Estimating the origin and evolution characteristics for Korean HIV type 1 subtype B using Bayesian phylogenetic analysis

Abstract

The majority of Korean human immunodeficiency virus type 1 (HIV-1) isolates are composed of the Korean clade B strain that is distinct from the subtype B prevalent in North America and Europe. However, it is still not clear how HIV-1 was introduced, transmitted, and evolved within the Korean population. To identify the evolutionary characteristics of Korean HIV-1, we estimate the molecular epidemic history of HIV-1 subtype B gp120 env in Korea in comparison with sequences isolated from other geographic locations. A Bayesian Markov chain Monte Carlo (MCMC) statistical inference was used to estimate the time of divergence of subtype B. The estimated time of divergence of subtype B and the distinct monophyletic Korean B cluster was estimated to be in the early and mid-1960s, respectively. Substitution rates were estimated at 7.3×10(-3) and 8.0×10(-3) substitutions per site per year for HIV-1 subtype B and Korean clade B, respectively. The demographic dynamics of two Korean data sets showed that the effective number of infections in Korea increased rapidly until the early 1980s, and then the rate only slowly increased until the mid-1990s when the population growth approached a steady-state. These results suggest that the growth rate of prevalent HIV-1 strains in Korea was lower than in other countries, suggesting that the evolution of HIV-1 Korean clade B was relatively slow. Furthermore, the limited transmission of HIV-1 within the Korean population likely led to the independent evolution of this virus to form the HIV-1 Korean clade B.

FIG. 1.

Neighbor-joining phylogenetic relationship generated from 2907 HIV-1 subtype B gp120 env sequences. Korean clade B (in red) formed a distinct cluster from worldwide HIV-1 subtype B. This tree showed the U.S. and European strains in different colors (Spain in cyan, France in blue, Great Britain in violet). U.S. and European sequences are scattered widely through tree.

FIG. 2.

Demographic history estimated from all subtype B samples in the env gp120 region: (A) HIV-1 subtype B and (B) Korean HIV-1 clade B. The demographic histories were estimated by Bayesian Markov chain Monte Carlo (MCMC) inference with the Skyline plot and show changes in the effective number of infections through time (time scale in year). The solid lines are the median estimate and the dashed lines indicate the 95% upper and lower highest posterior density intervals.