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Coldbeck-Shackley RC, Adamson PJ, Whybrow D, Selway CA, Papanicolas LE, Turra M, Leong LEX. Direct whole-genome sequencing of HIV-1 for clinical drug-resistance analysis and public health surveillance. J Clin Virol 2024; 174:105709. [PMID: 38924832 DOI: 10.1016/j.jcv.2024.105709] [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: 03/11/2024] [Revised: 06/14/2024] [Accepted: 06/20/2024] [Indexed: 06/28/2024]
Abstract
BACKGROUND Human Immunodeficiency virus type 1 (HIV-1) remains a significant global health threat partly due to its ability to develop resistance to anti-retroviral therapies. HIV-1 genotype and drug resistance analysis of the polymerase (pol) sequence is a mainstay of its clinical and public health management. However, as new treatments and resistances evolve, analysis methods must change accordingly. In this study, we outline the development and implementation of a direct whole-genome sequencing approach (dWGS) using probe-capture target-enrichment for HIV-1 genotype and drug resistance analysis. METHODS We implemented dWGS and performed parallel pol Sanger sequencing for clinical samples, followed by comparative genotype and drug-resistance analysis. These HIV-1 WGS sequences were also utilised for a novel partitioned phylogenetic analysis. RESULTS Optimised nucleic acid extraction and DNAse I treatment significantly increased HIV-1 whole-genome coverage and depth, and improved recovery of high-quality genomes from low viral load clinical samples, enabling routine sequencing of viral loads as low as 1000 copies/mL. Overall, dWGS was robust, accurate and more sensitive for detecting low-frequency variants at drug-resistance sites compared to Sanger sequencing. Analysis of multiple sequence regions improved phylogenetic reconstruction for recombinant HIV-1 sequences compared to analysis of pol sequence alone. CONCLUSIONS These findings demonstrate dWGS enhances HIV-1 drug-resistance analysis by quantitative variant detection and improves reconstruction of HIV-1 phylogenies compared to traditional pol sequencing. This work supports that HIV-1 dWGS is a viable option to replace Sanger sequencing for clinical and public health applications.
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Affiliation(s)
| | - Penelope J Adamson
- Microbiology and Infectious Diseases, SA Pathology, Adelaide 5000 Australia
| | - Daryn Whybrow
- Microbiology and Infectious Diseases, SA Pathology, Adelaide 5000 Australia
| | - Caitlin A Selway
- Microbiology and Infectious Diseases, SA Pathology, Adelaide 5000 Australia
| | - Lito E Papanicolas
- Microbiology and Infectious Diseases, SA Pathology, Adelaide 5000 Australia
| | - Mark Turra
- Microbiology and Infectious Diseases, SA Pathology, Adelaide 5000 Australia
| | - Lex E X Leong
- Microbiology and Infectious Diseases, SA Pathology, Adelaide 5000 Australia; UniSA Clinical and Health Sciences, University of South Australia, Adelaide 5000 Australia
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2
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Egger M, Sauermann M, Loosli T, Hossmann S, Riedo S, Beerenwinkel N, Jaquet A, Minga A, Ross J, Giandhari J, Kouyos RD, Lessells R. HIV-1 subtype-specific drug resistance on dolutegravir-based antiretroviral therapy: protocol for a multicentre study (DTG RESIST). BMJ Open 2024; 14:e085819. [PMID: 39174068 PMCID: PMC11340720 DOI: 10.1136/bmjopen-2024-085819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 07/31/2024] [Indexed: 08/24/2024] Open
Abstract
INTRODUCTION HIV drug resistance poses a challenge to the United Nation's goal of ending the HIV/AIDS epidemic. The integrase strand transfer inhibitor (InSTI) dolutegravir, which has a higher resistance barrier, was endorsed by the WHO in 2019 for first-line, second-line and third-line antiretroviral therapy (ART). This multiplicity of roles of dolutegravir in ART may facilitate the emergence of dolutegravir resistance. METHODS AND ANALYSIS Nested within the International epidemiology Databases to Evaluate AIDS (IeDEA), DTG RESIST is a multicentre study of adults and adolescents living with HIV in sub-Saharan Africa, Asia, and South and Central America who experienced virological failure on dolutegravir-based ART. At the time of virological failure, whole blood will be collected and processed to prepare plasma or dried blood spots. Laboratories in Durban, Mexico City and Bangkok will perform genotyping. Analyses will focus on (1) individuals who experienced virological failure on dolutegravir and (2) those who started or switched to such a regimen and were at risk of virological failure. For population (1), the outcome will be any InSTI drug resistance mutations, and for population (2) virological failure is defined as a viral load >1000 copies/mL. Phenotypic testing will focus on non-B subtype viruses with major InSTI resistance mutations. Bayesian evolutionary models will explore and predict treatment failure genotypes. The study will have intermediate statistical power to detect differences in resistance mutation prevalence between major HIV-1 subtypes; ample power to identify risk factors for virological failure and limited power for analysing factors associated with individual InSTI drug resistance mutations. ETHICS AND DISSEMINATION The research protocol was approved by the Biomedical Research Ethics Committee at the University of KwaZulu-Natal, South Africa and the Ethics Committee of the Canton of Bern, Switzerland. All sites participate in International epidemiology Databases to Evaluate AIDS and have obtained ethics approval from their local ethics committee to collect additional data. TRIAL REGISTRATION NUMBER NCT06285110.
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Affiliation(s)
- Matthias Egger
- Institute of Social & Preventive Medicine, University of Bern, Bern, Switzerland
- Centre for Infectious Disease Epidemiology and Research, University of Cape Town Faculty of Health Sciences, Cape Town, Western Cape, South Africa
| | - Mamatha Sauermann
- Institute of Social & Preventive Medicine, University of Bern, Bern, Switzerland
| | - Tom Loosli
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Stefanie Hossmann
- Institute of Social & Preventive Medicine, University of Bern, Bern, Switzerland
| | - Selma Riedo
- Institute of Social & Preventive Medicine, University of Bern, Bern, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Antoine Jaquet
- National Institute for Health and Medical Research (INSERM) UMR 1219, Research Institute for Sustainable Development (IRD) EMR 271, Bordeaux Population Health Centre, University of Bordeaux, Bordeaux, France
| | - Albert Minga
- Centre Médical de Suivi des Donneurs de Sang, Abidjan, Côte d'Ivoire
| | - Jeremy Ross
- TREAT Asia/amfAR – The Foundation for AIDS Research, Bangkok, Thailand
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), University of KwaZulu-Natal, Durban, South Africa
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), University of KwaZulu-Natal, Durban, South Africa
- Centre for the Aids Programme of Research in South Africa (CAPRISA), Durban, South Africa
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3
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Egger M, Sauermann M, Loosli T, Hossmann S, Riedo S, Beerenwinkel N, Jaquet A, Minga A, Ross JL, Giandhari J, Kouyos R, Lessells R. HIV-1 subtype-specific drug resistance on dolutegravir-based antiretroviral therapy: protocol for a multicentre longitudinal study (DTG RESIST). MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.23.24307850. [PMID: 38952780 PMCID: PMC11216534 DOI: 10.1101/2024.05.23.24307850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
Introduction HIV drug resistance poses a challenge to the United Nation's goal of ending the HIV/AIDS epidemic. The integrase strand transfer inhibitor (InSTI) dolutegravir, which has a higher resistance barrier, was endorsed by the World Health Organization in 2019 for first-, second-, and third-line antiretroviral therapy (ART). This multiplicity of roles of dolutegravir in ART may facilitate the emergence of dolutegravir resistance. Methods and analysis DTG RESIST is a multicentre longitudinal study of adults and adolescents living with HIV in sub-Saharan Africa, Asia, and South and Central America who experienced virologic failure on dolutegravir-based ART. At the time of virologic failure whole blood will be collected and processed to prepare plasma or dried blood spots. Laboratories in Durban, Mexico City and Bangkok will perform genotyping. Analyses will focus on (i) individuals who experienced virologic failure on dolutegravir, and (ii) on those who started or switched to such a regimen and were at risk of virologic failure. For population (i), the outcome will be any InSTI drug resistance mutations, and for population (ii) virologic failure defined as a viral load >1000 copies/mL. Phenotypic testing will focus on non-B subtype viruses with major InSTI resistance mutations. Bayesian evolutionary models will explore and predict treatment failure genotypes. The study will have intermediate statistical power to detect differences in resistance mutation prevalence between major HIV-1 subtypes; ample power to identify risk factors for virologic failure and limited power for analysing factors associated with individual InSTI drug resistance mutations. Ethics and dissemination The research protocol was approved by the Biomedical Research Ethics Committee at the University of KwaZulu-Natal, South Africa, and the Ethics Committee of the Canton of Bern, Switzerland. All sites participate in IeDEA and have obtained ethics approval from their local ethics committee to conduct the additional data collection. Registration NCT06285110. Strengths and limitations of this study - DTG RESIST is a large international study to prospectively examine emergent dolutegravir resistance in diverse settings characterised by different HIV-1 subtypes, provision of ART, and guidelines on resistance testing. - Embedded within the International epidemiology Databases to Evaluate AIDS (IeDEA), DTG RESIST will benefit from harmonized clinical data across participating sites and expertise in clinical, epidemiological, biological, and computational fields. - Procedures for sequencing and assembling genomes from different HIV-1 strains will be developed at the heart of the HIV epidemic, by the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), in Durban, South Africa. Phenotypic testing, Genome Wide Association Study (GWAS) methods and Bayesian evolutionary models will explore and predict treatment failure genotypes. - A significant limitation is the absence of genotypic resistance data from participants before they started dolutegravir treatment, as collecting and bio-banking pre-treatment samples was not feasible at most IeDEA sites. Consistent and harmonized data on adherence to treatment are also lacking. - The distribution of HIV-1 subtypes across different sites is uncertain, which may limit the statistical power of the study in analysing patterns and risk factors for dolutegravir resistance. The results from GWAS and Bayesian modelling analyses will be preliminary and hypothesis-generating.
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4
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Kim S, Kigozi G, Martin MA, Galiwango RM, Quinn TC, Redd AD, Ssekubugu R, Bonsall D, Ssemwanga D, Rambaut A, Herbeck JT, Reynolds SJ, Foley B, Abeler-Dörner L, Fraser C, Ratmann O, Kagaayi J, Laeyendecker O, Grabowski MK. Increasing intra- and inter-subtype HIV diversity despite declining HIV incidence in Uganda. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.14.24303990. [PMID: 38558994 PMCID: PMC10980117 DOI: 10.1101/2024.03.14.24303990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
HIV incidence has been declining in Africa with scale-up of HIV interventions. However, there is limited data on HIV evolutionary trends in African populations with waning epidemics. We evaluated changes in HIV viral diversity and genetic divergence in southern Uganda over a twenty-five-year period spanning the introduction and scale-up of HIV prevention and treatment programs using HIV sequence and survey data from the Rakai Community Cohort Study, an open longitudinal population-based HIV surveillance cohort. Gag (p24) and env (gp41) HIV data were generated from persons living with HIV (PLHIV) in 31 inland semi-urban trading and agrarian communities (1994 to 2018) and four hyperendemic Lake Victoria fishing communities (2011 to 2018) under continuous surveillance. HIV subtype was assigned using the Recombination Identification Program with phylogenetic confirmation. Inter-subtype diversity was estimated using the Shannon diversity index and intra-subtype diversity with the nucleotide diversity and pairwise TN93 genetic distance. Genetic divergence was measured using root-to-tip distance and pairwise TN93 genetic distance analyses. Evolutionary dynamics were assessed among demographic and behavioral sub-groups, including by migration status. 9,931 HIV sequences were available from 4,999 PLHIV, including 3,060 and 1,939 persons residing in inland and fishing communities, respectively. In inland communities, subtype A1 viruses proportionately increased from 14.3% in 1995 to 25.9% in 2017 (p<0.001), while those of subtype D declined from 73.2% in 1995 to 28.2% in 2017 (p<0.001). The proportion of viruses classified as recombinants significantly increased by more than four-fold. Inter-subtype HIV diversity has generally increased. While p24 intra-subtype genetic diversity and divergence leveled off after 2014, diversity and divergence of gp41 increased through 2017. Inter- and intra-subtype viral diversity increased across all population sub-groups, including among individuals with no recent migration history or extra-community sexual partners. This study provides insights into population-level HIV evolutionary dynamics in declining African HIV epidemics following the scale-up of HIV prevention and treatment programs. Continued molecular surveillance may provide a better understanding of the dynamics driving population HIV evolution and yield important insights for epidemic control and vaccine development.
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Affiliation(s)
- Seungwon Kim
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | - Michael A. Martin
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | - Thomas C. Quinn
- Rakai Health Sciences Program, Kalisizo, Uganda
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andrew D. Redd
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - David Bonsall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Deogratius Ssemwanga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Joshua T. Herbeck
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Steven J. Reynolds
- Rakai Health Sciences Program, Kalisizo, Uganda
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Brian Foley
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Lucie Abeler-Dörner
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | - Christophe Fraser
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | - Oliver Ratmann
- Department of Mathematics, Imperial College London, London, England, United Kingdom
| | - Joseph Kagaayi
- Rakai Health Sciences Program, Kalisizo, Uganda
- Makerere University School of Public Health, Kampala, Uganda
| | - Oliver Laeyendecker
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - M. Kate Grabowski
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Rakai Health Sciences Program, Kalisizo, Uganda
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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5
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Monod M, Brizzi A, Galiwango RM, Ssekubugu R, Chen Y, Xi X, Kankaka EN, Ssempijja V, Abeler-Dörner L, Akullian A, Blenkinsop A, Bonsall D, Chang LW, Dan S, Fraser C, Golubchik T, Gray RH, Hall M, Jackson JC, Kigozi G, Laeyendecker O, Mills LA, Quinn TC, Reynolds SJ, Santelli J, Sewankambo NK, Spencer SEF, Ssekasanvu J, Thomson L, Wawer MJ, Serwadda D, Godfrey-Faussett P, Kagaayi J, Grabowski MK, Ratmann O. Longitudinal population-level HIV epidemiologic and genomic surveillance highlights growing gender disparity of HIV transmission in Uganda. Nat Microbiol 2024; 9:35-54. [PMID: 38052974 PMCID: PMC10769880 DOI: 10.1038/s41564-023-01530-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 10/16/2023] [Indexed: 12/07/2023]
Abstract
HIV incidence in eastern and southern Africa has historically been concentrated among girls and women aged 15-24 years. As new cases decline with HIV interventions, population-level infection dynamics may shift by age and gender. Here, we integrated population-based surveillance of 38,749 participants in the Rakai Community Cohort Study and longitudinal deep-sequence viral phylogenetics to assess how HIV incidence and population groups driving transmission have changed from 2003 to 2018 in Uganda. We observed 1,117 individuals in the incidence cohort and 1,978 individuals in the transmission cohort. HIV viral suppression increased more rapidly in women than men, however incidence declined more slowly in women than men. We found that age-specific transmission flows shifted: whereas HIV transmission to girls and women (aged 15-24 years) from older men declined by about one-third, transmission to women (aged 25-34 years) from men that were 0-6 years older increased by half in 2003 to 2018. Based on changes in transmission flows, we estimated that closing the gender gap in viral suppression could have reduced HIV incidence in women by half in 2018. This study suggests that HIV programmes to increase HIV suppression in men are critical to reduce incidence in women, close gender gaps in infection burden and improve men's health in Africa.
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Affiliation(s)
- Mélodie Monod
- Department of Mathematics, Imperial College London, London, UK
| | - Andrea Brizzi
- Department of Mathematics, Imperial College London, London, UK
| | | | | | - Yu Chen
- Department of Mathematics, Imperial College London, London, UK
| | - Xiaoyue Xi
- Department of Mathematics, Imperial College London, London, UK
| | - Edward Nelson Kankaka
- Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Research Department, Rakai Health Sciences Program, Rakai, Uganda
| | - Victor Ssempijja
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Statistics Department, Rakai Health Sciences Program, Rakai, Uganda
| | | | | | | | - David Bonsall
- Wellcome Centre for Human Genomics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | - Larry W Chang
- Rakai Health Sciences Program, Kalisizo, Uganda
- Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Shozen Dan
- Department of Mathematics, Imperial College London, London, UK
| | - Christophe Fraser
- Big Data Institute, University of Oxford, Oxford, UK
- Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | - Tanya Golubchik
- Big Data Institute, University of Oxford, Oxford, UK
- Sydney Infectious Diseases Institute, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Ronald H Gray
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Matthew Hall
- Big Data Institute, University of Oxford, Oxford, UK
| | - Jade C Jackson
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | - Oliver Laeyendecker
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Lisa A Mills
- Division of Global HIV and TB, US Centers for Disease Control and Prevention, Kampala, Uganda
| | - Thomas C Quinn
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Steven J Reynolds
- Rakai Health Sciences Program, Kalisizo, Uganda
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - John Santelli
- Population and Family Health and Pediatrics, Columbia Mailman School of Public Health, New York, NY, USA
| | - Nelson K Sewankambo
- College of Health Sciences, School of Medicine, Makerere University, Kampala, Uganda
| | | | - Joseph Ssekasanvu
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Laura Thomson
- Big Data Institute, University of Oxford, Oxford, UK
| | - Maria J Wawer
- Rakai Health Sciences Program, Kalisizo, Uganda
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - David Serwadda
- Rakai Health Sciences Program, Kalisizo, Uganda
- College of Health Sciences, School of Medicine, Makerere University, Kampala, Uganda
| | - Peter Godfrey-Faussett
- Department of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | | | - M Kate Grabowski
- Rakai Health Sciences Program, Kalisizo, Uganda.
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA.
| | - Oliver Ratmann
- Department of Mathematics, Imperial College London, London, UK.
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Monod M, Brizzi A, Galiwango RM, Ssekubugu R, Chen Y, Xi X, Kankaka EN, Ssempijja V, Dörner LA, Akullian A, Blenkinsop A, Bonsall D, Chang LW, Dan S, Fraser C, Golubchik T, Gray RH, Hall M, Jackson JC, Kigozi G, Laeyendecker O, Mills LA, Quinn TC, Reynolds SJ, Santelli J, Sewankambo NK, Spencer SE, Ssekasanvu J, Thomson L, Wawer MJ, Serwadda D, Godfrey-Faussett P, Kagaayi J, Grabowski MK, Ratmann O. Longitudinal population-level HIV epidemiologic and genomic surveillance highlights growing gender disparity of HIV transmission in Uganda. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.16.23287351. [PMID: 36993261 PMCID: PMC10055554 DOI: 10.1101/2023.03.16.23287351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
HIV incidence in eastern and southern Africa has historically been concentrated among girls and women aged 15-24 years. As new cases decline with HIV interventions, population-level infection dynamics may shift by age and gender. Here, we integrated population-based surveillance of 38,749 participants in the Rakai Community Cohort Study and longitudinal deep sequence viral phylogenetics to assess how HIV incidence and population groups driving transmission have changed from 2003 to 2018 in Uganda. We observed 1,117 individuals in the incidence cohort and 1,978 individuals in the transmission cohort. HIV viral suppression increased more rapidly in women than men, however incidence declined more slowly in women than men. We found that age-specific transmission flows shifted, while HIV transmission to girls and women (aged 15-24 years) from older men declined by about one third, transmission to women (aged 25-34 years) from men that were 0-6 years older increased by half in 2003 to 2018. Based on changes in transmission flows, we estimated that closing the gender gap in viral suppression could have reduced HIV incidence in women by half in 2018. This study suggests that HIV programs to increase HIV suppression in men are critical to reduce incidence in women, close gender gaps in infection burden and improve men's health in Africa.
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7
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Wulan WN, Yunihastuti E, Arlinda D, Merati TP, Wisaksana R, Lokida D, Grossman Z, Huik K, Lau CY, Susanto NH, Kosasih H, Aman AT, Ang S, Evalina R, Ayu Yuli Gayatri AA, Hayuningsih C, Indrati AR, Kumalawati J, Mutiawati VK, Realino Nara MB, Nurulita A, Rahmawati R, Rusli A, Rusli M, Sari DY, Sembiring J, Udji Sofro MA, Susanti WE, Tandraeliene J, Tanzil FL, Neal A, Karyana M, Sudarmono P, Maldarelli F. Development of a multiassay algorithm (MAA) to identify recent HIV infection in newly diagnosed individuals in Indonesia. iScience 2023; 26:107986. [PMID: 37854696 PMCID: PMC10579430 DOI: 10.1016/j.isci.2023.107986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 07/12/2023] [Accepted: 09/16/2023] [Indexed: 10/20/2023] Open
Abstract
Ongoing HIV transmission is a public health priority in Indonesia. We developed a new multiassay algorithm (MAA) to identify recent HIV infection. The MAA is a sequential decision tree based on multiple biomarkers, starting with CD4+ T cells >200/μL, followed by plasma viral load (pVL) > 1,000 copies/ml, avidity index (AI) < 0 · 7, and pol ambiguity <0 · 47%. Plasma from 140 HIV-infected adults from 19 hospitals across Indonesia (January 2018 - June 2020) was studied, consisting of a training set (N = 60) of longstanding infection (>12-month) and a test set (N = 80) of newly diagnosed (≤1-month) antiretroviral (ARV) drug naive individuals. Ten of eighty (12 · 5%) newly diagnosed individuals were classified as recent infections. Drug resistance mutations (DRMs) against reverse transcriptase inhibitors were identified in two individuals: one infected with HIV subtype C (K219Q, V179T) and the other with CRF01_AE (V179D). Ongoing HIV transmission, including infections with DRMs, is substantial in Indonesia.
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Affiliation(s)
- Wahyu Nawang Wulan
- Doctoral Program in Biomedical Sciences, Faculty of Medicine Universitas Indonesia, Jakarta 10430, Indonesia
- The Indonesia Research Partnership on Infectious Disease (INA-RESPOND), Jakarta 10560, Indonesia
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Evy Yunihastuti
- Department of Internal Medicine, Faculty of Medicine Universitas Indonesia – HIV Integrated Clinic, Cipto Mangunkusumo Hospital, Jakarta 10430, Indonesia
| | - Dona Arlinda
- The Indonesia Research Partnership on Infectious Disease (INA-RESPOND), Jakarta 10560, Indonesia
- Health Policy Agency, Ministry of Health Republic of Indonesia, Jakarta 10560, Indonesia
| | | | | | - Dewi Lokida
- The Indonesia Research Partnership on Infectious Disease (INA-RESPOND), Jakarta 10560, Indonesia
- Tangerang District Hospital, Tangerang 15111, Indonesia
| | - Zehava Grossman
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, USA
- School of Public Health, Tel Aviv University, Tel Aviv 69978, Israel
| | - Kristi Huik
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, USA
- Department of Microbiology, University of Tartu, 50090 Tartu, Estonia
| | - Chuen-Yen Lau
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Nugroho Harry Susanto
- The Indonesia Research Partnership on Infectious Disease (INA-RESPOND), Jakarta 10560, Indonesia
| | - Herman Kosasih
- The Indonesia Research Partnership on Infectious Disease (INA-RESPOND), Jakarta 10560, Indonesia
| | | | - Sunarto Ang
- A. Wahab Sjahranie Hospital, Samarinda 75123, Indonesia
| | | | | | | | | | | | | | | | - Asvin Nurulita
- dr. Wahidin Sudirohusodo Hospital, Makassar 90245, Indonesia
| | | | - Adria Rusli
- Prof. Dr. Sulianti Saroso Infectious Hospital, Jakarta 14340, Indonesia
| | - Musofa Rusli
- Department of Internal Medicine, Faculty of Medicine, Universitas Airlangga / Dr. Soetomo Hospital, Surabaya 60286, Indonesia
| | | | | | | | | | | | | | - Aaron Neal
- Collaborative Clinical Research Branch, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
| | - Muhammad Karyana
- The Indonesia Research Partnership on Infectious Disease (INA-RESPOND), Jakarta 10560, Indonesia
- Health Policy Agency, Ministry of Health Republic of Indonesia, Jakarta 10560, Indonesia
| | - Pratiwi Sudarmono
- Department of Microbiology, Faculty of Medicine, Universitas Indonesia – Cipto Mangunkusumo Hospital, Jakarta 10430, Indonesia
| | - Frank Maldarelli
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, USA
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8
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Nouhin J, Tzou PL, Rhee SY, Sahoo MK, Pinsky BA, Krupkin M, Puglisi JD, Puglisi EV, Shafer RW. Human immunodeficiency virus 1 5'-leader mutations in plasma viruses before and after the development of reverse transcriptase inhibitor-resistance mutations. J Gen Virol 2023; 104:001898. [PMID: 37801004 PMCID: PMC10721937 DOI: 10.1099/jgv.0.001898] [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: 08/29/2023] [Accepted: 09/20/2023] [Indexed: 10/07/2023] Open
Abstract
Human immunodeficiency virus 1 (HIV-1) reverse transcriptase (RT) initiation depends on interaction between viral 5'-leader RNA, RT and host tRNA3Lys. Therefore, we sought to identify co-evolutionary changes between the 5'-leader and RT in viruses developing RT-inhibitor resistance mutations. We sequenced 5'-leader positions 37-356 of paired plasma virus samples from 29 individuals developing the nucleoside RT inhibitor (NRTI)-resistance mutation M184V, 19 developing a non-nucleoside RT inhibitor (NNRTI)-resistance mutation and 32 untreated controls. 5'-Leader variants were defined as positions where ≥20 % of next-generation sequencing (NGS) reads differed from the HXB2 sequence. Emergent mutations were defined as nucleotides undergoing a ≥4-fold change in proportion between baseline and follow-up. Mixtures were defined as positions containing ≥2 nucleotides each present in ≥20 % of NGS reads. Among 80 baseline sequences, 87 positions (27.2 %) contained a variant; 52 contained a mixture. Position 201 was the only position more likely to develop a mutation in the M184V (9/29 vs 0/32; P=0.0006) or NNRTI-resistance (4/19 vs 0/32; P=0.02; Fisher's exact test) groups than the control group. Mixtures at positions 200 and 201 occurred in 45.0 and 28.8 %, respectively, of baseline samples. Because of the high proportion of mixtures at these positions, we analysed 5'-leader mixture frequencies in two additional datasets: five publications reporting 294 dideoxyterminator clonal GenBank sequences from 42 individuals and six National Center for Biotechnology Information (NCBI) BioProjects reporting NGS datasets from 295 individuals. These analyses demonstrated position 200 and 201 mixtures at proportions similar to those in our samples and at frequencies several times higher than at all other 5'-leader positions. Although we did not convincingly document co-evolutionary changes between RT and 5'-leader sequences, we identified a novel phenomenon, wherein positions 200 and 201 immediately downstream of the HIV-1 primer binding site exhibited an extraordinarily high likelihood of containing a nucleotide mixture. Possible explanations for the high mixture rates are that these positions are particularly error-prone or provide a viral fitness advantage.
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Affiliation(s)
- Janin Nouhin
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
- Virology Unit, Institut Pasteur du Cambodge, Pasteur Network, Phnom Penh, Cambodia
| | - Philip Lei Tzou
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Soo-Yon Rhee
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Malaya K. Sahoo
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Benjamin A. Pinsky
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Miri Krupkin
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Joseph D. Puglisi
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Elisabetta V. Puglisi
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Robert W. Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
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9
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Jaha B, Schenkel CD, Jörimann L, Huber M, Zaheri M, Neumann K, Leemann C, Calmy A, Cavassini M, Kouyos RD, Günthard HF, Metzner KJ. Prevalence of HIV-1 drug resistance mutations in proviral DNA in the Swiss HIV Cohort Study, a retrospective study from 1995 to 2018. J Antimicrob Chemother 2023; 78:2323-2334. [PMID: 37545164 PMCID: PMC10477134 DOI: 10.1093/jac/dkad240] [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: 04/26/2023] [Accepted: 07/19/2023] [Indexed: 08/08/2023] Open
Abstract
BACKGROUND Genotypic resistance testing (GRT) is routinely performed upon diagnosis of HIV-1 infection or during virological failure using plasma viral RNA. An alternative source for GRT could be cellular HIV-1 DNA. OBJECTIVES A substantial number of participants in the Swiss HIV Cohort Study (SHCS) never received GRT. We applied a method that enables access to the near full-length proviral HIV-1 genome without requiring detectable viraemia. METHODS Nine hundred and sixty-two PBMC specimens were received. Our two-step nested PCR protocol was applied to generate two overlapping long-range amplicons of the HIV-1 genome, sequenced by next-generation sequencing (NGS) and analysed by MinVar, a pipeline to detect drug resistance mutations (DRMs). RESULTS Six hundred and eighty-one (70.8%) of the samples were successfully amplified, sequenced and analysed by MinVar. Only partial information of the pol gene was contained in 82/681 (12%), probably due to naturally occurring deletions in the proviral sequence. All common HIV-1 subtypes were successfully sequenced. We detected at least one major DRM at high frequency (≥15%) in 331/599 (55.3%) individuals. Excluding APOBEC-signature (G-to-A mutation) DRMs, 145/599 (24.2%) individuals carried at least one major DRM. RT-inhibitor DRMs were most prevalent. The experienced time on ART was significantly longer in DRM carriers (P = 0.001) independent of inclusion or exclusion of APOBEC-signature DRMs. CONCLUSIONS We successfully applied a reliable and efficient method to analyse near full-length HIV-1 proviral DNA and investigated DRMs in individuals with undetectable or low viraemia. Additionally, our data underscore the need for new computational tools to exclude APOBEC-related hypermutated NGS sequence reads for reporting DRMs.
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Affiliation(s)
- Bashkim Jaha
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Corinne D Schenkel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Lisa Jörimann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Maryam Zaheri
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Kathrin Neumann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Christine Leemann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Alexandra Calmy
- Division of Infectious Diseases, University Hospital Geneva, University of Geneva, Geneva, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, University Hospital Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Karin J Metzner
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
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10
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Nouhin J, Tzou PL, Rhee SY, Sahoo MK, Pinsky BA, Krupkin M, Puglisi JD, Puglisi EV, Shafer RW. HIV-1 5'-Leader Mutations in Plasma Viruses Before and After the Development of Reverse Transcriptase Inhibitor-Resistance Mutations. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.04.23290942. [PMID: 37333388 PMCID: PMC10274971 DOI: 10.1101/2023.06.04.23290942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Background HIV-1 RT initiation depends on interaction between viral 5'-leader RNA, RT, and host tRNA3Lys. We therefore sought to identify co-evolutionary changes between the 5'-leader and RT in viruses developing RT-inhibitor resistance mutations. Methods We sequenced 5'-leader positions 37-356 of paired plasma virus samples from 29 individuals developing the NRTI-resistance mutation M184V, 19 developing an NNRTI-resistance mutation, and 32 untreated controls. 5'-leader variants were defined as positions where ≥20% of NGS reads differed from the HXB2 sequence. Emergent mutations were defined as nucleotides undergoing ≥4-fold change in proportion between baseline and follow-up. Mixtures were defined as positions containing ≥2 nucleotides each present in ≥20% of NGS reads. Results Among 80 baseline sequences, 87 positions (27.2%) contained a variant; 52 contained a mixture. Position 201 was the only position more likely to develop a mutation in the M184V (9/29 vs. 0/32; p=0.0006) or NNRTI-resistance (4/19 vs. 0/32; p=0.02; Fisher's Exact Test) groups than the control group. Mixtures at positions 200 and 201 occurred in 45.0% and 28.8%, respectively, of baseline samples. Because of the high proportion of mixtures at these positions, we analyzed 5'-leader mixture frequencies in two additional datasets: five publications reporting 294 dideoxyterminator clonal GenBank sequences from 42 individuals and six NCBI BioProjects reporting NGS datasets from 295 individuals. These analyses demonstrated position 200 and 201 mixtures at proportions similar to those in our samples and at frequencies several times higher than at all other 5'-leader positions. Conclusions Although we did not convincingly document co-evolutionary changes between RT and 5'-leader sequences, we identified a novel phenomenon, wherein positions 200 and 201, immediately downstream of the HIV-1 primer binding site exhibited an extraordinarily high likelihood of containing a nucleotide mixture. Possible explanations for the high mixture rates are that these positions are particularly error-prone or provide a viral fitness advantage.
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Affiliation(s)
- Janin Nouhin
- Division of Infectious Diseases, Stanford University, Stanford, CA, USA and Virology Unit, Institut Pasteur du Cambodge, Pasteur Network, Phnom Penh, Cambodia
| | - Philip L Tzou
- Division of Infectious Diseases, Stanford University, Stanford, CA, USA
| | - Soo-Yon Rhee
- Division of Infectious Diseases, Stanford University, Stanford, CA, USA
| | - Malaya K Sahoo
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Benjamin A Pinsky
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, Stanford University, Stanford, CA, USA
| | - Miri Krupkin
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Elisabetta V Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Robert W Shafer
- Division of Infectious Diseases, Stanford University, Stanford, CA, USA
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11
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Balakrishna S, Loosli T, Zaheri M, Frischknecht P, Huber M, Kusejko K, Yerly S, Leuzinger K, Perreau M, Ramette A, Wymant C, Fraser C, Kellam P, Gall A, Hirsch HH, Stoeckle M, Rauch A, Cavassini M, Bernasconi E, Notter J, Calmy A, Günthard HF, Metzner KJ, Kouyos RD. Frequency matters: comparison of drug resistance mutation detection by Sanger and next-generation sequencing in HIV-1. J Antimicrob Chemother 2023; 78:656-664. [PMID: 36738248 DOI: 10.1093/jac/dkac430] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/18/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) is gradually replacing Sanger sequencing (SS) as the primary method for HIV genotypic resistance testing. However, there are limited systematic data on comparability of these methods in a clinical setting for the presence of low-abundance drug resistance mutations (DRMs) and their dependency on the variant-calling thresholds. METHODS To compare the HIV-DRMs detected by SS and NGS, we included participants enrolled in the Swiss HIV Cohort Study (SHCS) with SS and NGS sequences available with sample collection dates ≤7 days apart. We tested for the presence of HIV-DRMs and compared the agreement between SS and NGS at different variant-calling thresholds. RESULTS We included 594 pairs of SS and NGS from 527 SHCS participants. Males accounted for 80.5% of the participants, 76.3% were ART naive at sample collection and 78.1% of the sequences were subtype B. Overall, we observed a good agreement (Cohen's kappa >0.80) for HIV-DRMs for variant-calling thresholds ≥5%. We observed an increase in low-abundance HIV-DRMs detected at lower thresholds [28/417 (6.7%) at 10%-25% to 293/812 (36.1%) at 1%-2% threshold]. However, such low-abundance HIV-DRMs were overrepresented in ART-naive participants and were in most cases not detected in previously sampled sequences suggesting high sequencing error for thresholds <3%. CONCLUSIONS We found high concordance between SS and NGS but also a substantial number of low-abundance HIV-DRMs detected only by NGS at lower variant-calling thresholds. Our findings suggest that a substantial fraction of the low-abundance HIV-DRMs detected at thresholds <3% may represent sequencing errors and hence should not be overinterpreted in clinical practice.
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Affiliation(s)
- Suraj Balakrishna
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Tom Loosli
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Maryam Zaheri
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.,Swiss National Center for Retroviruses, University of Zurich, Zurich, Switzerland
| | - Paul Frischknecht
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.,Swiss National Center for Retroviruses, University of Zurich, Zurich, Switzerland
| | - Katharina Kusejko
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Sabine Yerly
- Laboratory of Virology, University Hospital Geneva, University of Geneva, Geneva, Switzerland
| | - Karoline Leuzinger
- Clinical Virology Division, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | - Matthieu Perreau
- Division of Immunology and Allergy, University Hospital Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Chris Wymant
- Nuffield Department of Medicine, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Christophe Fraser
- Nuffield Department of Medicine, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.,Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Paul Kellam
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Astrid Gall
- Excellence in Life Sciences (EMBO), Heidelberg, Germany
| | - Hans H Hirsch
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Marcel Stoeckle
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | - Julia Notter
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St Gallen, St Gallen, Switzerland
| | - Alexandra Calmy
- Division of Infectious Diseases, University Hospital Geneva, University of Geneva, Geneva, Switzerland
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Karin J Metzner
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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12
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Grant HE, Roy S, Williams R, Tutill H, Ferns B, Cane PA, Carswell JW, Ssemwanga D, Kaleebu P, Breuer J, Leigh Brown AJ. A large population sample of African HIV genomes from the 1980s reveals a reduction in subtype D over time associated with propensity for CXCR4 tropism. Retrovirology 2022; 19:28. [PMID: 36514107 PMCID: PMC9746199 DOI: 10.1186/s12977-022-00612-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/12/2022] [Indexed: 12/15/2022] Open
Abstract
We present 109 near full-length HIV genomes amplified from blood serum samples obtained during early 1986 from across Uganda, which to our knowledge is the earliest and largest population sample from the initial phase of the HIV epidemic in Africa. Consensus sequences were made from paired-end Illumina reads with a target-capture approach to amplify HIV material following poor success with standard approaches. In comparisons with a smaller 'intermediate' genome dataset from 1998 to 1999 and a 'modern' genome dataset from 2007 to 2016, the proportion of subtype D was significantly higher initially, dropping from 67% (73/109), to 57% (26/46) to 17% (82/465) respectively (p < 0.0001). Subtype D has previously been shown to have a faster rate of disease progression than other subtypes in East African population studies, and to have a higher propensity to use the CXCR4 co-receptor ("X4 tropism"); associated with a decrease in time to AIDS. Here we find significant differences in predicted tropism between A1 and D subtypes in all three sample periods considered, which is particularly striking the 1986 sample: 66% (53/80) of subtype D env sequences were predicted to be X4 tropic compared with none of the 24 subtype A1. We also analysed the frequency of subtype in the envelope region of inter-subtype recombinants, and found that subtype A1 is over-represented in env, suggesting recombination and selection have acted to remove subtype D env from circulation. The reduction of subtype D frequency over three decades therefore appears to be a result of selective pressure against X4 tropism and its higher virulence. Lastly, we find a subtype D specific codon deletion at position 24 of the V3 loop, which may explain the higher propensity for subtype D to utilise X4 tropism.
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Affiliation(s)
- Heather E Grant
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK.
| | - Sunando Roy
- Division of Infection and Immunity, University College London, London, UK
| | - Rachel Williams
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Helena Tutill
- Division of Infection and Immunity, University College London, London, UK
| | - Bridget Ferns
- Department of Virology, University College London Hospitals NHS Foundation Trust, London, UK
| | | | | | - Deogratius Ssemwanga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Pontiano Kaleebu
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, UK
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13
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Advances in Molecular Genetics Enabling Studies of Highly Pathogenic RNA Viruses. Viruses 2022; 14:v14122682. [PMID: 36560685 PMCID: PMC9784166 DOI: 10.3390/v14122682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022] Open
Abstract
Experimental work with viruses that are highly pathogenic for humans and animals requires specialized Biosafety Level 3 or 4 facilities. Such pathogens include some spectacular but also rather seldomly studied examples such as Ebola virus (requiring BSL-4), more wide-spread and commonly studied viruses such as HIV, and the most recent example, SARS-CoV-2, which causes COVID-19. A common characteristic of these virus examples is that their genomes consist of single-stranded RNA, which requires the conversion of their genomes into a DNA copy for easy manipulation; this can be performed to study the viral life cycle in detail, develop novel therapies and vaccines, and monitor the disease course over time for chronic virus infections. We summarize the recent advances in such new genetic applications for RNA viruses in Switzerland over the last 25 years, from the early days of the HIV/AIDS epidemic to the most recent developments in research on the SARS-CoV-2 coronavirus. We highlight game-changing collaborative efforts between clinical and molecular disciplines in HIV research on the path to optimal clinical disease management. Moreover, we summarize how the modern technical evolution enabled the molecular studies of emerging RNA viruses, confirming that Switzerland is at the forefront of SARS-CoV-2 research and potentially other newly emerging viruses.
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14
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Kemp SA, Charles OJ, Derache A, Smidt W, Martin DP, Iwuji C, Adamson J, Govender K, de Oliveira T, Dabis F, Pillay D, Goldstein RA, Gupta RK. HIV-1 Evolutionary Dynamics under Nonsuppressive Antiretroviral Therapy. mBio 2022; 13:e0026922. [PMID: 35446121 PMCID: PMC9239331 DOI: 10.1128/mbio.00269-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/28/2022] [Indexed: 12/19/2022] Open
Abstract
Prolonged virologic failure on 2nd-line protease inhibitor (PI)-based antiretroviral therapy (ART) without emergence of major protease mutations is well recognized and provides an opportunity to study within-host evolution in long-term viremic individuals. Using next-generation sequencing and in silico haplotype reconstruction, we analyzed whole-genome sequences from longitudinal plasma samples of eight chronically infected HIV-1-positive individuals failing 2nd-line regimens from the French National Agency for AIDS and Viral Hepatitis Research (ANRS) 12249 Treatment as Prevention (TasP) trial. On nonsuppressive ART, there were large fluctuations in synonymous and nonsynonymous variant frequencies despite stable viremia. Reconstructed haplotypes provided evidence for selective sweeps during periods of partial adherence, and viral haplotype competition, during periods of low drug exposure. Drug resistance mutations in reverse transcriptase (RT) were used as markers of viral haplotypes in the reservoir, and their distribution over time indicated recombination. We independently observed linkage disequilibrium decay, indicative of recombination. These data highlight dramatic changes in virus population structure that occur during stable viremia under nonsuppressive ART. IMPORTANCE HIV-1 infections are most commonly initiated with a single founder virus and are characterized by extensive inter- and intraparticipant genetic diversity. However, existing literature on HIV-1 intrahost population dynamics is largely limited to untreated infections, predominantly in subtype B-infected individuals. The manuscript characterizes viral population dynamics in long-term viremic treatment-experienced individuals, which has not been previously characterized. These data are particularly relevant for understanding HIV dynamics but can also be applied to other RNA viruses. With this unique data set we propose that the virus is highly unstable, and we have found compelling evidence of HIV-1 within-host viral diversification, recombination, and haplotype competition during nonsuppressive ART.
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Affiliation(s)
- Steven A. Kemp
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, United Kingdom
| | - Oscar J. Charles
- Division of Infection & Immunity, University College London, London, United Kingdom
| | - Anne Derache
- Africa Health Research Institute, Durban, South Africa
| | - Werner Smidt
- Africa Health Research Institute, Durban, South Africa
| | - Darren P. Martin
- Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Collins Iwuji
- Africa Health Research Institute, Durban, South Africa
- Research Department of Infection and Population Health, University College London, United Kingdom
| | - John Adamson
- Africa Health Research Institute, Durban, South Africa
| | | | - Tulio de Oliveira
- Africa Health Research Institute, Durban, South Africa
- KRISP - KwaZulu-Natal Research and Innovation Sequencing Platform, UKZN, Durban, South Africa
| | - Francois Dabis
- INSERM U1219-Centre Inserm Bordeaux Population Health, Université de Bordeaux, France
- Université de Bordeaux, ISPED, Centre INSERM U1219-Bordeaux Population Health, France
| | - Deenan Pillay
- Division of Infection & Immunity, University College London, London, United Kingdom
| | - Richard A. Goldstein
- Division of Infection & Immunity, University College London, London, United Kingdom
| | - Ravindra K. Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, United Kingdom
- Africa Health Research Institute, Durban, South Africa
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15
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Xing J, Zheng Z, Cao X, Wang Z, Xu Z, Gao H, Liu J, Xu S, Lin J, Chen S, Wang H, Zhang G, Sun Y. Whole genome sequencing of clinical specimens reveals the genomic diversity of porcine reproductive and respiratory syndrome viruses emerging in China. Transbound Emerg Dis 2022; 69:e2530-e2540. [DOI: 10.1111/tbed.14597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 04/28/2022] [Accepted: 05/12/2022] [Indexed: 11/27/2022]
Affiliation(s)
- Jia‐bao Xing
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine South China Agricultural University Guangzhou 510642 China
- Guangdong Laboratory for Lingnan Modern Agriculture Guangzhou 510642 China
- National Engineering Research Center for Breeding Swine Industry South China Agricultural University Guangzhou 510642 China
- Maoming Branch Guangdong Laboratory for Lingnan Modern Agriculture Maoming 525000 China
| | - Ze‐zhong Zheng
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine South China Agricultural University Guangzhou 510642 China
- Guangdong Laboratory for Lingnan Modern Agriculture Guangzhou 510642 China
- National Engineering Research Center for Breeding Swine Industry South China Agricultural University Guangzhou 510642 China
- Maoming Branch Guangdong Laboratory for Lingnan Modern Agriculture Maoming 525000 China
| | - Xin‐yu Cao
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine South China Agricultural University Guangzhou 510642 China
- Guangdong Laboratory for Lingnan Modern Agriculture Guangzhou 510642 China
- National Engineering Research Center for Breeding Swine Industry South China Agricultural University Guangzhou 510642 China
- Maoming Branch Guangdong Laboratory for Lingnan Modern Agriculture Maoming 525000 China
| | - Zhi‐yuan Wang
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine South China Agricultural University Guangzhou 510642 China
- Guangdong Laboratory for Lingnan Modern Agriculture Guangzhou 510642 China
- National Engineering Research Center for Breeding Swine Industry South China Agricultural University Guangzhou 510642 China
- Maoming Branch Guangdong Laboratory for Lingnan Modern Agriculture Maoming 525000 China
| | - Zhi‐ying Xu
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine South China Agricultural University Guangzhou 510642 China
- Guangdong Laboratory for Lingnan Modern Agriculture Guangzhou 510642 China
- National Engineering Research Center for Breeding Swine Industry South China Agricultural University Guangzhou 510642 China
- Maoming Branch Guangdong Laboratory for Lingnan Modern Agriculture Maoming 525000 China
| | - Han Gao
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine South China Agricultural University Guangzhou 510642 China
- Guangdong Laboratory for Lingnan Modern Agriculture Guangzhou 510642 China
- National Engineering Research Center for Breeding Swine Industry South China Agricultural University Guangzhou 510642 China
- Maoming Branch Guangdong Laboratory for Lingnan Modern Agriculture Maoming 525000 China
| | - Jing Liu
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine South China Agricultural University Guangzhou 510642 China
- Guangdong Laboratory for Lingnan Modern Agriculture Guangzhou 510642 China
- National Engineering Research Center for Breeding Swine Industry South China Agricultural University Guangzhou 510642 China
- Maoming Branch Guangdong Laboratory for Lingnan Modern Agriculture Maoming 525000 China
| | - Si‐jia Xu
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine South China Agricultural University Guangzhou 510642 China
- Guangdong Laboratory for Lingnan Modern Agriculture Guangzhou 510642 China
- National Engineering Research Center for Breeding Swine Industry South China Agricultural University Guangzhou 510642 China
- Maoming Branch Guangdong Laboratory for Lingnan Modern Agriculture Maoming 525000 China
| | - Jin‐sen Lin
- Guangzhou Sino‐science Gene Testing Service Co., Ltd Guangzhou 510700 China
| | - Sheng‐nan Chen
- Guangzhou Sino‐science Gene Testing Service Co., Ltd Guangzhou 510700 China
| | - Heng Wang
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine South China Agricultural University Guangzhou 510642 China
- Guangdong Laboratory for Lingnan Modern Agriculture Guangzhou 510642 China
- National Engineering Research Center for Breeding Swine Industry South China Agricultural University Guangzhou 510642 China
- Maoming Branch Guangdong Laboratory for Lingnan Modern Agriculture Maoming 525000 China
| | - Gui‐hong Zhang
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine South China Agricultural University Guangzhou 510642 China
- Guangdong Laboratory for Lingnan Modern Agriculture Guangzhou 510642 China
- National Engineering Research Center for Breeding Swine Industry South China Agricultural University Guangzhou 510642 China
- Maoming Branch Guangdong Laboratory for Lingnan Modern Agriculture Maoming 525000 China
| | - Yan‐kuo Sun
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine South China Agricultural University Guangzhou 510642 China
- Guangdong Laboratory for Lingnan Modern Agriculture Guangzhou 510642 China
- National Engineering Research Center for Breeding Swine Industry South China Agricultural University Guangzhou 510642 China
- Maoming Branch Guangdong Laboratory for Lingnan Modern Agriculture Maoming 525000 China
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Droplet-microfluidics-assisted sequencing of HIV proviruses and their integration sites in cells from people on antiretroviral therapy. Nat Biomed Eng 2022; 6:1004-1012. [PMID: 35347274 PMCID: PMC9398922 DOI: 10.1038/s41551-022-00864-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 01/28/2022] [Indexed: 01/03/2023]
Abstract
The human immunodeficiency virus (HIV) integrates its genome in that of infected cells and may enter an inactive state of reversible latency that cannot be targeted using antiretroviral therapy. The resulting HIV DNA is termed a provirus. Sequencing individual proviruses with the adjacent human cellular junctions may elucidate mechanisms of infected cell persistence in humans. Here, we introduce a high throughput microfluidic assay where droplet-based whole genome amplification of the HIV DNA in its native context is followed by a polymerase chain reaction to tag droplets containing proviruses for sequencing, resulting in the assembly of full-length viral genomes connected to their contiguous HIV-human DNA junctions, regardless of the 150 million-fold higher amount of human DNA present in the background. We analyzed infected cells from patients with HIV receiving suppressive antiretroviral therapy, resulting in the detection and sequencing of paired proviral genomes and integration sites, 90% of which weren’t recovered by commonly used nested PCR methods. The sequencing of individual proviral genomes with their integration sites could improve the genetic analysis of persistent HIV-infected cell reservoirs.
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Zhao L, Wymant C, Blanquart F, Golubchik T, Gall A, Bakker M, Bezemer D, Hall M, Ong SH, Albert J, Bannert N, Fellay J, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos RD, Laeyendecker O, Meyer L, Porter K, van Sighem A, van der Valk M, Berkhout B, Kellam P, Cornelissen M, Reiss P, Fraser C, Ferretti L. Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load. Virus Evol 2022; 8:veac022. [PMID: 35402002 PMCID: PMC8986633 DOI: 10.1093/ve/veac022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 02/25/2022] [Accepted: 03/15/2022] [Indexed: 11/16/2022] Open
Abstract
Set-point viral load (SPVL), a common measure of human immunodeficiency virus (HIV)-1 virulence, is partially determined by viral genotype. Epidemiological evidence suggests that this viral property has been under stabilising selection, with a typical optimum for the virus between 104 and 105 copies of viral RNA per ml. Here we aimed to detect transmission fitness differences between viruses from individuals with different SPVLs directly from phylogenetic trees inferred from whole-genome sequences. We used the local branching index (LBI) as a proxy for transmission fitness. We found that LBI is more sensitive to differences in infectiousness than to differences in the duration of the infectious state. By analysing subtype-B samples from the Bridging the Evolution and Epidemiology of HIV in Europe project, we inferred a significant positive relationship between SPVL and LBI up to approximately 105 copies/ml, with some evidence for a peak around this value of SPVL. This is evidence of selection against low values of SPVL in HIV-1 subtype-B strains, likely related to lower infectiousness, and perhaps a peak in the transmission fitness in the expected range of SPVL. The less prominent signatures of selection against higher SPVL could be explained by an inherent limit of the method or the deployment of antiretroviral therapy.
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Affiliation(s)
- Lele Zhao
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Headington, Oxford OX3 7LF, UK
| | - Chris Wymant
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Headington, Oxford OX3 7LF, UK
| | - François Blanquart
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Cedex 05, Paris 75231, France
| | - Tanya Golubchik
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Headington, Oxford OX3 7LF, UK
| | - Astrid Gall
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - Margreet Bakker
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, MB 1007, Netherlands
| | - Daniela Bezemer
- Stichting HIV Monitoring, Amsterdam, Amsterdam, AZ 1105, Netherlands
| | - Matthew Hall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Headington, Oxford OX3 7LF, UK
| | - Swee Hoe Ong
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Stockholm 171 77, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Solna, Stockholm S-171 76, Sweden
| | - Norbert Bannert
- Division for HIV and Other Retroviruses, Department of Infectious Diseases, Robert Koch Institute, Berlin 13353, Germany
| | - Jacques Fellay
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne CH-1015, Switzerland
| | - M Kate Grabowski
- Department of Pathology, John Hopkins University, Baltimore, MD 21287, USA
| | | | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich CH-8091, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich 8057, Switzerland
| | - Pia Kivelä
- Department of Infectious Diseases, Helsinki University Hospital, Helsinki FI-00029, Finland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich CH-8091, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich 8057, Switzerland
| | | | - Laurence Meyer
- INSERM CESP U1018, Université Paris Saclay, APHP, Service de Santé Publique, Hôpital de Bicêtre, Le Kremlin-Bicêtre 94270, France
| | - Kholoud Porter
- Institute for Global Health, University College London, London WC1N 1EH, UK
| | - Ard van Sighem
- Stichting HIV Monitoring, Amsterdam, Amsterdam, AZ 1105, Netherlands
| | - Marc van der Valk
- Stichting HIV Monitoring, Amsterdam, Amsterdam, AZ 1105, Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, MB 1007, Netherlands
| | - Paul Kellam
- Kymab Ltd, Babraham Research Campus, Cambridge CB22 3AT, UK
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Marion Cornelissen
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, MB 1007, Netherlands
- Molecular Diagnostic Unit, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, MB 1007, Netherlands
| | - Peter Reiss
- Stichting HIV Monitoring, Amsterdam, Amsterdam, AZ 1105, Netherlands
- Department of Global Health, Amsterdam University Medical Centers, University of Amsterdam and Amsterdam Institute for Global Health and Development, Amsterdam, DE 1100, Netherlands
| | - Christophe Fraser
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Headington, Oxford OX3 7LF, UK
| | - Luca Ferretti
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Headington, Oxford OX3 7LF, UK
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18
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Xi X, Spencer SEF, Hall M, Grabowski MK, Kagaayi J, Ratmann O. Inferring the sources of HIV infection in Africa from deep‐sequence data with semi‐parametric Bayesian Poisson flow models. J R Stat Soc Ser C Appl Stat 2022. [DOI: 10.1111/rssc.12544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xiaoyue Xi
- Department of MathematicsImperial College London LondonUK
| | | | - Matthew Hall
- Big Data Institute, Nuffield Department of MedicineUniversity of Oxford OxfordUK
| | - M. Kate Grabowski
- Department of PathologyJohns Hopkins University BaltimoreMDUSA
- Rakai Health Sciences Program KalisizoUganda
| | - Joseph Kagaayi
- Rakai Health Sciences Program KalisizoUganda
- Makerere University School of Public Health KampalaUganda
| | - Oliver Ratmann
- Department of MathematicsImperial College London LondonUK
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19
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Abstract
Genetically-characterizing full-length HIV-1 RNA is critical for identifying genetically-intact genomes and for comparing these RNA genomes to proviral DNA. We have developed a method for sequencing plasma-derived RNA using long-range sequencing (PRLS assay; ∼8.3 kb from gag to the 3′ end or ∼5 kb from integrase to the 3′ end). We employed the gag-3′ PRLS assay to sequence HIV-1 RNA genomes from ART-naive participants during acute/early infection (n = 6) or chronic infection (n = 2). On average, only 65% of plasma-derived genomes were genetically-intact. Defects were found in all genomic regions but were concentrated in env and pol. We compared these genomes to near-full-length proviral sequences from paired peripheral blood mononuclear cell (PBMC) samples for the acute/early group and found that near-identical (>99.98% identical) sequences were identified only during acute infection. For three participants who initiated therapy during acute infection, we used the int-3′ PRLS assay to sequence plasma-derived genomes from an analytical treatment interruption and identified 100% identical genomes between pretherapy and rebound time points. The PRLS assay provides a new level of sensitivity for understanding the genetic composition of plasma-derived HIV-1 RNA from viremic individuals either pretherapy or after treatment interruption, which will be invaluable in assessing possible HIV-1 curative strategies. IMPORTANCE We developed novel plasma-derived RNA using long-range sequencing assays (PRLS assay; 8.3 kb, gag-3′, and 5.0 kb, int-3′). Employing the gag-3′ PRLS assay, we found that 26% to 51% of plasma-derived genomes are genetically-defective, largely as a result of frameshift mutations and deletions. These genetic defects were concentrated in the env region compared to gag and pol, likely a reflection of viral immune escape in env during untreated HIV-1 infection. Employing the int-3′ PRLS assay, we found that analytical treatment interruption (ATI) plasma-derived sequences were identical and genetically-intact. Several sequences from the ATI plasma samples were identical to viral sequences from pretherapy plasma and PBMC samples, indicating that HIV-1 reservoirs established prior to therapy contribute to viral rebound during an ATI. Therefore, near-full-length sequencing of HIV-1 particles is required to gain an accurate picture of the genetic landscape of plasma HIV-1 virions in studies of HIV-1 replication and persistence.
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20
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Wymant C, Bezemer D, Blanquart F, Ferretti L, Gall A, Hall M, Golubchik T, Bakker M, Ong SH, Zhao L, Bonsall D, de Cesare M, MacIntyre-Cockett G, Abeler-Dörner L, Albert J, Bannert N, Fellay J, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos RD, Laeyendecker O, Meyer L, Porter K, Ristola M, van Sighem A, Berkhout B, Kellam P, Cornelissen M, Reiss P, Fraser C, Aubert V, Battegay M, Bernasconi E, Böni J, Braun DL, Bucher HC, Burton-Jeangros C, Calmy A, Cavassini M, Dollenmaier G, Egger M, Elzi L, Fehr J, Fellay J, Furrer H, Fux CA, Gorgievski M, Günthard H, Haerry D, Hasse B, Hirsch HH, Hoffmann M, Hösli I, Kahlert C, Kaiser L, Keiser O, Klimkait T, Kouyos R, Kovari H, Ledergerber B, Martinetti G, de Tejada BM, Marzolini C, Metzner K, Müller N, Nadal D, Nicca D, Pantaleo G, Rauch A, Regenass S, Rudin C, Schöni-Affolter F, Schmid P, Speck R, Stöckle M, Tarr P, Trkola A, Vernazza P, Weber R, Yerly S, van der Valk M, Geerlings SE, Goorhuis A, Hovius JW, Lempkes B, Nellen FJB, van der Poll T, Prins JM, Reiss P, van Vugt M, Wiersinga WJ, Wit FWMN, van Duinen M, van Eden J, Hazenberg A, van Hes AMH, Rajamanoharan S, Robinson T, Taylor B, Brewer C, Mayr C, Schmidt W, Speidel A, Strohbach F, Arastéh K, Cordes C, Pijnappel FJJ, Stündel M, Claus J, Baumgarten A, Carganico A, Ingiliz P, Dupke S, Freiwald M, Rausch M, Moll A, Schleehauf D, Smalhout SY, Hintsche B, Klausen G, Jessen H, Jessen A, Köppe S, Kreckel P, Schranz D, Fischer K, Schulbin H, Speer M, Weijsenfeld AM, Glaunsinger T, Wicke T, Bieniek B, Hillenbrand H, Schlote F, Lauenroth-Mai E, Schuler C, Schürmann D, Wesselmann H, Brockmeyer N, Jurriaans S, Gehring P, Schmalöer D, Hower M, Spornraft-Ragaller P, Häussinger D, Reuter S, Esser S, Markus R, Kreft B, Berzow D, Back NKT, Christl A, Meyer A, Plettenberg A, Stoehr A, Graefe K, Lorenzen T, Adam A, Schewe K, Weitner L, Fenske S, Zaaijer HL, Hansen S, Stellbrink HJ, Wiemer D, Hertling S, Schmidt R, Arbter P, Claus B, Galle P, Jäger H, Jä Gel-Guedes E, Berkhout B, Postel N, Fröschl M, Spinner C, Bogner J, Salzberger B, Schölmerich J, Audebert F, Marquardt T, Schaffert A, Schnaitmann E, Cornelissen MTE, Trein A, Frietsch B, Müller M, Ulmer A, Detering-Hübner B, Kern P, Schubert F, Dehn G, Schreiber M, Güler C, Schinkel CJ, Gunsenheimer-Bartmeyer B, Schmidt D, Meixenberger K, Bannert N, Wolthers KC, Peters EJG, van Agtmael MA, Autar RS, Bomers M, Sigaloff KCE, Heitmuller M, Laan LM, Ang CW, van Houdt R, Jonges M, Kuijpers TW, Pajkrt D, Scherpbier HJ, de Boer C, van der Plas A, van den Berge M, Stegeman A, Baas S, Hage de Looff L, Buiting A, Reuwer A, Veenemans J, Wintermans B, Pronk MJH, Ammerlaan HSM, van den Bersselaar DNJ, de Munnik ES, Deiman B, Jansz AR, Scharnhorst V, Tjhie J, Wegdam MCA, van Eeden A, Nellen J, Brokking W, Elsenburg LJM, Nobel H, van Kasteren MEE, Berrevoets MAH, Brouwer AE, Adams A, van Erve R, de Kruijf-van de Wiel BAFM, Keelan-Phaf S, van de Ven B, van der Ven B, Buiting AGM, Murck JL, de Vries-Sluijs TEMS, Bax HI, van Gorp ECM, de Jong-Peltenburg NC, de Mendonç A Melo M, van Nood E, Nouwen JL, Rijnders BJA, Rokx C, Schurink CAM, Slobbe L, Verbon A, Bassant N, van Beek JEA, Vriesde M, van Zonneveld LM, de Groot J, Boucher CAB, Koopmans MPG, van Kampen JJA, Fraaij PLA, van Rossum AMC, Vermont CL, van der Knaap LC, Visser E, Branger J, Douma RA, Cents-Bosma AS, Duijf-van de Ven CJHM, Schippers EF, van Nieuwkoop C, van Ijperen JM, Geilings J, van der Hut G, van Burgel ND, Leyten EMS, Gelinck LBS, Mollema F, Davids-Veldhuis S, Tearno C, Wildenbeest GS, Heikens E, Groeneveld PHP, Bouwhuis JW, Lammers AJJ, Kraan S, van Hulzen AGW, Kruiper MSM, van der Bliek GL, Bor PCJ, Debast SB, Wagenvoort GHJ, Kroon FP, de Boer MGJ, Jolink H, Lambregts MMC, Roukens AHE, Scheper H, Dorama W, van Holten N, Claas ECJ, Wessels E, den Hollander JG, El Moussaoui R, Pogany K, Brouwer CJ, Smit JV, Struik-Kalkman D, van Niekerk T, Pontesilli O, Lowe SH, Oude Lashof AML, Posthouwer D, van Wolfswinkel ME, Ackens RP, Burgers K, Schippers J, Weijenberg-Maes B, van Loo IHM, Havenith TRA, van Vonderen MGA, Kampschreur LM, Faber S, Steeman-Bouma R, Al Moujahid A, Kootstra GJ, Delsing CE, van der Burg-van de Plas M, Scheiberlich L, Kortmann W, van Twillert G, Renckens R, Ruiter-Pronk D, van Truijen-Oud FA, Cohen Stuart JWT, Jansen ER, Hoogewerf M, Rozemeijer W, van der Reijden WA, Sinnige JC, Brinkman K, van den Berk GEL, Blok WL, Lettinga KD, de Regt M, Schouten WEM, Stalenhoef JE, Veenstra J, Vrouenraets SME, Blaauw H, Geerders GF, Kleene MJ, Kok M, Knapen M, van der Meché IB, Mulder-Seeleman E, Toonen AJM, Wijnands S, Wttewaal E, Kwa D, van Crevel R, van Aerde K, Dofferhoff ASM, Henriet SSV, Ter Hofstede HJM, Hoogerwerf J, Keuter M, Richel O, Albers M, Grintjes-Huisman KJT, de Haan M, Marneef M, Strik-Albers R, Rahamat-Langendoen J, Stelma FF, Burger D, Gisolf EH, Hassing RJ, Claassen M, Ter Beest G, van Bentum PHM, Langebeek N, Tiemessen R, Swanink CMA, van Lelyveld SFL, Soetekouw R, van der Prijt LMM, van der Swaluw J, Bermon N, van der Reijden WA, Jansen R, Herpers BL, Veenendaal D, Verhagen DWM, Lauw FN, van Broekhuizen MC, van Wijk M, Bierman WFW, Bakker M, Kleinnijenhuis J, Kloeze E, Middel A, Postma DF, Schölvinck EH, Stienstra Y, Verhage AR, Wouthuyzen-Bakker M, Boonstra A, de Groot-de Jonge H, van der Meulen PA, de Weerd DA, Niesters HGM, van Leer-Buter CC, Knoester M, Hoepelman AIM, Arends JE, Barth RE, Bruns AHW, Ellerbroek PM, Mudrikova T, Oosterheert JJ, Schadd EM, van Welzen BJ, Aarsman K, Griffioen-van Santen BMG, de Kroon I, van Berkel M, van Rooijen CSAM, Schuurman R, Verduyn-Lunel F, Wensing AMJ, Bont LJ, Geelen SPM, Loeffen YGT, Wolfs TFW, Nauta N, Rooijakkers EOW, Holtsema H, Voigt R, van de Wetering D, Alberto A, van der Meer I, Rosingh A, Halaby T, Zaheri S, Boyd AC, Bezemer DO, van Sighem AI, Smit C, Hillebregt M, de Jong A, Woudstra T, Bergsma D, Meijering R, van de Sande L, Rutkens T, van der Vliet S, de Groot L, van den Akker M, Bakker Y, El Berkaoui A, Bezemer M, Brétin N, Djoechro E, Groters M, Kruijne E, Lelivelt KJ, Lodewijk C, Lucas E, Munjishvili L, Paling F, Peeck B, Ree C, Regtop R, Ruijs Y, Schoorl M, Schnörr P, Scheigrond A, Tuijn E, Veenenberg L, Visser KM, Witte EC, Ruijs Y, Van Frankenhuijsen M, Allegre T, Makhloufi D, Livrozet JM, Chiarello P, Godinot M, Brunel-Dalmas F, Gibert S, Trepo C, Peyramond D, Miailhes P, Koffi J, Thoirain V, Brochier C, Baudry T, Pailhes S, Lafeuillade A, Philip G, Hittinger G, Assi A, Lambry V, Rosenthal E, Naqvi A, Dunais B, Cua E, Pradier C, Durant J, Joulie A, Quinsat D, Tempesta S, Ravaux I, Martin IP, Faucher O, Cloarec N, Champagne H, Pichancourt G, Morlat P, Pistone T, Bonnet F, Mercie P, Faure I, Hessamfar M, Malvy D, Lacoste D, Pertusa MC, Vandenhende MA, Bernard N, Paccalin F, Martell C, Roger-Schmelz J, Receveur MC, Duffau P, Dondia D, Ribeiro E, Caltado S, Neau D, Dupont M, Dutronc H, Dauchy F, Cazanave C, Vareil MO, Wirth G, Le Puil S, Pellegrin JL, Raymond I, Viallard JF, Chaigne de Lalande S, Garipuy D, Delobel P, Obadia M, Cuzin L, Alvarez M, Biezunski N, Porte L, Massip P, Debard A, Balsarin F, Lagarrigue M, Prevoteau du Clary F, Aquilina C, Reynes J, Baillat V, Merle C, Lemoing V, Atoui N, Makinson A, Jacquet JM, Psomas C, Tramoni C, Aumaitre H, Saada M, Medus M, Malet M, Eden A, Neuville S, Ferreyra M, Sotto A, Barbuat C, Rouanet I, Leureillard D, Mauboussin JM, Lechiche C, Donsesco R, Cabie A, Abel S, Pierre-Francois S, Batala AS, Cerland C, Rangom C, Theresine N, Hoen B, Lamaury I, Fabre I, Schepers K, Curlier E, Ouissa R, Gaud C, Ricaud C, Rodet R, Wartel G, Sautron C, Beck-Wirth G, Michel C, Beck C, Halna JM, Kowalczyk J, Benomar M, Drobacheff-Thiebaut C, Chirouze C, Faucher JF, Parcelier F, Foltzer A, Haffner-Mauvais C, Hustache Mathieu M, Proust A, Piroth L, Chavanet P, Duong M, Buisson M, Waldner A, Mahy S, Gohier S, Croisier D, May T, Delestan M, Andre M, Zadeh MM, Martinot M, Rosolen B, Pachart A, Martha B, Jeunet N, Rey D, Cheneau C, Partisani M, Priester M, Bernard-Henry C, Batard ML, Fischer P, Berger JL, Kmiec I, Robineau O, Huleux T, Ajana F, Alcaraz I, Allienne C, Baclet V, Meybeck A, Valette M, Viget N, Aissi E, Biekre R, Cornavin P, Merrien D, Seghezzi JC, Machado M, Diab G, Raffi F, Bonnet B, Allavena C, Grossi O, Reliquet V, Billaud E, Brunet C, Bouchez S, Morineau-Le Houssine P, Sauser F, Boutoille D, Besnier M, Hue H, Hall N, Brosseau D, Souala F, Michelet C, Tattevin P, Arvieux C, Revest M, Leroy H, Chapplain JM, Dupont M, Fily F, Patra-Delo S, Lefeuvre C, Bernard L, Bastides F, Nau P, Verdon R, de la Blanchardiere A, Martin A, Feret P, Geffray L, Daniel C, Rohan J, Fialaire P, Chennebault JM, Rabier V, Abgueguen P, Rehaiem S, Luycx O, Niault M, Moreau P, Poinsignon Y, Goussef M, Mouton-Rioux V, Houlbert D, Alvarez-Huve S, Barbe F, Haret S, Perre P, Leantez-Nainville S, Esnault JL, Guimard T, Suaud I, Girard JJ, Simonet V, Debab Y, Schmit JL, Jacomet C, Weinberck P, Genet C, Pinet P, Ducroix S, Durox H, Denes É, Abraham B, Gourdon F, Antoniotti O, Molina JM, Ferret S, Lascoux-Combe C, Lafaurie M, Colin de Verdiere N, Ponscarme D, De Castro N, Aslan A, Rozenbaum W, Pintado C, Clavel F, Taulera O, Gatey C, Munier AL, Gazaigne S, Penot P, Conort G, Lerolle N, Leplatois A, Balausine S, Delgado J, Timsit J, Tabet M, Gerard L, Girard PM, Picard O, Tredup J, Bollens D, Valin N, Campa P, Bottero J, Lefebvre B, Tourneur M, Fonquernie L, Wemmert C, Lagneau JL, Yazdanpanah Y, Phung B, Pinto A, Vallois D, Cabras O, Louni F, Pialoux G, Lyavanc T, Berrebi V, Chas J, Lenagat S, Rami A, Diemer M, Parrinello M, Depond A, Salmon D, Guillevin L, Tahi T, Belarbi L, Loulergue P, Zak Dit Zbar O, Launay O, Silbermann B, Leport C, Alagna L, Pietri MP, Simon A, Bonmarchand M, Amirat N, Pichon F, Kirstetter M, Katlama C, Valantin MA, Tubiana R, Caby F, Schneider L, Ktorza N, Calin R, Merlet A, Ben Abdallah S, Weiss L, Buisson M, Batisse D, Karmochine M, Pavie J, Minozzi C, Jayle D, Castel P, Derouineau J, Kousignan P, Eliazevitch M, Pierre I, Collias L, Viard JP, Gilquin J, Sobel A, Slama L, Ghosn J, Hadacek B, Thu-Huyn N, Nait-Ighil L, Cros A, Maignan A, Duvivier C, Consigny PH, Lanternier F, Shoai-Tehrani M, Touam F, Jerbi S, Bodard L, Jung C, Goujard C, Quertainmont Y, Duracinsky M, Segeral O, Blanc A, Peretti D, Cheret A, Chantalat C, Dulucq MJ, Levy Y, Lelievre JD, Lascaux AS, Dumont C, Boue F, Chambrin V, Abgrall S, Kansau I, Raho-Moussa M, De Truchis P, Dinh A, Davido B, Marigot D, Berthe H, Devidas A, Chevojon P, Chabrol A, Agher N, Lemercier Y, Chaix F, Turpault I, Bouchaud O, Honore P, Rouveix E, Reimann E, Belan AG, Godin Collet C, Souak S, Mortier E, Bloch M, Simonpoli AM, Manceron V, Cahitte I, Hiraux E, Lafon E, Cordonnier F, Zeng AF, Zucman D, Majerholc C, Bornarel D, Uludag A, Gellen-Dautremer J, Lefort A, Bazin C, Daneluzzi V, Gerbe J, Jeantils V, Coupard M, Patey O, Bantsimba J, Delllion S, Paz PC, Cazenave B, Richier L, Garrait V, Delacroix I, Elharrar B, Vittecoq D, Bolliot C, Lepretre A, Genet P, Masse V, Perrone V, Boussard JL, Chardon P, Froguel E, Simon P, Tassi S, Avettand Fenoel V, Barin F, Bourgeois C, Cardon F, Chaix ML, Delfraissy JF, Essat A, Fischer H, Lecuroux C, Meyer L, Petrov-Sanchez V, Rouzioux C, Saez-Cirion A, Seng R, Kuldanek K, Mullaney S, Young C, Zucchetti A, Bevan MA, McKernan S, Wandolo E, Richardson C, Youssef E, Green P, Faulkner S, Faville R, Herman S, Care C, Blackman H, Bellenger K, Fairbrother K, Phillips A, Babiker A, Delpech V, Fidler S, Clarke M, Fox J, Gilson R, Goldberg D, Hawkins D, Johnson A, Johnson M, McLean K, Nastouli E, Post F, Kennedy N, Pritchard J, Andrady U, Rajda N, Donnelly C, McKernan S, Drake S, Gilleran G, White D, Ross J, Harding J, Faville R, Sweeney J, Flegg P, Toomer S, Wilding H, Woodward R, Dean G, Richardson C, Perry N, Gompels M, Jennings L, Bansaal D, Browing M, Connolly L, Stanley B, Estreich S, Magdy A, O'Mahony C, Fraser P, Jebakumar SPR, David L, Mette R, Summerfield H, Evans M, White C, Robertson R, Lean C, Morris S, Winter A, Faulkner S, Goorney B, Howard L, Fairley I, Stemp C, Short L, Gomez M, Young F, Roberts M, Green S, Sivakumar K, Minton J, Siminoni A, Calderwood J, Greenhough D, DeSouza C, Muthern L, Orkin C, Murphy S, Truvedi M, McLean K, Hawkins D, Higgs C, Moyes A, Antonucci S, McCormack S, Lynn W, Bevan M, Fox J, Teague A, Anderson J, Mguni S, Post F, Campbell L, Mazhude C, Russell H, Gilson R, Carrick G, Ainsworth J, Waters A, Byrne P, Johnson M, Fidler S, Kuldanek K, Mullaney S, Lawlor V, Melville R, Sukthankar A, Thorpe S, Murphy C, Wilkins E, Ahmad S, Green P, Tayal S, Ong E, Meaden J, Riddell L, Loay D, Peacock K, Blackman H, Harindra V, Saeed AM, Allen S, Natarajan U, Williams O, Lacey H, Care C, Bowman C, Herman S, Devendra SV, Wither J, Bridgwood A, Singh G, Bushby S, Kellock D, Young S, Rooney G, Snart B, Currie J, Fitzgerald M, Arumainayyagam J, Chandramani S. A highly virulent variant of HIV-1 circulating in the Netherlands. Science 2022; 375:540-545. [PMID: 35113714 DOI: 10.1126/science.abk1688] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We discovered a highly virulent variant of subtype-B HIV-1 in the Netherlands. One hundred nine individuals with this variant had a 0.54 to 0.74 log10 increase (i.e., a ~3.5-fold to 5.5-fold increase) in viral load compared with, and exhibited CD4 cell decline twice as fast as, 6604 individuals with other subtype-B strains. Without treatment, advanced HIV-CD4 cell counts below 350 cells per cubic millimeter, with long-term clinical consequences-is expected to be reached, on average, 9 months after diagnosis for individuals in their thirties with this variant. Age, sex, suspected mode of transmission, and place of birth for the aforementioned 109 individuals were typical for HIV-positive people in the Netherlands, which suggests that the increased virulence is attributable to the viral strain. Genetic sequence analysis suggests that this variant arose in the 1990s from de novo mutation, not recombination, with increased transmissibility and an unfamiliar molecular mechanism of virulence.
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Affiliation(s)
- Chris Wymant
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - François Blanquart
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France.,IAME, UMR 1137, INSERM, Université de Paris, Paris, France
| | - Luca Ferretti
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Astrid Gall
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Matthew Hall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tanya Golubchik
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Margreet Bakker
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Swee Hoe Ong
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Lele Zhao
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - David Bonsall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mariateresa de Cesare
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - George MacIntyre-Cockett
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lucie Abeler-Dörner
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Norbert Bannert
- Division for HIV and Other Retroviruses, Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Jacques Fellay
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - M Kate Grabowski
- Department of Pathology, John Hopkins University, Baltimore, MD, USA
| | | | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Pia Kivelä
- Department of Infectious Diseases, Helsinki University Hospital, Helsinki, Finland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | | | - Laurence Meyer
- INSERM CESP U1018, Université Paris Saclay, APHP, Service de Santé Publique, Hôpital de Bicêtre, Le Kremlin-Bicêtre, France
| | - Kholoud Porter
- Institute for Global Health, University College London, London, UK
| | - Matti Ristola
- Department of Infectious Diseases, Helsinki University Hospital, Helsinki, Finland
| | | | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Paul Kellam
- Kymab Ltd., Cambridge, UK.,Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Marion Cornelissen
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands.,Molecular Diagnostic Unit, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Peter Reiss
- Stichting HIV Monitoring, Amsterdam, Netherlands.,Department of Global Health, Amsterdam University Medical Centers, University of Amsterdam and Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands
| | - Christophe Fraser
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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21
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Abad CL, Bello JAG, Cruz AB, Danilovic A, Elias J, Bremer JW, Huang DD. Prevalent subtypes and one-year outcomes of an HIV-cohort from an urban Philippine center. Medicine (Baltimore) 2021; 100:e28315. [PMID: 34941127 PMCID: PMC8701963 DOI: 10.1097/md.0000000000028315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 01/05/2023] Open
Abstract
ABSTRACT Circulating HIV subtypes in the Philippines have increasingly diversified, potentially affecting treatment. We monitored outcomes of a treatment-naïve cohort and their virus subtype prevalence.Retrospective/prospective study cohort.HIV-I-REACT clinic patients co-enrolled in the Virology Quality Assurance Program (RUSH-VQA) from 7/2017-6/2019 were included. Relevant demographic and laboratory information were collected. The ViroSeq HIV-1 Genotyping System v.3 and HIV-1 Integrase Genotyping Kit identified protease-reverse transcriptase and integrase drug resistance mutations (DRM). Sequence subtyping followed using the Stanford University Drug Resistance Database and the REGA HIV-1 Subtyping Tool v.3. The jpHMM HIV-1 Tool and REGA HIV-1 Subtyping Tool provided additional subtype analysis of this cohort's 5'LTR-VIF regions after Sanger sequencing. One-year outcomes included virologic suppression, mortality, and follow-up.86/88 patients were males. Median age was 30 (range 19-65) years; 61/88 were MSM. 15/85 carried baseline DRM. ViroSeq-generated sequences included subtypes CRF01_AE (66/85), B (14/85), and newer recombinants (4/85). Extensive sequencing (n = 71) of the 5'-LTR-GAG-Pol genes showed CRF01_AE (n = 50), subtype B (n = 7), and other recombinants (n = 13). Bootstrap analysis identified 7 pairs of highly related strains. Discordant DRM appeared in 2/7 pairs, where 1/2 strains displayed DRM. After 1 year, 87 individuals were alive, with 19 lost to care. Viral load (VL) was repeated for only 31/77 (40.2%). Follow-up CD4 testing for 39/77 (50.6%) showed an increase to a median of 327 cells/mm3.Our cohort currently carries subtype CRF01_AE (∼68%-70%), followed by subtype B and CRF01_AE/B recombinants. Outcomes were favorable, regardless of subtype after 1 year on cART.
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Affiliation(s)
- Cybele L. Abad
- Department of Medicine, Section of Infectious Diseases, The Medical City, Ortigas Ave, Pasig, Philippines
- Department of Medicine, Division of Infectious Diseases, University of the Philippines Manila, Philippine General Hospital, Taft Avenue Manila, Philippines
| | - Jia An G. Bello
- Department of Medicine, Section of Infectious Diseases, The Medical City, Ortigas Ave, Pasig, Philippines
| | - Angela Beatriz Cruz
- Department of Medicine, Section of Infectious Diseases, The Medical City, Ortigas Ave, Pasig, Philippines
| | - Aleksandra Danilovic
- Department of Microbial Pathogens and Immunology, Rush University Medical College, 1653 West Congress Parkway, Chicago, IL
| | - Juan Elias
- Department of Microbial Pathogens and Immunology, Rush University Medical College, 1653 West Congress Parkway, Chicago, IL
| | - James W. Bremer
- Department of Microbial Pathogens and Immunology, Rush University Medical College, 1653 West Congress Parkway, Chicago, IL
| | - Diana D. Huang
- Department of Microbial Pathogens and Immunology, Rush University Medical College, 1653 West Congress Parkway, Chicago, IL
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22
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Dronina J, Samukaite-Bubniene U, Ramanavicius A. Advances and insights in the diagnosis of viral infections. J Nanobiotechnology 2021; 19:348. [PMID: 34717656 PMCID: PMC8556785 DOI: 10.1186/s12951-021-01081-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 10/11/2021] [Indexed: 12/15/2022] Open
Abstract
Viral infections are the most common among diseases that globally require around 60 percent of medical care. However, in the heat of the pandemic, there was a lack of medical equipment and inpatient facilities to provide all patients with viral infections. The detection of viral infections is possible in three general ways such as (i) direct virus detection, which is performed immediately 1-3 days after the infection, (ii) determination of antibodies against some virus proteins mainly observed during/after virus incubation period, (iii) detection of virus-induced disease when specific tissue changes in the organism. This review surveys some global pandemics from 1889 to 2020, virus types, which induced these pandemics, and symptoms of some viral diseases. Non-analytical methods such as radiology and microscopy also are overviewed. This review overlooks molecular analysis methods such as nucleic acid amplification, antibody-antigen complex determination, CRISPR-Cas system-based viral genome determination methods. Methods widely used in the certificated diagnostic laboratory for SARS-CoV-2, Influenza A, B, C, HIV, and other viruses during a viral pandemic are outlined. A comprehensive overview of molecular analytical methods has shown that the assay's sensitivity, accuracy, and suitability for virus detection depends on the choice of the number of regions in the viral open reading frame (ORF) genome sequence and the validity of the selected analytical method.
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Affiliation(s)
- Julija Dronina
- Laboratory of Nanotechnology, Department of Functional Materials and Electronics, Center for Physical Sciences and Technology, Sauletekio av. 3, Vilnius, Lithuania
- Department of Physical Chemistry, Faculty of Chemistry and Geoscience, Vilnius University, Naugarduko str. 24, 03225, Vilnius, Lithuania
| | - Urte Samukaite-Bubniene
- Department of Physical Chemistry, Faculty of Chemistry and Geoscience, Vilnius University, Naugarduko str. 24, 03225, Vilnius, Lithuania
| | - Arunas Ramanavicius
- Department of Physical Chemistry, Faculty of Chemistry and Geoscience, Vilnius University, Naugarduko str. 24, 03225, Vilnius, Lithuania.
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23
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Kao SW, Liu ZH, Wu TS, Ku SWW, Tsai CL, Shie SS, Huang PY, Wu YM, Hsiao YH, Chen NY. Prevalence of drug resistance mutations in HIV-infected individuals with low-level viraemia under combination antiretroviral therapy: an observational study in a tertiary hospital in Northern Taiwan, 2017-19. J Antimicrob Chemother 2021; 76:722-728. [PMID: 33331635 DOI: 10.1093/jac/dkaa510] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 11/09/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Effective ART is crucial for combating the HIV pandemic. Clinically, plasma viral load monitoring to achieve virological suppression is the guide for an optimal ART. The presence of low-level viraemia (LLV) below the definition level of virological failure is a risk factor for ART failure. However, there is no treatment consensus over LLV yet, mainly due to the limitation of standard HIV-RNA genotyping and the resultant insufficient understanding of LLV characteristics. OBJECTIVES To better profile drug resistance mutations (DRMs) and the associated factors in cases experiencing LLV. METHODS A prospective observational study was conducted from 2017 to 2019. HIV-DNA was used as an alternative to HIV-RNA for HIV genotyping coupled with deep sequencing for ART-naive and ART-failure cases, as well as those with LLV. RESULTS Eighty-one ART-naive, 18 ART-failure and 16 LLV cases received HIV genotyping in the study. Three-quarters (12/16) of cases experiencing LLV harboured DRMs. Cases with LLV had higher prevalence of DRMs to NNRTIs than the ART-naive group (69% versus 20%, P < 0.001), but lower DRM prevalence to NRTIs than the ART-failure group (25% versus 61%, P < 0.001). Approximately half of the LLV cases had issues of suboptimal ART compliance/ART interruption, and 68.8% (11/16) did not display drug resistance to their ART at the time of LLV. CONCLUSIONS HIV DRM profiles in LLV cases were significantly different to those in ART-naive and ART-failure cases. Approaches to consolidate ART compliance and early exploration of potential ART resistance may be needed for cases experiencing LLV episodes.
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Affiliation(s)
- Shu-Wei Kao
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital Linkou Branch, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Zhuo-Hao Liu
- Department of Neurosurgery, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan
| | - Ting-Shu Wu
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital Linkou Branch, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Stephane Wen-Wei Ku
- Division of Infectious Diseases, Department of Medicine, Taipei City Hospital Ren-Ai Branch, Taipei, Taiwan.,Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chia-Lung Tsai
- Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Shian-Sen Shie
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital Linkou Branch, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Po-Yen Huang
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital Linkou Branch, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Yen-Mu Wu
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital Linkou Branch, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Yu-Hsiang Hsiao
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital Linkou Branch, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Nan-Yu Chen
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital Linkou Branch, Chang Gung University College of Medicine, Taoyuan, Taiwan
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Bennedbæk M, Zhukova A, Tang MHE, Bennet J, Munderi P, Ruxrungtham K, Gisslen M, Worobey M, Lundgren JD, Marvig RL. Phylogenetic analysis of HIV-1 shows frequent cross-country transmission and local population expansions. Virus Evol 2021; 7:veab055. [PMID: 34532059 PMCID: PMC8438898 DOI: 10.1093/ve/veab055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 05/26/2021] [Accepted: 06/09/2021] [Indexed: 12/03/2022] Open
Abstract
Understanding of pandemics depends on the characterization of pathogen collections from well-defined and demographically diverse cohorts. Since its emergence in Congo almost a century ago, Human Immunodeficiency Virus Type 1 (HIV-1) has geographically spread and genetically diversified into distinct viral subtypes. Phylogenetic analysis can be used to reconstruct the ancestry of the virus to better understand the origin and distribution of subtypes. We sequenced two 3.6-kb amplicons of HIV-1 genomes from 3,197 participants in a clinical trial with consistent and uniform sampling at sites across 35 countries and analyzed our data with another 2,632 genomes that comprehensively reflect the HIV-1 genetic diversity. We used maximum likelihood phylogenetic analysis coupled with geographical information to infer the state of ancestors. The majority of our sequenced genomes (n = 2,501) were either pure subtypes (A-D, F, and G) or CRF01_AE. The diversity and distribution of subtypes across geographical regions differed; USA showed the most homogenous subtype population, whereas African samples were most diverse. We delineated transmission of the four most prevalent subtypes in our dataset (A, B, C, and CRF01_AE), and our results suggest both continuous and frequent transmission of HIV-1 over country borders, as well as single transmission events being the seed of endemic population expansions. Overall, we show that coupling of genetic and geographical information of HIV-1 can be used to understand the origin and spread of pandemic pathogens.
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Affiliation(s)
| | - Anna Zhukova
- Unité Bioinformatique Evolutive, Hub Bioinformatique et Biostatistique, USR3756 (C3BI//DBC), Institut Pasteur and CNRS, 25-28 Rue du Dr Roux, 75015 Paris, France
| | | | | | - Paula Munderi
- MRC Uganda Research Unit on AIDS, UVRI P.O.Box 49, Plot 51-59 Nakiwogo Road, Entebbe-Uganda
| | - Kiat Ruxrungtham
- HIV-NAT, Thai Red Cross AIDS Research Center, and School of Global Health, Faculty Medicine, Chulalongkorn University, Chamchuri 5 Bld. 6th Fl., Phayathai Rd., Wangmai, Pathumwan Bangkok 10330, Thailand
| | - Magnus Gisslen
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Universitetsplatsen 1, 405 30 Gothenburg, Sweden,Department of Infectious Diseases, Region Västra Götaland, Sahlgrenska University Hospital, Universitetsplatsen 1, 405 30 Gothenburg, Sweden
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Biological Sciences West, Rm. 324 Tucson, AZ 85721, USA
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Baxter JD, Dunn D, Tostevin A, Marvig RL, Bennedbaek M, Cozzi-Lepri A, Sharma S, Kozal MJ, Gompels M, Pinto AN, Lundgren J. Transmitted HIV-1 drug resistance in a large international cohort using next-generation sequencing: results from the Strategic Timing of Antiretroviral Treatment (START) study. HIV Med 2021; 22:360-371. [PMID: 33369017 PMCID: PMC8049964 DOI: 10.1111/hiv.13038] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/11/2020] [Accepted: 11/10/2020] [Indexed: 01/13/2023]
Abstract
OBJECTIVES The aim of this analysis was to characterize transmitted drug resistance (TDR) in Strategic Timing of Antiretroviral Treatment (START) study participants by next-generation sequencing (NGS), a sensitive assay capable of detecting low-frequency variants. METHODS Stored plasma from participants with entry HIV RNA > 1000 copies/mL were analysed by NGS (Illumina MiSeq). TDR was based on the WHO 2009 surveillance definition with the addition of reverse transcriptase (RT) mutations T215N and E138K, and integrase strand transfer inhibitor (INSTI) surveillance mutations (Stanford HIVdb). Drug resistance mutations (DRMs) detected at three thresholds are reported: > 2%, 5% and 20% of the viral population. RESULTS Between 2009 and 2013, START enrolled 4684 antiretroviral therapy (ART)-naïve individuals in 35 countries. Baseline NGS data at study entry were available for 2902 participants. Overall prevalence rates of TDR using a detection threshold of 2%/5%/20% were 9.2%/5.6%/3.2% for nucleoside reverse transcriptase inhibitors (NRTIs), 9.2%/6.6%/4.9% for non-NRTIs, 11.4%/5.5%/2.4% for protease inhibitors (PIs) and 3.5%/1.6%/0.1% for INSTI DRMs and varied by geographic region. Using the 2% detection threshold, individual DRMs with the highest prevalence were: PI M46IL (5.5%), RT K103NS (3.5%), RT G190ASE (3.1%), T215ISCDVEN (2.5%), RT M41L (2.2%), RT K219QENR (1.7%) and PI D30N (1.6%). INSTI DRMs were detected almost exclusively below the 20% detection threshold, most commonly Y143H (0.4%), Q148R (0.4%) and T66I (0.4%). CONCLUSIONS Use of NGS in this study population resulted in the detection of a large proportion of low-level variants which would not have been detected by traditional Sanger sequencing. Global surveillance studies utilizing NGS should provide a more comprehensive assessment of TDR prevalence in different regions of the world.
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Affiliation(s)
- J D Baxter
- Cooper University Hospital/Cooper Medical School of Rowan University, Camden, NJ, USA
| | - D Dunn
- Institute for Global Health, UCL, London, UK
| | - A Tostevin
- Institute for Global Health, UCL, London, UK
| | - R L Marvig
- Center for Genomic Medicine, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - M Bennedbaek
- Copenhagen HIV Programme, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | | | - S Sharma
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - M J Kozal
- Yale University School of Medicine, New Haven, CT, USA
| | - M Gompels
- North Bristol NHS Trust, Westbury on Trym, UK
| | - A N Pinto
- The Kirby Institute, University of New South Wales, Sydney, Australia
| | - J Lundgren
- Copenhagen HIV Programme, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
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26
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Olusola BA, Olaleye DO, Odaibo GN. New infections and HIV-1 subtypes among febrile persons and blood donors in Oyo State, Nigeria. J Med Virol 2021; 93:4891-4900. [PMID: 33590935 DOI: 10.1002/jmv.26872] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 01/29/2021] [Accepted: 02/05/2021] [Indexed: 12/28/2022]
Abstract
PURPOSE There were approximately 37.9 million persons infected with HIV in 2018 globally, resulting in 770,000 deaths annually. Over 50% of this infection and deaths occur in sub-Saharan Africa, with countries like Nigeria being seriously affected. Nigeria has one of the highest rates of new infections globally. To control HIV infection in Nigeria, there is a need to continually screen high-risk groups for early HIV infection and subtypes using very sensitive methods. In this study, new HIV-1 infection and circulating HIV-1 subtypes among febrile persons and blood donors were determined. Performance characteristics of three commercial EIA kits were also evaluated. METHODS In total, 1028 participants were recruited for the study. New HIV-1 infection and subtypes were determined using enzyme immunoassays and molecular techniques, respectively. Sensitivity, specificity, predictive values, and agreements were compared among the EIA kits using PCR-confirmed HIV-positive and negative samples. RESULTS The overall prevalence of HIV infection in this study was 5.35%. The rate of new HIV infection was significantly different (p < .03674) among 1028 febrile persons (Ibadan: 2.22%; Saki: 1.36%) and blood donors (5.07%) studied. Three subtypes, CRF02_AG, A, and G, were found among those with new HIV infection. Whereas the commercial ELISA kits had very high specificities (94.12%, 100%, and 100%) for HIV-1 detection, Alere Determine HIV-1 antibody rapid kit had the lowest sensitivity score (50%). CONCLUSION Genetic diversity of HIV-1 strains among infected individuals in Oyo State, Nigeria, is still relatively high. This high level of diversity of HIV-1 strains may impact the reliability of diagnosis of the virus in Nigeria and other African countries where many of the virus strains co-circulate.
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Affiliation(s)
- Babatunde A Olusola
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - David O Olaleye
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Georgina N Odaibo
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria
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27
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Kim KW, Choi S, Shin SK, Lee I, Ku KB, Kim SJ, Kim S, Yi H. A Half-Day Genome Sequencing Protocol for Middle East Respiratory Syndrome Coronavirus. Front Microbiol 2021; 12:602754. [PMID: 33679631 PMCID: PMC7933487 DOI: 10.3389/fmicb.2021.602754] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 01/29/2021] [Indexed: 12/17/2022] Open
Abstract
Recent coronavirus (CoV) outbreaks, including that of Middle East respiratory syndrome (MERS), have presented a threat to public health worldwide. A primary concern in these outbreaks is the extent of mutations in the CoV, and the content of viral variation that can be determined only by whole genome sequencing (WGS). We aimed to develop a time efficient WGS protocol, using universal primers spanning the entire MERS-CoV genome. MERS and synthetic Neoromicia capensis bat CoV genomes were successfully amplified using our developed PCR primer set and sequenced with MinION. All experimental and analytical processes took 6 h to complete and were also applied to synthetic animal serum samples, wherein the MERS-CoV genome sequence was completely recovered. Results showed that the complete genome of MERS-CoV and related variants could be directly obtained from clinical samples within half a day. Consequently, this method will contribute to rapid MERS diagnosis, particularly in future CoV epidemics.
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Affiliation(s)
- Kwan Woo Kim
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, South Korea
| | - Sungmi Choi
- Institute for Biomaterials, Korea University, Seoul, South Korea
| | - Su-Kyoung Shin
- Institute for Biomaterials, Korea University, Seoul, South Korea
| | - Imchang Lee
- Institute for Biomaterials, Korea University, Seoul, South Korea
| | - Keun Bon Ku
- Korea Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, South Korea
| | - Seong Jun Kim
- Korea Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, South Korea
| | - Seil Kim
- Korea Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, South Korea
- Microbiological Analysis Team, Group for Biometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon, South Korea
- Department of Bio-Analysis Science, University of Science and Technology, Daejeon, South Korea
| | - Hana Yi
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, South Korea
- Institute for Biomaterials, Korea University, Seoul, South Korea
- School of Biosystems and Biomedical Sciences, Korea University, Seoul, South Korea
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28
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Characterization of HIV-1 recombinant and subtype B near full-length genome among men who have sex with men in South Korea. Sci Rep 2021; 11:4122. [PMID: 33602986 PMCID: PMC7892834 DOI: 10.1038/s41598-021-82872-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 01/25/2021] [Indexed: 11/08/2022] Open
Abstract
In Korea, subtype B is the predominant variant of HIV-1, but full genome sequencing and analysis of its viral variants are lacking. We performed near full-length genome (NFLG) sequencing and phylogenetic and recombination analyses of fifty plasma samples from HIV-positive men who have sex with men (MSM) from a Korea HIV/AIDS cohort study. Viral genomes were amplified and the near-full-length sequences were determined using next-generation sequencing (NGS) and Sanger sequencing. We focused on the HIV-1 subtype classification and identification of HIV recombinants. Twelve HIV-1 NFLGs were determined: ten were subtyped as pure HIV-1 subtype B and two recombinant strains as a common subtype CRF07_BC, and a novel subtype CRF43_02G recombined with CRF02_AG again, or a new CRF02_AG and subtype G recombinant. For the ten NFLGs determined by NGS, “the novel recombinant emerged at approximately 2003 and the other nine subtype B about 2004 or 2005”. This is the first report analyzing HIV-1 NFLG, including recombinants and clinical characteristics, by subtype among MSM in Korea. Our results provide novel insights for understanding the recombinants in the HIV-1 epidemic in Korea.
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29
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Zhang Y, Wymant C, Laeyendecker O, Grabowski MK, Hall M, Hudelson S, Piwowar-Manning E, McCauley M, Gamble T, Hosseinipour MC, Kumarasamy N, Hakim JG, Kumwenda J, Mills LA, Santos BR, Grinsztejn B, Pilotto JH, Chariyalertsak S, Makhema J, Chen YQ, Cohen MS, Fraser C, Eshleman SH. Evaluation of Phylogenetic Methods for Inferring the Direction of Human Immunodeficiency Virus (HIV) Transmission: HIV Prevention Trials Network (HPTN) 052. Clin Infect Dis 2021; 72:30-37. [PMID: 31922537 PMCID: PMC7823077 DOI: 10.1093/cid/ciz1247] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 01/07/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Phylogenetic analysis can be used to assess human immunodeficiency virus (HIV) transmission in populations. We inferred the direction of HIV transmission using whole-genome HIV sequences from couples with known linked infection and known transmission direction. METHODS Complete next-generation sequencing (NGS) data were obtained for 105 unique index-partner sample pairs from 32 couples enrolled in the HIV Prevention Trials Network (HPTN) 052 study (up to 2 samples/person). Index samples were obtained up to 5.5 years before partner infection; partner samples were obtained near the time of seroconversion. The bioinformatics method, phyloscanner, was used to infer transmission direction. Analyses were performed using samples from individual sample pairs, samples from all couples (1 sample/person; group analysis), and all available samples (multisample group analysis). Analysis was also performed using NGS data from defined regions of the HIV genome (gag, pol, env). RESULTS Using whole-genome NGS data, transmission direction was inferred correctly (index to partner) for 98 of 105 (93.3%) of the individual sample pairs, 99 of 105 (94.3%) sample pairs using group analysis, and 31 of the 32 couples (96.9%) using multisample group analysis. There were no cases where the incorrect transmission direction (partner to index) was inferred. The accuracy of the method was higher with greater time between index and partner sample collection. Pol region sequences performed better than env or gag sequences for inferring transmission direction. CONCLUSIONS We demonstrate the potential of a phylogenetic method to infer the direction of HIV transmission between 2 individuals using whole-genome and pol NGS data.
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Affiliation(s)
- Yinfeng Zhang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Chris Wymant
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Oliver Laeyendecker
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - M Kathryn Grabowski
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Matthew Hall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Sarah Hudelson
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Estelle Piwowar-Manning
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Marybeth McCauley
- HIV Prevention Trials Network Leadership and Operations Center, FHI, Washington, District of Columbia, USA
| | - Theresa Gamble
- HIV Prevention Trials Network Leadership and Operations Center, FHI, Durham, North Carolina, USA
| | - Mina C Hosseinipour
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- University of North Carolina Project–Malawi, Institute for Global Health and Infectious Diseases, Lilongwe, Malawi
| | - Nagalingeswaran Kumarasamy
- Chennai Antiviral Research and Treatment Clinical Research Site, Infectious Diseases Medical Centre, Voluntary Health Services, Chennai, India
| | - James G Hakim
- Department of Medicine, University of Zimbabwe, Harare, Zimbabwe
| | | | - Lisa A Mills
- US Centers for Disease Control and Prevention, HIV Research Branch, Kisumu, Kenya
| | - Breno R Santos
- Department of Infectious Diseases, Hospital Nossa Senhora da Conceição, Porto Alegre, Brazil
| | - Beatriz Grinsztejn
- Instituto Nacional de Infectologia Evandro Chagas-Fiocruz, Rio de Janeiro, Brazil
| | - Jose H Pilotto
- Hospital Geral de Nova Iguacu and Laboratorio de AIDS e Imunologia Molecular–Instituto Oswaldo Cruz/Fiocruz, Rio de Janeiro, Brazil
| | - Suwat Chariyalertsak
- Research Institute for Health Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Joseph Makhema
- Botswana-Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Ying Q Chen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Myron S Cohen
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Christophe Fraser
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Susan H Eshleman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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30
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Olusola BA, Olaleye DO, Odaibo GN. Non-synonymous Substitutions in HIV-1 GAG Are Frequent in Epitopes Outside the Functionally Conserved Regions and Associated With Subtype Differences. Front Microbiol 2021; 11:615721. [PMID: 33505382 PMCID: PMC7829476 DOI: 10.3389/fmicb.2020.615721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/15/2020] [Indexed: 12/22/2022] Open
Abstract
In 2019, 38 million people lived with HIV-1 infection resulting in 690,000 deaths. Over 50% of this infection and its associated deaths occurred in Sub-Saharan Africa. The West African region is a known hotspot of the HIV-1 epidemic. There is a need to develop an HIV-1 vaccine if the HIV epidemic would be effectively controlled. Few protective cytotoxic T Lymphocytes (CTL) epitopes within the HIV-1 GAG (HIV_gagconsv) have been previously identified to be functionally conserved among the HIV-1 M group. These epitopes are currently the focus of universal HIV-1 T cell-based vaccine studies. However, these epitopes' phenotypic and genetic properties have not been observed in natural settings for HIV-1 strains circulating in the West African region. This information is critical as the usefulness of universal HIV-1 vaccines in the West African region depends on these epitopes' occurrence in strains circulating in the area. This study describes non-synonymous substitutions within and without HIV_gagconsv genes isolated from 10 infected Nigerians at the early stages of HIV-1 infection. Furthermore, we analyzed these substitutions longitudinally in five infected individuals from the early stages of infection till after seroconversion. We identified three non-synonymous substitutions within HIV_gagconsv genes isolated from early HIV infected individuals. Fourteen and nineteen mutations outside the HIV_gagconsv were observed before and after seroconversion, respectively, while we found four mutations within the HIV_gagconsv. These substitutions include previously mapped CTL epitope immune escape mutants. CTL immune pressure likely leaves different footprints on HIV-1 GAG epitopes within and outside the HIV_gagconsv. This information is crucial for universal HIV-1 vaccine designs for use in the West African region.
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Affiliation(s)
| | | | - Georgina N. Odaibo
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
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31
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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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32
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Modern diagnostic technologies for HIV. Lancet HIV 2020; 7:e574-e581. [PMID: 32763220 DOI: 10.1016/s2352-3018(20)30190-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/30/2020] [Accepted: 05/14/2020] [Indexed: 12/14/2022]
Abstract
Novel diagnostic technologies, including nanotechnology, microfluidics, -omics science, next-generation sequencing, genomics big data, and machine learning, could contribute to meeting the UNAIDS 95-95-95 targets to end the HIV epidemic by 2030. Novel technologies include multiplexed technologies (including biomarker-based point-of-care tests and molecular platform technologies), biomarker-based combination antibody and antigen technologies, dried-blood-spot testing, and self-testing. Although biomarker-based rapid tests, in particular antibody-based tests, have dominated HIV diagnostics since the development of the first HIV test in the mid-1980s, targets such as nucleic acids and genes are now used in nanomedicine, biosensors, microfluidics, and -omics to enable early diagnosis of HIV. These novel technologies show promise as they are associated with ease of use, high diagnostic accuracy, rapid detection, and the ability to detect HIV-specific markers. Additional clinical and implementation research is needed to generate evidence for use of novel technologies and a public health approach will be required to address clinical and operational challenges to optimise their global deployment.
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Perrier M, Castain L, Regad L, Todesco E, Landman R, Visseaux B, Yazdanpanah Y, Rodriguez C, Joly V, Calvez V, Marcelin AG, Descamps D, Charpentier C. HIV-1 protease, Gag and gp41 baseline substitutions associated with virological response to a PI-based regimen. J Antimicrob Chemother 2020; 74:1679-1692. [PMID: 30768160 DOI: 10.1093/jac/dkz043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 01/04/2019] [Accepted: 01/08/2019] [Indexed: 12/29/2022] Open
Abstract
OBJECTIVES To assess, at ART initiation, the impact of baseline substitutions in protease, Gag and gp41 regions on the virological response to a first-line PI-based regimen. PATIENTS AND METHODS One hundred and fifty-four HIV-infected ART-naive patients initiating a PI-based regimen including darunavir (n = 129) or atazanavir (n = 25) were assessed, including 36 experiencing virological failure (VF). Whole pol, gag and gp41 genes were sequenced at ART baseline by ultra-deep sequencing (UDS) using Illumina® technology. Supervised data-mining analyses were performed to identify mutations associated with virological response. Structural analyses were performed to assess the impact of mutations on protease conformation. RESULTS UDS was successful in 127, 138 and 134 samples for protease, Gag and gp41, respectively (31% subtype B and 38% CRF02_AG). Overall, T4A and S37T mutations in protease were identified as being associated with VF (P = 0.02 and P = 0.005, respectively). Among CRF02_AG sequences, I72M and E21D mutations were associated with VF (P = 0.03 for both). They all induced some conformational changes of some protease side-chain residues located near mutated residues. In Gag, mutations associated with VF were G62D, N315H and Y441S (P = 0.005, P = 0.007 and P = 0.0003, respectively). All were localized outside Gag cleavage sites (G62D, matrix; N315H, capsid; and Y441S, p1). In gp41, the I270T mutation, localized in the cytoplasmic tail, was associated with VF (P = 0.003), and the I4L mutation, in the fusion peptide, was associated with virological success (P = 0.004). CONCLUSIONS In this study, new baseline substitutions in Gag, protease and g41, potentially impacting PI-based regimen outcome, were evidenced. Phenotypic analyses are required to confirm their role in the PI-resistance mechanism.
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Affiliation(s)
- Marine Perrier
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat, AP-HP, Paris, France
| | - Louise Castain
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de Virologie, F-75013 Paris, France
| | - Leslie Regad
- Sorbonne Paris Cité, Université Paris-Diderot, CNRS, INSERM, Biologie Fonctionnelle et Adaptative UMR 8251, Computational Modeling of Protein Ligand Interactions U1133, Paris, France
| | - Eve Todesco
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de Virologie, F-75013 Paris, France
| | - Roland Landman
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Service de Maladies Infectieuses et Tropicales, Hôpital Bichat, AP-HP, Paris, France
| | - Benoit Visseaux
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat, AP-HP, Paris, France
| | - Yazdan Yazdanpanah
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Service de Maladies Infectieuses et Tropicales, Hôpital Bichat, AP-HP, Paris, France
| | - Christophe Rodriguez
- INSERM U955 Eq18, CNR hépatites virales B, C et delta, Laboratoire de Virologie, Hôpital Henri Mondor, AP-HP, Paris, France
| | - Véronique Joly
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Service de Maladies Infectieuses et Tropicales, Hôpital Bichat, AP-HP, Paris, France
| | - Vincent Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de Virologie, F-75013 Paris, France
| | - Anne-Geneviève Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de Virologie, F-75013 Paris, France
| | - Diane Descamps
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat, AP-HP, Paris, France
| | - Charlotte Charpentier
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat, AP-HP, Paris, France
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Capoferri AA, Lamers SL, Grabowski MK, Rose R, Wawer MJ, Serwadda D, Gray RH, Quinn TC, Kigozi G, Kagaayi J, Laeyendecker O, Abeler-Dörner L, Ayles H, Bonsall D, Bowden R, Calvez V, Cohen M, Denis A, Frampton D, de Oliveira T, Essex M, Fidler S, Fraser C, Golubchik T, Hayes R, Herbeck JT, Hoppe A, Kaleebu P, Kellam P, Kityo C, Leigh-Brown A, Lingappa JR, Novitsky V, Paton N, Pillay D, Rambaut A, Ratmann O, Seeley J, Ssemwanga D, Tanser F. Recombination Analysis of Near Full-Length HIV-1 Sequences and the Identification of a Potential New Circulating Recombinant Form from Rakai, Uganda. AIDS Res Hum Retroviruses 2020; 36:467-474. [PMID: 31914792 DOI: 10.1089/aid.2019.0150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Phylogenetics And Networks for Generalized HIV Epidemics in Africa (PANGEA-HIV) consortium has been vital in the generation and examination of near full-length HIV-1 sequences generated from Sub-Saharan Africa. In this study, we examined a subset (n = 275) of sequences from Rakai, Uganda, collected between August 2011 and January 2015. Sequences were initially screened with COMET for subtyping and then evaluated using bootscanning and phylogenetic inference. Among 275 sequences, 38.6% were subtype D, 19.3% were subtype A, 2.9% were subtype C, and 39.3% were recombinant. The recombinants were structurally diverse in the number of breakpoints observed, the location of recombinant segments, and represented subtypes, with AD recombinants accounting for the majority of all recombinants (29.8%). Within the AD subpopulation, we identified a potential new circulating recombinant form in five individuals where the polymerase gene was subtype D and most of env was subtype A (D-A junctures at HXB2 6760 and 8709). While the breakpoints were identical for the viruses from these individuals, the viral fragments did not cluster together. These results suggest selection for a viral strain where properties of the subtype A and subtype D portions of the virus confer a survival advantage. The continued study of recombinants will increase our breadth of knowledge for the genetic diversity and evolution of HIV-1, which can further contribute to our understanding toward a universal HIV-1 vaccine.
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Affiliation(s)
- Adam A. Capoferri
- The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Mary Kate Grabowski
- The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Rakai Health Sciences Program, Entebbe, Uganda
| | | | - Maria J. Wawer
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Rakai Health Sciences Program, Entebbe, Uganda
| | - David Serwadda
- Rakai Health Sciences Program, Entebbe, Uganda
- Makerere University School of Public Health, Kampala, Uganda
| | - Ronald H. Gray
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Rakai Health Sciences Program, Entebbe, Uganda
| | - Thomas C. Quinn
- The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, Maryland, USA
| | | | | | - Oliver Laeyendecker
- The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, Maryland, USA
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35
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Lamers SL, Rose R, Cross S, Rodriguez CW, Redd AD, Quinn TC, Serwadda D, Kagaayi J, Kigozi G, Galiwango R, Gray RH, Grabowski MK, Laeyendecker O. HIV-1 Subtype Distribution and Diversity Over 18 Years in Rakai, Uganda. AIDS Res Hum Retroviruses 2020; 36:522-526. [PMID: 32281387 DOI: 10.1089/aid.2020.0062] [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: 11/13/2022] Open
Abstract
The Rakai Community Cohort Study in south central Uganda has surveyed people aged 15-49 since 1994. Antiretroviral therapy (ART) was introduced in 2004. HIV p24 and gp41 subtype distribution and viral diversity were studied from blood samples collected at three surveys in 1994-1995, 2002-2003, and 2008-2009, which were compared with a new survey round from 2011 to 2012. These included 1364 HIV+ individuals. For both p24 and gp41 domains, the genetic diversity within subtypes A and D was significantly increasing in the pre-ART era and decreased between the last two survey rounds in the ART era (p < .01). This study suggests that despite ongoing mixing of viral subtypes, an association with the introduction of ART to a reduction of intra-subtype viral genomic diversity may be occurring, which can be explored in ongoing studies.
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Affiliation(s)
| | | | - Sissy Cross
- BioInfoExperts LLC, Thibodaux, Louisiana, USA
| | | | - Andrew D. Redd
- Laboratory of Immunoregulation, Division of Intramural Research, NIAID, NIH, Baltimore, Maryland, USA
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Thomas C. Quinn
- Laboratory of Immunoregulation, Division of Intramural Research, NIAID, NIH, Baltimore, Maryland, USA
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - David Serwadda
- Makerere University, School of Medicine, Kampala, Uganda
- Rakai Health Sciences Program, Kalisizo, Uganda
| | | | | | | | - Ronald H. Gray
- Rakai Health Sciences Program, Kalisizo, Uganda
- Department of Epidemiology, JHSPH, Baltimore, Maryland, USA
| | - M. Kate Grabowski
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
- Rakai Health Sciences Program, Kalisizo, Uganda
| | - Oliver Laeyendecker
- Laboratory of Immunoregulation, Division of Intramural Research, NIAID, NIH, Baltimore, Maryland, USA
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
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36
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Chen NY, Kao SW, Liu ZH, Wu TS, Tsai CL, Lin HH, Wong WW, Chang YY, Chen SS, Ku SWW. Shall I trust the report? Variable performance of Sanger sequencing revealed by deep sequencing on HIV drug resistance mutation detection. Int J Infect Dis 2020; 93:182-191. [PMID: 32061862 DOI: 10.1016/j.ijid.2020.02.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 01/31/2020] [Accepted: 02/06/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The clinical utilisation of deep sequencing in HIV treatment has been hindered due to its unknown correlation with standard Sanger genotyping and the undetermined value of minority drug resistance mutation (DRM) detection. OBJECTIVES To compare deep sequencing performance to standard Sanger genotyping with clinical samples, in an effort to delineate the correlation between the results from the two methods and to find the optimal deep sequencing threshold for clinical utilisation. METHODS We conducted a retrospective study using stored plasma collected from August 2014 to March 2018 for HIV genotyping with the commercial Sanger genotyping kit. Samples with available Sanger genotyping reports were further deep sequenced. Drug resistance was interpreted according to the Stanford HIV drug resistance database algorithm. RESULTS At 15-25% minority detection thresholds, 9-15% cases had underestimated DRMs by Sanger sequencing. The concordance between the Sanger and deep sequencing reports was 68-82% in protease-reverse transcriptase region and 88-97% in integrase region at 5-25% thresholds. The undetected drug resistant minority variants by Sanger sequencing contributed to the lower negative predictive value of Sanger genotyping in cases harbouring DRMs. CONCLUSIONS Use of deep sequencing improved detection of antiretroviral resistance mutations especially in cases with virological failure or previous treatment interruption. Deep sequencing with 10-15% detection thresholds may be considered a suitable substitute for Sanger sequencing on antiretroviral DRM detection.
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Affiliation(s)
- Nan-Yu Chen
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital Linkou Branch, Chang Gung University College of Medicine, Taiwan
| | - Shu-Wei Kao
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital Linkou Branch, Chang Gung University College of Medicine, Taiwan
| | - Zhuo-Hao Liu
- Department of Neurosurgery, Chang Gung Memorial Hospital Linkou Branch, Taiwan
| | - Ting-Shu Wu
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital Linkou Branch, Chang Gung University College of Medicine, Taiwan
| | - Chia-Lung Tsai
- Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Taiwan
| | - Hsi-Hsun Lin
- General Clinical Research Centre, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan; Institute of Public Health, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Wing-Wai Wong
- Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yea-Yuan Chang
- Division of Infectious Diseases, Department of Internal Medicine, National Yang-Ming University Hospital, Yilan, Taiwan; Institute of Clinical Medicine and AIDS Prevention and Research Centre, National Yang-Ming University, Taipei, Taiwan; Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan; Division of Infectious Diseases, Department of Medicine, Taipei City Hospital Ren-Ai Branch, Taiwan
| | - Shu-Sheng Chen
- Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Stephane Wen-Wei Ku
- Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan; Division of Infectious Diseases, Department of Medicine, Taipei City Hospital Ren-Ai Branch, Taiwan.
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37
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Ratmann O, Kagaayi J, Hall M, Golubchick T, Kigozi G, Xi X, Wymant C, Nakigozi G, Abeler-Dörner L, Bonsall D, Gall A, Hoppe A, Kellam P, Bazaale J, Kalibbala S, Laeyendecker O, Lessler J, Nalugoda F, Chang LW, de Oliveira T, Pillay D, Quinn TC, Reynolds SJ, Spencer SEF, Ssekubugu R, Serwadda D, Wawer MJ, Gray RH, Fraser C, Grabowski MK. Quantifying HIV transmission flow between high-prevalence hotspots and surrounding communities: a population-based study in Rakai, Uganda. Lancet HIV 2020; 7:e173-e183. [PMID: 31953184 PMCID: PMC7167508 DOI: 10.1016/s2352-3018(19)30378-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 11/11/2019] [Accepted: 11/15/2019] [Indexed: 06/02/2023]
Abstract
BACKGROUND International and global organisations advocate targeting interventions to areas of high HIV prevalence (ie, hotspots). To better understand the potential benefits of geo-targeted control, we assessed the extent to which HIV hotspots along Lake Victoria sustain transmission in neighbouring populations in south-central Uganda. METHODS We did a population-based survey in Rakai, Uganda, using data from the Rakai Community Cohort Study. The study surveyed all individuals aged 15-49 years in four high-prevalence Lake Victoria fishing communities and 36 neighbouring inland communities. Viral RNA was deep sequenced from participants infected with HIV who were antiretroviral therapy-naive during the observation period. Phylogenetic analysis was used to infer partial HIV transmission networks, including direction of transmission. Reconstructed networks were interpreted through data for current residence and migration history. HIV transmission flows within and between high-prevalence and low-prevalence areas were quantified adjusting for incomplete sampling of the population. FINDINGS Between Aug 10, 2011, and Jan 30, 2015, data were collected for the Rakai Community Cohort Study. 25 882 individuals participated, including an estimated 75·7% of the lakeside population and 16·2% of the inland population in the Rakai region of Uganda. 5142 participants were HIV-positive (2703 [13·7%] in inland and 2439 [40·1%] in fishing communities). 3878 (75·4%) people who were HIV-positive did not report antiretroviral therapy use, of whom 2652 (68·4%) had virus deep-sequenced at sufficient quality for phylogenetic analysis. 446 transmission networks were reconstructed, including 293 linked pairs with inferred direction of transmission. Adjusting for incomplete sampling, an estimated 5·7% (95% credibility interval 4·4-7·3) of transmissions occurred within lakeside areas, 89·2% (86·0-91·8) within inland areas, 1·3% (0·6-2·6) from lakeside to inland areas, and 3·7% (2·3-5·8) from inland to lakeside areas. INTERPRETATION Cross-community HIV transmissions between Lake Victoria hotspots and surrounding inland populations are infrequent and when they occur, virus more commonly flows into rather than out of hotspots. This result suggests that targeted interventions to these hotspots will not alone control the epidemic in inland populations, where most transmissions occur. Thus, geographical targeting of high prevalence areas might not be effective for broader epidemic control depending on underlying epidemic dynamics. FUNDING The Bill & Melinda Gates Foundation, the National Institute of Allergy and Infectious Diseases, the National Institute of Mental Health, the National Institute of Child Health and Development, the Division of Intramural Research of the National Institute for Allergy and Infectious Diseases, the World Bank, the Doris Duke Charitable Foundation, the Johns Hopkins University Center for AIDS Research, and the President's Emergency Plan for AIDS Relief through the Centers for Disease Control and Prevention.
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Affiliation(s)
- Oliver Ratmann
- Department of Mathematics, Imperial College London, London, UK.
| | - Joseph Kagaayi
- Rakai Health Sciences Program, Kalisizo, Old-Bukoba Road, Uganda
| | - Matthew Hall
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tanya Golubchick
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Godfrey Kigozi
- Rakai Health Sciences Program, Kalisizo, Old-Bukoba Road, Uganda
| | - Xiaoyue Xi
- Department of Mathematics, Imperial College London, London, UK
| | - Chris Wymant
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Lucie Abeler-Dörner
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - David Bonsall
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Astrid Gall
- European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Anne Hoppe
- Division of Infection and Immunity, University College London, London, UK
| | - Paul Kellam
- Department of Medicine, Imperial College London, London, UK
| | - Jeremiah Bazaale
- Rakai Health Sciences Program, Kalisizo, Old-Bukoba Road, Uganda
| | - Sarah Kalibbala
- Rakai Health Sciences Program, Kalisizo, Old-Bukoba Road, Uganda
| | - Oliver Laeyendecker
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA; Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Justin Lessler
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Fred Nalugoda
- Rakai Health Sciences Program, Kalisizo, Old-Bukoba Road, Uganda
| | - Larry W Chang
- Rakai Health Sciences Program, Kalisizo, Old-Bukoba Road, Uganda; Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Deenan Pillay
- Division of Infection and Immunity, University College London, London, UK
| | - Thomas C Quinn
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA; Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Steven J Reynolds
- Rakai Health Sciences Program, Kalisizo, Old-Bukoba Road, Uganda; Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA; Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | | | - Robert Ssekubugu
- Rakai Health Sciences Program, Kalisizo, Old-Bukoba Road, Uganda
| | - David Serwadda
- Rakai Health Sciences Program, Kalisizo, Old-Bukoba Road, Uganda; Makerere University School of Public Health, Kampala, Uganda
| | - Maria J Wawer
- Rakai Health Sciences Program, Kalisizo, Old-Bukoba Road, Uganda; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Ronald H Gray
- Rakai Health Sciences Program, Kalisizo, Old-Bukoba Road, Uganda; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Christophe Fraser
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - M Kate Grabowski
- Rakai Health Sciences Program, Kalisizo, Old-Bukoba Road, Uganda; Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA; KwaZulu-Natal Research Innovation and Sequencing Platform College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
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Carlisle LA, Turk T, Kusejko K, Metzner KJ, Leemann C, Schenkel CD, Bachmann N, Posada S, Beerenwinkel N, Böni J, Yerly S, Klimkait T, Perreau M, Braun DL, Rauch A, Calmy A, Cavassini M, Battegay M, Vernazza P, Bernasconi E, Günthard HF, Kouyos RD. Viral Diversity Based on Next-Generation Sequencing of HIV-1 Provides Precise Estimates of Infection Recency and Time Since Infection. J Infect Dis 2020; 220:254-265. [PMID: 30835266 DOI: 10.1093/infdis/jiz094] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/01/2019] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Human immunodeficiency virus type 1 (HIV-1) genetic diversity increases over the course of infection and can be used to infer the time since infection and, consequently, infection recency, which are crucial for HIV-1 surveillance and the understanding of viral pathogenesis. METHODS We considered 313 HIV-infected individuals for whom reliable estimates of infection dates and next-generation sequencing (NGS)-derived nucleotide frequency data were available. Fractions of ambiguous nucleotides, obtained by population sequencing, were available for 207 samples. We assessed whether the average pairwise diversity calculated using NGS sequences provided a more exact prediction of the time since infection and classification of infection recency (<1 year after infection), compared with the fraction of ambiguous nucleotides. RESULTS NGS-derived average pairwise diversity classified an infection as recent with a sensitivity of 88% and a specificity of 85%. When considering only the 207 samples for which fractions of ambiguous nucleotides were available, the NGS-derived average pairwise diversity exhibited a higher sensitivity (90% vs 78%) and specificity (95% vs 67%) than the fraction of ambiguous nucleotides. Additionally, the average pairwise diversity could be used to estimate the time since infection with a mean absolute error of 0.84 years, compared with 1.03 years for the fraction of ambiguous nucleotides. CONCLUSIONS Viral diversity based on NGS data is more precise than that based on population sequencing in its ability to predict infection recency and provides an estimated time since infection that has a mean absolute error of <1 year.
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Affiliation(s)
- Louisa A Carlisle
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich.,Institute of Medical Virology, University of Zurich, Zurich
| | - Teja Turk
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich.,Institute of Medical Virology, University of Zurich, Zurich
| | - Katharina Kusejko
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich.,Institute of Medical Virology, University of Zurich, Zurich
| | - Karin J Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich.,Institute of Medical Virology, University of Zurich, Zurich
| | - Christine Leemann
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich.,Institute of Medical Virology, University of Zurich, Zurich
| | - Corinne D Schenkel
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich.,Institute of Medical Virology, University of Zurich, Zurich
| | - Nadine Bachmann
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich.,Institute of Medical Virology, University of Zurich, Zurich
| | - Susana Posada
- Department of Biosystems Science and Engineering, ETH Zurich.,SIB Swiss Institute of Bioinformatics, University of Basel, Basel
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich.,SIB Swiss Institute of Bioinformatics, University of Basel, Basel
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Zurich.,Swiss National Center for Retroviruses, University of Zurich, Zurich
| | - Sabine Yerly
- Laboratory of Virology and Division of Infectious Diseases, Geneva University Hospital, Geneva
| | - Thomas Klimkait
- Molecular Virology, Department of Biomedicine-Petersplatz, University of Basel, Basel
| | - Matthieu Perreau
- Division of Immunology and Allergy, Lausanne University Hospital, Lausanne
| | - Dominique L Braun
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich.,Institute of Medical Virology, University of Zurich, Zurich
| | - Andri Rauch
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern
| | - Alexandra Calmy
- Laboratory of Virology and Division of Infectious Diseases, Geneva University Hospital, Geneva
| | | | - Manuel Battegay
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel
| | - Pietro Vernazza
- Division of Infectious Diseases, Cantonal Hospital St. Gallen, St. Gallen
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich.,Institute of Medical Virology, University of Zurich, Zurich
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich.,Institute of Medical Virology, University of Zurich, Zurich
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39
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Lunar MM, Mlakar J, Zorec TM, Poljak M. HIV-1 Unique Recombinant Forms Identified in Slovenia and Their Characterization by Near Full-Length Genome Sequencing. Viruses 2020; 12:v12010063. [PMID: 31947872 PMCID: PMC7019782 DOI: 10.3390/v12010063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 12/28/2019] [Accepted: 12/31/2019] [Indexed: 11/30/2022] Open
Abstract
Surveillance of HIV circulating recombinant forms (CRFs) is important because HIV diversity can affect various aspects of HIV infection from prevention to diagnosis and patient management. A comprehensive collection of pol sequences obtained from individuals diagnosed with HIV-1 from 2000 to 2016 in Slovenia was subtyped to identify possible unique recombinant forms (URFs). Selected samples were subjected to near full-length genome (NFLG) sequencing and detailed recombination analyses. Discordant subtyping results were observed for 68/387 (17.6%) sequences and 20 sequences were identified as the most probable URFs and selected for NFLG characterization. Further, 11 NFLGs and two sequences of >7000 base pairs were obtained. Seven sequences were identified as “pure” subtypes or already characterized CRFs: subtype B (n = 5), sub-subtype A6 (n = 1), and CRF01_AE (n = 1). The remaining six sequences were determined to be URFs; four displayed a single recombination event and two exhibited a complex recombination pattern involving several subtypes or CRFs. Finally, three HIV strains were recognized as having epidemic potential and could be further characterized as new CRFs. Our study shows that the identification of new CRFs is possible, even in countries where HIV diversity is considered limited, emphasizing the importance of the surveillance of HIV recombinant forms.
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Grant HE, Hodcroft EB, Ssemwanga D, Kitayimbwa JM, Yebra G, Esquivel Gomez LR, Frampton D, Gall A, Kellam P, de Oliveira T, Bbosa N, Nsubuga RN, Kibengo F, Kwan TH, Lycett S, Kao R, Robertson DL, Ratmann O, Fraser C, Pillay D, Kaleebu P, Leigh Brown AJ. Pervasive and non-random recombination in near full-length HIV genomes from Uganda. Virus Evol 2020; 6:veaa004. [PMID: 32395255 PMCID: PMC7204518 DOI: 10.1093/ve/veaa004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Recombination is an important feature of HIV evolution, occurring both within and between the major branches of diversity (subtypes). The Ugandan epidemic is primarily composed of two subtypes, A1 and D, that have been co-circulating for 50 years, frequently recombining in dually infected patients. Here, we investigate the frequency of recombinants in this population and the location of breakpoints along the genome. As part of the PANGEA-HIV consortium, 1,472 consensus genome sequences over 5 kb have been obtained from 1,857 samples collected by the MRC/UVRI & LSHTM Research unit in Uganda, 465 (31.6 per cent) of which were near full-length sequences (>8 kb). Using the subtyping tool SCUEAL, we find that of the near full-length dataset, 233 (50.1 per cent) genomes contained only one subtype, 30.8 per cent A1 (n = 143), 17.6 per cent D (n = 82), and 1.7 per cent C (n = 8), while 49.9 per cent (n = 232) contained more than one subtype (including A1/D (n = 164), A1/C (n = 13), C/D (n = 9); A1/C/D (n = 13), and 33 complex types). K-means clustering of the recombinant A1/D genomes revealed a section of envelope (C2gp120-TMgp41) is often inherited intact, whilst a generalized linear model was used to demonstrate significantly fewer breakpoints in the gag-pol and envelope C2-TM regions compared with accessory gene regions. Despite similar recombination patterns in many recombinants, no clearly supported circulating recombinant form (CRF) was found, there was limited evidence of the transmission of breakpoints, and the vast majority (153/164; 93 per cent) of the A1/D recombinants appear to be unique recombinant forms. Thus, recombination is pervasive with clear biases in breakpoint location, but CRFs are not a significant feature, characteristic of a complex, and diverse epidemic.
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Affiliation(s)
- Heather E Grant
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Emma B Hodcroft
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Deogratius Ssemwanga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
| | | | - Gonzalo Yebra
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Dan Frampton
- Division of Infection and Immunity, University College London, London, UK
| | - Astrid Gall
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Paul Kellam
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Tulio de Oliveira
- Nelson R. Mandela School of Medicine, Africa Health Research Institute, Durban, South Africa
| | - Nicholas Bbosa
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Rebecca N Nsubuga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Freddie Kibengo
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Tsz Ho Kwan
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Samantha Lycett
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Rowland Kao
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Oliver Ratmann
- Department of Mathematics, Imperial College London, London, UK
| | - Christophe Fraser
- Nuffield Department of Medicine, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Deenan Pillay
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
- Nelson R. Mandela School of Medicine, Africa Health Research Institute, Durban, South Africa
| | - Pontiano Kaleebu
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
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Hebberecht L, Vancoillie L, Schauvliege M, Staelens D, Demecheleer E, Hardy J, Mortier V, Verhofstede C. Single genome sequencing of near full-length HIV-1 RNA using a limiting dilution approach. J Virol Methods 2019; 274:113737. [PMID: 31562885 DOI: 10.1016/j.jviromet.2019.113737] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 09/20/2019] [Accepted: 09/22/2019] [Indexed: 11/18/2022]
Abstract
Sequencing very long stretches of the HIV-1 genome can advance studies on virus evolution and in vivo recombination but remains technically challenging. We developed an efficient procedure to sequence near full-length HIV-1 RNA using a two-amplicon approach. The whole genome was successfully amplified for 107 (88%) of 121 plasma samples including samples from patients infected with HIV-1 subtype A1, B, C, D, F1, G, H, CRF01_AE and CRF02_AG. For the 17 samples with a viral load below 1000 c/ml and the 104 samples with a viral load above 1000 c/ml, the amplification efficiency was respectively 53% and 94%. The sensitivity of the method was further evaluated using limiting dilution of RNA extracted from a plasma pool containing an equimolar mixture of three HIV-1 subtypes (B, C and CRF02_AG) and diluted before and after cDNA generation. Both RNA and cDNA dilution showed comparable sensitivity and equal accuracy in reflecting the subtype distribution of the plasma pool. One single event of in vitro recombination was detected amongst the 41 sequences obtained after cDNA dilution but no indications for in vitro recombination were found after RNA dilution. In conclusion, a two-amplicon strategy and limiting dilution of viral RNA followed by reverse transcription, nested PCR and Sanger sequencing, allows near full genome sequencing of individual HIV-1 RNA molecules. This method will be a valuable tool in the study of virus evolution and recombination.
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Affiliation(s)
- Laura Hebberecht
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Leen Vancoillie
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Marlies Schauvliege
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Delfien Staelens
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Els Demecheleer
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Jarryt Hardy
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Virginie Mortier
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Chris Verhofstede
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium.
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Budayanti NS, Merati TP, Bela B, Mahardika GN. Molecular Antiretroviral Resistance Markers of Human Immunodeficiency Virus-1 of CRF01_AE Subtype in Bali, Indonesia. Curr HIV Res 2019; 16:374-382. [PMID: 30714528 PMCID: PMC6446452 DOI: 10.2174/1570162x17666190204101154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 01/27/2019] [Accepted: 01/30/2019] [Indexed: 11/22/2022]
Abstract
Background: Molecular epidemiological study of human immunodeficiency virus drug-resistant (HIVDR) markers is challenging in areas where the dominant subtype is non-B. Objective: Here we provide molecular data for HIVDR in the CRF01_AE subtype in Bali, Indonesia. Method: Seventy patients were enrolled in this study and grouped into treatment failure and treatment naïve groups. The full-length pol gene was amplified using nested reverse transcriptase polymerase chain reaction and the product was then sequenced. The readable sequence was then subjected to Stan-ford HIV Drug Resistance Database genotyping. Results: We found that clinical classification was in accordance with the presence of HIVDR markers in the pol gene. Independent of therapy history, the treatment failure group showed resistance markers against nucleoside reverse transcriptase inhibitors (NRTI) and non-nucleoside reverse transcriptase in-hibitors (NNRTI), ranging from 72%–100% of patients. Only a small proportion of naïve patients harbored HIV with drug resistance markers to NNRTI. No protease inhibitor-resistant marker was found in either patient group. Molecular marker mutations, which were found in more than 50% of treatment failure patients, were M184V (100%), T215A/Y/F (88.2%), D67N/G (76.5%), and M41L (58.8%). Conclusion: The protocol used in this study to determine genetic markers of HIVDR based on sub-type B can be applied for the rapid determination of resistance of the CRF01_AE subtype. All patients with progressive clinical signs and increased viral load should be recommended to undergo second-line treatment of the ARV regimen.
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Affiliation(s)
- Nyoman Sri Budayanti
- Microbiology Department, Faculty of Medicine, Udayana University, Jl. PB Sudirman, Denpasar, Bali, Indonesia
| | - Tuti Parwati Merati
- Internal Medicine Department, Faculty of Medicine, Udayana University, Jl. PB Sudirman, Denpasar, Bali, Indonesia
| | - Budiman Bela
- Microbiology Department, Faculty of Medicine, Indonesia University, Jakarta, Indonesia
| | - Gusti Ngurah Mahardika
- Animal Biomedical and Molecular Biology Laboratory, Faculty of Veterinary Medicine, Udayana University, Jl. Sesetan-Markisa 6, Denpasar 80226, Bali, Indonesia
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Wu ZL, Guan GY, Zhao JH, Ma XM, Wang XM, Yang DZ, Cao M, Rawle DJ. Dynamic Characteristics and HIV Infection of Men who have Sex with Men from 2011 to 2017 in Yinchuan, Ningxia, China. Curr HIV Res 2019; 16:364-373. [PMID: 30659545 PMCID: PMC6446446 DOI: 10.2174/1570162x17666190119094035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 01/10/2019] [Accepted: 01/13/2019] [Indexed: 11/22/2022]
Abstract
OBJECTIVES Ningxia Hui Autonomous Region, an important area for ethnic Hui settlement in Northwest China, is a low HIV prevalence region. However, HIV infection rates among men who have sex with men (MSM) in Ningxia have increased to an alarming level, despite scale-up of control measures in recent years. This study aimed to understand the demographical and sexual behavior dynamics of MSM and to explore the factors associated with HIV infection. METHODS Annual cross-sectional surveys were carried out among MSM during 2011~2017 in Yinchuan, the capital city of Ningxia. Information regarding social demographics, sexual behavior and HIV prevention knowledge was collected. Blood samples were taken for HIV, HCV serological and genetic analysis, and syphilis serological analysis. The dynamic trend was analyzed with trend χ2 test and factors associated with HIV infection were identified by multivariate logistic regression analysis. RESULTS The study found a decreasing trend for mean age of the MSM population over the study period. MSMs with a college education or higher increased significantly, while the proportions that were in a marriage significantly decreased over the study period. The rate of HIV positive among MSM increased during the study period (p<0.05), however, the rate of recently diagnosed infections decreased from 2012 (p<0.05). Overall, a very high proportion (98%) of MSM had basic knowledge of HIV prevention, however, only approximately 40% of them used condoms consistently during anal sex with male partners. Unprotected anal sex was identified as a risk factor associated with HIV infection, as was syphilis infection. Local residency status and MSM who received intervention and detection services were the factors that decreased HIV infection risk. Sequence analysis identified the HIV-1 CRF55_01B subtype from MSM for the first time in Yinchuan. CONCLUSION The reduction of recent HIV diagnoses is an encouraging sign of successful HIV control measures in MSM in Ningxia. The finding that a high proportion of MSM had knowledge of HIV prevention but still conducted unprotected sex highlights the need for further control measures to change unsafe sexual practices among MSM.
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Affiliation(s)
- Zhong-Lan Wu
- Ningxia Center for Disease Control and Prevention, 470 Shengli St. Yinchuan, Ningxia 750001, China
| | - Guang-Yu Guan
- Ningxia Center for Disease Control and Prevention, 470 Shengli St. Yinchuan, Ningxia 750001, China
| | - Jian-Hua Zhao
- Ningxia Center for Disease Control and Prevention, 470 Shengli St. Yinchuan, Ningxia 750001, China
| | - Xue-Min Ma
- Ningxia Center for Disease Control and Prevention, 470 Shengli St. Yinchuan, Ningxia 750001, China
| | - Xue-Min Wang
- Ningxia Center for Disease Control and Prevention, 470 Shengli St. Yinchuan, Ningxia 750001, China
| | - Dong-Zhi Yang
- Ningxia Center for Disease Control and Prevention, 470 Shengli St. Yinchuan, Ningxia 750001, China
| | - Min Cao
- Ningxia Center for Disease Control and Prevention, 470 Shengli St. Yinchuan, Ningxia 750001, China
| | - Daniel J Rawle
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
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44
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Bachmann N, von Siebenthal C, Vongrad V, Turk T, Neumann K, Beerenwinkel N, Bogojeska J, Fellay J, Roth V, Kok YL, Thorball CW, Borghesi A, Parbhoo S, Wieser M, Böni J, Perreau M, Klimkait T, Yerly S, Battegay M, Rauch A, Hoffmann M, Bernasconi E, Cavassini M, Kouyos RD, Günthard HF, Metzner KJ. Determinants of HIV-1 reservoir size and long-term dynamics during suppressive ART. Nat Commun 2019; 10:3193. [PMID: 31324762 PMCID: PMC6642170 DOI: 10.1038/s41467-019-10884-9] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 06/05/2019] [Indexed: 12/20/2022] Open
Abstract
The HIV-1 reservoir is the major hurdle to a cure. We here evaluate viral and host characteristics associated with reservoir size and long-term dynamics in 1,057 individuals on suppressive antiretroviral therapy for a median of 5.4 years. At the population level, the reservoir decreases with diminishing differences over time, but increases in 26.6% of individuals. Viral blips and low-level viremia are significantly associated with slower reservoir decay. Initiation of ART within the first year of infection, pretreatment viral load, and ethnicity affect reservoir size, but less so long-term dynamics. Viral blips and low-level viremia are thus relevant for reservoir and cure studies. Here, Bachmann et al. provide data on long-term dynamics of the HIV-1 reservoir in 1,057 individuals on suppressive antiretroviral therapy and show that in 26.6% of individuals the reservoir increases. Viral blips and low-level viremia are significantly associated with a slower reservoir decay.
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Affiliation(s)
- Nadine Bachmann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
| | - Chantal von Siebenthal
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
| | - Valentina Vongrad
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
| | - Teja Turk
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
| | - Kathrin Neumann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, 4057 Basel, Switzerland
| | | | - Jaques Fellay
- School of Life Sciences, EPFL, 1015, Lausanne, Switzerland.,Precision Medicine Unit, Lausanne University Hospital, 1011, Lausanne, Switzerland
| | - Volker Roth
- Department of Mathematics and Computer Science, University of Basel, 4001, Basel, Switzerland
| | - Yik Lim Kok
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
| | | | - Alessandro Borghesi
- School of Life Sciences, EPFL, 1015, Lausanne, Switzerland.,Neonatal Intensive Care Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, 27100, Italy
| | - Sonali Parbhoo
- Department of Mathematics and Computer Science, University of Basel, 4001, Basel, Switzerland
| | - Mario Wieser
- Department of Mathematics and Computer Science, University of Basel, 4001, Basel, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
| | - Matthieu Perreau
- Division of Immunology and Allergy, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1015, Lausanne, Switzerland
| | - Thomas Klimkait
- Division Infection Diagnostics, Department Biomedicine-Petersplatz, University of Basel, 4001, Basel, Switzerland
| | - Sabine Yerly
- Division of Infectious Diseases and Laboratory of Virology, University Hospital Geneva, University of Geneva, 1211, Geneva, Switzerland
| | - Manuel Battegay
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, 4031, Basel, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, University Hospital Bern, 3010, Bern, Switzerland
| | - Matthias Hoffmann
- Division of Infectious Diseases, Cantonal Hospital of St. Gallen, 9007, St. Gallen, Switzerland
| | - Enos Bernasconi
- Infectious Diseases Service, Regional Hospital, 6900, Lugano, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1015, Lausanne, Switzerland
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland. .,Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland.
| | - Karin J Metzner
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
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Derache A, Iwuji CC, Baisley K, Danaviah S, Marcelin AG, Calvez V, de Oliveira T, Dabis F, Porter K, Pillay D. Impact of Next-generation Sequencing Defined Human Immunodeficiency Virus Pretreatment Drug Resistance on Virological Outcomes in the ANRS 12249 Treatment-as-Prevention Trial. Clin Infect Dis 2019; 69:207-214. [PMID: 30321314 PMCID: PMC6603266 DOI: 10.1093/cid/ciy881] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 10/09/2018] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Previous studies in human immunodeficiency virus (HIV)-positive individuals on thymidine analogue backbone antiretroviral therapy (ART) with either nevirapine or efavirenz have suggested poorer virological outcomes in the presence of pretreatment drug resistance (PDR). We assessed the impact of PDR on virological suppression (VS; <50 copies/mL) in individuals prescribed primarily tenofovir/emtricitabine/efavirenz in rural KwaZulu-Natal within a treatment-as-prevention trial. METHODS Among 1557 HIV-positive individuals who reported no prior ART at study entry and provided plasma samples, 1328 individuals with entry viral load (VL) >1000 copies/mL had next-generation sequencing (NGS) of the HIV pol gene with MiSeq technology. Results were obtained for 1148 individuals, and the presence of PDR was assessed at 5% and 20% detection thresholds. Virological outcome was assessed using Cox regression in 837 of 920 ART initiators with at least 1 follow-up VL after ART initiation. RESULTS PDR prevalence was 9.5% (109/1148) and 12.8% (147/1148) at 20% and 5% thresholds, respectively. After a median of 1.36 years (interquartile range, 0.91-2.13), mostly on fixed-dose combination tenofovir/emtricitabine/efavirenz, presence of both nonnucleoside reverse transcriptase inhibitor (NNRTI)/nucleoside reverse transcriptase inhibitor PDR vs no PDR was associated with longer time to VS (adjusted hazard ratio [aHR], 0.32; 95% confidence interval [CI], 0.12-0.86), while there was no difference between those with only NNRTI PDR vs no PDR (aHR, 1.05; 95% CI, 0.82-1.34) at the 5% threshold. Similar differences were observed for mutations detected at the 20% threshold, although without statistical significance. CONCLUSIONS NGS uncovered a high prevalence of PDR among participants enrolled in trial clinics in rural KwaZulu-Natal. Dual-class PDR to a mainly tenofovir/emtricitabine/efavirenz regimen was associated with poorer VS. However, there was no impact of NNRTI PDR alone. CLINICAL TRIALS TEGISTRATION NCT01509508; South African National Clinical Trials Register: DOH-27-0512-3974.
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Affiliation(s)
- Anne Derache
- Africa Health Research Institute, Mtubatuba, South Africa
- Sorbonne University, l’université Pierre et Marie Curie, Institut national de la santé et de la recherche médicale, Institut Pierre Louis d’Epidémiologie et de Santé Publique Unité Mixte de Recherche en Santé (IPLESP UMRS 1136), Paris, France
| | - Collins C Iwuji
- Africa Health Research Institute, Mtubatuba, South Africa
- Department of Global Health and Infection, Brighton and Sussex Medical School
- Institute for Global Health, University College London, United Kingdom
| | - Kathy Baisley
- Sorbonne University, l’université Pierre et Marie Curie, Institut national de la santé et de la recherche médicale, Institut Pierre Louis d’Epidémiologie et de Santé Publique Unité Mixte de Recherche en Santé (IPLESP UMRS 1136), Paris, France
| | - Siva Danaviah
- Africa Health Research Institute, Mtubatuba, South Africa
| | - Anne-Geneviève Marcelin
- Sorbonne University, l’université Pierre et Marie Curie, Institut national de la santé et de la recherche médicale, Institut Pierre Louis d’Epidémiologie et de Santé Publique Unité Mixte de Recherche en Santé (IPLESP UMRS 1136), Paris, France
| | - Vincent Calvez
- Sorbonne University, l’université Pierre et Marie Curie, Institut national de la santé et de la recherche médicale, Institut Pierre Louis d’Epidémiologie et de Santé Publique Unité Mixte de Recherche en Santé (IPLESP UMRS 1136), Paris, France
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - François Dabis
- Université de Bordeaux, Institut de Santé Publique d’Epidémiologie et de Développement, Centre Institut national de la santé et de la recherche médicale 1219, France
| | - Kholoud Porter
- Institute for Global Health, University College London, United Kingdom
| | - Deenan Pillay
- Africa Health Research Institute, Mtubatuba, South Africa
- Division of Infection and Immunity, University College London, United Kingdom
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Nili M, Tayeri K, Gholami M, Moallemi S, Sabahi F, Kalhori S, Baesi K, Hasibi M. There is no Difference Between Sequences of HIV-1 Infected Patients with Stable Clinical Status and HIV-1 Reference Sequence. Infect Disord Drug Targets 2019; 19:67-72. [PMID: 29473526 DOI: 10.2174/1871526518666180222111611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 12/27/2017] [Accepted: 02/17/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND The rate of human immunodeficiency virus type 1 (HIV-1) infection in Iran has increased dramatically in the past few years. HIV-1 genome sequences are pivotal for large-scale studies of inter- and intra-host evolution. To understand the molecular difference between reference HIV-1 isolate and two HIV-1 infected patients in Iran, we conducted this study to analyze some genome segments of Iranian HIV-1 isolates. METHODS Two HIV-1-infected individuals who were under antiretroviral therapy (ARV) for 8 years with stable clinical status were enrolled. The patient's plasma samples were used for the Gag-Pol genome sequences (4500 nt). The phylogenetic tree and similarity plotty were obtained based on Gag-Pol sequences. RESULTS Both HIV-1-infected isolates belonged to CRF35_AD subtype even though one of them had drug resistance. The HIV genome and protein sequences showed no clear difference between genome and protein sequences of our samples and the reference sequence. CONCLUSIONS Our patient's stable clinical status had no connection to genome sequence; which could be owing to immunological factors or other patient's mode which are still unknown.
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Affiliation(s)
- Marzyeh Nili
- Department of Virology, Tarbiat Modares University, Tehran, Iran
| | - Katayoon Tayeri
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High Risk Behaviors, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohamad Gholami
- Department of Virology, Tarbiat Modares University, Tehran, Iran
| | - Samaneh Moallemi
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High Risk Behaviors, Tehran University of Medical Sciences, Tehran, Iran
| | - Farzaneh Sabahi
- Department of Virology, Tarbiat Modares University, Tehran, Iran
| | | | - Kazem Baesi
- Hepatitis and AIDS Department, Pasteur Institute of Iran, Tehran, Iran
| | - Mehrdad Hasibi
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High Risk Behaviors, Tehran University of Medical Sciences, Tehran, Iran
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Sacktor N, Saylor D, Nakigozi G, Nakasujja N, Robertson K, Grabowski MK, Kisakye A, Batte J, Mayanja R, Anok A, Gray RH, Wawer MJ. Effect of HIV Subtype and Antiretroviral Therapy on HIV-Associated Neurocognitive Disorder Stage in Rakai, Uganda. J Acquir Immune Defic Syndr 2019; 81:216-223. [PMID: 30865184 PMCID: PMC6522269 DOI: 10.1097/qai.0000000000001992] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Combination antiretroviral therapy (ART) improves HIV-associated neurocognitive disorder (HAND) stage in the United States where subtype B predominates, but the effect of ART and subtype on HAND stage in individuals in Uganda with subtypes D and A is largely unknown. SETTING A community-based cohort of participants residing in Rakai, Uganda. METHODS Three hundred ninety-nine initially ART-naive HIV-seropositive (HIV+) individuals were followed up over 2 years. Neurological and neuropsychological tests and functional assessments were used to determine HAND stage. Frequency and predictors of HAND and HIV-associated dementia (HAD) were assessed at baseline and at follow-up after ART initiation in 312 HIV+ individuals. HIV subtype was determined from gag and env sequences. RESULTS At 2-year follow-up, HAD frequency among HIV+ individuals on ART (n = 312) decreased from 13% to 5% (P < 0.001), but the overall frequency of HAND remained unchanged (56%-51%). Subtype D was associated with higher rates of impaired cognition (global deficit score ≥ 0.5) compared with HIV+ individuals with subtype A (55% vs. 24%) (P = 0.008). Factors associated with HAD at baseline were older age, depression, and plasma HIV viral load >100,000 copies/mL. At follow-up, age and depression remained significantly associated with HAD. CONCLUSIONS HIV+ individuals on ART in rural Uganda had a significant decrease in the frequency of HAD, but HAND persists after 2 years on ART. The current guideline of immediate ART initiation after HIV diagnosis is likely to greatly reduce HAD in sub-Saharan Africa. Further studies of the effect of HIV subtype and neurocognitive performance are warranted.
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Affiliation(s)
- Ned Sacktor
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Deanna Saylor
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
| | | | | | - Kevin Robertson
- Department of Neurology, University of North Carolina-Chapel Hill, Chapel Hill, NC
| | - M. Kate Grabowski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | | | - James Batte
- Rakai Health Sciences Program, Kalisizo, Uganda
| | | | - Aggrey Anok
- Rakai Health Sciences Program, Kalisizo, Uganda
| | - Ronald H. Gray
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Maria J. Wawer
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
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48
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Liu CC, Ji H. PCR Amplification Strategies Towards Full-length HIV-1 Genome Sequencing. Curr HIV Res 2019; 16:98-105. [PMID: 29943704 DOI: 10.2174/1570162x16666180626152252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 05/05/2018] [Accepted: 06/20/2018] [Indexed: 11/22/2022]
Abstract
The advent of next-generation sequencing has enabled greater resolution of viral diversity and improved feasibility of full viral genome sequencing allowing routine HIV-1 full genome sequencing in both research and diagnostic settings. Regardless of the sequencing platform selected, successful PCR amplification of the HIV-1 genome is essential for sequencing template preparation. As such, full HIV-1 genome amplification is a crucial step in dictating the successful and reliable sequencing downstream. Here we reviewed existing PCR protocols leading to HIV-1 full genome sequencing. In addition to the discussion on basic considerations on relevant PCR design, the advantages as well as the pitfalls of the published protocols were reviewed.
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Affiliation(s)
- Chao Chun Liu
- National Microbiology Laboratory at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, Canada
| | - Hezhao Ji
- National Microbiology Laboratory at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
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49
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Banin AN, Tuen M, Bimela JS, Tongo M, Zappile P, Khodadadi-Jamayran A, Nanfack AJ, Meli J, Wang X, Mbanya D, Ngogang J, Heguy A, Nyambi PN, Fokunang C, Duerr R. Development of a Versatile, Near Full Genome Amplification and Sequencing Approach for a Broad Variety of HIV-1 Group M Variants. Viruses 2019; 11:E317. [PMID: 30939815 PMCID: PMC6520859 DOI: 10.3390/v11040317] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 11/17/2022] Open
Abstract
Near full genome sequencing (NFGS) of HIV-1 is required to assess the genetic composition of HIV-1 strains comprehensively. Population-wide, it enables a determination of the heterogeneity of HIV-1 and the emergence of novel/recombinant strains, while for each individual it constitutes a diagnostic instrument to assist targeted therapeutic measures against viral components. There is still a lack of robust and adaptable techniques for efficient NFGS from miscellaneous HIV-1 subtypes. Using rational primer design, a broad primer set was developed for the amplification and sequencing of diverse HIV-1 group M variants from plasma. Using pure subtypes as well as diverse, unique recombinant forms (URF), variable amplicon approaches were developed for NFGS comprising all functional genes. Twenty-three different genomes composed of subtypes A (A1), B, F (F2), G, CRF01_AE, CRF02_AG, and CRF22_01A1 were successfully determined. The NFGS approach was robust irrespective of viral loads (≥306 copies/mL) and amplification method. Third-generation sequencing (TGS), single genome amplification (SGA), cloning, and bulk sequencing yielded similar outcomes concerning subtype composition and recombinant breakpoint patterns. The introduction of a simple and versatile near full genome amplification, sequencing, and cloning method enables broad application in phylogenetic studies of diverse HIV-1 subtypes and can contribute to personalized HIV therapy and diagnosis.
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Affiliation(s)
- Andrew N Banin
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA.
- Faculty of Medicine and Biomedical Sciences, Department of Biochemistry, University of Yaoundé 1, BP 1364 Yaoundé, Cameroon.
| | - Michael Tuen
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA.
| | - Jude S Bimela
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA.
- Faculty of Science, Department of Biochemistry, BP 1364 Yaoundé, Cameroon.
| | - Marcel Tongo
- Center of Research for Emerging and Re-Emerging Diseases (CREMER), Institute of Medical Research and Study of Medicinal Plants, BP 906 Yaoundé, Cameroon.
| | - Paul Zappile
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA.
| | - Alireza Khodadadi-Jamayran
- Applied Bioinformatics Laboratories (ABL) and Genome Technology Center (GTC), Division of Advanced Research Technologies (DART), New York University Langone Medical Center, New York, NY 10016, USA.
| | - Aubin J Nanfack
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA.
- Medical Diagnostic Center, BP 15810 Yaoundé, Cameroon.
- Chantal Biya International Reference Center for Research on HIV/AIDS Prevention and Management, BP 3077 Messa Yaoundé, Cameroon.
| | | | - Xiaohong Wang
- Manhattan Veterans Affairs New York Harbor Healthcare System, New York, NY 10010, USA.
| | - Dora Mbanya
- Faculty of Medicine and Biomedical Sciences, Department of Microbiology, Parasitology and Infectious Diseases, University of Yaoundé 1, BP 1364 Yaoundé, Cameroon.
| | - Jeanne Ngogang
- Faculty of Medicine and Biomedical Sciences, Department of Biochemistry, University of Yaoundé 1, BP 1364 Yaoundé, Cameroon.
| | - Adriana Heguy
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA.
| | - Phillipe N Nyambi
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA.
- Manhattan Veterans Affairs New York Harbor Healthcare System, New York, NY 10010, USA.
| | - Charles Fokunang
- Faculty of Medicine and Biomedical Sciences, Department of Pharmacotoxicology & Pharmacokinetics, University of Yaoundé 1, BP 1364 Yaoundé, Cameroon.
| | - Ralf Duerr
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA.
- Manhattan Veterans Affairs New York Harbor Healthcare System, New York, NY 10010, USA.
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50
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Ratmann O, Grabowski MK, Hall M, Golubchik T, Wymant C, Abeler-Dörner L, Bonsall D, Hoppe A, Brown AL, de Oliveira T, Gall A, Kellam P, Pillay D, Kagaayi J, Kigozi G, Quinn TC, Wawer MJ, Laeyendecker O, Serwadda D, Gray RH, Fraser C. Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis. Nat Commun 2019; 10:1411. [PMID: 30926780 PMCID: PMC6441045 DOI: 10.1038/s41467-019-09139-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 02/22/2019] [Indexed: 11/09/2022] Open
Abstract
To prevent new infections with human immunodeficiency virus type 1 (HIV-1) in sub-Saharan Africa, UNAIDS recommends targeting interventions to populations that are at high risk of acquiring and passing on the virus. Yet it is often unclear who and where these 'source' populations are. Here we demonstrate how viral deep-sequencing can be used to reconstruct HIV-1 transmission networks and to infer the direction of transmission in these networks. We are able to deep-sequence virus from a large population-based sample of infected individuals in Rakai District, Uganda, reconstruct partial transmission networks, and infer the direction of transmission within them at an estimated error rate of 16.3% [8.8-28.3%]. With this error rate, deep-sequence phylogenetics cannot be used against individuals in legal contexts, but is sufficiently low for population-level inferences into the sources of epidemic spread. The technique presents new opportunities for characterizing source populations and for targeting of HIV-1 prevention interventions in Africa.
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Affiliation(s)
- Oliver Ratmann
- Department of Mathematics, Imperial College London, London, SW72AZ, UK.
- Department of Infectious Disease, Epidemiology School of Public Health, Imperial College London, London, W21PG, UK.
| | - M Kate Grabowski
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, 21205-2196, USA
- Rakai Health Sciences Program, Entebbe, P.O.Box 49, Uganda
| | - Matthew Hall
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford, OX3 7BN, UK
| | - Tanya Golubchik
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford, OX3 7BN, UK
| | - Chris Wymant
- Department of Infectious Disease, Epidemiology School of Public Health, Imperial College London, London, W21PG, UK
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford, OX3 7BN, UK
| | - Lucie Abeler-Dörner
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford, OX3 7BN, UK
| | - David Bonsall
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford, OX3 7BN, UK
| | - Anne Hoppe
- Division of Infection and Immunity, University College London, London, WC1E 6BT, UK
| | - Andrew Leigh Brown
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Tulio de Oliveira
- College of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa
| | - Astrid Gall
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Paul Kellam
- Department of Medicine, Imperial College London, London, W12 0HS, UK
| | - Deenan Pillay
- Division of Infection and Immunity, University College London, London, WC1E 6BT, UK
- Africa Health Research Institute, Private Bag X7, Durban, 4013, South Africa
| | - Joseph Kagaayi
- Rakai Health Sciences Program, Entebbe, P.O.Box 49, Uganda
| | - Godfrey Kigozi
- Rakai Health Sciences Program, Entebbe, P.O.Box 49, Uganda
| | - Thomas C Quinn
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, 21205-2196, USA
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892-9806, USA
| | - Maria J Wawer
- Rakai Health Sciences Program, Entebbe, P.O.Box 49, Uganda
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Oliver Laeyendecker
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, 21205-2196, USA
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892-9806, USA
| | - David Serwadda
- Rakai Health Sciences Program, Entebbe, P.O.Box 49, Uganda
- Makerere University School of Public Health, Kampala, 8HQG+3V, Uganda
| | - Ronald H Gray
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, 21205-2196, USA
- Rakai Health Sciences Program, Entebbe, P.O.Box 49, Uganda
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Christophe Fraser
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford, OX3 7BN, UK
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