Chronology and evolution of the HIV-1 subtype C epidemic in Ethiopia

Abstract

To reconstruct the onset date and evolutionary history of the HIV-1 subtype C epidemic in Ethiopia - one of the earliest recorded subtype C epidemics in the world. HIV-1 C env sequences with a known sampling year isolated from HIV-1 positive patients from Ethiopia between 1984 and 2003. Evolutionary parameters including origin and demographic growth patterns were estimated using a Bayesian coalescent-based approach under either strict or relaxed molecular clock models. Bayesian evolutionary analysis indicated a most recent common ancestor date of 1965 with three distinct epidemic growth phases. Regression analysis of root-to-tip distances revealed a highly similar estimate for the origin of the clade. In addition, we reveal that the HIV-1C epidemic in Ethiopia has grown at a faster rate than the epidemic of subtype C in sub-Saharan Africa. Reconstruction of the epidemic history in Ethiopia revealed that subtype C likely originated from either a single lineage or multiple descendents in the late 1960s or early 1970s where it grew exponentially throughout the mid-1970s and early 1980s, corresponding to a wave of urbanization and migration. In light of these findings, we suggest that subtype C strains were circulating at least a decade before previous estimates and the first recognition of symptomatic patients in Ethiopia. The timing of the Ethiopian epidemic is also in agreement with similar HIV-1 epidemics in sub-Saharan Africa.