panels, which were discussed in the Second International Winnipeg Symposium themed for EQA strategies for NGS HIVDR assays.
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Affiliation(s)
- Marc Noguera-Julian
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, s/n, Catalonia, 08196 Badalona, Spain
- Chair in AIDS and Related Illnesses, Centre for Health and Social Care Research (CESS), Faculty of Medicine, University of Vic, Central University of Catalonia, Can Baumann. Ctra. de Roda, 70, 08500 Vic, Spain
- Correspondence:
| | - Emma R. Lee
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; (E.R.L.); (H.J.)
| | | | - Rami Kantor
- Division of Infectious Diseases, Brown University Alpert Medical School, Providence, RI 02903, USA;
| | - Hezhao Ji
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; (E.R.L.); (H.J.)
- Department of Medical Microbiology and Infectious Diseases, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
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Ji H, Parkin N, Gao F, Denny T, Jennings C, Sandstrom P, Kantor R. External Quality Assessment Program for Next-Generation Sequencing-Based HIV Drug Resistance Testing: Logistical Considerations. Viruses 2020; 12:E556. [PMID: 32443529 PMCID: PMC7291315 DOI: 10.3390/v12050556] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 01/23/2023] Open
Abstract
Next-generation sequencing (NGS) is likely to become the new standard method for HIV drug resistance (HIVDR) genotyping. Despite the significant advances in the development of wet-lab protocols and bioinformatic data processing pipelines, one often-missing critical component of an NGS HIVDR assay for clinical use is external quality assessment (EQA). EQA is essential for ensuring assay consistency and laboratory competency in performing routine biomedical assays, and the rollout of NGS HIVDR tests in clinical practice will require an EQA. In September 2019, the 2nd International Symposium on NGS HIVDR was held in Winnipeg, Canada. It convened a multidisciplinary panel of experts, including research scientists, clinicians, bioinformaticians, laboratory biologists, biostatisticians, and EQA experts. A themed discussion was conducted on EQA strategies towards such assays during the symposium. This article describes the logistical challenges identified and summarizes the opinions and recommendations derived from these discussions, which may inform the development of an inaugural EQA program for NGS HIVDR in the near future.
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Affiliation(s)
- Hezhao Ji
- National HIV and Retrovirology Laboratories at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada;
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Neil Parkin
- Data First Consulting Inc., Sebastopol, CA 95472, USA;
| | - Feng Gao
- Duke Human Vaccine Institute and Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (F.G.); (T.D.)
| | - Thomas Denny
- Duke Human Vaccine Institute and Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (F.G.); (T.D.)
| | - Cheryl Jennings
- Department of Molecular Pathogens and Immunity, Rush University, Chicago, IL 60612, USA;
| | - Paul Sandstrom
- National HIV and Retrovirology Laboratories at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada;
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Rami Kantor
- Division of Infectious Diseases, Brown University Alpert Medical School, Providence, RI 02906, USA;
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External Quality Assessment for Next-Generation Sequencing-Based HIV Drug Resistance Testing: Unique Requirements and Challenges. Viruses 2020; 12:v12050550. [PMID: 32429382 PMCID: PMC7291216 DOI: 10.3390/v12050550] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/09/2020] [Accepted: 05/14/2020] [Indexed: 12/25/2022] Open
Abstract
Over the past decade, there has been an increase in the adoption of next generation sequencing (NGS) technologies for HIV drug resistance (HIVDR) testing. NGS far outweighs conventional Sanger sequencing as it has much higher throughput, lower cost when samples are batched and, most importantly, significantly higher sensitivities for variants present at low frequencies, which may have significant clinical implications. Despite the advantages of NGS, Sanger sequencing remains the gold standard for HIVDR testing, largely due to the lack of standardization of NGS-based HIVDR testing. One important aspect of standardization includes external quality assessment (EQA) strategies and programs. Current EQA for Sanger-based HIVDR testing includes proficiency testing where samples are sent to labs and the performance of the lab conducting such assays is evaluated. The current methods for Sanger-based EQA may not apply to NGS-based tests because of the fundamental differences in their technologies and outputs. Sanger-based genotyping reports drug resistance mutations (DRMs) data as dichotomous, whereas NGS-based HIVDR genotyping also reports DRMs as numerical data (percent abundance). Here we present an overview of the need to develop EQA for NGS-based HIVDR testing and some unique challenges that may be encountered.
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Colby DJ, Sarnecki M, Barouch DH, Tipsuk S, Stieh DJ, Kroon E, Schuetz A, Intasan J, Sacdalan C, Pinyakorn S, Grandin P, Song H, Tovanabutra S, Shubin Z, Kim D, Paquin-Proulx D, Eller MA, Thomas R, de Souza M, Wieczorek L, Polonis VR, Pagliuzza A, Chomont N, Peter L, Nkolola JP, Vingerhoets J, Truyers C, Pau MG, Schuitemaker H, Phanuphak N, Michael N, Robb ML, Tomaka FL, Ananworanich J. Safety and immunogenicity of Ad26 and MVA vaccines in acutely treated HIV and effect on viral rebound after antiretroviral therapy interruption. Nat Med 2020; 26:498-501. [DOI: 10.1038/s41591-020-0774-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 01/24/2020] [Indexed: 01/29/2023]
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Saeng-aroon S, Saipradit N, Loket R, Klamkhai N, Boonmuang R, Kaewprommal P, Prommajan K, Takeda N, Sungkanuparph S, Shioda T, Sangkitporn S, Motomura K. External Quality Assessment Scheme for HIV-1 Drug-Resistance Genotyping in Thailand. AIDS Res Hum Retroviruses 2018; 34:1028-1035. [PMID: 30215266 DOI: 10.1089/aid.2017.0299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The efficacy of antiretroviral (ARV) therapy can be compromised by the emergence and transmission of HIV-1 drug-resistant strains. HIV-1 drug-resistance (DR) genotypic testing thus plays an important role in the selection of optimal treatment regimens for HIV-infected individuals. Given the complexities of the testing procedures and the variety of approaches used, there is considerable potential for results to vary between laboratories. In Thailand, the national External Quality Assessment (EQA) scheme assesses the DR genotype testing performance of laboratories. Here, we evaluated the performance of laboratories in nucleotide sequencing and compared drug-resistance-associated mutations (DRMs) in the HIV-1 protease (PR) and reverse transcriptase (RT) genes during 2010-2015. The EQA samples in the 12 panels showed predominance for the CRF01_AE (85%) and subtype B (15%). Fourteen laboratory datasets were generated: eight using TruGene (TG), two using ViroSeq (VS), and four using in-house (IH) assays. All IH and VS laboratories had penalty scores <7, whereas five of the eight TG laboratories had fluctuating penalty scores. Moreover, seven and six TG laboratories could not amplify the two identical samples, 10B and 10E samples, or the CRF01_AE. Our findings demonstrate the requirement for laboratory participation in the ongoing EQA program and the optimization of kit assays using CRF01_AE samples. Our results also indicate that one advantage of participation is that the laboratories can monitor and investigate the source of laboratory errors.
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Affiliation(s)
- Siriphan Saeng-aroon
- Department of Medical Sciences, Ministry of Public Health, National Institute of Health, Nonthaburi, Thailand
| | - Nonglak Saipradit
- Department of Medical Sciences, Ministry of Public Health, National Institute of Health, Nonthaburi, Thailand
| | - Ruangchai Loket
- Department of Medical Sciences, Ministry of Public Health, National Institute of Health, Nonthaburi, Thailand
| | - Nattapong Klamkhai
- Department of Medical Sciences, Ministry of Public Health, National Institute of Health, Nonthaburi, Thailand
| | - Ratrawee Boonmuang
- Department of Medical Sciences, Ministry of Public Health, National Institute of Health, Nonthaburi, Thailand
| | - Pavita Kaewprommal
- Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Nonthaburi, Thailand
| | - Korrakot Prommajan
- Department of Medical Sciences, Ministry of Public Health, National Institute of Health, Nonthaburi, Thailand
| | - Naokazu Takeda
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections (RCC-ERI), Nonthaburi, Thailand
| | - Somnuek Sungkanuparph
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Nonthaburi, Thailand
| | - Tatsuo Shioda
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections (RCC-ERI), Nonthaburi, Thailand
| | - Somchai Sangkitporn
- Department of Medical Sciences, Ministry of Public Health, National Institute of Health, Nonthaburi, Thailand
| | - Kazushi Motomura
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections (RCC-ERI), Nonthaburi, Thailand
- Research Institute of Microbial Diseases, Osaka University, Suita, Japan
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
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Transmission dynamics among participants initiating antiretroviral therapy upon diagnosis of early acute HIV-1 infection in Thailand. AIDS 2018; 32:2373-2381. [PMID: 30096068 DOI: 10.1097/qad.0000000000001956] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE To assess transmission characteristics in a predominantly MSM cohort initiating antiretroviral therapy (ART) immediately following diagnosis of acute HIV-1infection (AHI). METHODS A longitudinal study (2009-2017) was performed in participants with AHI (n = 439) attending a single clinic in Bangkok. Plasma samples obtained prior to ART were used to obtain HIV-1 pol sequences and combined with clinical and epidemiologic data to assess transmission dynamics (cluster formation and size) using phylogenetic analysis. Clusters were estimated using maximum likelihood, genetic distance of 1.5% and visual inspection. The potential transmitter(s) in a cluster was determined using time to viral suppression and interview data. RESULTS The cohort was predominantly MSM (93%) and infected with HIV-1 CRF01_AE (87%). Medians (ranges) for age and viral load prior to ART were 26 (18-70) years and 5.9 (2.5-8.2) log10 HIV-1 RNA copies/ml. Median time from history of HIV-1 exposure to diagnosis was 19 (3-61) days. Viral suppression was observed in 388 of 412 (94%) participants at a median time of 12 weeks following ART. Twenty-six clusters with median cluster size of 2 (2-5) representing 62 of 439 (14%) participants were observed. Younger age was associated with cluster formation: median 28 versus 30 years for unique infections (P = 0.01). A potential transmitter was identified in 11 of 26 (42%) clusters. CONCLUSION Despite high rates of viral suppression following diagnosis and treatment of AHI within a cohort of young Thai MSM, HIV-1 transmission continued, reflecting the need to expand awareness and treatment access to the entire MSM population.
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Colby DJ, Trautmann L, Pinyakorn S, Leyre L, Pagliuzza A, Kroon E, Rolland M, Takata H, Buranapraditkun S, Intasan J, Chomchey N, Muir R, Haddad EK, Tovanabutra S, Ubolyam S, Bolton DL, Fullmer BA, Gorelick RJ, Fox L, Crowell TA, Trichavaroj R, O'Connell R, Chomont N, Kim JH, Michael NL, Robb ML, Phanuphak N, Ananworanich J. Rapid HIV RNA rebound after antiretroviral treatment interruption in persons durably suppressed in Fiebig I acute HIV infection. Nat Med 2018; 24:923-926. [PMID: 29892063 PMCID: PMC6092240 DOI: 10.1038/s41591-018-0026-6] [Citation(s) in RCA: 215] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 03/23/2018] [Indexed: 01/24/2023]
Abstract
Antiretroviral therapy during the earliest stage of acute HIV infection (Fiebig I) might minimize establishment of a latent HIV reservoir and thereby facilitate viremic control after analytical treatment interruption. We show that 8 participants, who initiated treatment during Fiebig I and were treated for a median of 2.8 years, all experienced rapid viral load rebound following analytical treatment interruption, indicating that additional strategies are required to control or eradicate HIV.
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Affiliation(s)
- Donn J Colby
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok, Thailand
| | - Lydie Trautmann
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Suteeraporn Pinyakorn
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Louise Leyre
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Amélie Pagliuzza
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Eugène Kroon
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok, Thailand
| | - Morgane Rolland
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Hiroshi Takata
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Supranee Buranapraditkun
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- Division of Allergy and Clinical Immunology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Chulalongkorn Vaccine Research Center, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Jintana Intasan
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok, Thailand
| | - Nitiya Chomchey
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok, Thailand
| | - Roshell Muir
- Department of Medicine, Division of Infectious Diseases & HIV Medicine at Drexel University College of Medicine, Philadelphia, PA, USA
| | - Elias K Haddad
- Department of Medicine, Division of Infectious Diseases & HIV Medicine at Drexel University College of Medicine, Philadelphia, PA, USA
| | - Sodsai Tovanabutra
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | | | - Diane L Bolton
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Brandie A Fullmer
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Robert J Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Lawrence Fox
- Division of AIDS, National Institute of Allergy and Infectious Diseases, Rockville, MD, USA
| | - Trevor A Crowell
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Rapee Trichavaroj
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences United States Component, Bangkok, Thailand
| | - Robert O'Connell
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences United States Component, Bangkok, Thailand
| | - Nicolas Chomont
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Jerome H Kim
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- International Vaccine Institute, Seoul, Korea
| | - Nelson L Michael
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Merlin L Robb
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | | | - Jintanat Ananworanich
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok, Thailand.
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.
- Department of Global Health, University of Amsterdam, Amsterdam, the Netherlands.
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Hiransuthikul A, Wongkanya R, Sirivichayakul S, Trachunthong D, Sungsing T, Pankam T, Phanuphak P, Phanuphak N. Short Communication: Discordance in Drug Resistance Mutations Between Blood Plasma and Semen or Rectal Secretions Among Newly Diagnosed HIV-1-Infected Thai Men Who Have Sex with Men. AIDS Res Hum Retroviruses 2018; 34:626-628. [PMID: 29756454 DOI: 10.1089/aid.2018.0029] [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: 11/12/2022] Open
Abstract
Human immunodeficiency virus 1 (HIV-1) infection is most commonly transmitted by sexual contact across mucosal surfaces. Information on concordance in drug resistance profile between blood plasma and anogenital compartments in resource-limited settings is limited. We aimed to determine discordances in genotypic drug resistance-associated mutations (DRAMs) between blood plasma and semen or rectal secretions among newly diagnosed, antiretroviral therapy (ART)-naive, HIV-1-infected Thai men who have sex with men (MSM). Blood plasma, semen, and rectal secretions of HIV-1-infected Thai MSM enrolled from the Test and Treat cohort were tested for genotypic mutations in the reverse transcriptase and protease genes. Seven participants with baseline DRAMs in blood plasma were included in this analysis. In anogenital samples, HIV-1 RNA could be fully amplified for DRAMs assessment in semen from three participants and in rectal secretions from four participants. DRAMs were identified in semen from two of three participants and in rectal secretions from four of four participants. Three participants had DRAMs in anogenital compartments that were not detected in blood plasma-one had DRAMs in semen that was not detected in blood plasma (I54FI) and two had DRAMs in rectal secretions that was not detected in blood plasma (I47IM; K70N, L74I, Y115F, M184V, K103N, V108I, and H221Y). Discordance in DRAMs between blood plasma and anogenital compartments is not uncommon among newly diagnosed, ART-naive, HIV-1-infected Thai MSM. Monitoring of drug-resistant virus in these vector compartments is warranted particularly as pre-exposure prophylaxis and treatment as prevention are increasingly used as the mainstay strategies to end the AIDS epidemic.
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Affiliation(s)
| | | | - Sunee Sirivichayakul
- Vaccine and Cellular Immunology Laboratory, Chulalongkorn Medical Research Center (ChulaMRC), Chulalongkorn University, Bangkok, Thailand
- Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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Puller V, Neher R, Albert J. Estimating time of HIV-1 infection from next-generation sequence diversity. PLoS Comput Biol 2017; 13:e1005775. [PMID: 28968389 PMCID: PMC5638550 DOI: 10.1371/journal.pcbi.1005775] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 10/12/2017] [Accepted: 09/15/2017] [Indexed: 01/16/2023] Open
Abstract
Estimating the time since infection (TI) in newly diagnosed HIV-1 patients is challenging, but important to understand the epidemiology of the infection. Here we explore the utility of virus diversity estimated by next-generation sequencing (NGS) as novel biomarker by using a recent genome-wide longitudinal dataset obtained from 11 untreated HIV-1-infected patients with known dates of infection. The results were validated on a second dataset from 31 patients. Virus diversity increased linearly with time, particularly at 3rd codon positions, with little inter-patient variation. The precision of the TI estimate improved with increasing sequencing depth, showing that diversity in NGS data yields superior estimates to the number of ambiguous sites in Sanger sequences, which is one of the alternative biomarkers. The full advantage of deep NGS was utilized with continuous diversity measures such as average pairwise distance or site entropy, rather than the fraction of polymorphic sites. The precision depended on the genomic region and codon position and was highest when 3rd codon positions in the entire pol gene were used. For these data, TI estimates had a mean absolute error of around 1 year. The error increased only slightly from around 0.6 years at a TI of 6 months to around 1.1 years at 6 years. Our results show that virus diversity determined by NGS can be used to estimate time since HIV-1 infection many years after the infection, in contrast to most alternative biomarkers. We provide the regression coefficients as well as web tool for TI estimation. HIV-1 establishes a chronic infection, which may last for many years before the infected person is diagnosed. The resulting uncertainty in the date of infection leads to difficulties in estimating the number of infected but undiagnosed persons as well as the number of new infections, which is necessary for developing appropriate public health policies and interventions. Such estimates would be much easier if the time since HIV-1 infection for newly diagnosed cases could be accurately estimated. Three types of biomarkers have been shown to contain information about the time since HIV-1 infection, but unfortunately, they only distinguish between recent and long-term infections (concentration of HIV-1-specific antibodies) or are imprecise (immune status as measured by levels of CD4+ T-lymphocytes and viral sequence diversity measured by polymorphisms in Sanger sequences). In this paper, we show that recent advances in sequencing technologies, i.e. the development of next generation sequencing, enable significantly more precise determination of the time since HIV-1 infection, even many years after the infection event. This is a significant advance which could translate into more effective HIV-1 prevention.
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Affiliation(s)
- Vadim Puller
- Max Planck Institute for Developmental Biology, Tübingen, Germany
- Biozentrum, University of Basel, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
- * E-mail:
| | - Richard Neher
- Max Planck Institute for Developmental Biology, Tübingen, Germany
- Biozentrum, University of Basel, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
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Praparattanapan J, Tragoolpua Y, Wongtrakul J, Kotarathitithum W, Chaiwarith R, Nuntachit N, Sirisanthana T, Supparatpinyo K. Comparison of in-house HIV-1 genotypic drug resistant test with commercial HIV-1 genotypic test kit. ASIAN BIOMED 2017. [DOI: 10.5372/1905-7415.0502.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Abstract
Background: The use of combination antiretroviral therapy (cART) has become a standard of care in the treatment of HIV infection. However, antiretroviral drug resistance occurs in a substantial number of patients. In resource-limited settings, genotypic resistance assay using a commercial kit is costly.
Objective: Focus on the validation of an in-house HIV-1 specific genotypic drug resistance assay in Thai patients failing cART.
Materials and methods: Results of HIV-1 genotypic drug resistance assay was evaluated by comparing an inhouse method to a commercial test. The TRUGENE HIV-1 genotyping kit was used in 79 plasma specimens (49 from HIV patients failing cART therapy and 30 from proficiency testing panels).
Results: The results from the in-house assay were comparable to those obtained from the TRUGENE HIV-1 genotyping kit with >99.0% codon-to-codon agreement. The lower limit of detection by the in-house assay was approximately 100 copies/mL of HIV-1 RNA. In addition, this in-house assay would allow testing of samples from patients infected with HIV-1 subtype other than B.
Conclusion: The in-house HIV-1 genotypic drug resistance assay may be used as an alternative to commercial kits, particularly in resource limited settings.
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Affiliation(s)
- Jutarat Praparattanapan
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand Thailand
- Department of Medicine, Faculty of Medicine; Chiang Mai University, Chiang Mai 50200, Thailand
| | - Yingmanee Tragoolpua
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Jeerang Wongtrakul
- Research Institute for Health Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Wilai Kotarathitithum
- Department of Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Romanee Chaiwarith
- Department of Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Nontakan Nuntachit
- Department of Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Thira Sirisanthana
- Research Institute for Health Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Khuanchai Supparatpinyo
- Correspondence to: Department of Medicine, Faculty of Medicine Chiang Mai University, Chiang Mai 50200, Thailand Thailand
- Research Institute for Health Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
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Declining trend in transmitted drug resistance detected in a prospective cohort study of acute HIV infection in Bangkok, Thailand. J Int AIDS Soc 2016; 19:20966. [PMID: 27802846 PMCID: PMC5090107 DOI: 10.7448/ias.19.1.20966] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 07/18/2016] [Accepted: 08/22/2016] [Indexed: 12/14/2022] Open
Abstract
Introduction As availability of antiretroviral therapy expands in developing countries, the risk for transmission of drug-resistant HIV also increases. Patients with acute HIV infection (AHI) provide an opportunity for real-time monitoring of transmitted drug resistance (TDR). SEARCH 010/RV 254 study is a prospective, longitudinal study of AHI. This analysis was performed to characterize changes in TDR over time in persons enrolled in the AHI cohort. Methods Genotype testing for TDR mutations was performed on 229 subjects enrolled from 2009 to 2014. Results The cohort was predominantly male (95%) and men who have sex with men (92%). TDR prevalence was 7.0%, declining from 12.5% in 2009–2010 to 4.8% in 2013–2014 (p=0.08). By drug class, resistance prevalence was 3.6% for proteases inhibitors, 2.6% for nucleoside/nucleotide reverse transcriptase inhibitors and 2.2% for non-nucleoside reverse transcriptase inhibitors. The greatest decline in prevalence was seen in the non-nucleoside reverses transcriptase inhibitors, from 9.4% in 2009–2010 to 0.7% in 2013–2014 (p=0.005). Conclusions TDR appears to be declining among individuals with AHI in Bangkok and in 2013 to 2014 met the World Health Organization definition for low prevalence. Continued surveillance is necessary to determine if this trend persists.
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High prevalence of transmitted drug resistance in acute HIV-infected Thai men who have sex with men. J Acquir Immune Defic Syndr 2015; 68:481-5. [PMID: 25559593 DOI: 10.1097/qai.0000000000000502] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
: As use of antiretroviral therapy in Thailand increases, so does the potential for transmission of drug-resistant HIV. We describe the prevalence of WHO surveillance drug resistance mutations among 120 subjects who underwent genotypic testing during acute HIV infection in Bangkok, Thailand. In this cohort of predominantly men who have sex with men, we observed an overall transmitted drug resistance prevalence of 9.2%, including nucleoside/nucleotide analog reverse transcriptase inhibitor 5.0%, nonnucleoside analog reverse transcriptase inhibitor 3.4%, and protease inhibitor 3.4%. These prevalence estimates are higher than previous reports of transmitted drug resistance in Thailand. Baseline drug resistance testing may be warranted, particularly among men who have sex with men.
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Yoshida S, Hattori J, Matsuda M, Okada K, Kazuyama Y, Hashimoto O, Ibe S, Fujisawa SI, Chiba H, Tatsumi M, Kato S, Sugiura W. Japanese external quality assessment program to standardize HIV-1 drug-resistance testing (JEQS2010 program) using in vitro transcribed RNA as reference material. AIDS Res Hum Retroviruses 2015; 31:318-25. [PMID: 25469535 DOI: 10.1089/aid.2014.0059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To design appropriate antiretroviral therapy regimens and avoid the emergence of human immunodeficiency virus (HIV)-1 variants with reduced susceptibility to antiretroviral drugs, genotypic drug-resistance testing (HIV genotyping) is strongly recommended. To monitor the quality of HIV genotyping in Japan, we performed an external quality assessment (EQA), named the Japanese external quality assessment program, to standardize HIV genotyping (JEQS). To accurately evaluate the quality of HIV genotyping, we employed as reference material (RM) a well-characterized sample, in vitro transcribed RNA (trRNA) that includes the HIV gag-pol sequence, and created a JEQS2010 panel consisting of three single variant and three mixed trRNA samples. All 11 participating laboratories showed high concordance rates (>96%) for the single variant samples. Eight laboratories also showed good rates of detecting minor variants, but three laboratories failed to detect the variants comprising one-half of the sample. These three laboratories used a common primer that had four internal mismatches to the minor trRNA clone. This program showed the usefulness of trRNA as RM, the high quality of HIV genotyping, and extensive interlaboratory variation in the ability to detect minor variants. These results suggest that improving the quality of HIV genotyping in Japan requires regularly implementing the EQA program and improving the HIV genotyping protocol in each laboratory.
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Affiliation(s)
- Shigeru Yoshida
- Faculty of Health Sciences, Hokkaido University, Sapporo, Japan
| | - Junko Hattori
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Masakazu Matsuda
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Kiyomi Okada
- Kitasato Otsuka Biomedical Assay Laboratories Co., Ltd., Kanagawa, Japan
| | - Yukumasa Kazuyama
- Kitasato Otsuka Biomedical Assay Laboratories Co., Ltd., Kanagawa, Japan
| | - Osamu Hashimoto
- Mitsubishi Chemical Medience Corporation Central Laboratory, Tokyo, Japan
| | - Shiro Ibe
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Shin-ichi Fujisawa
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, Japan
| | - Hitoshi Chiba
- Faculty of Health Sciences, Hokkaido University, Sapporo, Japan
| | | | - Shingo Kato
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Wataru Sugiura
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
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HIV multi-drug resistance at first-line antiretroviral failure and subsequent virological response in Asia. J Int AIDS Soc 2014; 17:19053. [PMID: 25141905 PMCID: PMC4139921 DOI: 10.7448/ias.17.1.19053] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 06/01/2014] [Accepted: 06/20/2014] [Indexed: 11/08/2022] Open
Abstract
Introduction First-line antiretroviral therapy (ART) failure often results from the development of resistance-associated mutations (RAMs). Three patterns, including thymidine analogue mutations (TAMs), 69 Insertion (69Ins) and the Q151M complex, are associated with resistance to multiple-nucleoside reverse transcriptase inhibitors (NRTIs) and may compromise treatment options for second-line ART. Methods We investigated patterns and factors associated with multi-NRTI RAMs at first-line failure in patients from The TREAT Asia Studies to Evaluate Resistance – Monitoring study (TASER-M), and evaluated their impact on virological responses at 12 months after switching to second-line ART. RAMs were compared with the IAS-USA 2013 mutations list. We defined multi-NRTI RAMs as the presence of either Q151M; 69Ins; ≥2 TAMs; or M184V+≥1 TAM. Virological suppression was defined as viral load (VL) <400 copies/ml at 12 months from switch to second-line. Logistic regression was used to analyze (1) factors associated with multi-NRTI RAMs at first-line failure and (2) factors associated with virological suppression after 12 months on second-line. Results A total of 105 patients from 10 sites in Thailand, Hong Kong, Indonesia, Malaysia and Philippines were included. There were 97/105 (92%) patients harbouring ≥1 RAMs at first-line failure, 39/105 with multi-NRTI RAMs: six with Q151M; 24 with ≥2 TAMs; and 32 with M184V+≥1 TAM. Factors associated with multi-NRTI RAMs were CD4 ≤200 cells/µL at genotyping (OR=4.43, 95% CI [1.59–12.37], p=0.004) and ART duration >2 years (OR=6.25, 95% CI [2.39–16.36], p<0.001). Among 87/105 patients with available VL at 12 months after switch to second-line ART, virological suppression was achieved in 85%. The median genotypic susceptibility score (GSS) for the second-line regimen was 2.00. Patients with ART adherence ≥95% were more likely to be virologically suppressed (OR=9.33, 95% CI (2.43–35.81), p=0.001). Measures of patient resistance to second-line ART, including the GSS, were not significantly associated with virological outcome. Conclusions Multi-NRTI RAMs at first-line failure were associated with low CD4 level and longer duration of ART. With many patients switching to highly susceptible regimens, good adherence was still crucial in achieving virological response. This emphasizes the importance of continued adherence counselling well into second-line therapy.
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Transmitted drug resistance and antiretroviral treatment outcomes in non-subtype B HIV-1-infected patients in South East Asia. J Acquir Immune Defic Syndr 2014; 66:74-9. [PMID: 24413039 DOI: 10.1097/qai.0000000000000108] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND We compared treatment outcomes of transmitted drug resistance (TDR) in patients on fully or partially sensitive drug regimens. METHODS Factors associated with survival and failure were analyzed using Cox proportional hazards and discrete time conditional logistic models. RESULTS TDR, found in 60 (4.1%) of 1471 Asian treatment-naive patients, was one of the significant predictors of failure. Patients with TDR to >1 drug in their regimen were >3 times as likely to fail compared to no TDR. CONCLUSIONS TDR was associated with failure in the context of non-fully sensitive regimens. Efforts are needed to incorporate resistance testing into national treatment programs.
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Ong LY, Razak SNH, Lee YM, Sri La Sri Ponnampalavanar S, Syed Omar SF, Azwa RI, Tee KK, Kamarulzaman A. Molecular diversity of HIV-1 and surveillance of transmitted drug resistance variants among treatment Naïve patients, 5 years after active introduction of HAART in Kuala Lumpur, Malaysia. J Med Virol 2013; 86:38-44. [PMID: 24127302 DOI: 10.1002/jmv.23772] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2013] [Indexed: 12/14/2022]
Abstract
Expansion of antiretroviral treatment programs have led to the growing concern for the development of antiretroviral drug resistance. The aims were to assess the prevalence of drug resistant HIV-1 variants and to identify circulating subtypes among HAART-naïve patients. Plasma specimens from N = 100 HIV+ HAART-naïve adult were collected between March 2008 and August 2010 and viral RNA were extracted for nested PCR and sequenced. PR-RT sequences were protein aligned and checked for transmitted drug resistance mutations. Phylogenetic reconstruction and recombination analysis were performed to determine the genotypes. Based on the WHO consensus guidelines, none of the recruited patients had any transmitted drug resistance mutations. When analyzed against the Stanford guidelines, 35% of patients had at least one reported mutation that may reduce drug susceptibility to PI (24%), NRTI (5%), and NNRTI (14%). The commonly detected mutation that may affect current first line therapy was V179D (3%), which may lead to reduced susceptibility to NNRTI. The predominant circulating HIV-1 genotypes were CRF01_AE (51%) and CRF33_01B (17%). The prevalence of unique recombinant forms (URF) was 7%; five distinct recombinant structures involving CRF01_AE and subtype B' were observed, among them a cluster of three isolates that could form a novel circulating recombinant form (CRF) candidate. Transmitted drug resistance prevalence among HAART-naïve patients was low in this cohort of patients in Kuala Lumpur despite introduction of HAART 5 years ago. Owing to the high genetic diversity, continued molecular surveillance can identify the persistent emergence of HIV-1 URF and novel CRF with significant epidemiological impact.
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Affiliation(s)
- Lai Yee Ong
- Faculty of Medicine, Centre of Excellence for Research in AIDS (CERiA), University of Malaya, Kuala Lumpur, Malaysia
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Katzenstein DA. HIV RNA and genotype in resource-limited settings: can we do better? Clin Infect Dis 2013; 58:110-2. [PMID: 24076967 DOI: 10.1093/cid/cit634] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Land S, Zhou J, Cunningham P, Sohn AH, Singtoroj T, Katzenstein D, Mann M, Sayer D, Kantor R. Capacity building and predictors of success for HIV-1 drug resistance testing in the Asia-Pacific region and Africa. J Int AIDS Soc 2013; 16:18580. [PMID: 23845227 PMCID: PMC3709369 DOI: 10.7448/ias.16.1.18580] [Citation(s) in RCA: 8] [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: 02/04/2013] [Revised: 05/13/2013] [Accepted: 06/06/2013] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The TREAT Asia Quality Assessment Scheme (TAQAS) was developed as a quality assessment programme through expert education and training, for laboratories in the Asia-Pacific and Africa that perform HIV drug-resistance (HIVDR) genotyping. We evaluated the programme performance and factors associated with high-quality HIVDR genotyping. METHODS Laboratories used their standard protocols to test panels of human immunodeficiency virus (HIV)-positive plasma samples or electropherograms. Protocols were documented and performance was evaluated according to a newly developed scoring system, agreement with panel-specific consensus sequence, and detection of drug-resistance mutations (DRMs) and mixtures of wild-type and resistant virus (mixtures). High-quality performance was defined as detection of ≥95% DRMs. RESULTS Over 4.5 years, 23 participating laboratories in 13 countries tested 45 samples (30 HIV-1 subtype B; 15 non-B subtypes) in nine panels. Median detection of DRMs was 88-98% in plasma panels and 90-97% in electropherogram panels. Laboratories were supported to amend and improve their test outcomes as appropriate. Three laboratories that detected <80% DRMs in early panels demonstrated subsequent improvement. Sample complexity factors - number of DRMs (p<0.001) and number of DRMs as mixtures (p<0.001); and laboratory performance factors - detection of mixtures (p<0.001) and agreement with consensus sequence (p<0.001), were associated with high performance; sample format (plasma or electropherogram), subtype and genotyping protocol were not. CONCLUSION High-quality HIVDR genotyping was achieved in the TAQAS collaborative laboratory network. Sample complexity and detection of mixtures were associated with performance quality. Laboratories conducting HIVDR genotyping are encouraged to participate in quality assessment programmes.
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Kiertiburanakul S, Chaiwarith R, Sirivichayakul S, Ditangco R, Jiamsakul A, Li PCK, Kantipong P, Lee C, Ratanasuwan W, Kamarulzaman A, Sohn AH, Sungkanuparph S. Comparisons of Primary HIV-1 Drug Resistance between Recent and Chronic HIV-1 Infection within a Sub-Regional Cohort of Asian Patients. PLoS One 2013; 8:e62057. [PMID: 23826076 PMCID: PMC3694952 DOI: 10.1371/journal.pone.0062057] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 03/17/2013] [Indexed: 12/30/2022] Open
Abstract
Background The emergence and transmission of HIV-1 drug resistance (HIVDR) has raised concerns after rapid global antiretroviral therapy (ART) scale-up. There are limited data on the epidemiology of primary HIVDR in resource-limited settings in Asia. We aimed to determine the prevalence and compare the distribution of HIVDR in a cohort of ART-naïve Asian patients with recent and chronic HIV-1 infection. Methods Multicenter prospective study was conducted in ART-naïve patients between 2007 and 2010. Resistance-associated mutations (RAMs) were assessed using the World Health Organization 2009 list for surveillance of primary HIVDR. Results A total of 458 patients with recent and 1,340 patients with chronic HIV-1 infection were included in the analysis. The overall prevalence of primary HIVDR was 4.6%. Recently infected patients had a higher prevalence of primary HIVDR (6.1% vs. 4.0%, p = 0.065) and frequencies of RAMs to protease inhibitors (PIs; 3.9% vs. 1.0%, p<0.001). Among those with recent infection, the most common RAMs to nucleoside reverse transcriptase inhibitors (NRTIs) were M184I/V and T215D/E/F/I/S/Y (1.1%), to non-NRTIs was Y181C (1.3%), and to PIs was M46I (1.5%). Of patients with chronic infection, T215D/E/F/I/S/Y (0.8%; NRTI), Y181C (0.5%; non-NRTI), and M46I (0.4%; PI) were the most common RAMs. K70R (p = 0.016) and M46I (p = 0.026) were found more frequently among recently infected patients. In multivariate logistic regression analysis in patients with chronic infection, heterosexual contact as a risk factor for HIV-1 infection was less likely to be associated with primary HIVDR compared to other risk categories (odds ratio 0.34, 95% confidence interval 0.20–0.59, p<0.001). Conclusions The prevalence of primary HIVDR was higher among patients with recent than chronic HIV-1 infection in our cohort, but of borderline statistical significance. Chronically infected patients with non-heterosexual risks for HIV were more likely to have primary HIVDR.
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Affiliation(s)
| | - Romanee Chaiwarith
- Research Institute for Health Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Sunee Sirivichayakul
- Faculty of Medicine, Chulalongkorn University and HIV-NAT/Thai Red Cross AIDS Research Centre, Bangkok, Thailand
| | | | | | | | | | | | - Winai Ratanasuwan
- Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Annette H. Sohn
- TREAT Asia, amfAR - The Foundation for AIDS Research, Bangkok, Thailand
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Jiamsakul A, Kantor R, Li PCK, Sirivichayakul S, Sirisanthana T, Kantipong P, Lee CKC, Kamarulzaman A, Ratanasuwan W, Ditangco R, Singtoroj T, Sungkanuparph S. Comparison of predicted susceptibility between genotype and virtual phenotype HIV drug resistance interpretation systems among treatment-naive HIV-infected patients in Asia: TASER-M cohort analysis. BMC Res Notes 2012; 5:582. [PMID: 23095645 PMCID: PMC3505153 DOI: 10.1186/1756-0500-5-582] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 10/19/2012] [Indexed: 01/19/2023] Open
Abstract
Background Accurate interpretation of HIV drug resistance (HIVDR) testing is challenging, yet important for patient care. We compared genotyping interpretation, based on the Stanford University HIV Drug Resistance Database (Stanford HIVdb), and virtual phenotyping, based on the Janssen Diagnostics BVBA’s vircoTYPE™ HIV-1, and investigated their level of agreement in antiretroviral (ARV) naive patients in Asia, where non-B subtypes predominate. Methods Sequences from 1301 ARV-naive patients enrolled in the TREAT Asia Studies to Evaluate Resistance – Monitoring Study (TASER-M) were analysed by both interpreting systems. Interpretations from both Stanford HIVdb and vircoTYPE™ HIV-1 were initially grouped into 2 levels: susceptible and non-susceptible. Discrepancy was defined as a discordant result between the susceptible and non-susceptible interpretations from the two systems for the same ARV. Further analysis was performed when interpretations from both systems were categorised into 3 levels: susceptible, intermediate and resistant; whereby discrepancies could be categorised as major discrepancies and minor discrepancies. Major discrepancy was defined as having a susceptible result from one system and resistant from the other. Minor discrepancy corresponded to having an intermediate interpretation in one system, with a susceptible or resistant result in the other. The level of agreement was analysed using the prevalence adjusted bias adjusted kappa (PABAK). Results Overall, the agreement was high, with each ARV being in “almost perfect agreement”, using Landis and Koch’s categorisation. Highest discordance was observed for efavirenz (75/1301, 5.8%), all arising from susceptible Stanford HIVdb versus non-susceptible vircoTYPE™ HIV-1 predictions. Protease Inhibitors had highest level of concordance with PABAKs all above 0.99, followed by Nucleoside Reverse Transcriptase Inhibitors with PABAKs above 0.97 and non-NRTIs with the lowest PABAK of 0.88. The 68/75 patients with discordant efavirenz results harboured the V179D/E mutations compared to 7/1226 with no efavirenz discrepancy (p-value <0.001). In the 3-level comparison, all but one of the discrepancies was minor. Conclusions The two systems agreed well with lowest concordance observed for efavirenz. When interpreting HIVDR, especially in non-B subtypes, clinical correlation is crucial, in particular when efavirenz resistance is interpreted based on V179D/E.
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Hamers RL, Straatsma E, Kityo C, Wallis CL, Stevens WS, Sigaloff KCE, Siwale M, Conradie F, Botes ME, Mandaliya K, Wellington M, Osibogun A, van Vugt M, Rinke de Wit TF. Building capacity for the assessment of HIV drug resistance: experiences from the PharmAccess African Studies to Evaluate Resistance network. Clin Infect Dis 2012; 54 Suppl 4:S261-5. [PMID: 22544185 DOI: 10.1093/cid/cir995] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The PharmAccess African Studies to Evaluate Resistance (PASER) network was established as a collaborative partnership of clinical sites, laboratories, and research groups in 6 African countries; its purpose is to build research and laboratory capacity in support of a coordinated effort to assess population-level acquired and transmitted human immunodeficiency virus type-1 drug resistance (HIVDR), thus contributing to the goals of the World Health Organization Global HIV Drug Resistance Network. PASER disseminates information to medical professionals and policy makers and conducts observational research related to HIVDR. The sustainability of the network is challenged by funding limitations, constraints in human resources, a vulnerable general health infrastructure, and high cost and complexity of molecular diagnostic testing. This report highlights experiences and challenges in the PASER network from 2006 to 2010.
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Affiliation(s)
- Raph L Hamers
- PharmAccess Foundation and Department of Global Health, Academic Medical Center of the University of Amsterdam, Amsterdam Institute for Global Health and Development, the Netherlands.
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DeLong AK, Wu M, Bennett D, Parkin N, Wu Z, Hogan JW, Kantor R. Sequence quality analysis tool for HIV type 1 protease and reverse transcriptase. AIDS Res Hum Retroviruses 2012; 28:894-901. [PMID: 21916749 DOI: 10.1089/aid.2011.0120] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Access to antiretroviral therapy is increasing globally and drug resistance evolution is anticipated. Currently, protease (PR) and reverse transcriptase (RT) sequence generation is increasing, including the use of in-house sequencing assays, and quality assessment prior to sequence analysis is essential. We created a computational HIV PR/RT Sequence Quality Analysis Tool (SQUAT) that runs in the R statistical environment. Sequence quality thresholds are calculated from a large dataset (46,802 PR and 44,432 RT sequences) from the published literature ( http://hivdb.Stanford.edu ). Nucleic acid sequences are read into SQUAT, identified, aligned, and translated. Nucleic acid sequences are flagged if with >five 1-2-base insertions; >one 3-base insertion; >one deletion; >six PR or >18 RT ambiguous bases; >three consecutive PR or >four RT nucleic acid mutations; >zero stop codons; >three PR or >six RT ambiguous amino acids; >three consecutive PR or >four RT amino acid mutations; >zero unique amino acids; or <0.5% or >15% genetic distance from another submitted sequence. Thresholds are user modifiable. SQUAT output includes a summary report with detailed comments for troubleshooting of flagged sequences, histograms of pairwise genetic distances, neighbor joining phylogenetic trees, and aligned nucleic and amino acid sequences. SQUAT is a stand-alone, free, web-independent tool to ensure use of high-quality HIV PR/RT sequences in interpretation and reporting of drug resistance, while increasing awareness and expertise and facilitating troubleshooting of potentially problematic sequences.
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Affiliation(s)
- Allison K. DeLong
- Center for Statistical Sciences, Brown University, Providence, Rhode Island
| | - Mingham Wu
- Department of Research and Development, CardioDx Inc., Palo Alto, California
| | - Diane Bennett
- U.S. Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Zhijin Wu
- Department of Biostatistics and Center for Statistical Sciences, Brown University, Providence, Rhode Island
| | - Joseph W. Hogan
- Department of Biostatistics and Center for Statistical Sciences, Brown University, Providence, Rhode Island
| | - Rami Kantor
- Division of Infectious Diseases, Brown University Alpert Medical School, Providence, Rhode Island
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Bunupuradah T, Chetchotisakd P, Ananworanich J, Munsakul W, Jirajariyavej S, Kantipong P, Prasithsirikul W, Sungkanuparph S, Bowonwatanuwong C, Klinbuayaem V, Kerr SJ, Sophonphan J, Bhakeecheep S, Hirschel B, Ruxrungtham K. A randomized comparison of second-line lopinavir/ritonavir monotherapy versus tenofovir/lamivudine/lopinavir/ritonavir in patients failing NNRTI regimens: the HIV STAR study. Antivir Ther 2012; 17:1351-61. [PMID: 23075703 DOI: 10.3851/imp2443] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/26/2012] [Indexed: 10/27/2022]
Abstract
BACKGROUND Data informing the use of boosted protease inhibitor (PI) monotherapy as second-line treatment are limited. There are also no randomized trials addressing treatment options after failing first-line non-nucleoside reverse transcriptase inhibitor (NNRTI)-regimens. METHODS HIV-infected subjects ≥18 years, with HIV RNA≥1,000 copies/ml while using NNRTI plus 2 NRTIs, and naive to PIs were randomized to lopinavir/ritonavir (LPV/r) 400/100 mg twice daily monotherapy (mono-LPV/r) or tenofovir disoproxil fumarate (TDF) once daily plus lamivudine (3TC) twice daily plus LPV/r 400/100 mg twice daily (TDF/3TC/LPV/r) at nine sites in Thailand. The primary outcome was time-weighted area under curve (TWAUC) change in HIV RNA over 48 weeks. The a priori hypothesis was that the mono-LPV/r arm would be considered non-inferior if the upper 95% confidence limit in TWAUC mean difference was ≤0.5 log(10) copies/ml. RESULTS The intention-to-treat (ITT) population comprised 195 patients (mono-LPV/r n=98 and TDF/3TC/LPV/r n=97): male 58%, baseline mean (sd) age of 38 (7) years, CD4(+) T-cell count of 204 (135) cells/mm(3) and HIV RNA of 4.1 (0.6) log(10) copies/ml. The majority had HIV-1 recombinant CRF01_AE infection, and thymidine analogue mutation (TAM)-2 was 3× more common than TAM-1. At 48 weeks, the difference in TWAUC HIV RNA between arms was 0.15 (95% CI -0.04, 0.33) log(10) copies/ml, consistent with our definition of non-inferiority. However, the proportion with HIV RNA<50 copies/ml was significantly lower in the mono-LPV/r arm: 61% versus 83% (ITT, P<0.01). Baseline HIV RNA≥5 log(10) copies/ml (P<0.001) and mono-LPV/r use (P=0.003) were predictors of virological failure. Baseline genotypic sensitivity scores ≥2 and TAM-2 were associated with better virological control in subjects treated with the TDF-containing regimen. CONCLUSIONS In PI-naive patients failing NNRTI-based first-line HAART, mono-LPV/r had a significantly lower proportion of patients with HIV RNA<50 copies/ml compared to the TDF/3TC/LPV/r treatment. Thus, mono-LPV/r should not be recommended as a second-line option.
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Huang A, Hogan JW, Istrail S, Delong A, Katzenstein DA, Kantor R. Global analysis of sequence diversity within HIV-1 subtypes across geographic regions. Future Virol 2012; 7:505-517. [PMID: 22822410 DOI: 10.2217/fvl.12.37] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
AIMS: HIV-1 sequence diversity can affect host immune responses and phenotypic characteristics such as antiretroviral drug resistance. Current HIV-1 sequence diversity classification uses phylogeny-based methods to identify subtypes and recombinants, which may overlook distinct subpopulations within subtypes. While local epidemic studies have characterized sequence-level clustering within subtypes using phylogeny, identification of new genotype - phenotype associations are based on mutational correlations at individual sequence positions. We perform a systematic, global analysis of position-specific pol gene sequence variation across geographic regions within HIV-1 subtypes to characterize subpopulation differences that may be missed by standard subtyping methods and sequence-level phylogenetic clustering analyses. MATERIALS #ENTITYSTARTX00026; METHODS: Analysis was performed on a large, globally diverse, cross-sectional pol sequence dataset. Sequences were partitioned into subtypes and geographic subpopulations within subtypes. For each subtype, we identified positions that varied according to geography using VESPA (viral epidemiology signature pattern analysis) to identify sequence signature differences and a likelihood ratio test adjusted for multiple comparisons to characterize differences in amino acid (AA) frequencies, including minority mutations. Synonymous nonsynonymous analysis program (SNAP) was used to explore the role of evolutionary selection witihin subtype C. RESULTS: In 7693 protease (PR) and reverse transcriptase (RT) sequences from untreated patients in multiple geographic regions, 11 PR and 11 RT positions exhibited sequence signature differences within subtypes. Thirty six PR and 80 RT positions exhibited within-subtype geography-dependent differences in AA distributions, including minority mutations, at both conserved and variable loci. Among subtype C samples from India and South Africa, nine PR and nine RT positions had significantly different AA distributions, including one PR and five RT positions that differed in consensus AA between regions. A selection analysis of subtype C using SNAP demonstrated that estimated rates of nonsynonymous and synonymous mutations are consistent with the possibility of positive selection across geographic subpopulations within subtypes. CONCLUSION: We characterized systematic genotypic pol differences across geographic regions within subtypes that are not captured by the subtyping nomenclature. Awareness of such differences may improve the interpretation of future studies determining the phenotypic consequences of genetic backgrounds.
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Affiliation(s)
- Austin Huang
- Division of Infectious Diseases, Brown University, Providence, RI, USA
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29
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Bunupuradah T, Ananworanich J, Chetchotisakd P, Kantipong P, Jirajariyavej S, Sirivichayakul S, Munsakul W, Prasithsirikul W, Sungkanuparph S, Bowonwattanuwong C, Klinbuayaem V, Petoumenos K, Hirschel B, Bhakeecheep S, Ruxrungtham K. Etravirine and rilpivirine resistance in HIV-1 subtype CRF01_AE-infected adults failing non-nucleoside reverse transcriptase inhibitor-based regimens. Antivir Ther 2012; 16:1113-21. [PMID: 22024527 DOI: 10.3851/imp1906] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
BACKGROUND We studied prevalence of etravirine (ETR) and rilpivirine (RPV) resistance in HIV-1 subtype CRF01_AE infection with first-line non-nucleoside reverse transcriptase inhibitor (NNRTI) failure. METHODS A total of 225 adults failing two nucleoside reverse transcriptase inhibitors (NRTIs) plus 1 NNRTI in Thailand with HIV RNA>1,000 copies/ml were included. Genotypic resistance results and HIV-1 subtype were interpreted by Stanford DR database. ETR resistance was calculated by the new Monogram weighted score (Monogram WS; ≥ 4 indicating high-level ETR resistance) and by DUET weighted score (DUET WS; 2.5-3.5 and ≥ 4 resulted in intermediate and reduce ETR response, respectively). RPV resistance interpretation was based on previous reports. RESULTS Median (IQR) age was 38 (34-42) years, 41% were female and CDC A:B:C were 22%:21%:57%. HIV subtypes were 96% CRF01_AE and 4% B. Antiretrovirals at failure were lamivudine (100%), stavudine (93%), nevirapine (90%) and efavirenz (10%) with a median (IQR) duration of 3.4 (1.8-4.5) years. Median (IQR) CD4(+) T-cell count and HIV RNA were 194 (121-280) cells/mm³ and 4.1 (3.6-4.6) log₁₀ copies/ml, respectively. The common NNRTI mutations were Y181C (41%), G190A (22%) and K103N (19%). The proportion of patients with Monogram WS score ≥ 4 was 61.3%. By DUET WS, 49.8% and 7.5% of patients were scored 2.5-3.5 and ≥4, respectively. Only HIV RNA ≥ 4 log₁₀ copies/ml at failure was associated with both Monogram WS ≥ 4 (OR 2.3, 95% CI 1.3-3.9; P=0.003) and DUET WS ≥ 2.5 (OR 1.9, 95% CI 1.1-3.3; P=0.02). The RVP resistance-associated mutations (RAMs) detected were K101P (1.8%), Y181I (2.7%) and Y181V (3.6%). All patients with RPV mutation had ETR resistance. No E138R/E138K mutations were detected. CONCLUSIONS Approximately 60% of patients had high-level ETR resistance. The role of ETR in second-line therapy is limited in late NNRTI failure settings. RVP RAMs were uncommon, but cross-resistance between ETR and RVP was high.
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Praparattanapan J, Tragoolpua Y, Pathom-aree W, Kotarathitithum W, Chaiwarith R, Nuntachit N, Sirisanthana T, Supparatpinyo K. Current molecular epidemiology and recombination of HIV type 1 subtypes in northern Thailand. AIDS Res Hum Retroviruses 2011; 27:1201-6. [PMID: 21449850 DOI: 10.1089/aid.2010.0257] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
HIV subtype characterization is an important tool to monitor the genetic variation of the HIV epidemic. This study investigated the current HIV subtype distribution and recombination among the northern Thai population. An in-house genotypic assay of HIV protease and reverse transcriptase genes was performed on 420 plasma specimens from HIV-infected patients residing in several northern Thai provinces. HIV subtyping was determined by phylogenetic analysis. Three hundred and ninety-eight sequences (94.8%) were identified as CRF01_AE with the genetic distance of 1.848 ± 0.957% and 12 (2.9%) as subtype B with the genetic distance of 4.186 ± 0.849%. In addition, two sequences (0.5%) of HIV subtype C were found, suggesting that these patients were either immigrants from another country or were infected through heterosexual contact with HIV-infected subjects from another country. Bootscan analysis showed that there were eight (1.9%) unique recombinant forms (URFs) consisting of a recombinant of CRF01_AE with subtype B or subtype C. The information from this study is useful for prevention programs to halt the onward transmission of a particular HIV outbreak. However, characterization of the full genome of these CRF01_AE/B and CRF01_AE/C intersubtype recombinants, and also subtype C, is required for confirmation and elucidation.
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Affiliation(s)
- Jutarat Praparattanapan
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Department of Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Yingmanee Tragoolpua
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Wasu Pathom-aree
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Wilai Kotarathitithum
- Department of Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Romanee Chaiwarith
- Department of Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Nontakan Nuntachit
- Department of Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Thira Sirisanthana
- Research Institute for Health Science, Chiang Mai University, Chiang Mai, Thailand
| | - Khuanchai Supparatpinyo
- Department of Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Research Institute for Health Science, Chiang Mai University, Chiang Mai, Thailand
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Hamers RL, Wallis CL, Kityo C, Siwale M, Mandaliya K, Conradie F, Botes ME, Wellington M, Osibogun A, Sigaloff KCE, Nankya I, Schuurman R, Wit FW, Stevens WS, van Vugt M, de Wit TFR. HIV-1 drug resistance in antiretroviral-naive individuals in sub-Saharan Africa after rollout of antiretroviral therapy: a multicentre observational study. THE LANCET. INFECTIOUS DISEASES 2011; 11:750-9. [PMID: 21802367 DOI: 10.1016/s1473-3099(11)70149-9] [Citation(s) in RCA: 235] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND There are few data on the epidemiology of primary HIV-1 drug resistance after the roll-out of antiretroviral treatment (ART) in sub-Saharan Africa. We aimed to assess the prevalence of primary resistance in six African countries after ART roll-out and if wider use of ART in sub-Saharan Africa is associated with rising prevalence of drug resistance. METHODS We did a cross-sectional study in antiretroviral-naive adults infected with HIV-1 who had not started first-line ART, recruited between 2007 and 2009 from 11 regions in Kenya, Nigeria, South Africa, Uganda, Zambia, and Zimbabwe. We did population-based sequencing of the pol gene on plasma specimens with greater than 1000 copies per mL of HIV RNA. We identified drug-resistance mutations with the WHO list for transmitted resistance. The prevalence of sequences containing at least one drug-resistance mutation was calculated accounting for the sampling weights of the sites. We assessed the risk factors of resistance with multilevel logistic regression with random coefficients. FINDINGS 2436 (94.1%) of 2590 participants had a pretreatment genotypic resistance result. 1486 participants (57.4%) were women, 1575 (60.8%) had WHO clinical stage 3 or 4 disease, and the median CD4 count was 133 cells per μL (IQR 62-204). Overall sample-weighted drug-resistance prevalence was 5.6% (139 of 2436; 95% CI 4.6-6.7), ranging from 1.1% (two of 176; 0.0-2.7) in Pretoria, South Africa, to 12.3% (22 of 179; 7.5-17.1) in Kampala, Uganda. The pooled prevalence for all three Ugandan sites was 11.6% (66 of 570; 8.9-14.2), compared with 3.5% (73 of 1866; 2.5-4.5) for all other sites. Drug class-specific resistance prevalence was 2.5% (54 of 2436; 1.8-3.2) for nucleoside reverse-transcriptase inhibitors (NRTIs), 3.3% (83 of 2436; 2.5-4.2) for non-NRTIs (NNRTIs), 1.3% (31 of 2436; 0.8-1.8) for protease inhibitors, and 1.2% (25 of 2436; 0.7-1.7) for dual-class resistance to NRTIs and NNRTIs. The most common drug-resistance mutations were K103N (43 [1.8%] of 2436), thymidine analogue mutations (33 [1.6%] of 2436), M184V (25 [1.2%] of 2436), and Y181C/I (19 [0.7%] of 2436). The odds ratio for drug resistance associated with each additional year since the start of the ART roll-out in a region was 1.38 (95% CI 1.13-1.68; p=0.001). INTERPRETATION The higher prevalence of primary drug resistance in Uganda than in other African countries is probably related to the earlier start of ART roll-out in Uganda. Resistance surveillance and prevention should be prioritised in settings where ART programmes are scaled up. FUNDING Ministry of Foreign Affairs of the Netherlands.
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Affiliation(s)
- Raph L Hamers
- PharmAccess Foundation, Department of Global Health, Academic Medical Centre of University of Amsterdam, Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands.
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Sungkanuparph S, Oyomopito R, Sirivichayakul S, Sirisanthana T, Li PCK, Kantipong P, Lee CKC, Kamarulzaman A, Messerschmidt L, Law MG, Phanuphak P. HIV-1 drug resistance mutations among antiretroviral-naive HIV-1-infected patients in Asia: results from the TREAT Asia Studies to Evaluate Resistance-Monitoring Study. Clin Infect Dis 2011; 52:1053-7. [PMID: 21460324 DOI: 10.1093/cid/cir107] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Of 682 antiretroviral-naïve patients initiating antiretroviral therapy in a prospective, multicenter human immunodeficiency virus type 1 (HIV-1) drug resistance monitoring study involving 8 sites in Hong Kong, Malaysia, and Thailand, the prevalence of patients with ≥1 drug resistance mutation was 13.8%. Primary HIV drug resistance is emerging after rapid scaling-up of antiretroviral therapy use in Asia.
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33
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Hamers RL, Oyomopito R, Kityo C, Phanuphak P, Siwale M, Sungkanuparph S, Conradie F, Kumarasamy N, Botes ME, Sirisanthana T, Abdallah S, Li PCK, Ngorima N, Kantipong P, Osibogun A, Lee CKC, Stevens WS, Kamarulzaman A, Derdelinckx I, Chen YMA, Schuurman R, van Vugt M, Rinke de Wit TF. Cohort profile: The PharmAccess African (PASER-M) and the TREAT Asia (TASER-M) monitoring studies to evaluate resistance--HIV drug resistance in sub-Saharan Africa and the Asia-Pacific. Int J Epidemiol 2010; 41:43-54. [PMID: 21071386 PMCID: PMC3304520 DOI: 10.1093/ije/dyq192] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Affiliation(s)
- Raph L Hamers
- PharmAccess Foundation, Amsterdam Institute for Global Health and Development, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
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