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PANGEA stands for "Phylogenetics And Networks for Generalised Epidemics in Africa". The overarching goal of the PANGEA consortium is to identify individual and population level factors that drive the epidemic using HIV-1 phylogenetic data, analyse the dynamics of the epidemic, and translate these findings into information that can be used to more effectively target interventions. PANGEA consists of many partners in Africa, Europe and the US.


The most powerful tool available to study HIV transmission is phylogenetics. A viral phylogeny reveals who is close to whom in the transmission network. With additional epidemiological information or modelling one can identify which of these close individuals are likely sources of new infections. Following theoretical work on incorporating within-host diversity into phylogenetic inference, we have developed a tool called phyloscanner that can be used for source attribution in HIV next generation sequencing (NGS) data. Once sources have been identified with quantified uncertainty, epidemiological questions about the characteristics of transmitters can be addressed. For example, transmission networks will enable us to detect individuals that are at high risk of infecting others and quantify their contribution to transmission.