Timing of the HIV-1 subtype C epidemic in Ethiopia based on early virus strains and subsequent virus diversification

Abstract

Objective To trace the introduction of HIV-1 subtype C into Ethiopia based on virus diversification during the epidemic.Design A set of 474 serum samples obtained in Ethiopia in 1982–1985 was tested for HIV-1. HIV-1 env gp120 V3 and gag or pol regions were sequenced and analysed together with sequences from later stages of the epidemic.Results None of 98 samples from 1982–1983, one of 193 samples from 1984, and one of 183 samples from 1985 were HIV-1 positive. Phylogenetic analysis of virus sequences from positive samples revealed that they belong to the Ethiopian C, and not the C′, cluster. Analysis of 81 Ethiopian C V3 sequences from 1984–1997 revealed that the consensus sequence of the Ethiopian epidemic has been stable over time. Both the 1984 and 1985 V3 sequences, in contrast with three out of 27 (11%) of the 1988 and none out of 51 of the 1992–1997 sequences, had no synonymous substitutions compared to the reconstructed common ancestor of the Ethiopian C viruses. A highly significant correlation between sampling years of the V3 sequences and their synonymous distances to the common ancestor was demonstrated.Conclusions The increasing genetic heterogeneity together with stable consensus sequence of the Ethiopian HIV-1 C population demonstrates that evolution of the virus population is characterized by an unbiased expansion around a stationary consensus. Based on the rate of synonymous diversification of HIV-1 strains within the Ethiopian population, we were able to estimate 1983 (95% confidence interval, 1980–1984) as the year of HIV-1 C introduction into Ethiopia.