Title: Inferring population dynamics of HIV-1 subtype C epidemics in Eastern Africa and Southern Brazil applying different Bayesian phylodynamics approaches
Authors: Mir D, Graf T, Esteves de Matos Almeida S, Pinto AR, Delatorre E, Bello G.
Journal: Scientific Reports,8(1):877:doi: 10.1038/s41598-018-26824-4 (2018)
The subtype C Eastern Africa clade (CEA), a particularly successful HIV-1 subtype C lineage, has seeded several sub-epidemics in Eastern African countries and Southern Brazil during the 1960s and 1970s. Here, we characterized the past population dynamics of the major CEA sub-epidemics in Eastern Africa and Brazil by using Bayesian phylodynamic approaches based on coalescent and birth-death models. All phylodynamic models support similar epidemic dynamics and exponential growth rates until roughly the mid-1980s for all the CEA sub-epidemics. Divergent growth patterns, however, were supported afterwards. The Bayesian skygrid coalescent model (BSKG) and the birth-death skyline model (BDSKY) supported longer exponential growth phases than the Bayesian skyline coalescent model (BSKL). The BDSKY model uncovers patterns of a recent decline for the CEA sub-epidemics in Burundi/Rwanda and Tanzania (Re?1) and a recent growth for Southern Brazil (Re?>?1); whereas coalescent models infer an epidemic stabilization. To the contrary, the BSKG model captured a decline of Ethiopian CEA sub-epidemic between the mid-1990s and mid-2000s that was not uncovered by the BDSKY model. These results underscore that the joint use of different phylodynamic approaches may yield complementary insights into the past HIV population dynamics
Citation: Mir D, Graf T, Esteves de Matos Almeida S, Pinto AR, Delatorre E, Bello G. Inferring population dynamics of HIV-1 subtype C epidemics in Eastern Africa and Southern Brazil applying different Bayesian phylodynamics approaches Scientific Reports,8(1):877:doi: 10.1038/s41598-018-26824-4 (2018).