Dating the origin of the African human T-cell lymphotropic virus type-i (HTLV-I) subtypes

To investigate the origin of the African PTLV-I virus, we phylogenetically analyzed the available HTLV-I and STLV-I strains. We also attempted to date the presumed interspecies transmissions that resulted in the African HTLV-I subtypes. Molecular-clock analysis was performed using the Tamura-Nei substitution model and gamma distributed rate heterogeneity based on the maximum-likelihood topology of the combined long-terminal-repeat and env third-codon-position sequences. Since the molecular clock was not rejected and no evidence for saturation was found, a constant rate of evolution at these positions for all 33 HTLV-I and STLV-I strains was reasonably assumed. The spread of PTLV-I in Africa is estimated to have occurred at least 27,300 +/- 8,200 years ago. Using the available strains, the HTLV-If subtype appears to have emerged within the last 3,000 years, and the HTLV-Ia, HTLV-Ib, HTLV-Id, and HTLV-Ie subtypes appear to have diverged between 21,100 and 5,300 years ago. Interspecies transmissions, most probably simian to human, must have occurred around that time and probably continued later. When the synonymous and nonsynonymous substitution ratios were compared, it was clear that purifying selection was the driving force for PTLV-I evolution in the env gene, irrespective of the host species. Due to the small number of strains in some of the investigated groups, these data on selective pressure should be taken with caution.