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

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.

Keywords: CRF01_AE; China; HIV-1; cross-continental; dispersal.

FIGURE 1

The study flowchart used to screen and identify HIV-1 CRF01_AE strains associated with viral transmission in China. The Blast tool was used to search the sequence of interest in (i) the Los Alamos HIV sequence database and (ii) the United Kingdom HIV Drug Resistance Database. Five published Chinese major CRF01_AE clusters were used as queries (covering protease and partial reverse transcriptase nucleotide sequences). The top 200 sequences were selected and included in this analysis according to Blast scores. Phylogenetic and phylogeographic analyses were reconstructed to identify the relationship between Chinese CRF01_AE and CRF01_AE from other countries/regions globally.

FIGURE 2

Phylogenetic analysis of global CRF01_AE strains outside Mainland China together with five major Chinese clusters. After the online BLAST of the two databases, the phylogenetic analysis of all selected sequences related to viral transmission of five major Chinese HIV-1 CRF01_AE clusters of interest was performed to demonstrate any possible linkages of CRF01_AE strains between China and the rest of the world. The maximum likelihood (ML) tree was reconstructed using the 1.1-kb pol sequences under GTR + I + G sites substitution model. The sample countries of each sequence are represented by different colors. The ML tree is rooted with three subtype C sequences as outgroup. The sequences that un-clustered with major five Chinese clusters were deleted in this reconstruction and the Supplementary Figure S1 showed the raw phylogenetic ML tree using the whole 2150 sequences in online BLAST search.

FIGURE 3

The origins and dispersal history of HIV-1 CRF01_AE associated with viral transmission in Mainland China. The maximum clade credibility (MCC) tree was reconstructed using the subsampled sequences (n = 328) in an online web server of CD-HIT-EST program, under GTR + I + G sites substitution model, the uncorrelated relaxed clock model and the Bayesian SkyGrid model through the Bayesian inference approach. The colors of nodes and branches represent the locations of the estimated ancestors for clades and the sampling locations of each sequence. The size of node represents the strength of node support (posterior probability). The tMRCAs of the representative clusters are indicated at the node.

FIGURE 4

Proposed global dispersal and timeline map of HIV-1 CRF01_AE strains associated with transmission in China. The five CRF01_AE clusters related to HIV transmission in China are color-coded. The color lines represent global dispersal patterns of these different clusters. The black line represents that these related CRF01_AE strains originated from Africa and then spread to Thailand, which became the secondary and the most important source of CRF01_AE, and finally developed several distinct clusters in China. CRF01_AE clusters associated with viral transmission in China have spread to neighboring countries/regions as well as the United Kingdom and other countries. A number of United Kingdom or European sequences and Vietnam sequences were identified within CN.01AE.HST/IDU-2, which was the first out-dispersal cluster and the exportation event occurred around ∼1995. Most CN.01AE.HST/IDU-2 viruses in the United Kingdom were isolated from Asian immigrants. Two distinct sub-clusters within the clusters circulating among Chinese MSM were formed respectively, one of which is in neighboring Japan (designated JP-CN.01AE.MSM.4), and the other is in the United Kingdom with strains from Hong Kong and Thailand (designated UK-CN.01AE.MSM.5).