Secondary Logo

Institutional members access full text with Ovid®


Phylogenetics And Networks for Generalised Epidemics in Africa

Abeler-Dörner, Luciea; Grabowski, Mary K.b; Rambaut, Andrewc; Pillay, Deenand,e; Fraser, Christophea on behalf of the PANGEA consortium

Current Opinion in HIV and AIDS: May 2019 - Volume 14 - Issue 3 - p 173–180
doi: 10.1097/COH.0000000000000542
PHYLOGENETICS IN HIV TRANSMISSION: Edited by Morgane Rolland and Josh Herbeck

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.

aBig Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK

bDepartment of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Rakai Health Sciences Program, Baltimore, USA

cInstitute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, UK

dAfrica Health Research Institute, KwaZulu-Natal, South Africa

eDivision of Infection and Immunity, University College London, London, UK

Correspondence to Mary K. Grabowski, PhD, ScM, Johns Hopkins University, Baltimore, USA. E-mail:;

Copyright © 2019 Wolters Kluwer Health, Inc. All rights reserved.