Abstract
BackgroundIn this study, the prevalence of HIV-1 CRF01_AE intrasubtype recombinants in China is estimated and their contributions to the epidemic are explored.MethodsAvailable HIV-1 complete genomes of CRF01_AE were retrieved from the HIV database. The two alignments were evaluated with RDP3. Recombinants were defined as cases in which the recombination signal was supported by at least 3 methods with P-values of ≤0.05 after Bonferroni correction for multiple comparisons implemented in RDP3. Phylogenetic analysis was performed to further investigate the role of intrasubtype recombinants in epidemics.ResultsHere, 124 out of the 339 sequences from around the world (36.6 %) showed significant evidence of recombination. Here, 84 of these recombinants were from China, accounting for 54.9 % of local total sequences (84 out of 153). The results indicated non-negligible levels of intrasubtype recombination. Subsequent phylogenetic analysis indicated that a considerable proportion of CRF01_AE strains in China originated from circulating intrasubtype recombinant forms. Three large, well-supported intrasubtype recombinants clusters were identified here. Through a survey of risk factors and sampling cities and provinces, cluster I and cluster II were found to be prevalent primarily among men who have sex with men in major northern cities. Cluster III was prevalent among heterosexuals and intravenous drug users in southern and southwestern provinces.ConclusionsThe current work highlighted the remarkable prevalence of intrasubtype recombination within the CRF01_AE epidemic and emphasized the value of intrasubtype recombinants, which came to circulate in the same manner as intersubtype recombinants.Electronic supplementary materialThe online version of this article (doi:10.1186/s12879-015-1273-5) contains supplementary material, which is available to authorized users.
Highlights
In this study, the prevalence of human immunodeficiency virus type 1 (HIV-1) CRF01_AE intrasubtype recombinants in China is estimated and their contributions to the epidemic are explored
The results showed significantly high prevalence of intrasubtype recombinants in circulation and indicated that a considerable proportion of CRF01_AE strains in China originated from circulating intrasubtype recombinant forms
Phylogenetic and recombination analysis indicated that considerable CRF01_AE strains in China originated from circulating intrasubtype recombinant forms Among these 124 recombinants, 1 was from Afghanistan, and all the others were from China (84 recombinants), Thailand (14 recombinants), or Vietnam (25 recombinants), which are geographically close
Summary
The prevalence of HIV-1 CRF01_AE intrasubtype recombinants in China is estimated and their contributions to the epidemic are explored. Phylogenetic and recombination analysis indicated that considerable CRF01_AE strains in China originated from circulating intrasubtype recombinant forms Among these 124 recombinants, 1 was from Afghanistan, and all the others were from China (84 recombinants), Thailand (14 recombinants), or Vietnam (25 recombinants), which are geographically close Such clustering in geographic distribution and the fact that distinct CRF01_AE lineages were independently introduced to China from Southeast Asia suggest that these intrasubtype recombinants very likely originated within this region and that there have probably been epidemics caused by intrasubtype recombinants from the same recombination event. Three large (≥10 sequences), well-supported (SH values were 100 %) and distinct clusters of CRF01_AE strains being almost entirely composed of putative recombinants were indicated from clusters I–III.
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