title: A considerable proportion of CRF01_AE strains in China originated from circulating intrasubtype recombinant forms (CIRF).
abstract: BACKGROUND
  In this study, the prevalence of HIV-1 CRF01_AE intrasubtype recombinants in China is estimated and their contributions to the epidemic are explored.
  
  
  METHODS
  Available 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.
  
  
  RESULTS
  Here, 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.
  
  
  CONCLUSIONS
  The 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.
authors.affiliation: Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China. jialeihaowawa@gmail.com.
authors.forename: Lei
authors.initials: L
authors.lastname: Jia
authors.affiliation: Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China. guibaodj@126.com.
authors.forename: Tao
authors.initials: T
authors.lastname: Gui
authors.affiliation: Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China. dearwood@sina.com.
authors.forename: Lin
authors.initials: L
authors.lastname: Li
authors.affiliation: Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China. aliusy_0@sina.com.
authors.forename: Siyang
authors.initials: S
authors.lastname: Liu
authors.affiliation: Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China. hanpingline@163.com.
authors.forename: Hanping
authors.initials: H
authors.lastname: Li
authors.affiliation: Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China. bzy_6611@sina.com.
authors.forename: Zuoyi
authors.initials: Z
authors.lastname: Bao
authors.affiliation: Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China. woodsxl@163.com.
authors.forename: Xiaolin
authors.initials: X
authors.lastname: Wang
authors.affiliation: Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China. zdm0705@hotmail.com.
authors.forename: Daomin
authors.initials: D
authors.lastname: Zhuang
authors.affiliation: Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China. tianyili1983@gmail.com.
authors.forename: Tianyi
authors.initials: T
authors.lastname: Li
authors.affiliation: Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China. hanjingwan@gmail.com.
authors.forename: Jingwan
authors.initials: J
authors.lastname: Han
authors.affiliation: Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China. yongjian325@sina.com.
authors.forename: Yongjian
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China. lijy@bmi.ac.cn.
authors.forename: Jingyun
authors.initials: J
authors.lastname: Li
mesh_terms: D002681:China / Q000453:epidemiology; D055030:Drug Users; D015658:HIV Infections / Q000453:epidemiology / Q000821:virology*; D015497:HIV-1 / Q000235:genetics* / Q000472:pathogenicity; D020010:Heterosexuality; D006801:Humans; D008297:Male; D010802:Phylogeny; D011995:Recombination, Genetic