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PANGEA has been funded in two phases by the Bill & Melinda Gates Foundation. The first phase (2013-2017) establishing the network, obtaining viral sequences and clinical data, and creating a sequence database. Over 13,000 HIV genomes were sequenced during this first phase of the project. The second phase (2017-2021) will will see the generation of more sequences, but mainly focus on analysis.

PANGEA 1 was led by Deenan Pillay, with Andrew Leigh Brown, Christophe Fraser, Paul Kellam and Tulio de Oliveira as members of the executive committee, and Anne Hoppe as project manager. Members of the PANGEA 1 Steering Committee were Myron Cohen, Tulio de Oliveira, Ann Dennis, Max Essex, Sarah Fidler, Daniel Frampton, Christophe Fraser, Richard Hayes, Joshua Herbeck, Anne Hoppe, Pontiano Kaleebu, Paul Kellam, Cissy Kiyo, Andrew Leigh Brown, Jairam Lingappa, Vladimir Novitsky, Nick Paton, Deenan Pillay, Thomas Quinn, Oliver Ratmann, Deogratius Sseemwanga, Frank Tanser, and Maria Wawer. Members of the scientific advisory board were Kevin de Cock, Carl Dieffenbach, Eric Goosby, Simon Hay, Anne Johnson, Stuart Ray, and Christine Wasunna.