Abstract
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.
Highlights
The human immunodeficiency virus type 1 (HIV-1) subtype C accounts for approximately 48% of all people living with HIV, representing the most prevalent HIV-1 subtype in the world[1]
We characterized key features of the epidemic dynamics of major HIV-1 subtype CEA lineages circulating in East Africa and Southern Brazil through the use of different phylodynamic frameworks based in coalescent and birth-death process
The different coalescent models capture very similar epidemic dynamics over the earlier decades of the CEA lineages dissemination; but point to quite different epidemic dynamics from the mid-1980s onwards. Both phylodynamic approaches suggest an initial stage of fast exponential growth of all the CEA sub-epidemics during the period of cryptic transmission of HIV in human populations
Summary
The human immunodeficiency virus type 1 (HIV-1) subtype C accounts for approximately 48% of all people living with HIV, representing the most prevalent HIV-1 subtype in the world[1]. The CEA clade currently predominates among subtype C strains from Eastern African countries and Brazil, and accounts for almost 100%. Key epidemiological and population parameters, most notably the effective number of infections (Ne), the epidemic growth rate (r) and the basic (R0) and effective (Re) reproductive number, can be estimated from viral sequence data by using Bayesian phylodynamic approaches based on coalescent[15] and birth-death[16] models. These models have very different mathematical grounds as well as particular strengths and limitations. A potential disadvantage of the birth-death model is that credibility intervals grow wider the further we go into the past, which is not the case for the coalescent-based models[21]; simulation studies showed that the coalescent might not capture the true r because of the narrow credibility intervals around the median estimate attributed to its assumption of deterministic changes in the population size[20]
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