title: Identification of Two New HIV-1 Circulating Recombinant Forms (CRF87_cpx and CRF88_BC) from Reported Unique Recombinant Forms in Asia.
abstract: The on-going generation of HIV-1 intersubtype recombination has led to new circulating recombinant forms (CRFs) and unique recombinant forms (URFs) in Asia. In this study, we evaluated whether previously reported URFs were actually CRFs. All available complete or near full-length HIV-1 URF sequences from Asia were retrieved from the HIV Los Alamos National Laboratory Sequence database, and phylogenetic, transmission cluster, and bootscan analyses were performed using MEGA 6.0, Cluster Picker 1.2.1, and SimPlot3.5.1. According to the criterion of new CRFs, two new HIV-1 CRFs (CRF87_cpx and CRF88_BC) were identified from these available URFs. CRF87_cpx comprised HIV-1 subtypes B, C, and CRF01_AE, and CRF88_BC comprised subtypes B and C. HIV Blast and bootscan analysis revealed that besides the three representative strains, there were two additional CRF87_cpx strains. Furthermore, we defined seven dominant URFs (dURF01-dURF07), each of which contained two strains sharing same recombination map and can be used as sequence references to facilitate the finding of new potential CRFs in future. These results will benefit the molecular epidemiological investigation of HIV-1 in Asia.
authors.affiliation: 1 CAS Key Laboratory of Molecular Virology & Immunology, Pathogen Diagnostic Center, Institut Pasteur of Shanghai , Chinese Academy of Science, Shanghai, China .
authors.forename: Yihong
authors.initials: Y
authors.lastname: Hu
authors.affiliation: 2 Medical Laboratory of Taizhou Fourth People's Hospital , Taizhou, China .
authors.forename: Zhenzhou
authors.initials: Z
authors.lastname: Wan
authors.affiliation: 3 Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, College of Life Sciences, Yan'an University , Yan'an, China .
authors.forename: Yan-Heng
authors.initials: YH
authors.lastname: Zhou
authors.affiliation: 4 Division of Infectious Diseases, University of California San Diego , La Jolla, California.|5 Veterans Affairs Healthcare System San Diego , San Diego, California.
authors.forename: Davey
authors.initials: D
authors.lastname: Smith
authors.affiliation: 6 Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology , Chinese Academy of Sciences, Kunming, China .
authors.forename: Yong-Tang
authors.initials: YT
authors.lastname: Zheng
authors.affiliation: 1 CAS Key Laboratory of Molecular Virology & Immunology, Pathogen Diagnostic Center, Institut Pasteur of Shanghai , Chinese Academy of Science, Shanghai, China .
authors.forename: Chiyu
authors.initials: C
authors.lastname: Zhang
mesh_terms: D001208:Asia / Q000453:epidemiology; D016000:Cluster Analysis; D018562:Disease Transmission, Infectious; D016679:Genome, Viral; D005838:Genotype; D015658:HIV Infections / Q000453:epidemiology / Q000635:transmission / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D017720:Molecular Epidemiology; D010802:Phylogeny; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA
keywords: Asia; CRF; HIV-1; URF; cluster; subtype