HIV 2015: Using Phylogenetics to Enhance the HIV Response

HIV 2015: Using Phylogenetics to Enhance the HIV Response

Thursday, June 4, 2015

The New York Academy of Sciences

Rapid advances in molecular genetics and bio-informatics allow more and better data on the phylogeny of HIV to be collected. The genetic diversity among HIV strains within individual patients, communities and globally allows the dynamics of transmission and evolution of the virus to be studied in ever greater detail. The implications for drug resistance, vaccine development, transmission networks and evaluation of prevention interventions are beginning to be understood. The challenge is to translate the new science into more effective ways to prioritize the HIV response and to monitor the impact of different intervention approaches. This meeting brings together scientists, policy makers, and international organizations dedicated to advancing our scientific knowledge of HIV and translating that information into the most effective programs for reducing transmission of the virus.

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Presented by

  • Global Fund
  • UNAIDS
  • The New York Academy of Sciences

**Note: The HIV 2015: Using Phylogenetics to Enhance the HIV Response symposium is cosponsored by the Joint United Nations Programme on HIV/AIDS (UNAIDS). The views expressed in symposium materials or publications, by speakers and moderators, or by any symposium cosponsors do not necessarily reflect the official views or policies of UNAIDS; nor does mention of trade names, commercial practices, or organizations imply endorsement by UNAIDS.


The Microbiology & Infectious Diseases Discussion Group is proudly supported by

  • Pfizer

Agenda

* Presentation titles and times are subject to change.


Thursday, June 4, 2015

8:30 AM

Registration and Continental Breakfast

Session I. Situation Report

Moderator: Sonya Dougal, PhD, The New York Academy of Sciences

9:00 AM

Welcome Remarks
Sonya Dougal, PhD, The New York Academy of Sciences

9:10 AM

Opening Remarks
Luiz Loures, MD, MPH, UNAIDS

9:25 AM

PEPFAR 3.0
Maureen Goodenow, MD, Office of the U.S. Global AIDS Coordinator

9:40 AM

The Global Fund, New Funding Model; Focusing for Impact
Ade Fakoya, MSc, MB, BS, FRCP (UK), The Global Fund to Fight AIDS, Tuberculosis and Malaria

9:55 AM

Phlyogenetics of HIV – An Introduction and Latest Approaches – Laboratory Approaches and Bioinformatics
Tulio de Oliveira, PhD, Wellcome Trust Africa Centre for Health and Population Studies

10:10 AM

Discussion

10:30 AM

Networking Coffee Break

Session II. Recent Advances in the Phylogenetics of HIV – Relevance to Current Program Directions

Moderator: Morgane Rolland, PhD, Walter Reed Army Institute of Research

11:00 AM

Adapting to Changing Environments – The Role of Fitness and Intrinsic Immune Escape in Transmission and Progression
Jonathan M. Carlson, PhD, Microsoft Research

11:15 AM

Phylogenetics, Transmission Networks, and Drug Resistance: Bringing It All Together
Alexa Oster, MD, Centers for Disease Control and Prevention

11:30 AM

Phylogenetics and Transmission – Insights into Interrupting Transmission Chains
Christophe Fraser, PhD, Imperial College

12:00 PM

Discussion

12:30 PM

Networking Lunch Break

Session III. Phylogenetics to Support HIV Prevention Research

Moderator: Kate Thompson, The Global Fund to Fight AIDS, Tuberculosis and Malaria

1:30 PM

Phylogenetics and Vaccine Development – Diversity and What it Means
Morgane Rolland, PhD, Walter Reed Army Institute of Research

1:45 PM

Phylodynamic Analysis of Linkage between Key and General Populations in Abuja Nigeria
William A. Blattner, MD, MS, University of Maryland, College Park

2:00 PM

Phylogenetics and Recent Infections in Rakai, Uganda
Thomas Quinn, MD, Johns Hopkins University

2:15 PM

HIV Gene Sequencing: Identifying who is Infecting who in a Rural South African Community
Ayesha Kharsany, PhD, Center for the AIDS Program of Research in South Africa (CAPRISA)

2:30 PM

PANGEA-HIV: Phylogenetics for Generalised Epidemics in Africa
Tulio de Oliveira, PhD, Director of the Africa Centre for Health and Population Studies, University of KwaZulu-Natal; University College London

2:45 PM

Discussion

3:15 PM

Networking Break

Session IV. Discussion Panel – Uses (and abuses) of Phylogenetics

Moderator: Peter Godfrey-Faussett, BA, MBBS, DTM&H, FRCP (UK), UNAIDS

3:45 PM

Phylogenetics for Communities and Policy-makers – What do we Need to Know Now and Tomorrow

Panelists:
Ralf Jürgens, LLM, PhD, The Global Fund to Fight AIDS, Tuberculosis and Malaria
Joanne Csete, PhD, Columbia University Mailman School of Public Health
Mark Harrington, Treatment Action Group
Maureen Goodenow, MD, Office of the U.S. Global AIDS Coordinator
Kate Thompson, The Global Fund to Fight AIDS, Tuberculosis and Malaria

Session V. Closing Remarks

Moderator: Peter Godfrey-Faussett, BA, MBBS, DTM&H, FRCP (UK), UNAIDS

4.45 PM

Closing Thoughts on the Way Forward
The Joint United Nations Program on HIV/AIDS
Office of the U.S. Global AIDS Coordinator
The Global Fund to Fight AIDS, Tuberculosis and Malaria

5:00 PM

Networking Reception

6:00 PM

Adjourn

Speakers

Organizers

Tulio De Oliveira, PhD

Wellcome Trust Africa Centre for Health and Population Studies

Ade Fakoya, MD

The Global Fund to Fight AIDS, Tuberculosis and Malaria

Dr. Ade Fakoya, MD is a clinician and specialist in HIV and International Health with over 20 years national and international experience in HIV, STI clinical care, service management and programme delivery. He is currently Senior Disease Coordinator, HIV at the Global Fund to Fight AIDS, Tuberculosis and Malaria based in Geneva. Dr. Fakoya has previously held technical, senior management and research posts working in the UK and Internationally. Over the last 3 years his team have provided technical support and coordinated partner technical cooperation which has seen the approval of over 5 billion USD in Global Fund phase 2 and new funding model HIV grants.

His areas of experience include HIV clinical care and treatment, prevention, and care, ARV scale up and provision of STI clinical services. He has provided technical support to national HIV programmes in Africa, Asia and Latin America. He has sat on a number of national and international advisory committees including those for ARV treatment guidelines, prevention of mother to child transmission guidelines and Sexual and Reproductive Health (SRH). His current interests include improving access to anti-retroviral treatment, PMTCT implementation, HIV and TB integration and the role of disease specific funding initiatives in health systems strengthening.

Peter Godfrey-Faussett, BA, MBBS, DTM&H, FRCP(UK)

UNAIDS

Peter Godfrey-Faussett is a professor at the LSHTM and consultant physician at the Hospital for Tropical Diseases. After training in clinical infectious diseases and molecular genetics, he spent five years leading the Zambian AIDS-related TB (ZAMBART) project, an interdisciplinary collaborative research programme between the LSHTM, Lusaka Urban District Health Management Team and the University of Zambia. Thereafter he spent a year working with the Global Tuberculosis Programme of the World Health Organization, where he was responsible for developing strategies to address the combined epidemic of TB and HIV. Following his return to London he has maintained an interest in global policies around TB and HIV and served as chairman for the Technical Review Panel of the Global Fund against AIDS, Tuberculosis and Malaria. A regular member of WHO expert groups, his research interests remain focused on the impact that the HIV epidemic is having on TB control and on interventions to reduce both diseases.  He is currently seconded full-time to UNAIDS, where he is the Senior Science Adviser with a wide ranging portfolio including HIV cure, ARV-based HIV prevention, HIV vaccines and synergies between the HIV and the non-commnicable disease response.

Morgane Rolland, PhD

Walter Reed Army Institute of Research

Dr. Rolland is chief of the viral genetics section at the US Military HIV Research Program (MHRP) in Silver Spring, Maryland, United States. She obtained her PhD from the University of Bordeaux, France in 2003. She completed a post-doctoral fellowship with Professor James I. Mullins in the Microbiology department of the University of Washington in Seattle between 2004 and 2010.

Dr. Rolland's interests focus on understanding features of HIV-1 genetics and evolution that are important to HIV vaccine-related research. Her research work is centered on the interplay between HIV-1 genetics and the host immune pressure, principally focusing on HIV-1 vaccine design and the analysis of HIV-1 evolution during acute/early infection, including the study of HIV breakthrough infections in vaccine efficacy trials.

Sonya Dougal, PhD

The New York Academy of Sciences

Dr. Sonya Dougal serves as the Director of Life Sciences Discussion Groups at the New York Academy of Sciences. In this role, she provides strategic development and oversight of an annual portfolio of scientific workshops on pressing topics across the life sciences and biomedical research. Dr. Dougal has over 14 years of experience in scientific research and program management in academia, industry, and the non-profit sector. She received her bachelor's degree with honors from the University of Massachusetts, Amherst and her PhD in Cognitive Psychology from the University of Pittsburgh. She was the recipient of a Ruth L. Kirschstein National Research Service Award from the National Institutes of Health for her postdoctoral training as a cognitive neuroscientist in the laboratory of Dr. Elizabeth Phelps at New York University.

Speakers

William A. Blattner, MD

Institute of Human Virology, School of Medicine, University of Maryland

William A. Blattner MD, Co-Founder and Associate Director of the Institute of Human Virology (IHV) and Professor of Medicine, School of Medicine, University of Maryland, is share Principal Investigator of the NIH sponsored TRUST study. TRUST, building upon his research among key populations (KP) that date back to the early 1980’s, examines the impact of providing prevention and treatment as prevention services in a trusted community-based venue in Abuja Nigeria. TRUST engages a multi-institutional, multidisciplinary team that includes application of phylodynamic modeling approaches to gain insights for cost effective and impactful interventions among KP. His 400 plus publications include the first peer-reviewed publication of the sensitivity and specificity of the HIV blood test and molecular epidemiological analyses of HIV acquisition and natural history. Founder of IHV-Nigeria, he led the roll out of a President’s Emergency Plan for AIDS Relief (PEPFAR) program that screened over 2 million Nigerians for HIV infection, placed 160,000 on treatment while building with NIH Fogarty and research funding a Nigerian research center of excellence that includes the IHVN WHO Accredited Molecular Virology Laboratory that provided world class sequence data for the current presentation. He is founding Editor-in-Chief of the Journal of Acquired Immune Deficiency Syndromes.

Jonathan Carlson, PhD

Microsoft Research

Jonathan Carlson, Ph.D., is a researcher at Microsoft Research, where he studies viral evolution, immunology and vaccine design through statistical modeling. His models of viral escape have achieved broad recognition in the HIV community, where they have led to the discovery of important viral-host interactions and insights into mechanisms of natural immune control. He has served on advisory panels and committees for the Institute of Medicine, the Gates Foundation and the Center for HIV/AIDS Vaccine Immunology. In 2009, he received his Ph.D. in computer science and computational molecular biology from the University of Washington, where he studied under David Heckerman (Microsoft Research) and Larry Ruzzo (UW) and was given the university’s Distinguished Dissertation Award. He received his B.A. in Biology and Computer Science from Dartmouth in 2003, where he studied the bioinformatics of transcriptional regulation under Bob Gross.

Joanna Csete, PhD, MPH

Columbia University Mailman School of Public Health

Joanne Csete is an adjunct professor at the Columbia University Mailman School of Public Health where she was formerly a full-time associate professor. She was the founding director of the HIV Program at Human Rights Watch, executive director of the Canadian HIV/AIDS Legal Network and deputy director of the Global Drug Policy Program of the Open Society Foundations. She was a senior advisor for health and nutrition in UNICEF and chief of program planning in the UNICEF regional office in Nairobi. She worked on health programs in Africa for over ten years and has written widely on health services for criminalized populations, including people who use drugs, sex workers and prisoners. She was an assistant professor at the University of Wisconsin-Madison.

Tulio De Oliveira, PhD

Wellcome Trust Africa Centre for Health and Population Studies

Prof Tulio de Oliveira is A Professor in the Wellcome Trust Africa Centre for Health and Population Studies at School of Laboratory Medicine & Medical Sciences, College of Health Sciences, UKZN, South Africa. He was a Marie Curie research fellow at the University of Oxford, UK, where he received in depth training on virus genetic analysis and molecular evolution. He is recognized as an expert on HIV genetic data and bioinformatics and has published some high-impact articles including the one that presents the Rega Subtyping tools, one that proof the innocence of the six foreign medical personnel condemned to death for infecting with HIV 438 children in a hospital in Libya, open access and public HIV drug resistance databases in Africa and the first case of proven HIV surrogate transmission in South Africa. His group website (www.bioafrica.net) hosts popular open access bioinformatics tools and databases (Science Netwatch 2005; Nature 2010).

Ade Fakoya, MD

The Global Fund to Fight AIDS, Tuberculosis and Malaria

Dr. Ade Fakoya, MD is a clinician and specialist in HIV and International Health with over 20 years national and international experience in HIV, STI clinical care, service management and programme delivery. He is currently Senior Disease Coordinator, HIV at the Global Fund to Fight AIDS, Tuberculosis and Malaria based in Geneva. Dr. Fakoya has previously held technical, senior management and research posts working in the UK and Internationally. Over the last 3 years his team have provided technical support and coordinated partner technical cooperation which has seen the approval of over 5 billion USD in Global Fund phase 2 and new funding model HIV grants.

His areas of experience include HIV clinical care and treatment, prevention, and care, ARV scale up and provision of STI clinical services. He has provided technical support to national HIV programmes in Africa, Asia and Latin America. He has sat on a number of national and international advisory committees including those for ARV treatment guidelines, prevention of mother to child transmission guidelines and Sexual and Reproductive Health (SRH). His current interests include improving access to anti-retroviral treatment, PMTCT implementation, HIV and TB integration and the role of disease specific funding initiatives in health systems strengthening.

Christophe Fraser, PhD

Imperial College

Maureen M. Goodenow, PhD

US Department of State

Maureen M. Goodenow, PhD is newly appointed as Senior Advisor and Acting Director of the Office of Research and Science within the office of the US Global AIDS Coordinator and Health Diplomacy [S/GAC] at the US Department of State in Washington, DC.  At S/GAC, she is responsible for managing a portfolio of three large international combination HIV prevention clinical studies, a program of implementation science and impact evaluation projects, interagency relations related to PEPFAR, as well as the Scientific Advisory Board and Expert Working Groups for Ambassador Deborah Birx, the US Global AIDS Coordinator. Dr. Goodenow was a Jefferson Science Fellow from 2012 to 2013 in the Bureau of Asia Pacific Affairs/Office of Economic Policy where she was responsible for health, science, technology, and innovation within APEC [Asia Pacific Economic Cooperation], including organizing interagency working groups, participating in bilateral meetings with APEC economies, serving as US government lead at High Level Meetings for Health and the Economy attended by ministers of health from Asia Pacific region, and co-organizing international policy dialogues on HIV-1, health-care associated infections, multi-drug resistance tuberculosis, cervical cancer, and blood supply safety.

Dr.Goodenow’s activities at S/GAC are in partnership with the University of Florida, where she is Professor of Pathology, Immunology, and Laboratory Medicine in the College of Medicine, holds the Stephany W. Holloway Endowed Chair for HIV/AIDS Research, is the Chair of the Global Health Council, and is the Director of the Center for Research in Pediatric Immune Deficiency.  Professor Goodenow has a research program in molecular epidemiology, pathogenesis, and vaccines for HIV-1 and human papillomaviruses. Her research involves implementation of technology, including high-throughput next generation genomics, bioinformatics and systems biology, to solve problems of human-pathogen interactions from a global health perspective.

Professor Goodenow received a PhD in molecular genetics from the Sue Golding Graduate School at the Albert Einstein College of Medicine in New York.  Following a postdoctoral fellowship in molecular oncology at the Sloan Kettering Institute in New York, she was a visiting scientist at the Pasteur Institute in Paris before accepting a faculty position at the University of Florida in the College of Medicine. She has published over 100 articles and book chapters, serves on the editorial boards of numerous journals, advises the NIH on merits of scientific proposals and the Trans-NIH Plan for HIV-Related Research in the Office of AIDS Research, and is a former member of the AIDS Research Advisory Committee for the Division of AIDS in the National Institute of Allergy and Infectious Diseases at NIH. She provided advice to the combined program between NIH and Department of State for enhancing research between US and Russian scientists, as well as to Fogarty Programs in India and Kazakhstan and to medical fellowship training programs in Brazil.

Ayesha Kharsany, PhD

Center for the AIDS Program of Research in South Africa (CAPRISA)

Ayesha Kharsany, PhD, is a Senior Scientist at CAPRISA and has an honorary position as Professor in Medical Microbiology, University of KwaZulu-Natal. Her main research interests are in understanding the evolving HIV epidemic in South Africa, factors influencing acquisition and reducing young women’s vulnerability to HIV infection, and sexually transmitted infections. She has played a key role in CAPRISA’s research on young women and microbicides. She leads the HIV surveillance studies and is currently the PI of the CDC funded population-level HIV Incidence Provincial Surveillance System (HIPSS) platform and the NIH funded Adolescent HIV Transmission Network studies.

Luiz Loures, MD, MPH

UNAIDS

Luiz Loures joined UNAIDS in 1996 and was appointed Deputy Executive Director of Programme and Assistant Secretary-General of the United Nations in January 2013. He leads UNAIDS’ efforts in leveraging critical support to countries to meet the 2015 global AIDS targets and establish a sustainable response to AIDS.

Dr. Loures is a medical doctor with nearly 30 years’ experience in the AIDS response. His engagement ranges from providing medical care to people living with HIV in the early days of the epidemic––to his dynamic involvement in global policy framework development. In 2006, Dr. Loures was granted the Make a Difference Award for his long-standing contribution to the global response to AIDS by O Globo, one of Brazil’s largest newspapers.

Previously, Dr. Loures was Director of the Political and Public Affairs Branch of UNAIDS where he managed strategic and political processes to promote UNAIDS’ vision and enable effective implementation of the corporate agenda. Prior to this, Dr. Loures was the Director of UNAIDS’ Executive Office, overseeing strategic direction and assisting the Executive Director in implementing the UNAIDS strategy. He also managed UNAIDS’ activities in the Americas and Europe as the Associate Director of the Country and Regional Support Department.

Before joining UNAIDS Dr. Loures served in various capacities within the Ministry of Health in Brazil. He participated actively in the creation and consolidation of Brazil’s National AIDS Programme—which is widely recognized today as being one of the most effective in curbing the epidemic. Dr. Loures was directly responsible for designing the programme for universal access to antiretroviral therapy for people living with HIV in Brazil. In the early 1980’s as a pioneer in the AIDS response, Dr. Loures diagnosed some of the first patients with AIDS-related illnesses in Brazil.

Born, raised and educated in Brazil, Dr. Loures completed his medical studies at the Federal University of Minas Gerais, specializing in critical care. He holds an MPH degree from the University of California at Berkeley and speaks Portuguese, Spanish, English and French.

Alexa Oster, MD

Centers for Disease Control and Prevention

Alexa Oster is a medical epidemiologist in the Division of HIV/AIDS Prevention at the Centers for Disease Control and Prevention in Atlanta, Georgia, where she serves as Lead for Molecular HIV Surveillance. Alexa has worked in the Division of HIV/AIDS Prevention since 2007, and during that time has led analyses and publications of data from behavioral and clinical surveillance, case-control studies, phylogenetic analysis, and network analysis. Her areas of interest include sexual and transmission networks, racial and ethnic disparities, engagement in health care, and temporal trends in HIV infection and testing. Alexa graduated from Vanderbilt University with majors in Linguistics and Molecular Biology and a minor in Spanish. After attending the University of Pennsylvania School of Medicine, she completed her residency in Primary Care Internal Medicine at the University of California, San Francisco/San Francisco General Hospital.

Thomas Quinn, MD

Johns Hopkins University

Dr. Thomas Quinn is Senior Investigator and Head of the Section on International HIV/AIDS Research in the Laboratory of Immunoregulation at the National Institute of Allergy and Infectious Diseases. He is also Associate Director for International Research for the Division of Intramural Research at NIAID. In addition he is Professor of Medicine and Pathology in the Johns Hopkins School of Medicine and Professor of International Health, Epidemiology, and Immunology and Molecular Microbiology in The Johns Hopkins School of Public Health. In 2006 he was appointed founding Director of the Johns Hopkins Center for Global Health. His research interests have involved laboratory and field investigations that have helped define the biological factors involved in sexual and perinatal transmission of HIV, the natural history and treatment of HIV infections, and the molecular epidemiology of HIV. He is a member of the Institute of Medicine and Fellow of the American Association for the Advancement of Science. He is an author of over 950 publications on HIV, STDs, and infectious diseases.

Morgane Rolland, PhD

Walter Reed Army Institute of Research

Dr. Rolland is chief of the viral genetics section at the US Military HIV Research Program (MHRP) in Silver Spring, Maryland, United States. She obtained her PhD from the University of Bordeaux, France in 2003. She completed a post-doctoral fellowship with Professor James I. Mullins in the Microbiology department of the University of Washington in Seattle between 2004 and 2010.

Dr. Rolland's interests focus on understanding features of HIV-1 genetics and evolution that are important to HIV vaccine-related research. Her research work is centered on the interplay between HIV-1 genetics and the host immune pressure, principally focusing on HIV-1 vaccine design and the analysis of HIV-1 evolution during acute/early infection, including the study of HIV breakthrough infections in vaccine efficacy trials.

Doug Shaffer, RPh, MD, MHS

Office of the U.S. Global AIDS Coordinator, U.S. Department of State

Dr. Shaffer is the Chief Medical Officer for the Office of the U.S. Global AIDS Coordinator. Doug is focused on optimizing HIV prevention, care, and treatment services with parallel development of integrated research capacity and leadership. Prior to this appointment, Doug was a practicing physician and lecturer in Kenya, and was instrumental in leading the U.S. Government collaboration with the Government of Kenya during the roll out of HIV services under the President's Emergency Plan for AIDS Relief (PEPFAR). He was also a Principal Investigator for the U.S. Military HIV Research Program AIDS Clinical Trials Group (ACTG) where he joined and mentored researchers in Africa on over 40 studies covering HIV epidemiology, health economics, and Phase I-III vaccine and therapeutic clinical trials (including tuberculosis and malaria co-infections).

Kate Thompson, MA

The Global Fund

Kate Thomson is Head of the Community, Rights and Gender department at the Global Fund to Fight AIDS, Tuberculosis and Malaria, having joined in September 2013 when the department was created. She was previously at Global Fund from 2002 to 2004, moving to Geneva just after its establishment, working as the Civil Society Relations Manager.

From 2005-2013, Kate was based at the Geneva Headquarters of UNAIDS where she led the Civil Society partnerships team, and then the Community Mobilization division. Shortly after joining UNAIDS she and a number of other staff members formed the UN system HIV-Positive Staff Group (UN+) with over 200 members working across the UN system. In her role at UNAIDS, Kate had overall responsibility for collaboration with diverse civil society groups, such as faith based organizations, national and international NGOs, organizations of people living with HIV and key population networks. She oversaw civil society participation strategy and policy development and in events such as High Level Meetings in the UN General Assembly.

Kate has been active in the global AIDS response for more than a quarter century, beginning in early 1987 when she helped to establish Positively Women, a UK based peer led support organization for women living with HIV. She subsequently worked as its coordinator for several years. In 1992 she was among fifty or so women who formed the International Community of Women living with HIV/AIDS (ICW).

Panelists

Mark Harrington

Treatment Action Group

Mark Harrington joined the seminal AIDS activist group, ACT UP (the AIDS Coalition to Unleash Power) in 1988, five years after receiving his bachelor’s degree from Harvard University. As a member of ACT UP’s Treatment and Data Committee, Mark helped plan and execute ACT UP’s “Seize Control of the FDA” demonstration in 1988 and its “Storm the NIH” demonstration in 1990. The events helped initiate a fundamental shift in regard to how the U.S. Food and Drug Administration (FDA), the U.S. National Institutes of Health (NIH), and other government agencies addressed HIV community health priorities. He was a founding member of the US AIDS Clinical Trials Group (ACTG) Community Constituency Group, serving from 1990 to 1993 on the ACTG Opportunistic Infections and Primary Infection Committees. In 1992, Mark and 20 other AIDS activists cofounded the Treatment Action Group (TAG). The group scored its first major victory when a groundbreaking report he coauthored with Gregg Gonsalves, AIDS Research at the NIH: A Critical Review (1992), led to federal legislation restructuring the NIH AIDS research effort and strengthening the NIH Office of AIDS Research, signed into law by President Bill Clinton in June 1993. In 1993, he wrote The Crisis in Clinical AIDS Research, an exposé of inadequate clinical trials then being carried out by the ACTG, the U.S. Department of Defense, and others. He served as an ad hoc community representative at several meetings of the FDA Antiviral Drugs Advisory Committee, and  also served on the NIH AIDS Research Program Evaluation Working Group (the Levine Committee), whose 1996 report called for sweeping restructuring of the NIH AIDS research program. Mark served on the U.S. Department of Health and Human Services (DHHS) Panel on Antiretroviral Guidelines for Adults and Adolescents from 1996 to 2008. Mark has coauthored papers published in the Clinical Infectious Diseases, The Lancet, PloS Medicine, and Science. Since 2002 Mark has been executive director of Treatment Action Group (TAG), overseeing policy advocacy work on research, prevention, treatment, policy, and access for people living with and at risk for HIV, hepatitis C virus (HCV), and tuberculosis (TB). In 2012 the Health Global Access Project (HealthGAP) awarded Mark the Evan Ruderman Global Health Justice award. In October 2014 Mark was appointed to New York State Governor Andrew Cuomo’s Ending the Epidemic Task Force. He co-chaired the Task Force’s Data Committee. On April 29, 2015, Governor Cuomo accepted the Blueprint containing the Task Force’s recommendations to end AIDS as an epidemic by 2020.

Ralf Jürgens, LLM, PhD

Open Society Foundations

Ralf Jürgens recently joined the Global Fund to Fight AIDS, TB and Malaria in Geneva as its Senior Human Rights Adviser.

Until May 2015, he was director of programs for the Open Society Public Health Program in New York City, overseeing strategy development and implementation, staff learning, and day-to-day management. Prior to that role, Jürgens was the director of the Law and Health Initiative of the Open Society Public Health Program, where he supported legal strategies to advance the health and human rights of marginalized and vulnerable people.

Before joining the Open Society Foundations in 2012, Jürgens co-founded and served as executive director of the Canadian HIV/AIDS Legal Network and consulted on health policy and human rights for many organizations, including the International HIV/AIDS Alliance, the Global Fund to Fight AIDS, TB and Malaria, the World Health Organization, and the International Affairs Directorate of Health Canada.

Jürgens is a member of the UNAIDS Reference Group on HIV and Human Rights, and of the World Health Organization’s Strategic and Technical Advisory Committee for HIV/AIDS. He is the recipient of the International Rolleston Award and the Award for Action on HIV/AIDS and Human Rights.

Jürgens has a master’s degree in law from McGill University and a doctorate in law from the University of Munich.

Moderator

Peter Godfrey-Faussett, BA, MBBS, DTM&H, FRCP(UK)

UNAIDS, Geneva, Switzerland

Sponsors

Grant Support

This program is supported by an educational grant from Gilead Sciences, Inc.

Promotional Partner

AVAC

Buddies of NJ, Inc.

Caribbean Health Aids Day

Gene Therapy

Global HIV Vaccine Enterprise

Immunology & Cell Biology

Nature

Nature Reviews Nephrology

POPULATION COUNCIL

Presented by

  • Global Fund
  • UNAIDS
  • The New York Academy of Sciences

**Note: The HIV 2015: Using Phylogenetics to Enhance the HIV Response symposium is cosponsored by the Joint United Nations Programme on HIV/AIDS (UNAIDS). The views expressed in symposium materials or publications, by speakers and moderators, or by any symposium cosponsors do not necessarily reflect the official views or policies of UNAIDS; nor does mention of trade names, commercial practices, or organizations imply endorsement by UNAIDS.


The Microbiology & Infectious Diseases Discussion Group is proudly supported by

  • Pfizer

Abstracts

Phylodynamic Analysis of Linkage between Key and General Populations in Abuja Nigeria
William A. Blattner MD2

We analyzed HIV-1 pol sequences from a cohort of men who have sex with men (MSM)(N=151) in Abuja, Nigeria from 2012-2014, and compared to samples from the general population of Abuja (2011-2014)(N=150).  Data were examined for evidence of higher transmission rates in MSM and evidence that HIV in the general population is attributed to sex between men. We observed several clades of predominantly MSM patients in a paraphyletic relationship with samples from the general population, suggesting a source-sink epidemiological relationship. To estimate transmission rates within and between MSM and the general population, we developed a dynamical infectious disease model which accounted for stage of infection, sex, risk group, and variable force of infection through time. This model was fitted to merged time-scaled phylogenies for subtypes CRF02_AG and G using a structured-coalescent approach. This yields estimates of incidence of infection in MSM of 12.5% (95%CI: 9.0-17.6) per susceptible person year (similar to the rate observed in prospective follow up of the MSM TRUST cohort).  We estimate the population attributable fraction (PAF) of transmissions from MSM to females in the general population as 4.1% (95%CI: 2.7-5.7), and from the general population to MSM as 0.2%(95%CI: 0.06-0.3). While recent incidence of infection has fallen in Nigeria among the general population, prevalence and incidence have increased in the MSM population, highlighting the importance of addressing the prevention and treatment needs of key populations in the context of generalized epidemics of Sub-Saharan Africa in order to achieve full epidemiological control.
 
Coauthors: Erik Votz PhD1*, Man Charurat PhD2*, Nicaise Ndembi PhD3, Rebecca Nowak PhD2, Gustavo Kijak PhD4, Mark Dybul MD5, John Idoko MD6, Patrick Dakum MD3, Joyce Johnson2, Walter Royal MD2, Stefan Baral MD7
*Denotes Co-first author
1 Department of Infectious Disease Epidemiology, Imperial College, London UK
2 Institute of Human Virology, School of Medicine University of Maryland, Baltimore, Maryland USA
3 WHO Accredited Molecular Virology Laboratory, Institute of Human Virology Nigeria, Abuja Nigeria
4 Viral Sequencing Core, MHRP, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
5 Global Fund to Fight AIDS, Tuberculosis and Malaria, Geneva, Switzerland
6 National Agency for Control of AIDS, Abuja Nigeria
7 Center for Public Health and Human Rights, Johns Hopkins University, Baltimore, Maryland USA

 

Adapting to Changing Environments—The Role of Intrinsic Fitness and Immune Escape in Transmission and Progression
Jonathan M Carlson, PhD, Microsoft Research, Redmond, Washington, United States

The high rate of HIV-1 mutation provides an ideal evolutionary substrate for rapid adaptation to changing environments. In a typical donor-recipient transmission pair, the virus must navigate three distinct environments: 1) the adaptive immune response of the donor; 2) the immunologically naïve mucosal compartment of the prospective recipient; and 3) the adaptive immune response of the new recipient. In each of these stages, evolution selects for viral variants that maximize the “intrinsic” fitness of the virus while minimizing the costs imposed by the host immune responses. By studying large viral phylogenies with linked host genetics and clinical outcomes, the characteristics of the underlying fitness function begins to emerge. Intrinsic fitness has been shown to play a clear role in all stages, highlighting the role of viral genetics in shaping these events. However, strong interactions with the host environment are critical. In the context of transmission, modeling and empirical data indicate that intrinsic fitness is primarily important when the prospective new host is relatively resistant to infection, raising concerns about unintended consequences of certain prophylactic interventions. In the context of chronic infection, selection of cellular immune escape mutations, while frequently reducing intrinsic fitness, nevertheless associates with substantially faster rates of progression. When such mutations are transmitted, their effect depends on the genetics of the new host. More rapid progression is observed when mutations confer escape in the new host; slower progression is observed when they do not. Overall, the combination of host and viral genetics are critical to defining clinical outcomes, and thus have strong implications for the design and monitoring of intervention strategies.
 

HIV Phylogenetics and Human Rights:  How to Avoid Misuse of a New Tool
Joanne Csete, PhD, Columbia University, New York, New York

The advantages of the use of HIV phylogenetic testing and mapping for improving treatment and “treatment as prevention” outcomes should be weighed against the disadvantages of potential harms faced by those identified and singled out as “drivers” of the epidemic. Identifying traits of persons likely to be involved in transmission may be useful clinically, but it is potentially dangerous to especially to people already marginalized and stigmatized, including those facing unjust criminalization of sexual orientation, sex work and minor drug offenses. These persons may be harmed by any intervention that brings them or the places where they reside, work or socialize to the attention of the police and other authorities.  As UNAIDS has noted, in places where HIV transmission and exposure are criminalized, phylogenetic information may be used in criminal proceedings.  Misinterpretation of phylogenetic evidence can lead to unjust outcomes of court cases. This presentation will discuss measures that should be taken to protect against the use of phylogenetic data to undermine human rights.
 

PANGEA-HIV: phylogenetics for generalised epidemics in Africa
Tulio de Oliveira, Wellcome Trust Africa Centre for Health and Population Studies

The Phylogenetics and Networks for Generalized HIV Epidemics in Africa consortium (PANGEA-HIV) is an international partnership to use viral sequence analyses to assess the transmission of HIV in Africa. The aims of PANGEA-HIV include to sequence 20 000 total HIV genomes from several African study sites, with every genome sequence linked to clinical, demographic, and epidemiological data; and to direct the development of phylogenetic methods to address key challenges and opportunities in measuring, understanding, and controlling HIV transmission in generalised epidemics.
 
Coauthors: Pillay D, Herbeck J, Cohen MS, Fraser C, Ratmann O, Brown A-L, Kellam P, on behalf of the PANGEA-HIV Consortium
 

The Global Fund - Investing and Focusing for Impact
Ade Fakoya, MD and Kate Thompson, MA, The Global Fund

The Global Fund is an innovative public private partnership which to date has committed funds from bilateral, donor government and the private sector of over 43 billion USD. By mid-2014 HIV signed proposals totalled 16.7 billion USD.  Since its conception the Global Fund has invested resources based on national country proposals to deliver impact across HIV, Tuberculosis and Malaria in addition to directly and indirectly strengthening health and community systems.
Scientific and programmatic advances bring us to an era where ending HIV as a public health threat- that is gaining epidemiological control, is eminently conceivable within the next 15 years. This presentation will describe how the Global Fund, working in partnership aims to maximise impact by, differentiating responses based on local epidemiology,  supporting countries to focus on the highest impact  interventions,  addressing human rights and stigma constraints and leveraging partnerships in health diplomacy to increase domestic financial contributions.
The Global Fund is moving to the end of its current 2012-2016 strategy, and embarking on consultations for the needs assessment and strategic directions of the 2017-2021 period. Driving towards greater focus on data driven programming and the targeting of interventions continues to be critical particularly in a cost- constrained situation.
 

PEPFAR 3.0
Maureen M Goodenow, PhD1

Thirty million individuals are estimated to be living with HIV/AIDS. Although HIV-1 incidence is declining globally, the reduction is unequal across countries. The President’s Emergency Fund for AIDS Relief (PEPFAR) was initiated in 2003 as the largest response to the HIV/AIDS epidemic and is responsible for providing antiretroviral therapy to more than 7.7 million individuals. The current phase of PEPFAR, titled PEPFAR 3.0, aims to apply a fast track approach to achieve epidemic control by doing the right things in the right place, right now.  As compared to current programming approaches, this fast track approach has the potential to avert 28 million HIV infections over the next five years. PEPFAR 3.0 rests on the pillars of accountability, transparency and impact and will be achieved through a data driven approach to improve the quality of program planning and implementation.  Various data streams including cost data, program monitoring data, geospatial and epidemiologic data are being analyzed and triangulated to inform strategic program implementation at the most local level, the site.  Phylogenetic data can be utilized for PEPFAR’s fast track strategy due to recent developments in viral sequencing, bioinformatics and analytic techniques for large-scale data, and reductions in viral sequencing costs.  Phylogenetic data, when paired with geospatial and epidemiologic data, have the potential to provide a comprehensive understanding of current HIV transmission and inform more targeted programming of the right things, in the right place at the right time.

Coauthors: Delivette Castor, PhD,1,2Nancy Padian, PhD,3 Julia J Mackenzie, PhD,1 and Douglas N Shaffer, MD1

1 Office of the U.S. Global AIDS Coordinator, Office of Research and Science, U.S. Department of State, Washington, District of Columbia, USA
2 Office of HIV/AIDS, Technical Leadership and Research, United States Agency for International Development, Washington, District of Columbia, USA
3 Division of Epidemiology, School of Public Health, University of California, Berkeley, CA, USA

 

HIV Gene Sequencing: Identifying Who is Infecting Who in a Rural South African Community
Ayesha BM Kharsany, PhD1,2

Despite the availability of behavioral interventions to reduce sexual transmission of HIV, adolescent girls remain disproportionately affected by the HIV epidemic. Strategies to reduce HIV transmission in this key population would benefit greatly from a better understanding of the sexual networks that drive HIV transmission in adolescent girls. Furthermore, if HIV infection rates in adolescent girls can be reduced, this could break critical chains of transmission and decrease the spread of HIV in the general population. The goal of this project is to identify sexual networks that drive high HIV incidence in adolescent girls in rural KwaZulu-Natal (KZN), South Africa. To achieve a very high rate of population coverage we will extensively sample HIV infected individuals.  With phylogenetic analyses of HIV-1 sequences and traditional sexual networking methods we will identify networks of HIV-1 transmission clusters and viral linkages in adolescents and link these to community sequences.  The study area is uniquely suited for this research as it is rural, geographically well defined, is one of the highest HIV burden districts in South Africa and data collection on structural, behavioral and biological determinants of risks of HIV infection in this community is ongoing. We will build on our expertise in HIV surveillance in this area, including high-throughput sequencing, bioinformatics and network analysis to characterize transmission clusters and their members, describe the network characteristics of these transmission chains and analyze the contribution of HIV clusters to new infections. The data on HIV transmission networks will aid in the design of intervention packages aimed at reducing HIV transmission in adolescent girls.
 
Coauthors: Lyle McKinnon, PhD1,2, Carolyn Williamson, PhD3, Simon Travers, PhD4, Hans-Peter Kohler5, Cherie Cawood6, Tulio de Oliveira, PhD7, Salim S Abdool Karim PhD1,2 and Quarraisha Abdool Karim, PhD1,2
1 Centre for the AIDS Programme of Research in South Africa, Durban, South Africa.
2 University of KwaZulu-Natal, Durban, South Africa
3 University of Cape Town, Cape Town, South Africa
4 South African National Bioinformatics Institute, South African Medical Research Council Bioinformatics Unit, University of the Western Cape, Bellville, South Africa
5 Population Studies Center, University of Pennsylvania, Philadelphia USA
6 Epicentre, Durban, South Africa
7 Africa Centre for Health and Population Studies, South Africa

 

Phylogenetics, Transmission Networks, and Drug Resistance: Bringing It All Together
Alexandra M. Oster, MD1

HIV sequence data can provide insight into prevalence of HIV drug-resistant strains and can be used to identify clusters of HIV infection and therefore understand the spread of HIV among and between populations. Molecular HIV Surveillance (MHS), a component of the U.S. National HIV Surveillance System, collects HIV nucleotide sequences and analyzes these sequences to monitor drug resistance patterns and genetic diversity and improve understanding of HIV transmission networks. Twenty-seven U.S. states and cities participate in MHS and collaborate with commercial/private, public, and hospital-based laboratories to obtain genetic sequence data from resistance testing conducted as a part of HIV care. To date, MHS jurisdictions have collected sequences for >100,000 persons living with diagnosed HIV infection in the United States. For many years, we have used our molecular data to describe the prevalence of transmitted drug resistance in the United States. Recently, transmission network analysis has shed light on routes of HIV acquisition among women, the spread of HIV among young men who have sex with men, transmissions between the United States and other countries, and the growth of transmission clusters over time.  We have also combined drug resistance and transmission network analysis to understand the spread of HIV drug resistance and implications for treatment and prevention. We are currently expanding coverage of sequence data, enhancing state analytic capacity, improving data visualization methods, and considering ethical issues regarding using these data. Addressing these issues is critical to achieving the potential afforded by widespread availability of sequence data and new analytical tools.
 
Coauthors: Angela L. Hernandez, MD, MPH1, M. Cheryl Bañez Ocfemia, MPH1, Joel O. Wertheim, PhD2,3, Y. Omar Whiteside, PhD1, H. Irene Hall, PhD1
1 Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
2 ICF International, Atlanta, Georgia, United States
3 University of California, San Diego, California, United States

 

Phylogenetics and Recent Infections—Quantification and Relevance to the Epidemic— Population based studies in Rakai, Uganda
Thomas C. Quinn, MD1,2

Effective HIV control requires an understanding of how HIV spreads through sexual networks between individuals in households, between community members in different households, and between individuals from different communities. Using viral phylogenetics that examine the genetic relatedness of viruses, we investigated the spatial dynamics of HIV transmission in sexual networks in rural Uganda. We analyzed HIV transmission in a cohort of 14,594 individuals within 46 communities in Rakai, Uganda. Individuals living in households with HIV-incident (n = 189) or HIV-prevalent (n = 1,597) persons were 3.2 (95% CI: 2.7–3.7) times more likely to be HIV infected themselves compared to the population in general. Phylogenetic analyses of gag and env genes suggest that chains of transmission frequently cross community boundaries. A total of 95 phylogenetic clusters were identified; 44% of phylogenetic clusters were within households, and 40% of clusters crossed community borders. Using the locations of self-reported sexual partners, we estimated that 39% (95% CI: 34%–42%) of new viral transmissions occur within stable household partnerships, and that 62% (95% CI: 55%–70%) are infected by sexual partners outside their community. These results suggest that HIV introductions into communities are frequent and are likely to play an important role in sustaining HIV transmission in the Rakai District. Consequently, prevention efforts to halt the spread of HIV will need to be implemented at spatial scales broader than individual communities, and key populations that are likely to introduce HIV into communities will need to be targeted.
 
Coauthor: Mary K. Grabowski, PhD2
1 National Institute of Allergy and Infectious Diseases, Baltimore, Maryland, United States
2 Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States

 

Phylogenetics and Vaccine Development—Diversity and What it Means
Morgane Rolland, PhD
US Military HIV Research Program (MHRP), Silver Spring, Maryland, United States
Henry M. Jackson Foundation, Bethesda, Maryland, United States

HIV diversity is a major challenge for HIV vaccine development and several strategies have been explored to try to cope with it. Centralized antigens (consensus or ancestral) are designed in silico to represent the best approximation of global HIV diversity; then, appending common HIV variants to these centralized antigens allows to derive variability-inclusive antigens. However, to date, HIV vaccine efficacy trials have only tested antigens corresponding to circulating HIV strains, sometimes as multivalent combinations. While the extent of HIV diversity hinders the path towards a successful vaccine, it also offers opportunities to assess how a vaccine worked. Sieve analyses methods have been developed to leverage HIV diversity when comparing breakthrough infections from vaccine and placebo recipients. In the Step study, although the vaccine had no efficacy, we showed that it had a genetic impact on HIV breakthrough infections - with more mutations in predicted CTL epitopes from vaccine recipients’s sequences. In the RV144 study, the first HIV vaccine candidate to show some efficacy, we found two signatures associated with vaccine efficacy in the Env-V2 region of HIV breakthrough viruses. This sieve signal supported the hypothesis that antibodies directed against Env-V2, which were identified as a correlate of decreased risk of HIV infection in the RV144 trial, played a role in the protection afforded by the RV144 vaccine. These data highlight the dualism associated with HIV diversity, frustrating efforts to develop a vaccine while also helping garner insights on potential mechanisms of vaccine protection.
 

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