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Using Phylogenetics to Enhance the HIV Response

Using Phylogenetics to Enhance the HIV Response
Reported by
Hannah Rice

Posted August 31, 2015


Rapid advances in molecular genetics and bioinformatics allow scientists to track infectious diseases in ever greater detail. Phylogenetic and network data reveal highly specific information about disease spread, such as when and where infections occur and how infections in individuals are linked. As the global response to HIV shifts toward targeted interventions for high-risk populations with the greatest disease burdens, researchers seek to use insights from genetic data to reduce transmission and to control epidemics, with the goal of ending HIV/AIDS. Studies have demonstrated that such interventions can be more effective and cheaper than generalized treatment and prevention programs for whole populations.

However, the use of genetic data to map HIV transmission dynamics raises ethical concerns, particularly when groups with high HIV prevalence are marginalized, stigmatized, or criminalized. On June 4, 2015, Joint United Nations Programme on HIV/AIDS (UNAIDS), the Global Fund to Fight AIDS, Tuberculosis and Malaria, and the Academy's Microbiology and Infectious Diseases Discussion Group convened researchers and policy makers for HIV 2015: Using Phylogenetics to Enhance the HIV Response, to explore the science and ethics of genetic mapping in HIV research. Speakers described the high genetic diversity of HIV strains—in individual patients, in communities, and globally—and the implications for drug resistance, vaccine development, transmission networks, and prevention programs.

Use the tabs above to find a meeting report and multimedia from this event.

Presentations available from:
Jonathan M. Carlson, PhD (Microsoft Research)
Joanne Csete, PhD, MPH (Columbia University Mailman School of Public Health)
Ade Fakoya, MD (The Global Fund to Fight AIDS, Tuberculosis and Malaria)
Christophe Fraser, PhD (Imperial College London, UK)
Ayesha Kharsany, PhD (Center for the AIDS Program of Research in South Africa)
Luiz Loures, MD, MPH (UNAIDS)
Tulio de Oliveira, PhD (Wellcome Trust Africa Centre for Health and Population Studies, South Africa)
Alexa Oster, MD (Centers for Disease Control and Prevention)
Thomas Quinn, MD (Johns Hopkins University)
Morgane Rolland, PhD (Walter Reed Army Institute of Research)
Kate Thomson, MA (The Global Fund to Fight AIDS, Tuberculosis and Malaria)
Moderator: Peter Godfrey-Faussett, MBBS, DTM&H (UNAIDS)

Presented by

  • The Global Fund
  • The New York Academy of Sciences

**Note: The HIV 2015: Using Phylogenetics to Enhance the HIV Response symposium was 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

How to cite this eBriefing

The New York Academy of Sciences. Using Phylogenetics to Enhance the HIV Response. Academy eBriefings. 2015. Available at:


Situation report

Centers for Disease Control and Prevention. HIV/AIDS. HIV Surveillance Reports.

The Global Fund to Fight AIDS, Tuberculosis and Malaria. The Global Fund's New Funding Model. 2013.

Office of the U.S. Global AIDS Coordinator, U.S. Department of State. PEPFAR 3.0. Controlling the epidemic: delivering on the promise of an AIDS-free generation. 2014.

UNAIDS. 2015 progress reports submitted by countries.

UNAIDS. How AIDS changed everything. Fact sheet: 2014 global statistics.

United States President's Emergency Plan for AIDS Relief. Funding and Results.

U.S. Department of State. PEPFAR Dashboards.

Introduction to phylogenetics

Grenfell BT, Pybus OG, Gog JR, et al. Unifying the epidemiological and evolutionary dynamics of pathogens. Science. 2004;303(5656):327-32.

Hué S, Pillay D, Clewley JP, Pybus OG. Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups. Proc Natl Acad Sci U S A. 2005;102(12):4425-9.

Lewis F, Hughes GJ, Rambaut A, et al. Episodic sexual transmission of HIV revealed by molecular phylodynamics. PLoS Med. 2008;5(3):e50.

Pybus OG, Charleston MA, Gupta S, et al. The epidemic behavior of the hepatitis C virus. Science. 2001;292(5525):2323-5.

Stadler T, Kühnert D, Bonhoeffer S, Drummond AJ. Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV). Proc Natl Acad Sci U S A. 2013;110(1):228-33.

Vrancken B, Rambaut A, Suchard MA, et al. The genealogical population dynamics of HIV-1 in a large transmission chain: bridging within and among host evolutionary rates. PLoS Comput Biol. 2014;10(4):e1003505.

Viral fitness and intrinsic immune escape in HIV transmission and progression

Carlson JM, Schaefer M, Monaco DC, et al. HIV transmission. Selection bias at the heterosexual HIV-1 transmission bottleneck. Science. 2014;345(6193):1254031.

Garrett NJ, Werner L, Naicker N, et at. HIV disease progression in seroconvertors from the CAPRISA 004 tenofovir gel pre-exposure prophylaxis trial. J Acquir Immune Defic Syndr. 2015;68(1):55-61.

International HIV Controllers Study, Pereyra F, Jia X, et al. The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Science. 2010;330(6010):1551-7.

Kiepiela P, Ngumbela K, Thobakgale C, et al. CD8+ T-cell responses to different HIV proteins have discordant associations with viral load. Nat Med. 2007;13(1):46-53.

Prince JL, Claiborne DT, Carlson JM, et al. Role of transmitted Gag CTL polymorphisms in defining replicative capacity and early HIV-1 pathogenesis. PLoS Pathog. 2012;8(11):e1003041.

Transmission networks and drug resistance

Cooley LA, Pearl ML, Flynn C, et al. Low viral suppression and high HIV diagnosis rate among men who have sex with men with syphilis—Baltimore, Maryland. Sex Transm Dis. 2015;42(4):226-31.

Oster AM, Sternberg M, Lansky A, et al. Population size estimates for men who have sex with men and persons who inject drugs. J Urban Health. 2015;92(4):733-43.

Oster AM, Wertheim JO, Hernandez AL, et al. Using molecular HIV surveillance data to understand transmission between subpopulations in the United States. J Acquired Immune Defic Synd. 2015. [Epub ahead of print]

Sionean C, Le BC, Hageman K, et al. HIV Risk, prevention, and testing behaviors among heterosexuals at increased risk for HIV infection—National HIV Behavioral Surveillance System, 21 U.S. cities, 2010. MMWR Surveill Summ. 2014;63(14):1-39.

Simon Collins, HIV i-Base. Prevalence of transmitted drug resistance globally: highest in Australia, US and some European countries but between-country differences in all regions. HIV TREATMENT BULLETIN. 2015.

Wertheim JO, Leigh Brown AJ, Hepler NL, et al. The global transmission network of HIV-1. J Infect Dis. 2014;209(2):304-13.

Interrupting transmission chains

Bezemer D, de Wolf F, Boerlijst MC, et al. 27 years of the HIV epidemic amongst men having sex with men in the Netherlands: an in depth mathematical model-based analysis. Epidemics. 2010;2(2):66-79.

Bezemer D, de Wolf F, Boerlijst MC, et al. A resurgent HIV-1 epidemic among men who have sex with men in the era of potent antiretroviral therapy. AIDS. 2008;22(9):1071-7.

Cori A, Ferguson NM, Fraser C, Cauchemez S. A new framework and software to estimate time-varying reproduction numbers during epidemics. Am J Epidemiol. 2013;178(9):1505-12.

Jombart T, Aanensen DM, Baguelin M, et al. OutbreakTools: a new platform for disease outbreak analysis using the R software. Epidemics. 2014;7:28-34.

Van Sighem A, Jansen I, Bezemer D, et al. Increasing sexual risk behaviour among Dutch men who have sex with men: mathematical models versus prospective cohort data. AIDS. 2012;26(14):1840-3.

Vaccine development—diversity and what it means

Barouch DH, Stephenson KE, Borducchi EN, et al. Protective efficacy of a global HIV-1 mosaic vaccine against heterologous SHIV challenges in rhesus monkeys. Cell. 2013;155(3):531-9.

Chin'ombe N, Ruhanya V. HIV/AIDS vaccines for Africa: scientific opportunities, challenges and strategies. Pan Afr Med J. 2015;20:386.

Edlefsen PT, Rolland M, Hertz T, et al. Comprehensive sieve analysis of breakthrough HIV-1 sequences in the RV144 vaccine efficacy trial. PLoS Comput Biol. 2015;11(2):e1003973.

Herbeck JT, Rolland M, Liu Y, et al. Demographic processes affect HIV-1 evolution in primary infection before the onset of selective processes. J Virol. 2011;85(15):7523-34.

Ndhlovu ZM, Piechocka-Trocha A, Vine S, et al. Mosaic HIV-1 Gag antigens can be processed and presented to human HIV-specific CD8+ T cells. J Immunol. 2011;186(12):6914-24.

Nickle DC, Jojic N, Heckerman D, et al. Comparison of immunogen designs that optimize peptide coverage: reply to Fischer et al. PLoS Comput Biol. 2008;4(1):e25.

Mapping transmission in African communities

Abdool Karim Q, Dellar RC, Bearnot B, et al. HIV-positive status disclosure in patients in care in rural South Africa: implications for scaling up treatment and prevention interventions. AIDS Behav. 2015;19(2):322-9.

Grabowski MK, Lessler J, Redd AD, et al. The role of viral introductions in sustaining community-based HIV epidemics in rural Uganda: evidence from spatial clustering, phylogenetics, and egocentric transmission models. PLoS Med. 2014;11(3):e1001610.

Kharsany AB, Buthelezi TJ, Frohlich JA, et al. HIV infection in high school students in rural South Africa: role of transmissions among students. AIDS Res Hum Retroviruses. 2014;30(10):956-65.

Phylogenetics and Networks for Generalised HIV Epidemics in Africa (PANGEA-HIV)

Pillay D, Herbeck J, Cohen MS, et al. PANGEA-HIV: phylogenetics for generalised epidemics in Africa. Lancet Infect Dis. 2015;15(3):259-61.

Redd AD, Quinn TC, Tobian AA. Frequency and implications of HIV superinfection. Lancet Infect Dis. 2013;13(7):622-8.

Reynolds SJ, Makumbi F, Nakigozi G, et al. HIV-1 transmission among HIV-1 discordant couples before and after the introduction of antiretroviral therapy. AIDS. 2011;25(4):473-7.

Schwartz SR, Nowak RG, Orazulike I, et al. The immediate effect of the Same-Sex Marriage Prohibition Act on stigma, discrimination, and engagement on HIV prevention and treatment services in men who have sex with men in Nigeria: analysis of prospective data from the TRUST cohort. Lancet HIV. 2015;2(7):e299-306.

Uses (and abuses) of phylogenetics

Amnesty International. Making love a crime: criminalization of same-sex conduct in sub-Saharan Africa. Research Reports. 2013.

Buse K, Eba P, Sigurdson J, et al. Leveraging HIV-related human rights achievements through a Framework Convention on Global Health. Health Hum Rights. 2013;15(1):e96-110.

Csete J, Dube S. An inappropriate tool: criminal law and HIV in Asia. AIDS. 2010;24 Suppl 3:S80-5.

Csete J, Grob PJ. Switzerland, HIV, and the power of pragmatism: lessons for drug policy development. Int J Drug Policy. 2012;23(1):82-6.

Hayashi K, Small W, Csete J, et al. Experiences with policing among people who inject drugs in Bangkok, Thailand: a qualitative study. PLoS Med. 2013;10(12):e1001570; discussion e1001570.

Killen J, Harrington M, Fauci AS. MSM, AIDS research activism, and HAART. Lancet. 2012;380(9839):314-6.

Jürgens R, Cohen J, Girard F, Beyrer C. Increasing access to HIV testing and counselling while respecting human rights. HIV AIDS Policy Law Rev. 2007;12(2-3):63-6.

Jürgens R, Csete J, Amon JJ, et al. People who use drugs, HIV, and human rights. Lancet. 2010;376(9739):475-85.

Knight R, Small W, Pakula B, et al. A scoping study to identify opportunities to advance the ethical implementation and scale-up of HIV treatment as prevention: priorities for empirical research. BMC Med Ethics. 2014;15:54.

Shannon K, Csete J. Violence, condom negotiation, and HIV/STI risk among sex workers. JAMA. 2010;304(5):573-4.

Yi H, Zheng T, Wan Y, et al. Occupational safety and HIV risk among female sex workers in China: a mixed-methods analysis of sex-work harms and mommies. Glob Public Health. 2012;7(8):840-55.


Ade Fakoya, MD

The Global Fund to Fight AIDS, Tuberculosis and Malaria

Ade Fakoya is a clinician and specialist in HIV and international health with over 20 years' experience in clinical care, service management, and program delivery. He is senior disease coordinator for HIV at the Global Fund. His team provides technical support and coordinates partner cooperation, leading over the past 3 years to the approval of over $5 billion in Global Fund phase 2 and new funding model HIV grants. His experience is in HIV clinical care, treatment and prevention, antiretroviral (ARV) therapy scale-up, and provision of STI clinical services. He has supported national HIV programs in Africa, Asia, and Latin America and participated in several advisory committees, including for ARV treatment guidelines, prevention of mother-to-child transmission (PMTCT) guidelines, and sexual and reproductive health. His interests include improving access to ARV treatment, PMTCT implementation, HIV and TB integration, and the role of disease-specific funding initiatives in strengthening health systems.

Peter Godfrey-Faussett, MBBS, DTM&H

website | publications

Peter Godfrey-Faussett is a professor at the London School of Hygiene and Tropical Medicine (LSHTM) and a consultant physician at the Hospital for Tropical Diseases in London. After training in clinical infectious diseases and molecular genetics, he spent 5 years leading the Zambian AIDS-related TB (ZAMBART) project, an interdisciplinary collaborative research program of LSHTM, Lusaka Urban District Health Management Team, and the University of Zambia. He spent a year working with the World Health Organization (WHO) Global Tuberculosis Programme, focused on the combined epidemics of TB and HIV. He has maintained an interest in global policies around TB and HIV, serving as chairman for the Technical Review Panel of the Global Fund and as a regular member of WHO expert groups. He is currently seconded full time to UNAIDS as senior science adviser, with a portfolio including HIV cure, ARV-based HIV prevention, HIV vaccines, and interactions between HIV response and noncommunicable disease response.

Tulio de Oliveira, PhD

Wellcome Trust Africa Centre for Health and Population Studies, South Africa
website | publications

Tulio de Oliveira is a professor in the Wellcome Trust Africa Centre for Health and Population Studies at the School of Laboratory Medicine and Medical Sciences in the College of Health Sciences, University of KwaZulu-Natal, South Africa. He was previously a Marie Curie research fellow at the University of Oxford, UK, where he received training in virus genetic analysis and molecular evolution. He studies HIV genetic data and bioinformatics, publishing on Rega Subtyping tools and HIV drug resistance databases in Africa. He has also published work proving the innocence of six foreign medical personnel condemned to death for infecting with HIV 438 children in a hospital in Libya and documenting the first case of proven HIV surrogate transmission in South Africa. His group website ( hosts open-access bioinformatics tools and databases.

Morgane Rolland, PhD

Walter Reed Army Institute of Research
website | publications

Morgane Rolland is chief of the viral genetics section at the U.S. Military HIV Research Program (MHRP). She obtained her PhD from the University of Bordeaux, France, and completed a postdoctoral fellowship with Dr. James I. Mullins in the Microbiology Department of the University of Washington. Rolland is interested in understanding features of HIV-1 genetics and evolution that are important to HIV vaccine research. Her research focuses on the interplay between HIV-1 genetics and host immune pressure, particularly for HIV-1 vaccine design and the analysis of HIV-1 evolution during acute and early infection. She also studies HIV breakthrough infections in vaccine efficacy trials.

Sonya Dougal, PhD

The New York Academy of Sciences

Sonya Dougal is the director of Life Sciences Discussion Groups at the New York Academy of Sciences. She develops an annual portfolio of scientific symposia on life sciences and biomedical research. Dougal has over 14 years of experience in scientific research and program management in academia, industry, and nonprofits. She holds a 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.


William A. Blattner, MD

University of Maryland, College Park
website | publications

Jonathan M. Carlson, PhD

Microsoft Research
website | publications

Joanne Csete, PhD, MPH

Columbia University Mailman School of Public Health
website | publications

Christophe Fraser, PhD

Imperial College London, UK
website | publications

Maureen M. Goodenow, PhD

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

Mark Harrington

Treatment Action Group

Ralf Jürgens, LLM, PhD

The Global Fund to Fight AIDS, Tuberculosis and Malaria

Ayesha Kharsany, PhD

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

Luiz Loures, MD, MPH


Alexa Oster, MD

Centers for Disease Control and Prevention

Thomas Quinn, MD

Johns Hopkins University
website | publications

Kate Thomson, MA

The Global Fund to Fight AIDS, Tuberculosis and Malaria

Hannah Rice

Hannah Rice is editorial manager for eBriefings at the New York Academy of Sciences.


Grant Support

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

Presented by

  • The Global Fund
  • The New York Academy of Sciences

**Note: The HIV 2015: Using Phylogenetics to Enhance the HIV Response symposium was 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