Inferring population dynamics of HIV-1 subtype C epidemics in Eastern Africa and Southern Brazil applying different Bayesian phylodynamics approaches

Autor:	Tiago Gräf, Gonzalo Bello, Sabrina Esteves de Matos Almeida, Edson Delatorre, Aguinaldo R. Pinto, Daiana Mir
Jazyk:	angličtina
Rok vydání:	2018
Předmět:	0301 basic medicine Lineage (evolution) Bayesian probability Population Human immunodeficiency virus (HIV) lcsh:Medicine HIV Infections medicine.disease_cause Coalescent theory Evolution Molecular 03 medical and health sciences Bayes' theorem medicine Humans education Clade lcsh:Science Phylogeny education.field_of_study Multidisciplinary lcsh:R Bayes Theorem Africa Eastern 030104 developmental biology Geography Viral phylodynamics Evolutionary biology pol Gene Products Human Immunodeficiency Virus HIV-1 lcsh:Q Brazil
Zdroj:	Scientific Reports, Vol 8, Iss 1, Pp 1-10 (2018)
ISSN:	2045-2322
DOI:	10.1038/s41598-018-26824-4
Popis:	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 e > 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.
Databáze:	OpenAIRE
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