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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] [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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Jamrozik E, Munung NS, Abeler-Dorner L, Parker M. Public health use of HIV phylogenetic data in sub-Saharan Africa: ethical issues. BMJ Glob Health 2023; 8:e011884. [PMID: 37407228 PMCID: PMC10335518 DOI: 10.1136/bmjgh-2023-011884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 06/05/2023] [Indexed: 07/07/2023] Open
Abstract
Phylogenetic analyses of HIV are an increasingly accurate method of clarifying population-level patterns of transmission and linking individuals or groups with transmission events. Viral genetic data may be used by public health agencies to guide policy interventions focused on clusters of transmission or segments of the population in which transmission is concentrated. Analyses of HIV phylogenetics in high-income countries have often found that clusters of transmission play a significant role in HIV epidemics. In sub-Saharan Africa, HIV phylogenetic analyses to date suggest that clusters of transmission play a relatively minor role in local epidemics. Such analyses could nevertheless be used to guide priority setting and HIV public health programme design in Africa for sub-populations in which transmission events are more concentrated. Phylogenetic analysis raises ethical issues, in part due to the range of potential benefits and potential harms (ie, risks). Potential benefits include (1) improving knowledge of transmission patterns, (2) informing the design of focused public health interventions for subpopulations in which transmission is concentrated, (3) identifying and responding to clusters of transmission, (4) reducing stigma (in some cases) and (5) informing estimates of the (cost-)effectiveness of HIV treatment programmes. Potential harms include (1) privacy infringements, (2) increasing stigma (in some cases), (3) reducing trust in public health programmes, and (4) increased prosecution of legal cases where HIV transmission, homosexuality or sex work is criminalised. This paper provides analysis of relevant issues with a focus on sub-Saharan Africa in order to inform consultations regarding ethical best practice for HIV phylogenetics.
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Affiliation(s)
- Euzebiusz Jamrozik
- Ethox and the Wellcome Centre for Ethics and Humanities, University of Oxford, Oxford, UK
- Royal Melbourne Hospital Department of Medicine, University of Melbourne, Parkville, Victoria, Australia
- Monash Bioethics Centre, Monash University, Melbourne, Victoria, Australia
| | | | | | - Michael Parker
- Ethox and the Wellcome Centre for Ethics and Humanities, University of Oxford, Oxford, UK
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Tordoff DM, Minalga B, Trejo A, Shook A, Kerani RP, Herbeck JT. Lessons learned from community engagement regarding phylodynamic research with molecular HIV surveillance data. J Int AIDS Soc 2023; 26 Suppl 1:e26111. [PMID: 37408448 PMCID: PMC10323319 DOI: 10.1002/jia2.26111] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 05/09/2023] [Indexed: 07/07/2023] Open
Abstract
INTRODUCTION The widespread implementation of molecular HIV surveillance (MHS) has resulted in an increased discussion about the ethical, human rights and public health implications of MHS. We narrate our process of pausing our research that uses data collected through MHS in response to these growing concerns and summarize the key lessons we learned through conversations with community members. METHODS The original study aimed to describe HIV transmission patterns by age and race/ethnicity among men who have sex with men in King County, Washington, by applying probabilistic phylodynamic modelling methods to HIV-1 pol gene sequences collected through MHS. In September 2020, we paused the publication of this research to conduct community engagement: we held two public-facing online presentations, met with a national community coalition that included representatives of networks of people living with HIV, and invited two members of this coalition to provide feedback on our manuscript. During each of these meetings, we shared a brief presentation of our methods and findings and explicitly solicited feedback on the perceived public health benefit and potential harm of our analyses and results. RESULTS Some community concerns about MHS in public health practice also apply to research using MHS data, namely those related to informed consent, inference of transmission directionality and criminalization. Other critiques were specific to our research study and included feedback about the use of phylogenetic analyses to study assortativity by race/ethnicity and the importance of considering the broader context of stigma and structural racism. We ultimately decided the potential harms of publishing our study-perpetuating racialized stigma about men who have sex with men and eroding the trust between phylogenetics researchers and communities of people living with HIV-outweighed the potential benefits. CONCLUSIONS HIV phylogenetics research using data collected through MHS data is a powerful scientific technology with the potential to benefit and harm communities of people living with HIV. Addressing criminalization and including people living with HIV in decision-making processes have the potential to meaningfully address community concerns and strengthen the ethical justification for using MHS data in both research and public health practice. We close with specific opportunities for action and advocacy by researchers.
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Affiliation(s)
- Diana M. Tordoff
- Department of EpidemiologyUniversity of WashingtonSeattleWashingtonUSA
| | - Brian Minalga
- Fred Hutch, Office of HIV/AIDS Network CoordinationSeattleWashingtonUSA
| | - Alfredo Trejo
- Department of Political ScienceUniversity of California Los AngelesLos AngelesCaliforniaUSA
| | - Alic Shook
- Seattle University, College of NursingSeattleWashingtonUSA
- Seattle Children's Center for Pediatric Nursing ResearchSeattleWashingtonUSA
| | - Roxanne P. Kerani
- Department of EpidemiologyUniversity of WashingtonSeattleWashingtonUSA
- Public Health – Seattle & King County, HIV/STD ProgramSeattleWashingtonUSA
- Department of MedicineUniversity of WashingtonSeattleWashingtonUSA
| | - Joshua T. Herbeck
- Department of Global HealthUniversity of WashingtonSeattleWashingtonUSA
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Williams E, Moso M, Lim C, Chibo D, Nicholson S, Jackson K, Williamson DA. Laboratory diagnosis of HIV: a contemporary overview in the Australian context. Pathology 2023:S0031-3025(23)00125-3. [PMID: 37302942 DOI: 10.1016/j.pathol.2023.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 03/02/2023] [Accepted: 04/19/2023] [Indexed: 06/13/2023]
Abstract
Over the past decade there have been technical advances in human immunodeficiency virus (HIV) assays and updates to testing regulations that have substantially changed the landscape of laboratory testing for HIV. In addition, there have been significant changes in the epidemiology of HIV in Australia in the context of highly effective contemporary biomedical treatment and prevention strategies. Here, we provide an update on contemporary issues for the laboratory detection and confirmation of HIV in Australia. These include (1) the impact of early treatment and biological prevention strategies on the serological and virological detection of HIV; (2) the updated national HIV laboratory case definition and its interaction with testing regulations, public health and clinical guidelines; and (3) novel strategies for the laboratory detection of HIV, including the incorporation of HIV nucleic acid amplification tests (NAATs) into testing algorithms. These developments present an opportunity to develop a nationally consistent contemporary HIV testing algorithm that would result in optimisation and standardisation of HIV testing in Australia.
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Affiliation(s)
- Eloise Williams
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia; Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia.
| | - Michael Moso
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia; Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia; Department of Microbiology, The Royal Melbourne Hospital, Melbourne, Vic, Australia
| | - Chuan Lim
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
| | - Doris Chibo
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
| | - Suellen Nicholson
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
| | - Kathy Jackson
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
| | - Deborah Anne Williamson
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia; Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
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Cholette F, Lazarus L, Macharia P, Thompson LH, Githaiga S, Mathenge J, Walimbwa J, Kuria I, Okoth S, Wambua S, Albert H, Mwangi P, Adhiambo J, Kasiba R, Juma E, Battacharjee P, Kimani J, Sandstrom P, Meyers AFA, Joy JB, Thomann M, McLaren PJ, Shaw S, Mishra S, Becker ML, McKinnon L, Lorway R. Community Insights in Phylogenetic HIV Research: The CIPHR Project Protocol. Glob Public Health 2023; 18:2269435. [PMID: 37851872 DOI: 10.1080/17441692.2023.2269435] [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: 03/01/2023] [Accepted: 10/04/2023] [Indexed: 10/20/2023]
Abstract
Inferring HIV transmission networks from HIV sequences is gaining popularity in the field of HIV molecular epidemiology. However, HIV sequences are often analyzed at distance from those affected by HIV epidemics, namely without the involvement of communities most affected by HIV. These remote analyses often mean that knowledge is generated in absence of lived experiences and socio-economic realities that could inform the ethical application of network-derived information in 'real world' programmes. Procedures to engage communities are noticeably absent from the HIV molecular epidemiology literature. Here we present our team's protocol for engaging community activists living in Nairobi, Kenya in a knowledge exchange process - The CIPHR Project (Community Insights in Phylogenetic HIV Research). Drawing upon a community-based participatory approach, our team will (1) explore the possibilities and limitations of HIV molecular epidemiology for key population programmes, (2) pilot a community-based HIV molecular study, and (3) co-develop policy guidelines on conducting ethically safe HIV molecular epidemiology. Critical dialogue with activist communities will offer insight into the potential uses and abuses of using such information to sharpen HIV prevention programmes. The outcome of this process holds importance to the development of policy frameworks that will guide the next generation of the global response.
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Affiliation(s)
- François Cholette
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
- Sexually Transmitted and Blood-Borne Infections, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Canada
| | - Lisa Lazarus
- Institute for Global Public Health, Department of Community Health Sciences, University of Manitoba, Winnipeg, Canada
| | - Pascal Macharia
- Health Options for Young Men on HIV/AIDS and STIs (HOYMAS), Nairobi, Kenya
| | - Laura H Thompson
- Sexually Transmitted and Blood-Borne Infections Surveillance Division, Centre for Communicable Diseases and Infection Control, Public Health Agency of Canada, Ottawa, Canada
| | - Samuel Githaiga
- Health Options for Young Men on HIV/AIDS and STIs (HOYMAS), Nairobi, Kenya
| | - John Mathenge
- Health Options for Young Men on HIV/AIDS and STIs (HOYMAS), Nairobi, Kenya
| | | | - Irene Kuria
- Key Population Consortium of Kenya, Nairobi, Kenya
| | - Silvia Okoth
- Bar Hostess Empowerment and Support Programme, Nairobi, Kenya
| | | | - Harrison Albert
- Health Options for Young Men on HIV/AIDS and STIs (HOYMAS), Nairobi, Kenya
| | - Peninah Mwangi
- Bar Hostess Empowerment and Support Programme, Nairobi, Kenya
| | - Joyce Adhiambo
- Partners for Health Development in Africa (PHDA), Nairobi, Kenya
- Sex Worker Outreach Programme (SWOP), Nairobi, Kenya
| | | | - Esther Juma
- Sex Worker Outreach Programme (SWOP), Nairobi, Kenya
| | | | - Joshua Kimani
- Sex Worker Outreach Programme (SWOP), Nairobi, Kenya
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Paul Sandstrom
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
- Sexually Transmitted and Blood-Borne Infections, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Canada
| | - Adrienne F A Meyers
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
- Sexually Transmitted and Blood-Borne Infections, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Canada
| | - Jeffrey B Joy
- British Columbia Centre for Excellence in HIV/AIDS (BCCfE), St. Paul's Hospital, Vancouver, Canada
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, Canada
- Bioinformatics Programme, University of British Columbia, Vancouver, Canada
| | - Matthew Thomann
- Department of Anthropology, University of Maryland, College Park, MD, USA
| | - Paul J McLaren
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
- Sexually Transmitted and Blood-Borne Infections, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Canada
| | - Souradet Shaw
- Institute for Global Public Health, Department of Community Health Sciences, University of Manitoba, Winnipeg, Canada
| | - Sharmistha Mishra
- MAP Centre for Urban Health Solutions, St. Michael's Hospital, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Canada
| | - Marissa L Becker
- Institute for Global Public Health, Department of Community Health Sciences, University of Manitoba, Winnipeg, Canada
| | - Lyle McKinnon
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Robert Lorway
- Institute for Global Public Health, Department of Community Health Sciences, University of Manitoba, Winnipeg, Canada
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Liu M, Chato C, Poon AFY. From components to communities: bringing network science to clustering for molecular epidemiology. Virus Evol 2023; 9:vead026. [PMID: 37187604 PMCID: PMC10175948 DOI: 10.1093/ve/vead026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 01/30/2023] [Accepted: 04/17/2023] [Indexed: 05/17/2023] Open
Abstract
Defining clusters of epidemiologically related infections is a common problem in the surveillance of infectious disease. A popular method for generating clusters is pairwise distance clustering, which assigns pairs of sequences to the same cluster if their genetic distance falls below some threshold. The result is often represented as a network or graph of nodes. A connected component is a set of interconnected nodes in a graph that are not connected to any other node. The prevailing approach to pairwise clustering is to map clusters to the connected components of the graph on a one-to-one basis. We propose that this definition of clusters is unnecessarily rigid. For instance, the connected components can collapse into one cluster by the addition of a single sequence that bridges nodes in the respective components. Moreover, the distance thresholds typically used for viruses like HIV-1 tend to exclude a large proportion of new sequences, making it difficult to train models for predicting cluster growth. These issues may be resolved by revisiting how we define clusters from genetic distances. Community detection is a promising class of clustering methods from the field of network science. A community is a set of nodes that are more densely inter-connected relative to the number of their connections to external nodes. Thus, a connected component may be partitioned into two or more communities. Here we describe community detection methods in the context of genetic clustering for epidemiology, demonstrate how a popular method (Markov clustering) enables us to resolve variation in transmission rates within a giant connected component of HIV-1 sequences, and identify current challenges and directions for further work.
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Affiliation(s)
- Molly Liu
- Department of Pathology and Laboratory Medicine, Western University, Dental Sciences Building, Rm. 4044, London, ON N6A 5C1, Canada
| | - Connor Chato
- Department of Pathology and Laboratory Medicine, Western University, Dental Sciences Building, Rm. 4044, London, ON N6A 5C1, Canada
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Csete J, Elliott R, Bernard EJ. So many harms, so little benefit: a global review of the history and harms of HIV criminalisation. Lancet HIV 2023; 10:e52-e61. [PMID: 36202138 DOI: 10.1016/s2352-3018(22)00248-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 08/22/2022] [Accepted: 08/22/2022] [Indexed: 11/07/2022]
Abstract
Since the early years of HIV, many jurisdictions have criminalised HIV non-disclosure, potential or perceived exposure, and transmission. Many of these laws and prosecutions are without a scientific basis and reflect an inaccurate understanding of HIV-related risk and harm. Numerous studies of HIV criminal prosecutions show that women, sex workers, racial minorities, gay and bisexual men, transgender people, immigrants, and Indigenous people are disproportionately charged and convicted, often resulting in long custodial sentences. Data from molecular HIV surveillance, used to track HIV outbreaks in marginalised populations, are prone to be misused in HIV criminal cases. Scientific consensus statements and international standards have helped to guide advocacy to repeal or reform a number of these laws, resulting in fewer prosecutions in some jurisdictions. Many successful reform efforts have been led by people living with HIV and are notable at a moment of reckoning on racism and inequality in global health.
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Affiliation(s)
- Joanne Csete
- Department of Population and Family Health, Columbia University Mailman School of Public Health, New York, NY, USA.
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8
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Optimized phylogenetic clustering of HIV-1 sequence data for public health applications. PLoS Comput Biol 2022; 18:e1010745. [PMID: 36449514 PMCID: PMC9744331 DOI: 10.1371/journal.pcbi.1010745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 12/12/2022] [Accepted: 11/17/2022] [Indexed: 12/02/2022] Open
Abstract
Clusters of genetically similar infections suggest rapid transmission and may indicate priorities for public health action or reveal underlying epidemiological processes. However, clusters often require user-defined thresholds and are sensitive to non-epidemiological factors, such as non-random sampling. Consequently the ideal threshold for public health applications varies substantially across settings. Here, we show a method which selects optimal thresholds for phylogenetic (subset tree) clustering based on population. We evaluated this method on HIV-1 pol datasets (n = 14, 221 sequences) from four sites in USA (Tennessee, Washington), Canada (Northern Alberta) and China (Beijing). Clusters were defined by tips descending from an ancestral node (with a minimum bootstrap support of 95%) through a series of branches, each with a length below a given threshold. Next, we used pplacer to graft new cases to the fixed tree by maximum likelihood. We evaluated the effect of varying branch-length thresholds on cluster growth as a count outcome by fitting two Poisson regression models: a null model that predicts growth from cluster size, and an alternative model that includes mean collection date as an additional covariate. The alternative model was favoured by AIC across most thresholds, with optimal (greatest difference in AIC) thresholds ranging 0.007-0.013 across sites. The range of optimal thresholds was more variable when re-sampling 80% of the data by location (IQR 0.008 - 0.016, n = 100 replicates). Our results use prospective phylogenetic cluster growth and suggest that there is more variation in effective thresholds for public health than those typically used in clustering studies.
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Stockdale JE, Liu P, Colijn C. The potential of genomics for infectious disease forecasting. Nat Microbiol 2022; 7:1736-1743. [PMID: 36266338 DOI: 10.1038/s41564-022-01233-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 08/18/2022] [Indexed: 11/09/2022]
Abstract
Genomic technologies have led to tremendous gains in understanding how pathogens function, evolve and interact. Pathogen diversity is now measurable at high precision and resolution, in part because over the past decade, sequencing technologies have increased in speed and capacity, at decreased cost. Alongside this, the use of models that can forecast emergence and size of infectious disease outbreaks has risen, highlighted by the coronavirus disease 2019 pandemic but also due to modelling advances that allow for rapid estimates in emerging outbreaks to inform monitoring, coordination and resource deployment. However, genomics studies have remained largely retrospective. While they contain high-resolution views of pathogen diversification and evolution in the context of selection, they are often not aligned with designing interventions. This is a missed opportunity because pathogen diversification is at the core of the most pressing infectious public health challenges, and interventions need to take the mechanisms of virulence and understanding of pathogen diversification into account. In this Perspective, we assess these converging fields, discuss current challenges facing both surveillance specialists and modellers who want to harness genomic data, and propose next steps for integrating longitudinally sampled genomic data with statistical learning and interpretable modelling to make reliable predictions into the future.
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Affiliation(s)
- Jessica E Stockdale
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Pengyu Liu
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Caroline Colijn
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada.
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10
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Meumann EM, Krause VL, Baird R, Currie BJ. Using Genomics to Understand the Epidemiology of Infectious Diseases in the Northern Territory of Australia. Trop Med Infect Dis 2022; 7:tropicalmed7080181. [PMID: 36006273 PMCID: PMC9413455 DOI: 10.3390/tropicalmed7080181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 11/16/2022] Open
Abstract
The Northern Territory (NT) is a geographically remote region of northern and central Australia. Approximately a third of the population are First Nations Australians, many of whom live in remote regions. Due to the physical environment and climate, and scale of social inequity, the rates of many infectious diseases are the highest nationally. Molecular typing and genomic sequencing in research and public health have provided considerable new knowledge on the epidemiology of infectious diseases in the NT. We review the applications of genomic sequencing technology for molecular typing, identification of transmission clusters, phylogenomics, antimicrobial resistance prediction, and pathogen detection. We provide examples where these methodologies have been applied to infectious diseases in the NT and discuss the next steps in public health implementation of this technology.
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Affiliation(s)
- Ella M. Meumann
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin 0810, Australia
- Department of Infectious Diseases, Division of Medicine, Royal Darwin Hospital, Darwin 0810, Australia
- Correspondence:
| | - Vicki L. Krause
- Northern Territory Centre for Disease Control, Northern Territory Government, Darwin 0810, Australia
| | - Robert Baird
- Territory Pathology, Royal Darwin Hospital, Darwin 0810, Australia
| | - Bart J. Currie
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin 0810, Australia
- Department of Infectious Diseases, Division of Medicine, Royal Darwin Hospital, Darwin 0810, Australia
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11
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Ferdinand AS, Hocking JS, Denholm JT, Howden BP, Williamson DA. Patient-focused pathogen genetic counselling-has the time come? Genome Med 2021; 13:178. [PMID: 34749791 PMCID: PMC8574140 DOI: 10.1186/s13073-021-00993-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 10/13/2021] [Indexed: 12/11/2022] Open
Abstract
Ensuring accordance with principles of healthcare ethics requires improved communication of pathogen genomic data. This could include educating healthcare professionals in communicating pathogen genomic information to individuals, developing ethical frameworks for reporting pathogen genomic results to individuals, responsible media reporting guidelines, and counselling for individuals (‘pathogen genetic counselling’).
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Affiliation(s)
- Angeline S Ferdinand
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, 3100, Australia. .,Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Australia.
| | - Jane S Hocking
- Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - Justin T Denholm
- Victorian Tuberculosis Program, Melbourne Health, Melbourne, Australia.,Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, 3100, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, 3100, Australia
| | - Deborah A Williamson
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, 3100, Australia. .,Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, Australia. .,Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
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12
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Hughes SD, Woods WJ, O'Keefe KJ, Delgado V, Pipkin S, Scheer S, Truong HHM. Integrating Phylogenetic Biomarker Data and Qualitative Approaches: An example of HIV Transmission Clusters as a Sampling Frame for Semistructured Interviews and Implications for the COVID-19 Era. JOURNAL OF MIXED METHODS RESEARCH 2021; 15:327-347. [PMID: 38883973 PMCID: PMC11178346 DOI: 10.1177/15586898211012786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Mixed methods studies of human disease that combine surveillance, biomarker, and qualitative data can help elucidate what drives epidemiological trends. Viral genetic data are rarely coupled with other types of data due to legal and ethical concerns about patient privacy. We developed a novel approach to integrate phylogenetic and qualitative methods in order to better target HIV prevention efforts. The overall aim of our mixed methods study was to characterize HIV transmission clusters. We combined surveillance data with HIV genomic data to identify cases whose viruses share enough similarities to suggest a recent common source of infection or participation in linked transmission chains. Cases were recruited through a multi-phase process to obtain consent for recruitment to semi-structured interviews. Through linkage of viral genetic sequences with epidemiological data, we identified individuals in large transmission clusters, which then served as a sampling frame for the interviews. In this article, we describe the multi-phase process and the limitations and challenges encountered. Our approach contributes to the mixed methods research field by demonstrating that phylogenetic analysis and surveillance data can be harnessed to generate a sampling frame for subsequent qualitative data collection, using an explanatory sequential design. The process we developed also respected protections of patient confidentiality. The novel method we devised may offer an opportunity to implement a sampling frame that allows for the recruitment and interview of individuals in high-transmission clusters to better understand what contributes to spread of other infectious diseases, including COVID-19.
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Affiliation(s)
| | | | - Kara J O'Keefe
- San Francisco Department of Public Health, San Francisco, CA, USA
| | - Viva Delgado
- San Francisco Department of Public Health, San Francisco, CA, USA
| | - Sharon Pipkin
- San Francisco Department of Public Health, San Francisco, CA, USA
| | - Susan Scheer
- San Francisco Department of Public Health, San Francisco, CA, USA
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13
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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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14
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Lapointe HR, Harrigan PR. Human Immunodeficiency Virus Phylogenetics in the United States-and Elsewhere. J Infect Dis 2020; 222:1939-1940. [PMID: 32529243 DOI: 10.1093/infdis/jiaa108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 03/06/2020] [Indexed: 01/16/2023] Open
Affiliation(s)
- Hope R Lapointe
- Division of AIDS Department of Medicine, Vancouver, British Columbia, Canada
| | - P Richard Harrigan
- Division of AIDS Department of Medicine, Vancouver, British Columbia, Canada
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15
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Bernard EJ, McClelland A, Cardell B, Chung C, Castro-Bojorquez M, French M, Hursey D, Khanna N, Minalga MB, Spieldenner A, Strub S. We Are People, Not Clusters! THE AMERICAN JOURNAL OF BIOETHICS : AJOB 2020; 20:1-4. [PMID: 32945744 DOI: 10.1080/15265161.2020.1809550] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Affiliation(s)
| | | | - Barb Cardell
- Colorado Organizations and Individuals Responding to HIV/AIDS
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16
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Molldrem S, Smith AKJ. Reassessing the Ethics of Molecular HIV Surveillance in the Era of Cluster Detection and Response: Toward HIV Data Justice. THE AMERICAN JOURNAL OF BIOETHICS : AJOB 2020; 20:10-23. [PMID: 32945756 DOI: 10.1080/15265161.2020.1806373] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
In the United States, clinical HIV data reported to surveillance systems operated by jurisdictional departments of public health are re-used for epidemiology and prevention. In 2018, all jurisdictions began using HIV genetic sequence data from clinical drug resistance tests to identify people living with HIV in "clusters" of others with genetically similar strains. This is called "molecular HIV surveillance" (MHS). In 2019, "cluster detection and response" (CDR) programs that re-use MHS data became the "fourth pillar" of the national HIV strategy. Public health re-uses of HIV data are done without consent and are a source of concern among stakeholders. This article presents three cases that illuminate bioethical challenges associated with re-uses of clinical HIV data for public health. We focus on evidence-base, risk-benefit ratio, determining directionality of HIV transmission, consent, and ethical re-use. The conclusion offers strategies for "HIV data justice." The essay contributes to a "bioethics of the oppressed."
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17
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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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18
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What Should Health Departments Do with HIV Sequence Data? Viruses 2020; 12:v12091018. [PMID: 32932642 PMCID: PMC7551807 DOI: 10.3390/v12091018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/09/2020] [Accepted: 09/11/2020] [Indexed: 11/27/2022] Open
Abstract
Many countries and US states have mandatory statues that require reporting of HIV clinical data including genetic sequencing results to the public health departments. Because genetic sequencing is a part of routine care for HIV infected persons, health departments have extensive sequence collections spanning years and even decades of the HIV epidemic. How should these data be used (or not) in public health practice? This is a complex, multi-faceted question that weighs personal risks against public health benefit. The answer is neither straightforward nor universal. However, to make that judgement—of how genetic sequence data should be used in describing and combating the HIV epidemic—we need a clear image of what a phylogenetically enhanced HIV surveillance system can do and what benefit it might provide. In this paper, we present a positive case for how up-to-date analysis of HIV sequence databases managed by health departments can provide unique and actionable information of how HIV is spreading in local communities. We discuss this question broadly, with examples from the US, as it is globally relevant for all health authorities that collect HIV genetic data.
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19
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Jazieh AR, Kozlakidis Z. Healthcare Transformation in the Post-Coronavirus Pandemic Era. Front Med (Lausanne) 2020; 7:429. [PMID: 32850915 PMCID: PMC7399067 DOI: 10.3389/fmed.2020.00429] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 07/03/2020] [Indexed: 12/30/2022] Open
Affiliation(s)
- Abdul Rahman Jazieh
- Department of Oncology, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Zisis Kozlakidis
- Laboratory Services and Biobanking, International Agency for Research on Cancer, World Health Organization, Lyon, France
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20
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Rudolph AE, Martinez O, Davison R, Amuchi CB. Informed consent for HIV phylogenetic research: A case study of urban individuals living with HIV approached for enrollment in an HIV study. EHQUIDAD 2020; 2020:129-143. [PMID: 32954381 PMCID: PMC7497840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
INTRODUCTION Phylogenetic analyses can provide insights on HIV tansmission dynamics. Country and state-level differences in HIV criminalization and disclosure laws and advances in next generation sequencing could impact perceived study risks. METHODS We present study opt-out rates and the reasons provided during enrollment for a study conducted in Boston (6/2017-8/2018). RESULTS Of 90 patients approached to participate, 45 did not consent to participate. Reasons for not participating included unwillingness to discuss their HIV status, privacy and confidentiality concerns, disinterest, and lack of time. CONLUSIONS Given low participation rates and concerns related to HIV disclosure, privacy, and confidentiality, these questions remain (1) should informed consent be required for all phylogenetic analyses, including deidentified and surveillance data? (2) what additional steps can researchers take to protect the privacy of individuals, particularly in contexts where HIV is criminalized or there have been civil/criminal cases investigating HIV transmission? And (3) what role can community members play to minimize the potential risks, particularly for those most marginalized? These questions require input from both researchers and community members living with HIV/AIDS.
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Affiliation(s)
- Abby E. Rudolph
- Department of Epidemiology and Biostatistics, Temple
University College of Public Health, Philadelphia, USA
| | - Omar Martinez
- School of Social Work, Temple University College of Public
Health, Philadelphia, USA
| | - Robin Davison
- School of Social Work, Temple University College of Public
Health, Philadelphia, USA
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21
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Johnson S, Parker M. Ethical challenges in pathogen sequencing: a systematic scoping review. Wellcome Open Res 2020; 5:119. [PMID: 32864469 PMCID: PMC7445679 DOI: 10.12688/wellcomeopenres.15806.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/01/2020] [Indexed: 11/29/2022] Open
Abstract
Background: Going forward, the routine implementation of genomic surveillance activities and outbreak investigation is to be expected. We sought to systematically identify the emerging ethical challenges; and to systematically assess the gaps in ethical frameworks or thinking and identify where further work is needed to solve practical challenges. Methods: We systematically searched indexed academic literature from PubMed, Google Scholar, and Web of Science from 2000 to April 2019 for peer-reviewed articles that substantively engaged in discussion of ethical issues in the use of pathogen genome sequencing technologies for diagnostic, surveillance and outbreak investigation. Results: 28 articles were identified; nine United States, five United Kingdom, five The Netherlands, three Canada, two Switzerland, one Australia, two South Africa, and one Italy. Eight articles were specifically about the use of sequencing in HIV. Eleven were not specific to a particular disease. Results were organized into four themes: tensions between public and private interests; difficulties with translation from research to clinical and public health practice; the importance of community trust and support; equity and global partnerships; and the importance of context. Conclusion: While pathogen sequencing has the potential to be transformative for public health, there are a number of key ethical issues that must be addressed, particularly around the conditions of use for pathogen sequence data. Ethical standards should be informed by public values, and further empirical work investigating stakeholders’ views are required. Development in the field should also be under-pinned by a strong commitment to values of justice, in particular global health equity.
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Affiliation(s)
- Stephanie Johnson
- Wellcome Centre for Ethics and Humanities and Ethox Centre, University of Oxford, Oxford, OX3 7LF, UK
| | - Michael Parker
- Wellcome Centre for Ethics and Humanities and Ethox Centre, University of Oxford, Oxford, OX3 7LF, UK
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22
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Wertheim JO, Morris S, Ragonnet-Cronin M. Consent and criminalisation concerns over phylogenetic analysis of surveillance data - Authors' reply. Lancet HIV 2020; 6:e420-e421. [PMID: 31272659 DOI: 10.1016/s2352-3018(19)30142-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 04/18/2019] [Indexed: 10/26/2022]
Affiliation(s)
- Joel O Wertheim
- Department of Medicine, University of California, San Diego, CA, USA.
| | - Sheldon Morris
- Department of Medicine, University of California, San Diego, CA, USA
| | - Manon Ragonnet-Cronin
- Department of Medicine, University of California, San Diego, CA, USA; MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
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23
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Shahmanesh M, Harling G, Coltart CEM, Bailey H, King C, Gibbs J, Seeley J, Phillips A, Sabin CA, Aldridge RW, Sonnenberg P, Hart G, Rowson M, Pillay D, Johnson AM, Abubakar I, Field N. From the micro to the macro to improve health: microorganism ecology and society in teaching infectious disease epidemiology. THE LANCET. INFECTIOUS DISEASES 2020; 20:e142-e147. [PMID: 32386611 PMCID: PMC7252039 DOI: 10.1016/s1473-3099(20)30136-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 02/14/2020] [Accepted: 02/18/2020] [Indexed: 12/21/2022]
Abstract
Chronic and emerging infectious diseases and antimicrobial resistance remain a substantial global health threat. Microbiota are increasingly recognised to play an important role in health. Infections also have a profound effect beyond health, especially on global and local economies. To maximise health improvements, the field of infectious disease epidemiology needs to derive learning from ecology and traditional epidemiology. New methodologies and tools are transforming understanding of these systems, from a better understanding of socioeconomic, environmental, and cultural drivers of infection, to improved methods to detect microorganisms, describe the immunome, and understand the role of human microbiota. However, exploiting the potential of novel methods to improve global health remains elusive. We argue that to exploit these advances a shift is required in the teaching of infectious disease epidemiology to ensure that students are well versed in a breadth of disciplines, while maintaining core epidemiological skills. We discuss the following key points using a series of teaching vignettes: (1) integrated training in classic and novel techniques is needed to develop future scientists and professionals who can work from the micro (interactions between pathogens, their cohabiting microbiota, and the host at a molecular and cellular level), with the meso (the affected communities), and to the macro (wider contextual drivers of disease); (2) teach students to use a team-science multidisciplinary approach to effectively integrate biological, clinical, epidemiological, and social tools into public health; and (3) develop the intellectual skills to critically engage with emerging technologies and resolve evolving ethical dilemmas. Finally, students should appreciate that the voices of communities affected by infection need to be kept at the heart of their work.
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Affiliation(s)
- Maryam Shahmanesh
- Institute for Global Health, University College London, London, UK; Africa Health Research Institute, Durban, South Africa.
| | - Guy Harling
- Institute for Global Health, University College London, London, UK; Africa Health Research Institute, Durban, South Africa; MRC/Wits-Agincourt Unit, University of the Witwatersrand, Johannesburg, South Africa; Harvard Centre for Population and Development Studies, Harvard T H Chan School of Public Health, Boston, MA, USA
| | | | - Heather Bailey
- Institute for Global Health, University College London, London, UK
| | - Carina King
- Institute for Global Health, University College London, London, UK; Department of Public Health Sciences, Karolinska Institutet, Solna, Sweden
| | - Jo Gibbs
- Institute for Global Health, University College London, London, UK
| | - Janet Seeley
- Africa Health Research Institute, Durban, South Africa; London School of Hygiene and Tropical Medicine, London, UK
| | - Andrew Phillips
- Institute for Global Health, University College London, London, UK
| | - Caroline A Sabin
- Institute for Global Health, University College London, London, UK
| | - Robert W Aldridge
- Institute of Health Informatics, University College London, London, UK
| | - Pam Sonnenberg
- Institute for Global Health, University College London, London, UK
| | - Graham Hart
- Institute for Global Health, University College London, London, UK
| | - Mike Rowson
- Institute for Global Health, University College London, London, UK
| | - Deenan Pillay
- Division of infection and immunity, University College London, London, UK; Africa Health Research Institute, Durban, South Africa
| | - Anne M Johnson
- Institute for Global Health, University College London, London, UK
| | - Ibrahim Abubakar
- Institute for Global Health, University College London, London, UK
| | - Nigel Field
- Institute for Global Health, University College London, London, UK
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24
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Brown BJ, Sugarman J. Why ethics guidance needs to be updated for contemporary HIV prevention research. J Int AIDS Soc 2020; 23:e25500. [PMID: 32406990 PMCID: PMC7224307 DOI: 10.1002/jia2.25500] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/01/2020] [Accepted: 04/07/2020] [Indexed: 12/16/2022] Open
Affiliation(s)
- Brandon J Brown
- Center for Healthy CommunitiesSchool of MedicineUniversity of CaliforniaRiversideCAUSA
| | - Jeremy Sugarman
- Berman Institute of BioethicsJohns Hopkins UniversityBaltimoreMDUSA
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25
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Understanding disclosed and cryptic HIV transmission risk via genetic analysis: what are we missing and when does it matter? Curr Opin HIV AIDS 2020; 14:205-212. [PMID: 30946142 DOI: 10.1097/coh.0000000000000537] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
PURPOSE OF REVIEW To discuss the recent HIV phylogenetic analyses examining HIV transmission patterns among and within risk groups. RECENT FINDINGS Phylodynamic analysis has recently been applied to multiple HIV outbreaks among people who inject drugs to determine whether HIV transmission is ongoing. Large-scale analyses of datasets of HIV sequences collected for drug-resistance testing provide population-level insights into transmission patterns. One focus across world regions has been to investigate whether age-disparity is a driver of HIV transmission. In sub-Saharan Africa, researchers have examined transmission between heterosexuals and MSM and between high prevalence fishing communities and inland communities. In the US and the UK, cryptic risk groups such as nondisclosed MSM and the partners of transgender women are increasingly being uncovered based on their position in densely sampled molecular transmission networks. SUMMARY Analysis of HIV genetic sequence can resolve viral transmission patterns between risk groups at unprecedented scales and levels of detail. Future research should focus on understanding the effect of missing data on inferences and the biases of different methods. Uncovering groups and patterns obscured from traditional epidemiolocal analyses is exciting but should not compromise the privacy of the groups in question.
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26
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Harling G, Tsai AC. Using Social Networks to Understand and Overcome Implementation Barriers in the Global HIV Response. J Acquir Immune Defic Syndr 2019; 82 Suppl 3:S244-S252. [PMID: 31764260 PMCID: PMC6923140 DOI: 10.1097/qai.0000000000002203] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
BACKGROUND Despite the development of several efficacious HIV prevention and treatment methods in the past 2 decades, HIV continues to spread globally. Uptake of interventions is nonrandomly distributed across populations. Such inequality is socially patterned and reinforced by homophily arising from both social selection (becoming friends with similar people) and influence (becoming similar to friends). METHODS We conducted a narrative review to describe how social network analysis methods-including egocentric, sociocentric, and respondent-driven sampling designs-provide tools to measure key populations, to understand how epidemics spread, and to evaluate intervention take-up. RESULTS Social network analysis-informed designs can improve intervention effectiveness by reaching otherwise inaccessible populations. They can also improve intervention efficiency by maximizing spillovers, through social ties, to at-risk but susceptible individuals. Social network analysis-informed designs thus have the potential to be both more effective and less unequal in their effects, compared with social network analysis-naïve approaches. Although social network analysis-informed designs are often resource-intensive, we believe they provide unique insights that can help reach those most in need of HIV prevention and treatment interventions. CONCLUSION Increased collection of social network data during both research and implementation work would provide important information to improve the roll-out of existing studies in the present and to inform the design of more data-efficient, social network analysis-informed interventions in the future. Doing so will improve the reach of interventions, especially to key populations, and to maximize intervention impact once delivered.
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Affiliation(s)
- Guy Harling
- Institute for Global Health, University College London, London, United Kingdom
- Africa Health Research Institute, KwaZulu-Natal, South Africa
- Department of Epidemiology and Harvard Center for Population and Development Studies, Harvard University, Cambridge MA, United States
- MRC/Wits Rural Public Health & Health Transitions Research Unit (Agincourt), University of the Witwatersrand, Johannesburg, South Africa
| | - Alexander C. Tsai
- Department of Epidemiology and Harvard Center for Population and Development Studies, Harvard University, Cambridge MA, United States
- Chester M. Pierce, MD Division of Global Psychiatry, Massachusetts General Hospital, Boston MA United States
- Mbarara University of Science and Technology, Mbarara, Uganda
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27
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Günthard HF, Kouyos R. Can Directionality of HIV Transmission be Predicted by Next-Generation Sequencing Data? J Infect Dis 2019; 220:1393-1395. [PMID: 30590738 DOI: 10.1093/infdis/jiy737] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 12/21/2018] [Indexed: 11/12/2022] Open
Affiliation(s)
- Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich.,Institute of Medical Virology, University of Zurich, Switzerland
| | - Roger Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich.,Institute of Medical Virology, University of Zurich, Switzerland
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Schairer CE, Mehta SR, Vinterbo SA, Hoenigl M, Kalichman M, Little SJ. Trust and Expectations of Researchers and Public Health Departments for the Use of HIV Molecular Epidemiology. AJOB Empir Bioeth 2019; 10:201-213. [PMID: 31050604 DOI: 10.1080/23294515.2019.1601648] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Background: Molecular epidemiology (ME) is a technique used to study the dynamics of pathogen transmission through a population. When used to study HIV infections, ME generates powerful information about how HIV is transmitted, including epidemiologic patterns of linkage and, potentially, transmission direction. Thus, ME raises challenging questions about the most responsible way to protect individual privacy while acquiring and using these data to advance public health and inform HIV intervention strategies. Here, we report on stakeholders' expectations for how researchers and public health agencies might use HIV ME. Methods: We conducted in-depth semistructured interviews with 40 key stakeholders to find out how these individuals respond to the proposed risks and benefits of HIV ME. Transcripts were coded and analyzed using Atlas.ti. Expectations were assessed through analysis of responses to hypothetical scenarios designed to help interviewees think through the implications of this emerging technique in the contexts of research and public health. Results: Our analysis reveals a wide range of imagined responsibilities, capabilities, and trustworthiness of researchers and public health agencies. Specifically, many respondents expect researchers and public health agencies to use HIV ME carefully and maintain transparency about how data will be used. Informed consent was discussed as an important opportunity for notification of privacy risks. Furthermore, some respondents wished that public health agencies were held to the same form of oversight and accountability represented by informed consent in research. Conclusions: To prevent HIV ME from becoming a barrier to testing or a source of public mistrust, the sense of vulnerability expressed by some respondents must be addressed. In research, informed consent is an obvious opportunity for this. Without giving specimen donors a similar opportunity to opt out, public health agencies may find it difficult to adopt HIV ME without deterring testing and treatment.
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Affiliation(s)
- Cynthia E Schairer
- a Department of Psychiatry, University of California San Diego , La Jolla , California , USA
| | - Sanjay R Mehta
- b Department of Medicine, University of California San Diego , La Jolla , California , USA.,c Department of Medicine, San Diego Veterans Affairs Medical Center , San Diego , California , USA.,d Department of Pathology, University of California San Diego , La Jolla , California , USA
| | - Staal A Vinterbo
- e Department of Information Security and Communication Technology, Norwegian University of Science and Technology , Gjøvik , Norway
| | - Martin Hoenigl
- b Department of Medicine, University of California San Diego , La Jolla , California , USA
| | - Michael Kalichman
- d Department of Pathology, University of California San Diego , La Jolla , California , USA.,f Research Ethics Program, University of California San Diego , La Jolla , California , USA
| | - Susan J Little
- b Department of Medicine, University of California San Diego , La Jolla , California , USA
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Abeler-Dörner L, Grabowski MK, Rambaut A, Pillay D, Fraser C. PANGEA-HIV 2: Phylogenetics And Networks for Generalised Epidemics in Africa. Curr Opin HIV AIDS 2019; 14:173-180. [PMID: 30946141 PMCID: PMC6629166 DOI: 10.1097/coh.0000000000000542] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
PURPOSE OF REVIEW The HIV epidemic in sub-Saharan Africa is far from being under control and the ambitious UNAIDS targets are unlikely to be met by 2020 as declines in per-capita incidence being largely offset by demographic trends. There is an increasing number of proven and specific HIV prevention tools, but little consensus on how best to deploy them. RECENT FINDINGS Traditionally, phylogenetics has been used in HIV research to reconstruct the history of the epidemic and date zoonotic infections, whereas more recent publications focus on HIV diversity and drug resistance. However, it is also the most powerful method of source attribution available for the study of HIV transmission. The PANGEA (Phylogenetics And Networks for Generalized Epidemics in Africa) consortium has generated over 18 000 NGS HIV sequences from five countries in sub-Saharan Africa. Using phylogenetic methods, we will identify characteristics of individuals or groups, which are most likely to be at risk of infection or at risk of infecting others. SUMMARY Combining phylogenetics, phylodynamics and epidemiology will allow PANGEA to highlight where prevention efforts should be focussed to reduce the HIV epidemic most effectively. To maximise the public health benefit of the data, PANGEA offers accreditation to external researchers, allowing them to access the data and join the consortium. We also welcome submissions of other HIV sequences from sub-Saharan Africa to the database.
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Affiliation(s)
- Lucie Abeler-Dörner
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mary K. Grabowski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Rakai Health Sciences Program, Baltimore, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, UK
| | - Deenan Pillay
- Africa Health Research Institute, KwaZulu-Natal, South Africa
- Division of Infection and Immunity, University College London, London, UK
| | - Christophe Fraser
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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Abstract
PURPOSE OF REVIEW HIV phylogenetic and molecular epidemiology analyses are increasingly being performed with a goal of improving HIV prevention efforts. However, ethical, legal and social issues are associated with these analyses, and should be considered when performed. RECENT FINDINGS Several working groups have recently outlined the major issues surrounding the use of molecular epidemiology for HIV prevention. First, the benefits of HIV molecular epidemiology remain unclear, and further work is needed to quantitatively demonstrate the benefits that can be expected. Second, privacy loss is an important risk, with implications of disclosure varying by the regional legal and social climate. Inferential privacy risks will increase with technological improvements in sequencing and analysis. Third, data sharing, which enhances the utility of the data, may also increase the risk of inferential privacy loss. Mitigation strategies are available to address each of these issues. SUMMARY HIV molecular epidemiology for research and public health pose significant ethical issues that continue to evolve with improving technology, increased sampling and a changing legal and social climate. Guidance surrounding these issues needs to be developed for researchers and public health officials in an iterative and region specific manner that accounts for the potential benefits and risks of this technology.
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Affiliation(s)
- Sanjay R Mehta
- Departments of Medicine and Pathology, University of California San Diego
- Department of Medicine San Diego Veterans Affairs Medical Center
| | | | - Susan Little
- Department of Medicine, University of California San Diego, San Diego, California, USA
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31
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Wertheim JO, Chato C, Poon AFY. Comparative analysis of HIV sequences in real time for public health. Curr Opin HIV AIDS 2019; 14:213-220. [PMID: 30882486 DOI: 10.1097/coh.0000000000000539] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
PURPOSE OF REVIEW The purpose of this study is to summarize recent advances in public health applications of comparative methods for HIV-1 sequence analysis in real time, including genetic clustering methods. RECENT FINDINGS Over the past 2 years, several groups have reported the deployment of established genetic clustering methods to guide public health decisions for HIV prevention in 'near real time'. However, it remains unresolved how well the readouts of comparative methods like clusters translate to events that are actionable for public health. A small number of recent studies have begun to elucidate the linkage between clusters and HIV-1 incidence, whereas others continue to refine and develop new comparative methods for such applications. SUMMARY Although the use of established methods to cluster HIV-1 sequence databases has become a widespread activity, there remains a critical gap between clusters and public health value.
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Affiliation(s)
- Joel O Wertheim
- Department of Medicine, University of California, San Diego, California, USA
| | | | - Art F Y Poon
- Department of Pathology and Laboratory Medicine
- Department of Microbiology and Immunology, Western University, London, Ontario, Canada
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32
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Rhee SY, Magalis BR, Hurley L, Silverberg MJ, Marcus JL, Slome S, Kosakovsky Pond SL, Shafer RW. National and International Dimensions of Human Immunodeficiency Virus-1 Sequence Clusters in a Northern California Clinical Cohort. Open Forum Infect Dis 2019; 6:ofz135. [PMID: 31041344 PMCID: PMC6483754 DOI: 10.1093/ofid/ofz135] [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: 12/24/2018] [Accepted: 03/12/2019] [Indexed: 11/14/2022] Open
Abstract
Background Recent advances in high-throughput molecular epidemiology are transforming the analysis of viral infections. Methods Human immunodeficiency virus (HIV)-1 pol sequences from a Northern Californian cohort (NCC) of 4553 antiretroviral-naive individuals sampled between 1998 and 2016 were analyzed together with 140 000 previously published global pol sequences. The HIV-TRAnsmission Cluster Engine (HIV-TRACE) was used to infer a transmission network comprising links between NCC and previously published sequences having a genetic distance ≤1.5%. Results Twenty-five percent of NCC sequences were included in 264 clusters linked to a published sequence, and approximately one third of these (8.0% of the total) were linked to 1 or more non-US sequences. The largest cluster, containing 512 NCC sequences (11.2% of the total), comprised the subtype B lineage that traced its origin to the earliest North American sequences. Approximately 5 percent of NCC sequences belonged to a non-B subtype, and these were more likely to cluster with a non-US sequence. Twenty-two NCC sequences belonged to 1 of 4 large clusters containing sequences from rapidly growing regional epidemics: CRF07_BC (East Asia), subtype A6 (former Soviet Union), a Japanese subtype B lineage, and an East/Southeast Asian CRF01_AE lineage. Bayesian phylogenetics suggested that most non-B sequences resulted from separate introductions but that local spread within the largest CRF01_AE cluster occurred twice. Conclusions The NCC contains national and international links to previously published sequences including many to the subtype B strain that originated in North America and several to rapidly growing Asian epidemics. Despite their rapid regional growth, the Asian epidemic strains demonstrated limited NCC spread.
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Affiliation(s)
- Soo-Yon Rhee
- Division of Infectious Diseases, Department of Medicine, Stanford University, California
| | | | - Leo Hurley
- Division of Research, Kaiser Permanente Northern California, Oakland
| | | | - Julia L Marcus
- Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts
| | - Sally Slome
- Department of Infectious Diseases, Kaiser Permanente Northern California, Oakland
| | | | - Robert W Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, California
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Kavanagh MM, Baral SD, Milanga M, Sugarman J. Biometrics and public health surveillance in criminalised and key populations: policy, ethics, and human rights considerations. Lancet HIV 2018; 6:S2352-3018(18)30243-1. [PMID: 30305236 DOI: 10.1016/s2352-3018(18)30243-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 08/22/2018] [Accepted: 08/28/2018] [Indexed: 01/04/2023]
Abstract
Widespread public health surveillance efforts focused on key populations (men who have sex with men, sex workers, people who inject drugs, and others) gather data on population sizes, HIV prevalence, and other information for planning and resource allocation. Biometric identification might improve this data gathering. However, in the context of extensive criminalisation of these populations, the use of biometrics such as fingerprints raises concerns that are insufficiently addressed in current policies. These concerns include infringing privacy, exposing participants to risks of legal action or violence, biasing surveillance results, and undermining trust in the health system. We set out key ethics and human rights considerations regarding the use of biometrics in HIV surveillance among these populations, and outline a typology of jurisdictions wherein such methods might be considered, based on data about legal, political, and social environments. In this Review, we suggest that the biometrics approach is not currently likely to be appropriate in many jurisdictions.
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Affiliation(s)
- Matthew M Kavanagh
- O'Neill Institute of National & Global Health Law, Georgetown University, Washington, DC, USA.
| | - Stefan D Baral
- Department of Epidemiology, Johns Hopkins University, Baltimore, MD, USA
| | | | - Jeremy Sugarman
- Berman Institute of Bioethics and Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
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