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Prediction of HIV-1 Coreceptor Usage (Tropism) by Sequence Analysis using a Genotypic Approach

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Published on: December 1, 2011

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

Gab Jung Kim¹, Mi-Ran Yun, Min Jee Koo

¹Division of AIDS, Department of Immunology and Pathology, National Institute of Health South Korea, Cheongwon-gun, Chungcheongbuk-do, Korea. gabjkim@korea.kr

AIDS Research and Human Retroviruses

|November 3, 2011

Summary

The human immunodeficiency virus type 1 (HIV-1) Korean clade B strain diverged in the 1960s, evolving slowly due to limited transmission. This distinct viral lineage evolved independently within Korea.

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Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3

Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3

Published on: December 27, 2010

Area of Science:

Virology
Epidemiology
Molecular Evolution

Background:

The majority of Korean human immunodeficiency virus type 1 (HIV-1) isolates belong to the distinct Korean clade B strain.
The introduction, transmission, and evolutionary history of HIV-1 within the Korean population remain unclear.

Purpose of the Study:

To elucidate the evolutionary characteristics of the Korean HIV-1 subtype B gp120 env gene.
To compare the molecular epidemic history of Korean HIV-1 with strains from other geographic locations.

Main Methods:

Bayesian Markov chain Monte Carlo (MCMC) statistical inference was employed to estimate divergence times.
Substitution rates and demographic dynamics of HIV-1 in Korea were analyzed using molecular data.

Main Results:

The estimated time of divergence for HIV-1 subtype B and the Korean clade B cluster was 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.
Demographic analysis indicated a rapid increase in infections until the early 1980s, followed by slower growth, suggesting a lower overall growth rate compared to other countries.

Conclusions:

The evolution of HIV-1 Korean clade B appears to be relatively slow.
Limited transmission within the Korean population likely facilitated the independent evolution of the HIV-1 Korean clade B.