Cross-Continental Dispersal of Major HIV-1 CRF01_AE Clusters in China.

Minghui An,Suzanne English,Hong Shang,Simon D W Frost,Bin Zhao,Hongyi Zhang,Xiaoxu Han

doi:10.3389/fmicb.2020.00061

Abstract

Since the 1990s, several distinct clusters of human immunodeficiency virus-type 1 (HIV-1) CRF01_AE related to a large epidemic in China have been identified, but it is yet poorly understood whether its transmission has dispersed globally. We aimed to characterize and quantify the genetic relationship of HIV-1 CRF01_AEs circulating in China and other countries. Using representative sequences of Chinese clusters as queries, all relevant CRF01_AE pol sequences in two large databases (the Los Alamos HIV sequence database and the UK HIV Drug Resistance Database) were selected with the online basic local alignment search (BLAST) tool. Phylogenetic and phylogeographic analyses were then carried out to characterize possible linkage of CRF01_AE strains between China and the rest of the world. We identified that 269 strains isolated in other parts of the world were associated with five major Chinese CRF01_AE clusters. 80.7% were located within CN.01AE.HST/IDU-2, most of which were born in Southeast Asia. 17.8% were clustered with CN.01AE.MSM-4 and -5. Two distinct sub-clusters associated with Chinese men who have sex with men (MSM) emerged in HK-United Kingdom and Japan after 2000. Our analysis suggests that HIV-1 CRF01_AE strains related to viral transmission in China were initially brought to the United Kingdom or other countries during the 1990s by Asian immigrants or returning international tourists from Southeast Asia, and then after having circulated among MSM in China for several years, these Chinese strains dispersed outside again, possibly through MSM network. This study provided evidence of regional and global dispersal of Chinese CRF01_AE strains. It would also help understand the global landscape of HIV epidemic associated with CRF01_AE transmission and highlight the need for further international collaborative study in this field.

Highlights

MATERIALS AND METHODSThe human immunodeficiency virus-type 1 (HIV-1) pandemic is currently dominated by Group M, which has diversified into nine subtypes, seven sub-subtypes (A1, A2, A3, A4, A6, F1, and F2), 98 circulating recombinant forms (CRF) and numerous unique recombinant forms (URF)
In Mainland China, HIV-1 CRF01_AE has caused a large epidemic, and several distinct clusters related to transmission among various high-risk populations have been identified
Angelis et al (2015) reported that China was a sink and CRF01_AE strains were mainly imported from neighboring countries and evolved into “distinct” Chinese strains, based on a global dataset of 2736 CRF01-AE sequences acquired from many public databases and cohort studies

Summary

Introduction

MATERIALS AND METHODSThe HIV-1 pandemic is currently dominated by Group M, which has diversified into nine subtypes, seven sub-subtypes (A1, A2, A3, A4, A6, F1, and F2), 98 circulating recombinant forms (CRF) and numerous unique recombinant forms (URF). Strains of CRF01_AE and B co-circulate among high risk sexual population and injecting drug users (IDUs) in East and South-east Asia, in contrast to MSM population in Western Europe and North America, where circulating HIV-1 strains are dominated by subtype B (Peeters et al, 2013). Recent studies have reported the emergence and rapid increase of non-B subtypes in various populations globally (Cuevas et al, 2009; Liao et al, 2009; Hawke et al, 2013; Neogi et al, 2014; Beloukas et al, 2016; Nikolopoulos et al, 2016; Dennis et al, 2017), especially among men who have sex with men (MSM) in China (Zhang et al, 2015). Few studies have focused on the genetic links of HIV-1 CRF01_AE strains between countries or regions

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