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Jenkins F, Le T, Farhat R, Pinto A, Anzari A, Bonsall D, Golubchik T, Bowden R, Lee FJ, van Hal SJ. Validation of an HIV whole genome sequencing method for HIV drug resistance testing in an Australian clinical microbiology laboratory. J Med Virol 2023; 95:e29273. [PMID: 38050831 DOI: 10.1002/jmv.29273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/31/2023] [Accepted: 11/16/2023] [Indexed: 12/07/2023]
Abstract
Detection of HIV drug resistance (HIVDR) is vital to successful anti-retroviral therapy (ART). HIVDR testing to determine drug-resistance mutations is routinely performed in Australia to guide ART choice in newly diagnosed people living with HIV or in cases of treatment failure. In 2022, our clinical microbiology laboratory sought to validate a next-generation sequencing (NGS)-based HIVDR assay to replace the previous Sanger-sequencing (SS)-based ViroSeq. NGS solutions for HIVDR offer higher throughput, lower costs and higher sensitivity for variant detection. We sought to validate the previously described low-cost probe-based NGS method (veSEQ-HIV) for whole-genome recovery and HIVDR-testing in a diagnostic setting. veSEQ-HIV displayed 100% and 98% accuracy in major and minor mutation detection, respectively, and 100% accuracy of subtyping (provided > 1000 mapped reads were obtained). Pairwise comparison exhibited low inter-and intrarun variability across the whole-genome (Jaccard index [J] = 0.993; J = 0.972) and the Pol gene (J = 0.999; J = 0.999), respectively. veSEQ-HIV met all our pre-set criteria based on WHO recommendations and successfully replaced ViroSeq in our laboratory. Scaling-down veSEQ-HIV to a limited batch size and sequencing on Illumina iSeq. 100, allowed easy implementation of the assay into the workflow of a small sequencing laboratory with minimal staff and equipment and the ability to meet clinically relevant test turn-around times. As HIVDR-testing moves from SS- to NGS-based methods and new ART drugs come to market (particularly those with targets outside the Pol region), whole-genome recovery using veSEQ-HIV provides a robust, cost-effective and "future-proof" NGS method for HIVDR-testing.
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Affiliation(s)
- Frances Jenkins
- Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Thomas Le
- Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Rima Farhat
- Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Angie Pinto
- Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, Australia
- The Kirby Institute, UNSW Australia, Sydney, Australia
| | - Azim Anzari
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - David Bonsall
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Tanya Golubchik
- Department of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Rory Bowden
- The Walter and Eliza Hall Institute of Medical Research, Advanced Genomics Facility, Melbourne, Australia
| | - Frederick J Lee
- Department of Clinical Immunology and Allergy, Royal Prince Alfred Hospital, Sydney, Australia
- Sydney Medical School, University of Sydney, Sydney, Australia
| | - Sebastiaan J van Hal
- Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, Australia
- Sydney Medical School, University of Sydney, Sydney, Australia
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Abstract
PURPOSE OF REVIEW HIV-1 drug resistance (HIV DR) testing is routinely performed by genotyping plasma viruses using Sanger population sequencing. Next-generation sequencing (NGS) is increasingly replacing standardized Sanger sequencing. This opens up new opportunities, but also brings challenges. RECENT FINDINGS The number of NGS applications and protocols for HIV DR testing is increasing. All of them are noninferior to Sanger sequencing when comparing NGS-derived consensus sequences to Sanger sequencing-derived sequences. In addition, NGS enables high-throughput sequencing of near full-length HIV-1 genomes and detection of low-abundance drug-resistant HIV-1 variants, although their clinical implications need further investigation. Several groups have defined remaining challenges in implementing NGS protocols for HIV-1 resistance testing. Some of them are already being addressed. One of the most important needs is quality management and consequently, if possible, standardization. SUMMARY The use of NGS technologies on HIV DR testing will allow unprecedented insights into genomic structures of virus populations that may be of immediate relevance to both clinical and research areas such as personalized antiretroviral treatment. Efforts continue to tackle the remaining challenges in NGS-based HIV DR testing.
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Yu F, Li Q, Wang L, Zhao H, Wu H, Yang S, Tang Y, Xiao J, Zhang F. Drug Resistance to HIV-1 Integrase Inhibitors Among Treatment-Naive Patients in Beijing, China. Pharmgenomics Pers Med 2022; 15:195-203. [PMID: 35300056 PMCID: PMC8922317 DOI: 10.2147/pgpm.s345797] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 02/17/2022] [Indexed: 12/31/2022] Open
Abstract
Introduction Integrase strand transfer inhibitors (INSTIs) are important drugs that are currently used as the first line treatment for HIV-1 patients. The aim of this study was to characterize HIV-1 INSTI mutations among ART-naive patients in Beijing from 2019-2021. Methods 865 ART-naive patients were enrolled in this study between January 2019 and June 2021 in Beijing. The amplification of the entire pol gene containing the reverse transcriptase, protease and integrase regions was performed using a validated In-house SBS method. HIV-1 subtypes and circulating recombinant forms (CRFs) were determined using the COMET online tool (http://comet.retrovirology.lu). Stanford HIV-1 drug resistance database (HIVdb version 8.9) was used to analyze the mutations. Results 865 HIV-1 pol sequences were successfully amplified and sequenced. Among them, no major INSTI-related mutations were identified, but 12 polymorphic accessory mutations were found. Two patients have E138A and G163R mutations respectively and both could cause low-level resistance to RAL and EVG. Furthermore, one patient having S230R mutation resulted in low-level resistance to RAL, EVG, DTG and BIC. Conclusion The prevalence of INSTIs mutations remains low, which demonstrated that INSTIs have good applicability currently in our city. Nevertheless, it is very important to monitor the INSTI-related mutations in Beijing.
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Affiliation(s)
- Fengting Yu
- Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, People’s Republic of China
| | - Qun Li
- Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, People’s Republic of China
| | - Linghang Wang
- Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, People’s Republic of China
| | - Hongxin Zhao
- Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, People’s Republic of China
| | - Hao Wu
- Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Siyuan Yang
- Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, People’s Republic of China
| | - Yunxia Tang
- Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, People’s Republic of China
| | - Jiang Xiao
- Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, People’s Republic of China
| | - Fujie Zhang
- Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Clinical Center for HIV/AIDS, Capital Medical University, Beijing, People’s Republic of China
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Blassel L, Zhukova A, Villabona-Arenas CJ, Atkins KE, Hué S, Gascuel O. Drug resistance mutations in HIV: new bioinformatics approaches and challenges. Curr Opin Virol 2021; 51:56-64. [PMID: 34597873 DOI: 10.1016/j.coviro.2021.09.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 08/31/2021] [Accepted: 09/13/2021] [Indexed: 12/11/2022]
Abstract
Drug resistance mutations appear in HIV under treatment pressure. Resistant variants can be transmitted to treatment-naive individuals, which can lead to rapid virological failure and can limit treatment options. Consequently, quantifying the prevalence, emergence and transmission of drug resistance is critical to effectively treating patients and to shape health policies. We review recent bioinformatics developments and in particular describe: (1) the machine learning approaches intended to predict and explain the level of resistance of HIV variants from their sequence data; (2) the phylogenetic methods used to survey the emergence and dynamics of resistant HIV transmission clusters; (3) the impact of deep sequencing in studying within-host and between-host genetic diversity of HIV variants, notably regarding minority resistant variants.
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Affiliation(s)
- Luc Blassel
- Unité Bioinformatique Evolutive, Institut Pasteur, Paris, France; Sorbonne Université, Collège Doctoral, Paris, France
| | - Anna Zhukova
- Unité Bioinformatique Evolutive, Institut Pasteur, Paris, France; Hub de Bioinformatique et Biostatistique, Institut Pasteur, Paris, France
| | - Christian J Villabona-Arenas
- Centre for the Mathematical Modelling of Infectious Diseases (CMMID), London School of Hygiene & Tropical Medicine, London, UK; Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Katherine E Atkins
- Centre for the Mathematical Modelling of Infectious Diseases (CMMID), London School of Hygiene & Tropical Medicine, London, UK; Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK; Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Stéphane Hué
- Centre for the Mathematical Modelling of Infectious Diseases (CMMID), London School of Hygiene & Tropical Medicine, London, UK; Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Olivier Gascuel
- Institut de Systématique, Evolution, Biodiversité (ISYEB, UMR 7205 - CNRS, Muséum National d'Histoire Naturelle, EPHE, SU, UA), Paris, France.
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Frost JR, Schulz H, McLachlan E, Hiebert J, Severini A. An enrichment method for capturing mumps virus whole genome sequences directly from clinical specimens. J Virol Methods 2021; 294:114176. [PMID: 33957163 DOI: 10.1016/j.jviromet.2021.114176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/16/2021] [Accepted: 04/24/2021] [Indexed: 10/21/2022]
Abstract
Recently there has been a significant increase in the number of mumps outbreaks occurring in highly vaccinated populations. These outbreaks are often due to a mumps genotype G virus, where sequencing of the SH gene does not reveal enough genetic diversity to sufficient to resolve outbreaks. This has elevated the need to be able to sequence complete mumps viruses from clinical samples without laborious methods. Here we describe a probe enrichment method that allows for whole genome sequencing of the mumps virus directly from clinical specimens. Using 136 clinical samples, we show this method allows for a significant increase in the percentage of viral sequencing reads, resulting in the capture of mumps genomes. This method will be an asset in investigating future mumps outbreaks.
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Affiliation(s)
- Jasmine Rae Frost
- Department of Medical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Helene Schulz
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Elizabeth McLachlan
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Joanne Hiebert
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Alberto Severini
- Department of Medical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada; National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
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Li M, Liang S, Zhou C, Chen M, Liang S, Liu C, Zuo Z, Liu L, Feng Y, Song C, Xing H, Ruan Y, Shao Y, Liao L. HIV Drug Resistance Mutations Detection by Next-Generation Sequencing during Antiretroviral Therapy Interruption in China. Pathogens 2021; 10:pathogens10030264. [PMID: 33668946 PMCID: PMC7996606 DOI: 10.3390/pathogens10030264] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/17/2021] [Accepted: 02/20/2021] [Indexed: 11/24/2022] Open
Abstract
Patients with antiretroviral therapy interruption have a high risk of virological failure when re-initiating antiretroviral therapy (ART), especially those with HIV drug resistance. Next-generation sequencing may provide close scrutiny on their minority drug resistance variant. A cross-sectional study was conducted in patients with ART interruption in five regions in China in 2016. Through Sanger and next-generation sequencing in parallel, HIV drug resistance was genotyped on their plasma samples. Rates of HIV drug resistance were compared by the McNemar tests. In total, 174 patients were included in this study, with a median 12 (interquartile range (IQR), 6–24) months of ART interruption. Most (86.2%) of them had received efavirenz (EFV)/nevirapine (NVP)-based first-line therapy for a median 16 (IQR, 7–26) months before ART interruption. Sixty-one (35.1%) patients had CRF07_BC HIV-1 strains, 58 (33.3%) CRF08_BC and 35 (20.1%) CRF01_AE. Thirty-four (19.5%) of the 174 patients were detected to harbor HIV drug-resistant variants on Sanger sequencing. Thirty-six (20.7%), 37 (21.3%), 42 (24.1%), 79 (45.4%) and 139 (79.9) patients were identified to have HIV drug resistance by next-generation sequencing at 20% (v.s. Sanger, p = 0.317), 10% (v.s. Sanger, p = 0.180), 5% (v.s. Sanger, p = 0.011), 2% (v.s. Sanger, p < 0.001) and 1% (v.s. Sanger, p < 0.001) of detection thresholds, respectively. K65R was the most common minority mutation, of 95.1% (58/61) and 93.1% (54/58) in CRF07_BC and CRF08_BC, respectively, when compared with 5.7% (2/35) in CRF01_AE (p < 0.001). In 49 patients that followed-up a median 10 months later, HIV drug resistance mutations at >20% frequency such as K103N, M184VI and P225H still existed, but with decreased frequencies. The prevalence of HIV drug resistance in ART interruption was higher than 15% in the survey. Next-generation sequencing was able to detect more minority drug resistance variants than Sanger. There was a sharp increase in minority drug resistance variants when the detection threshold was below 5%.
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Affiliation(s)
- Miaomiao Li
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (M.L.); (Z.Z.); (L.L.); (Y.F.); (C.S.); (H.X.); (Y.R.); (Y.S.)
| | - Shujia Liang
- Guangxi Center for Disease Control and Prevention, Nanning 530028, China;
| | - Chao Zhou
- Chongqing Center for Disease Control and Prevention, Chongqing 400042, China;
| | - Min Chen
- Yunnan Center for Disease Control and Prevention, Kunming 650022, China;
| | - Shu Liang
- Sichuan Center for Disease Control and Prevention, Chengdu 610041, China;
| | - Chunhua Liu
- Henan Center for Disease Control and Prevention, Zhengzhou 450016, China;
| | - Zhongbao Zuo
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (M.L.); (Z.Z.); (L.L.); (Y.F.); (C.S.); (H.X.); (Y.R.); (Y.S.)
| | - Lei Liu
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (M.L.); (Z.Z.); (L.L.); (Y.F.); (C.S.); (H.X.); (Y.R.); (Y.S.)
| | - Yi Feng
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (M.L.); (Z.Z.); (L.L.); (Y.F.); (C.S.); (H.X.); (Y.R.); (Y.S.)
| | - Chang Song
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (M.L.); (Z.Z.); (L.L.); (Y.F.); (C.S.); (H.X.); (Y.R.); (Y.S.)
| | - Hui Xing
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (M.L.); (Z.Z.); (L.L.); (Y.F.); (C.S.); (H.X.); (Y.R.); (Y.S.)
| | - Yuhua Ruan
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (M.L.); (Z.Z.); (L.L.); (Y.F.); (C.S.); (H.X.); (Y.R.); (Y.S.)
| | - Yiming Shao
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (M.L.); (Z.Z.); (L.L.); (Y.F.); (C.S.); (H.X.); (Y.R.); (Y.S.)
| | - Lingjie Liao
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (M.L.); (Z.Z.); (L.L.); (Y.F.); (C.S.); (H.X.); (Y.R.); (Y.S.)
- Correspondence:
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Bonsall D, Golubchik T, de Cesare M, Limbada M, Kosloff B, MacIntyre-Cockett G, Hall M, Wymant C, Ansari MA, Abeler-Dörner L, Schaap A, Brown A, Barnes E, Piwowar-Manning E, Eshleman S, Wilson E, Emel L, Hayes R, Fidler S, Ayles H, Bowden R, Fraser C. A Comprehensive Genomics Solution for HIV Surveillance and Clinical Monitoring in Low-Income Settings. J Clin Microbiol 2020; 58:e00382-20. [PMID: 32669382 PMCID: PMC7512176 DOI: 10.1128/jcm.00382-20] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 07/10/2020] [Indexed: 01/01/2023] Open
Abstract
Viral genetic sequencing can be used to monitor the spread of HIV drug resistance, identify appropriate antiretroviral regimes, and characterize transmission dynamics. Despite decreasing costs, next-generation sequencing (NGS) is still prohibitively costly for routine use in generalized HIV epidemics in low- and middle-income countries. Here, we present veSEQ-HIV, a high-throughput, cost-effective NGS sequencing method and computational pipeline tailored specifically to HIV, which can be performed using leftover blood drawn for routine CD4 cell count testing. This method overcomes several major technical challenges that have prevented HIV sequencing from being used routinely in public health efforts; it is fast, robust, and cost-efficient, and generates full genomic sequences of diverse strains of HIV without bias. The complete veSEQ-HIV pipeline provides viral load estimates and quantitative summaries of drug resistance mutations; it also exploits information on within-host viral diversity to construct directed transmission networks. We evaluated the method's performance using 1,620 plasma samples collected from individuals attending 10 large urban clinics in Zambia as part of the HPTN 071-2 study (PopART Phylogenetics). Whole HIV genomes were recovered from 91% of samples with a viral load of >1,000 copies/ml. The cost of the assay (30 GBP per sample) compares favorably with existing VL and HIV genotyping tests, proving an affordable option for combining HIV clinical monitoring with molecular epidemiology and drug resistance surveillance in low-income settings.
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Affiliation(s)
- David Bonsall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Tanya Golubchik
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Mariateresa de Cesare
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Mohammed Limbada
- ZAMBART, University of Zambia, Lusaka, Zambia
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Barry Kosloff
- ZAMBART, University of Zambia, Lusaka, Zambia
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - George MacIntyre-Cockett
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Matthew Hall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Chris Wymant
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - M Azim Ansari
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Lucie Abeler-Dörner
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Ab Schaap
- ZAMBART, University of Zambia, Lusaka, Zambia
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Anthony Brown
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | | | - Susan Eshleman
- Dept. of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ethan Wilson
- Statistical Centre for HIV/AIDS Research, Fred Hutchinson Cancer Research Centre, Seattle, Washington, USA
| | - Lynda Emel
- Statistical Centre for HIV/AIDS Research, Fred Hutchinson Cancer Research Centre, Seattle, Washington, USA
| | - Richard Hayes
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Sarah Fidler
- Department of Infectious Disease, Imperial College London, Imperial College NIHR BRC, London, United Kingdom
| | - Helen Ayles
- ZAMBART, University of Zambia, Lusaka, Zambia
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Rory Bowden
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Christophe Fraser
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
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