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279 Precise Mapping of Recombination Breakpoints Reveals a Common Parent of Two BC Recombinant Strains Circulating in China
F. E. McCutchan*1, J. K. Carr1, D. Murphy1, S. Piyasirisilp1, F. Gao2, B. Hahn2, X.-F. Yu3, C. Beyrer3, and D. L. Birx4
1Henry M. Jackson Fndn., Rockville, MD, USA; 2Univ. of Alabama, Birmingham, USA; 3The Johns Hopkins Univ., Baltimore, MD, USA; and 4Walter Reed Army Inst. of Res., Washington, DC, USA
Background: Two BC recombinant HIV-1s have arisen recently and begun to circulate among intravenous drug users (IDU) in China. The 2 recombinants are mostly subtype C, but each contains a few small subtype B segments; because their structures are sufficiently different, they have been considered to have arisen independently. More near full-genome sequences of the 2 circulating recombinant forms (CRF), termed CRF07_BC and CRF08_BC, respectively, are now available for analysis.
Methods: Four sequences of CRF07_BC (97CN54, 97CN001, 98CN009, and 98CNGL-179) and 4 sequences of CRF08_BC (97CNGX-6, 97CNGX-7, 97CNGX-9, and 98CN006) were compared for their recombination breakpoints using bootscanning and a new software, Informative Site Analysis (ISA), which tabulates the subtype associations in 10-bp increments across the 9,000-bp genome.
Results: The 4 sequences of CRF07_BC shared an identical recombination structure, and the 4 sequences of CRF08_BC also shared an identical, but different recombination structure. ISA revealed that the 2 CRFs share 5 precise subtype B/C boundaries, although other segments differ between the 2 CRFs.
Conclusions: CRF07_BC and CRF08_BC are now more completely documented and defined. The possibility that these CRFs shared a common ancestor, itself a BC recombinant that separately "backcrossed" onto different subtype C strains to generate the 2 CRFs, should be strongly considered. The application of ISA to other CRFs and related recombinants may increase understanding of the generation and spread of recombinant HIV-1 in the pandemic and help to identify ancestral sequences as candidates for vaccine development.
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