Multiple Independent Introductions of HIV-1 CRF01_AE Identified in China: What Are the Implications for Prevention?

Yassir F Abubakar,Xiaoyan Zhang,Zhefeng Meng,Jianqing Xu,Wing-Cheong Yam

doi:10.1371/journal.pone.0080487

Yassir F Abubakar, Xiaoyan Zhang + Show 3 more

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https://doi.org/10.1371/journal.pone.0080487

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Abstract

BackgroundHIV-1 CRF01_AE accounts for an important fraction of HIV infections in Asia including China, but little is known about the phylogenetic and evolutionary history of this CRF (circulating recombinant form). In the current study, we collected a large number of 1,957 CRF01_AE gag p17 sequences with known sampling year (1990-2010) from 5 global regions representing 15 countries to better understand the phylogenetic relationships and epidemic history of CRF01_AE strains in China.Methodology/Principal FindingsCRF01_AE gag p17 sequences were retrieved from public databases to explore phylogenetic relationships and phylogeographic dynamics of CRF01_AE in Asia by using maximum-likelihood phylogenetics and Bayesian coalescent-based analyses. We found close phylogenetic relationships between sequences from Thailand, Vietnam and China. Moreover, at least 5 independent introductions and 5 independent autochthonous clades of CRF01_AE, which descended from Thailand or Vietnam were identified in China from 1991 through 2003.Conclusion/SignificanceThe current study not only defines the migration of CRF01_AE clades to/in Asia, but also demonstrates the criticalness of identifying the circulating strains in the population for the development of vaccine and microbicides.

Highlights

Human immunodeficiency virus type 1 (HIV-1) sequences belonging to the pandemic group M are classified into nine subtypes (A–D, F–H, J, and K), six sub-subtypes (A1-A4, and F1- F2), and a variety of inter-subtype recombinant forms (Los Alamos HIV sequence database: http://hiv-web.lanl.gov/)
The utilized dataset included a total of 1,957 CRF01_AE gag p17, covering all five geographic regions included in the study (West Africa, Central Africa, West and Central Europe, East Asia, and South and Southeast Asia) (Table 1)
This dataset was employed to characterize the phylogenetic relationships between CRF01_AE sequences of all involved regions, and to delineate with more confidence the relationships within Asian sequences, which was the main focus of the study

Summary

Introduction

Human immunodeficiency virus type 1 (HIV-1) sequences belonging to the pandemic group M are classified into nine subtypes (A–D, F–H, J, and K), six sub-subtypes (A1-A4, and F1- F2), and a variety of inter-subtype recombinant forms (Los Alamos HIV sequence database: http://hiv-web.lanl.gov/). CRF01_AE had been reported as prevalent and responsible for the vast majority of infections in South and South East Asia[1,2]. HIV-1 CRF01_AE accounts for an important fraction of HIV infections in Asia including China, but little is known about the phylogenetic and evolutionary history of this CRF (circulating recombinant form). We collected a large number of 1,957 CRF01_AE gag p17 sequences with known sampling year (1990-2010) from 5 global regions representing 15 countries to better understand the phylogenetic relationships and epidemic history of CRF01_AE strains in China. Conclusion/Significance: The current study defines the migration of CRF01_AE clades to/in Asia, and demonstrates the criticalness of identifying the circulating strains in the population for the development of vaccine and microbicides

Methods

Results

Conclusion