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Inzaule SC, Siedner MJ, Little SJ, Avila-Rios S, Ayitewala A, Bosch RJ, Calvez V, Ceccherini-Silberstein F, Charpentier C, Descamps D, Eshleman SH, Fokam J, Frenkel LM, Gupta RK, Ioannidis JP, Kaleebu P, Kantor R, Kassaye SG, Kosakovsky Pond SL, Kouamou V, Kouyos RD, Kuritzkes DR, Lessells R, Marcelin AG, Mbuagbaw L, Minalga B, Ndembi N, Neher RA, Paredes R, Pillay D, Raizes EG, Rhee SY, Richman DD, Ruxrungtham K, Sabeti PC, Schapiro JM, Sirivichayakul S, Steegen K, Sugiura W, van Zyl GU, Vandamme AM, Wensing AM, Wertheim JO, Gunthard HF, Jordan MR, Shafer RW. Recommendations on data sharing in HIV drug resistance research. PLoS Med 2023; 20:e1004293. [PMID: 37738247 PMCID: PMC10558071 DOI: 10.1371/journal.pmed.1004293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Revised: 10/06/2023] [Indexed: 09/24/2023] Open
Abstract
• Human immunodeficiency virus (HIV) drug resistance has implications for antiretroviral treatment strategies and for containing the HIV pandemic because the development of HIV drug resistance leads to the requirement for antiretroviral drugs that may be less effective, less well-tolerated, and more expensive than those used in first-line regimens. • HIV drug resistance studies are designed to determine which HIV mutations are selected by antiretroviral drugs and, in turn, how these mutations affect antiretroviral drug susceptibility and response to future antiretroviral treatment regimens. • Such studies collectively form a vital knowledge base essential for monitoring global HIV drug resistance trends, interpreting HIV genotypic tests, and updating HIV treatment guidelines. • Although HIV drug resistance data are collected in many studies, such data are often not publicly shared, prompting the need to recommend best practices to encourage and standardize HIV drug resistance data sharing. • In contrast to other viruses, sharing HIV sequences from phylogenetic studies of transmission dynamics requires additional precautions as HIV transmission is criminalized in many countries and regions. • Our recommendations are designed to ensure that the data that contribute to HIV drug resistance knowledge will be available without undue hardship to those publishing HIV drug resistance studies and without risk to people living with HIV.
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Affiliation(s)
- Seth C. Inzaule
- Amsterdam Institute for Global Health and Development, and Department of Global Health, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Mark J. Siedner
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Susan J. Little
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, San Diego, California, United States of America
| | - Santiago Avila-Rios
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Alisen Ayitewala
- National Health Laboratories and Diagnostic Services, Ministries of Health, Kampala, Uganda
| | - Ronald J. Bosch
- Center for Biostatistics in AIDS Research, Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Vincent Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France
| | | | - Charlotte Charpentier
- Service de Virologie, Université Paris Cité, INSERM, IAME, UMR 1137, AP-HP, Hôpital Bichat-Claude Bernard, F-75018 Paris, France
| | - Diane Descamps
- Service de Virologie, Université Paris Cité, INSERM, IAME, UMR 1137, AP-HP, Hôpital Bichat-Claude Bernard, F-75018 Paris, France
| | - Susan H. Eshleman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Joseph Fokam
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon, and Faculty of Health Sciences, University of Buea, Yaoundé, Cameroon
| | - Lisa M. Frenkel
- Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
| | - Ravindra K. Gupta
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, United Kingdom
| | - John P.A. Ioannidis
- Department of Medicine, Department of Epidemiology and Population Health, and Meta-Research Innovation Center at Stanford (METRICS), Stanford University, Stanford, California, United States of America
| | - Pontiano Kaleebu
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Entebbe, Uganda
| | - Rami Kantor
- Department of Medicine, Brown University, The Miriam Hospital, Providence, Rhode Island, United States of America
| | - Seble G. Kassaye
- Department of Medicine, Division of Infectious Diseases, Georgetown University, Washington DC, United States of America
| | - Sergei L. Kosakovsky Pond
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Vinie Kouamou
- Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Roger D. Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland and Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Daniel R. Kuritzkes
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Richard Lessells
- Affiliation is KwaZulu-Natal Research Innovation & Sequencing Platform, University of KwaZulu-Natal, Durban, South Africa
| | - Anne-Genevieve Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié-Salpêtrière—Charles Foix, Laboratoire de Virologie, Paris, France
| | - Lawrence Mbuagbaw
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - Brian Minalga
- Office of HIV/AIDS Network Coordination, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Nicaise Ndembi
- Institute of Human Virology Nigeria, Herbert Macaulay Way, Abuja, Nigeria
| | | | - Roger Paredes
- Department of Infectious Diseases & irsiCaixa, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spain
| | - Deenan Pillay
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Elliot G. Raizes
- United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Soo-Yon Rhee
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, United States of America
| | - Douglas D. Richman
- Center for AIDS Research, Department of Medicine, University of California San Diego, San Diego, California, United States of America
| | - Kiat Ruxrungtham
- School of Global Health, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Pardis C. Sabeti
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | | | | | - Kim Steegen
- Department of Molecular Medicine and Haematology, National Health Laboratory Service, Johannesburg, South Africa
| | - Wataru Sugiura
- Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo, Japan
| | - Gert U. van Zyl
- Division of Medical Virology, Stellenbosch University and National Health Laboratory Service, Cape Town, South Africa
| | - Anne-Mieke Vandamme
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium
- Center for Global Health And Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Annemarie M.J. Wensing
- University Medical Center Utrecht, the Netherlands and Wits Reproductive Health and HIV Institute, University of the Witwatersrand, Johannesburg, South Africa
| | - Joel O. Wertheim
- Department of Medicine, University of California San Diego, San Diego, La Jolla, California, United States of America
| | - Huldrych F. Gunthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland and Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Michael R. Jordan
- Department of Medicine, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Robert W. Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, United States of America
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Jordan MR, Hamunime N, Bikinesi L, Sawadogo S, Agolory S, Shiningavamwe AN, Negussie T, Fisher-Walker CL, Raizes EG, Mutenda N, Hunter CJ, Dean N, Steegen K, Kana V, Carmona S, Yang C, Tang AM, Parkin N, Hong SY. High levels of HIV drug resistance among adults failing second-line antiretroviral therapy in Namibia. Medicine (Baltimore) 2020; 99:e21661. [PMID: 32925712 PMCID: PMC7489739 DOI: 10.1097/md.0000000000021661] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
To support optimal third-line antiretroviral therapy (ART) selection in Namibia, we investigated the prevalence of HIV drug resistance (HIVDR) at time of failure of second-line ART. A cross-sectional study was conducted between August 2016 and February 2017. HIV-infected people ≥15 years of age with confirmed virological failure while receiving ritonavir-boosted protease inhibitor (PI/r)-based second-line ART were identified at 15 high-volume ART clinics representing over >70% of the total population receiving second-line ART. HIVDR genotyping of dried blood spots obtained from these individuals was performed using standard population sequencing methods. The Stanford HIVDR algorithm was used to identify sequences with predicted resistance; genotypic susceptibility scores for potential third-line regimens were calculated. Two hundred thirty-eight individuals were enrolled; 57.6% were female. The median age and duration on PI/r-based ART at time of enrolment were 37 years and 3.46 years, respectively. 97.5% received lopinavir/ritonavir-based regimens. The prevalence of nucleoside reverse transcriptase inhibitor (NRTI), non-nucleoside reverse transcriptase inhibitor (NNRTI), and PI/r resistance was 50.6%, 63.1%, and 13.1%, respectively. No significant association was observed between HIVDR prevalence and age or sex. This study demonstrates high levels of NRTI and NNRTI resistance and moderate levels of PI resistance in people receiving PI/r-based second-line ART in Namibia. Findings underscore the need for objective and inexpensive measures of adherence to identify those in need of intensive adherence counselling, routine viral load monitoring to promptly detect virological failure, and HIVDR genotyping to optimize selection of third-line drugs in Namibia.
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Affiliation(s)
- Michael R. Jordan
- Division of Geographic Medicine and Infectious Disease, Tufts Medical Center
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA, USA
| | - Ndapewa Hamunime
- Directorate of Special Programmes, Ministry of Health and Social Services, Windhoek, Namibia
| | - Leonard Bikinesi
- Directorate of Special Programmes, Ministry of Health and Social Services, Windhoek, Namibia
| | | | - Simon Agolory
- United States Centers for Disease Control and Prevention
| | | | - Taffa Negussie
- Directorate of Special Programmes, Ministry of Health and Social Services, Windhoek, Namibia
| | | | | | - Nicholus Mutenda
- Directorate of Special Programmes, Ministry of Health and Social Services, Windhoek, Namibia
| | | | - Natalie Dean
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
| | - Kim Steegen
- Department of Molecular Medicine and Haematology, University of Witwatersrand, Johannesburg, South Africa
| | - Vibha Kana
- Department of Molecular Medicine and Haematology, University of Witwatersrand, Johannesburg, South Africa
| | - Sergio Carmona
- Department of Molecular Medicine and Haematology, University of Witwatersrand, Johannesburg, South Africa
| | - Chunfu Yang
- United States Centers for Disease Control and Prevention, Atlanta, GA
| | - Alice M. Tang
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA, USA
| | - Neil Parkin
- Data First Consulting, Inc., Sebastopol, CA, USA
| | - Steven Y. Hong
- Division of Geographic Medicine and Infectious Disease, Tufts Medical Center
- United States Centers for Disease Control and Prevention
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