BACKGROUND: In this study, the prevalence of @entity2858 CRF01_AE intrasubtype recombinants in China is estimated and their contributions to the @entity3082 are explored. METHODS: Available @entity2858 complete genomes of CRF01_AE were retrieved from the @entity645 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 @entity13563 . 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 @entity1 who have sex with @entity1 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 @entity3082 and emphasized the value of intrasubtype recombinants, which came to circulate in the same manner as intersubtype recombinants.

A considerable proportion of CRF01_AE strains in China originated from @entity13563 ( XXXX ).

@entity1 :: ('9606', 'Species') :: ['men'] @entity13563 :: ('MESH:C535296', 'Disease') :: ['circulating intrasubtype recombinant forms'] @entity3082 :: ('MESH:D004671', 'Disease') :: ['epidemic'] @entity2858 :: ('11676', 'Species') :: ['HIV-1'] @entity645 :: ('57667', 'Species') :: ['HIV']
@entity13563 :: (MESH:C535296,Disease) :: ['CIRF']
