Viral phylogenetic tools can make substantial contributions to understand how HIV spreads in populations, and thereby guide the design of more effective prevention interventions. To direct the use of these tools to where the impact of HIV is greatest, the Phylogenetics And Networks for Generalised HIV Epidemics in Africa (PANGEA-HIV) consortium generates full genome viral sequences from across sub-Saharan Africa. However, the generalised epidemics in sub-Saharan Africa and sequence availability in these resource-poor settings differ fundamentally from those where phylogenetic tools have proven effective. I here discuss the PANGEA-HIV community-wide blinded methods comparison exercise, that aimed to assess if the latest generation of phylogenetic tools can be adapted for estimating recent transmission dynamics of generalised HIV epidemics in sub-Saharan Africa. The findings add confidence to using HIV phylogenetics, support using full genome HIV sequences more routinely to advance HIV surveillance and prevention in sub-Saharan Africa, and indicate particular areas for further methods improvement.
The simulation data sets are available from figshare and could be useful for broader benchmarking and to address the performance of phylogenetic tools on other aspects of generalised HIV epidemics.]