title: Precise mapping of recombination breakpoints suggests a common parent of two BC recombinant HIV type 1 strains circulating in China.
abstract: Two different BC recombinant HIV-1 strains have arisen and begun to circulate among intravenous drug users in China. The recombinants are mostly subtype C with a few small subtype B segments. Additional full-genome sequences of the two recombinants, termed CRF07_BC and CRFO&_BC, are now available for analysis. Four CRF07_BC strains, including c54, 97CNU01, 98CN009, and a new strain CNGL-179, described here, and four CRF08_BC strains, including 97CNGX-6, 97CNGX-7, 97CNGX-9, and 98CN006, were compared for their recombination breakpoints by bootscanning and software for fine mapping of recombinants. The four CRF07_BC strains shared an identical recombination structure and the four CRF08_BC strains shared an identical, but different, recombination structure. The two CRFs share five precise subtype B/C boundaries, although although other segments differ between them, suggesting that they shared a common ancestor, itself a BC recombinant that separately "back-crossed" onto different subtype C strains. Both CRFs are broadly distributed from north to south in western China and have maintained low interpatient diversity.
authors.affiliation: Henry M Jackson Foundation, Rockville, Maryland 20850, USA. fmccutchan@hivresearch.org
authors.forename: F E
authors.initials: FE
authors.lastname: McClutchan
authors.forename: J K
authors.initials: JK
authors.lastname: Carr
authors.forename: D
authors.initials: D
authors.lastname: Murphy
authors.forename: S
authors.initials: S
authors.lastname: Piyasirisilp
authors.forename: F
authors.initials: F
authors.lastname: Gao
authors.forename: B
authors.initials: B
authors.lastname: Hahn
authors.forename: X-F
authors.initials: XF
authors.lastname: Yu
authors.forename: C
authors.initials: C
authors.lastname: Beyrer
authors.forename: D L
authors.initials: DL
authors.lastname: Birx
mesh_terms: D002681:China / Q000453:epidemiology; D019295:Computational Biology; D016679:Genome, Viral; D015658:HIV Infections / Q000453:epidemiology* / Q000821:virology; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D011995:Recombination, Genetic; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012984:Software; D015819:Substance Abuse, Intravenous / Q000150:complications