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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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Multi-Laboratory Comparison of Next-Generation to Sanger-Based Sequencing for HIV-1 Drug Resistance Genotyping. Viruses 2020; 12:v12070694. [PMID: 32605062 PMCID: PMC7411816 DOI: 10.3390/v12070694] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/20/2020] [Accepted: 06/24/2020] [Indexed: 11/16/2022] Open
Abstract
Next-generation sequencing (NGS) is increasingly used for HIV-1 drug resistance genotyping. NGS methods have the potential for a more sensitive detection of low-abundance variants (LAV) compared to standard Sanger sequencing (SS) methods. A standardized threshold for reporting LAV that generates data comparable to those derived from SS is needed to allow for the comparability of data from laboratories using NGS and SS. Ten HIV-1 specimens were tested in ten laboratories using Illumina MiSeq-based methods. The consensus sequences for each specimen using LAV thresholds of 5%, 10%, 15%, and 20% were compared to each other and to the consensus of the SS sequences (protease 4-99; reverse transcriptase 38-247). The concordance among laboratories' sequences at different thresholds was evaluated by pairwise sequence comparisons. NGS sequences generated using the 20% threshold were the most similar to the SS consensus (average 99.6% identity, range 96.1-100%), compared to 15% (99.4%, 88.5-100%), 10% (99.2%, 87.4-100%), or 5% (98.5%, 86.4-100%). The average sequence identity between laboratories using thresholds of 20%, 15%, 10%, and 5% was 99.1%, 98.7%, 98.3%, and 97.3%, respectively. Using the 20% threshold, we observed an excellent agreement between NGS and SS, but significant differences at lower thresholds. Understanding how variation in NGS methods influences sequence quality is essential for NGS-based HIV-1 drug resistance genotyping.
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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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Performance comparison of next generation sequencing analysis pipelines for HIV-1 drug resistance testing. Sci Rep 2020; 10:1634. [PMID: 32005884 PMCID: PMC6994664 DOI: 10.1038/s41598-020-58544-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 01/09/2020] [Indexed: 01/13/2023] Open
Abstract
Next generation sequencing (NGS) is a trending new standard for genotypic HIV-1 drug resistance (HIVDR) testing. Many NGS HIVDR data analysis pipelines have been independently developed, each with variable outputs and data management protocols. Standardization of such analytical methods and comparison of available pipelines are lacking, yet may impact subsequent HIVDR interpretation and other downstream applications. Here we compared the performance of five NGS HIVDR pipelines using proficiency panel samples from NIAID Virology Quality Assurance (VQA) program. Ten VQA panel specimens were genotyped by each of six international laboratories using their own in-house NGS assays. Raw NGS data were then processed using each of the five different pipelines including HyDRA, MiCall, PASeq, Hivmmer and DEEPGEN. All pipelines detected amino acid variants (AAVs) at full range of frequencies (1~100%) and demonstrated good linearity as compared to the reference frequency values. While the sensitivity in detecting low abundance AAVs, with frequencies between 1~20%, is less a concern for all pipelines, their specificity dramatically decreased at AAV frequencies <2%, suggesting that 2% threshold may be a more reliable reporting threshold for ensured specificity in AAV calling and reporting. More variations were observed among the pipelines when low abundance AAVs are concerned, likely due to differences in their NGS read quality control strategies. Findings from this study highlight the need for standardized strategies for NGS HIVDR data analysis, especially for the detection of minority HIVDR variants.
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Magomere EO, Nyangahu DD, Kimoloi S, Webala BA, Ondigo BN. Performance characteristics of a modified HIV-1 drug resistance genotyping method for use in resource-limited settings. F1000Res 2019; 8:1518. [PMID: 31656591 PMCID: PMC6798314 DOI: 10.12688/f1000research.20083.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/14/2019] [Indexed: 11/20/2022] Open
Abstract
Background: HIV-1 drug resistance (HIVDR) assays are critical components of HIV clinical management programs in the face of emerging drug resistance. However, the high costs associated with existing commercial HIVDR assays prohibit their routine usage in resource-limited settings. We present the performance characteristics of a modified commercial HIVDR testing assay. Methods: A total of 26 plasma samples were used to validate and assess the accuracy, precision, reproducibility and amplification sensitivity of a modified HIVDR assay by HIV genotyping. In addition, a cost comparison between the original and the modified assay was performed using the ingredient costing approach. Results: The performance characteristics of the modified assay were in agreement with the original assay. Accuracy, precision and reproducibility showed nucleotide sequence identity of 98.5% (confidence interval (CI), 97.9-99.1%), 98.67% (CI, 98.1-99.23) and 98.7% (CI, 98.1-99.3), respectively. There was no difference in the type of mutations detected by the two assays (χ 2 = 2.36, p = 0.26). Precision and reproducibility showed significant mutation agreement between replicates (kappa = 0.79 and 0.78), respectively ( p < 0.05). The amplification sensitivity of the modified assay was 100% and 62.5% for viremia ≥1000 copies/ml and <1000 copies/ml respectively. Our assay modification translates to a 39.2% reduction in the cost of reagents. Conclusions: Our findings underscore the potential of modifying commercially available HIVDR testing assays into cost-effective, yet accurate assays for use in resource-limited settings.
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Affiliation(s)
- Edwin O. Magomere
- Department of Biochemistry and Molecular Biology, Egerton University, Nakuru, Nakuru, 20115, Kenya
| | - Donald D. Nyangahu
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Seattle, Washington, USA
| | - Sammy Kimoloi
- Department of Medical Laboratory Sciences, Masinde Muliro University of Science and Technology, Kakamega, Kakamega, Kenya
| | - Brenda A. Webala
- Faculty of Health Sciences, Egerton University, Nakuru, Nakuru, Kenya
| | - Bartholomew N. Ondigo
- Department of Biochemistry and Molecular Biology, Egerton University, Nakuru, Nakuru, 20115, Kenya
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kisumu, Kenya
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, NIH, USA, Bethesda, Maryland, USA
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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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Ji H, Enns E, Brumme CJ, Parkin N, Howison M, Lee ER, Capina R, Marinier E, Avila‐Rios S, Sandstrom P, Van Domselaar G, Harrigan R, Paredes R, Kantor R, Noguera‐Julian M. Bioinformatic data processing pipelines in support of next-generation sequencing-based HIV drug resistance testing: the Winnipeg Consensus. J Int AIDS Soc 2018; 21:e25193. [PMID: 30350345 PMCID: PMC6198166 DOI: 10.1002/jia2.25193] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 09/26/2018] [Indexed: 11/14/2022] Open
Abstract
INTRODUCTION Next-generation sequencing (NGS) has several advantages over conventional Sanger sequencing for HIV drug resistance (HIVDR) genotyping, including detection and quantitation of low-abundance variants bearing drug resistance mutations (DRMs). However, the high HIV genomic diversity, unprecedented large volume of data, complexity of analysis and potential for error pose significant challenges for data processing. Several NGS analysis pipelines have been developed and used in HIVDR research; however, the absence of uniformity in data processing strategies results in lack of consistency and comparability of outputs from different pipelines. To fill this gap, an international symposium on bioinformatic strategies for NGS-based HIVDR testing was held in February 2018 in Winnipeg, Canada, convening laboratory scientists, bioinformaticians and clinicians involved in four recently developed, publicly available NGS HIVDR pipelines. The goal of this symposium was to establish a consensus on effective bioinformatic strategies for NGS data management and its use for HIVDR reporting. DISCUSSION Essential functionalities of an NGS HIVDR pipeline were divided into five analytic blocks: (1) NGS read quality control (QC)/quality assurance (QA); (2) NGS read alignment and reference mapping; (3) HIV variant calling and variant QC; (4) NGS HIVDR reporting; and (5) extended data applications and additional considerations for data management. The consensuses reached among the participants on all major aspects of these blocks are summarized here. They encompass not only recommended data management and analysis strategies, but also detailed bioinformatic approaches that help ensure accuracy of the derived HIVDR analysis outputs for both research and potential clinical use. CONCLUSIONS While NGS is being adopted more broadly in HIVDR testing laboratories, data processing is often a bottleneck hindering its generalized application. The proposed standardization of NGS read QC/QA, read alignment and reference mapping, variant calling and QC, HIVDR reporting and relevant data management strategies in this "Winnipeg Consensus" may serve as a starting guideline for NGS HIVDR data processing that informs the refinement of existing pipelines and those yet to be developed. Moreover, the bioinformatic strategies presented here may apply more broadly to NGS data analysis of microbes harbouring significant genomic diversity.
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Affiliation(s)
- Hezhao Ji
- National HIV and Retrovirology Laboratories at JC Wilt Infectious Diseases Research CentrePublic Health Agency of CanadaWinnipegMBCanada
- Department of Medical Microbiology and Infectious DiseasesUniversity of ManitobaWinnipegMBCanada
| | - Eric Enns
- Bioinformatics Core at the National Microbiology LaboratoryPublic Health Agency of CanadaWinnipegMBCanada
| | | | | | - Mark Howison
- Watson Institute for International and Public AffairsBrown UniversityProvidenceRIUSA
| | - Emma R. Lee
- National HIV and Retrovirology Laboratories at JC Wilt Infectious Diseases Research CentrePublic Health Agency of CanadaWinnipegMBCanada
| | - Rupert Capina
- National HIV and Retrovirology Laboratories at JC Wilt Infectious Diseases Research CentrePublic Health Agency of CanadaWinnipegMBCanada
| | - Eric Marinier
- Bioinformatics Core at the National Microbiology LaboratoryPublic Health Agency of CanadaWinnipegMBCanada
| | - Santiago Avila‐Rios
- Centre for Research in Infectious DiseasesNational Institute of Respiratory DiseasesMexico CityMexico
| | - Paul Sandstrom
- National HIV and Retrovirology Laboratories at JC Wilt Infectious Diseases Research CentrePublic Health Agency of CanadaWinnipegMBCanada
- Department of Medical Microbiology and Infectious DiseasesUniversity of ManitobaWinnipegMBCanada
| | - Gary Van Domselaar
- Department of Medical Microbiology and Infectious DiseasesUniversity of ManitobaWinnipegMBCanada
- Bioinformatics Core at the National Microbiology LaboratoryPublic Health Agency of CanadaWinnipegMBCanada
| | - Richard Harrigan
- Division of AIDSDepartment of MedicineUniversity of British ColumbiaVancouverBCCanada
| | - Roger Paredes
- IrsiCaixa AIDS Research InstituteBadalonaCataloniaSpain
| | - Rami Kantor
- Division of Infectious DiseasesBrown University Alpert Medical SchoolProvidenceRIUSA
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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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A quality control program within a clinical trial Consortium for PCR protocols to detect Plasmodium species. J Clin Microbiol 2014; 52:2144-9. [PMID: 24740073 DOI: 10.1128/jcm.00565-14] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Malaria parasite infections that are only detectable by molecular methods are highly prevalent and represent a potential transmission reservoir. The methods used to detect these infections are not standardized, and their operating characteristics are often unknown. We designed a proficiency panel of Plasmodium spp. in order to compare the accuracy of parasite detection of molecular protocols used by labs in a clinical trial consortium. Ten dried blood spots (DBSs) were assembled that contained P. falciparum, P. vivax, P. malariae, and P. ovale; DBSs contained either a single species or a species mixed with P. falciparum. DBS panels were tested in 9 participating laboratories in a masked fashion. Of 90 tests, 68 (75.6%) were correct; there were 20 false-negative results and 2 false positives. The detection rate was 77.8% (49/63) for P. falciparum, 91.7% (11/12) for P. vivax, 83.3% (10/12) for P. malariae, and 70% (7/10) for P. ovale. Most false-negative P. falciparum results were from samples with an estimated ≤ 5 parasites per μl of blood. Between labs, accuracy ranged from 100% to 50%. In one lab, the inability to detect species in mixed-species infections prompted a redesign and improvement of the assay. Most PCR-based protocols were able to detect P. falciparum and P. vivax at higher densities, but these assays may not reliably detect parasites in samples with low P. falciparum densities. Accordingly, formal quality assurance for PCR should be employed whenever this method is used for diagnosis or surveillance. Such efforts will be important if PCR is to be widely employed to assist malaria elimination efforts.
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Yan H, Yu H, Xing W, Xiao Y, Zhang H, Pei L, Zhang N, Jiang Y. Development of a proficiency testing program for the HIV-1 BED incidence assay in China. Sci Rep 2014; 4:4512. [PMID: 24676229 PMCID: PMC3968539 DOI: 10.1038/srep04512] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 03/13/2014] [Indexed: 11/27/2022] Open
Abstract
The HIV-1 BED incidence assay was adopted in China in 2005 for HIV-1 incidence surveillance. A proficiency testing (PT) program was established in 2006 to provide quality assurance services. The BED PT program consisted of two components, an international program provided by the U.S. Centers for Disease Control and Prevention from 2006 and a domestic program started by the National HIV/HCV Reference Laboratory in 2011. Each PT panel consisted of eight coded specimens distributed to participating laboratories semi-annually, and testing results were collected and analyzed. The number of participating laboratories increased progressively from 2006 to 2012. The Chinese HIV-1 incidence laboratory network performed satisfactorily both in international and domestic PT programs. We also demonstrated that the BED assay was highly reproducible among participating laboratories. Our success and lessons learned can be readily replicated in other countries or regions contemplating the establishment of a PT program for assay-based HIV incidence estimation.
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Affiliation(s)
- Hao Yan
- National HIV/HCV Reference Laboratory, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Haiying Yu
- 1] National HIV/HCV Reference Laboratory, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China [2] HIV Confirmatory Central Laboratory, Shandong Provincial Center for Disease Control and Prevention, Jinan, China
| | - Wenge Xing
- National HIV/HCV Reference Laboratory, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yao Xiao
- National HIV/HCV Reference Laboratory, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hui Zhang
- National HIV/HCV Reference Laboratory, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lijian Pei
- National HIV/HCV Reference Laboratory, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Na Zhang
- 1] National HIV/HCV Reference Laboratory, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China [2] HIV Confirmatory Central Laboratory, Jiangxi Provincial Center for Disease Control and Prevention, Nanchang, China
| | - Yan Jiang
- National HIV/HCV Reference Laboratory, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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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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Parikh UM, Mellors JW. Pretreatment HIV-1 drug resistance is strongly associated with virologic failure in HIV-infected patients receiving partly active antiretroviral regimens. Future Microbiol 2013; 7:929-32. [PMID: 22913352 DOI: 10.2217/fmb.12.72] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The scale-up of antiretroviral therapy in sub-Saharan Africa has significantly reduced mortality from AIDS. Hamers et al. explores the impact of pretreatment HIV-1 drug resistance on virologic failure, immunologic response, and acquisition of drug resistance after 1 year of first-line antiretroviral therapy by longitudinally evaluating 2579 participants with pretreatment drug resistance results from the PharmAccess African Studies to Evaluate Resistance Monitoring (PASER-M) cohort. Participants with pretreatment drug resistance who were given a treatment regimen with reduced activity to at least one prescribed drug had a significantly greater risk of virologic failure and acquired drug resistance compared with both participants without pretreatment drug resistance, and participants with pretreatment drug resistance who were prescribed fully active regimens. This paper by Hamers et al. validates the need for at least three fully active antiretroviral drugs to prevent the acquisition of drug resistance and to optimize treatment success in resource limited settings.
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Affiliation(s)
- Urvi M Parikh
- University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.
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Emerging HIV-1 drug resistance after roll-out of antiretroviral therapy in sub-Saharan Africa. Curr Opin HIV AIDS 2013; 8:19-26. [DOI: 10.1097/coh.0b013e32835b7f94] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Jordan MR, Bennett DE, Wainberg MA, Havlir D, Hammer S, Yang C, Morris L, Peeters M, Wensing AM, Parkin N, Nachega JB, Phillips A, De Luca A, Geng E, Calmy A, Raizes E, Sandstrom P, Archibald CP, Perriëns J, McClure CM, Hong SY, McMahon JH, Dedes N, Sutherland D, Bertagnolio S. Update on World Health Organization HIV drug resistance prevention and assessment strategy: 2004-2011. Clin Infect Dis 2012; 54 Suppl 4:S245-9. [PMID: 22544182 DOI: 10.1093/cid/cis206] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The HIV drug resistance (HIVDR) prevention and assessment strategy, developed by the World Health Organization (WHO) in partnership with HIVResNet, includes monitoring of HIVDR early warning indicators, surveys to assess acquired and transmitted HIVDR, and development of an accredited HIVDR genotyping laboratory network to support survey implementation in resource-limited settings. As of June 2011, 52 countries had implemented at least 1 element of the strategy, and 27 laboratories had been accredited. As access to antiretrovirals expands under the WHO/Joint United Nations Programme on HIV/AIDS Treatment 2.0 initiative, it is essential to strengthen HIVDR surveillance efforts in the face of increasing concern about HIVDR emergence and transmission.
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Affiliation(s)
- M R Jordan
- World Health Organization, Geneva, Switzerland.
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Parkin N, de Mendoza C, Schuurman R, Jennings C, Bremer J, Jordan MR, Bertagnolio S. Evaluation of in-house genotyping assay performance using dried blood spot specimens in the Global World Health Organization laboratory network. Clin Infect Dis 2012; 54 Suppl 4:S273-9. [PMID: 22544187 DOI: 10.1093/cid/cir982] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In resource-limited settings, there is increased demand for human immunodeficiency virus type 1 drug resistance testing. Because preservation of plasma specimens is often not feasible in resource-limited settings, use of dried blood spots (DBSs) is being adopted. We used 2 panels of DBSs for genotyping assay validation and proficiency testing in selected laboratories in the World Health Organization laboratory network in 14 countries. An amplification sensitivity of 1000 copies/mL was achieved by 2 laboratories. Reproducibility and accuracy of nucleotide sequence determination and resistance-associated mutation identification from DBSs was similar to that previously determined for plasma. International shipping at ambient temperature had no significant effect on amplification success. These studies indicate that DBS-based genotyping is equally reproducible and reliable, although slightly less sensitive, compared with plasma.
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Affiliation(s)
- Neil Parkin
- Data First Consulting, Belmont, California 94002, USA.
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Gupta RK, Jordan MR, Sultan BJ, Hill A, Davis DHJ, Gregson J, Sawyer AW, Hamers RL, Ndembi N, Pillay D, Bertagnolio S. Global trends in antiretroviral resistance in treatment-naive individuals with HIV after rollout of antiretroviral treatment in resource-limited settings: a global collaborative study and meta-regression analysis. Lancet 2012; 380:1250-8. [PMID: 22828485 PMCID: PMC3790969 DOI: 10.1016/s0140-6736(12)61038-1] [Citation(s) in RCA: 278] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
BACKGROUND The emergence and spread of high levels of HIV-1 drug resistance in resource-limited settings where combination antiretroviral treatment has been scaled up could compromise the effectiveness of national HIV treatment programmes. We aimed to estimate changes in the prevalence of HIV-1 drug resistance in treatment-naive individuals with HIV since initiation of rollout in resource-limited settings. METHODS We did a systematic search for studies and conference abstracts published between January, 2001, and July, 2011, and included additional data from the WHO HIV drug resistance surveillance programme. We assessed the prevalence of drug-resistance mutations in untreated individuals with respect to time since rollout in a series of random-effects meta-regression models. FINDINGS Study-level data were available for 26,102 patients from sub-Saharan Africa, Asia, and Latin America. We recorded no difference between chronic and recent infection on the prevalence of one or more drug-resistance mutations for any region. East Africa had the highest estimated rate of increase at 29% per year (95% CI 15 to 45; p=0·0001) since rollout, with an estimated prevalence of HIV-1 drug resistance at 8 years after rollout of 7·4% (4·3 to 12·7). We recorded an annual increase of 14% (0% to 29%; p=0·054) in southern Africa and a non-significant increase of 3% (-0·9 to 16; p=0·618) in west and central Africa. There was no change in resistance over time in Latin America, and because of much country-level heterogeneity the meta-regression analysis was not appropriate for Asia. With respect to class of antiretroviral, there were substantial increases in resistance to non-nucleoside reverse transcriptase inhibitors (NNRTI) in east Africa (36% per year [21 to 52]; p<0·0001) and southern Africa (23% per year [7 to 42]; p=0·0049). No increase was noted for the other drug classes in any region. INTERPRETATION Our findings suggest a significant increase in prevalence of drug resistance over time since antiretroviral rollout in regions of sub-Saharan Africa; this rise is driven by NNRTI resistance in studies from east and southern Africa. The findings are of concern and draw attention to the need for enhanced surveillance and drug-resistance prevention efforts by national HIV treatment programmes. Nevertheless, estimated levels, although increasing, are not unexpected in view of the large expansion of antiretroviral treatment coverage seen in low-income and middle-income countries--no changes in antiretroviral treatment guidelines are warranted at the moment. FUNDING Bill & Melinda Gates Foundation and the European Community's Seventh Framework Programme.
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Affiliation(s)
| | | | - Binta J Sultan
- Mortimer Market Centre, Camden Provider Services PCT, London, UK
| | - Andrew Hill
- Pharmacology Research Laboratories, Liverpool University, Liverpool, UK
| | - Daniel HJ Davis
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - John Gregson
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | - Raph L Hamers
- PharmAccess Foundation, Academic Medical Centre of the University of Amsterdam, Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands
| | | | - Deenan Pillay
- Department of Infection, University College London, London, UK
| | - Silvia Bertagnolio
- WHO, Geneva, Switzerland
- Correspondence to: Dr Silvia Bertagnolio, HIV Department, WHO, Geneva, Switzerland
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