Identification of Hepatitis B virus putative intergenotype recombinants by using fragment typing

State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-sen (Zhongshan) University, Guangzhou 510275, People's Republic of China.
Journal of General Virology (Impact Factor: 3.18). 09/2006; 87(Pt 8):2203-15. DOI: 10.1099/vir.0.81752-0
Source: PubMed


Eight hundred and thirty-seven human Hepatitis B virus (HBV) genomes were categorized into pure genotypes and potential intergenotypes, according to their fragment types which were determined based on similarity and phylogenetic analyses of 13 contrived fragments of 250 bp against the corresponding fragments of the consensus sequences of genotypes A-H. Twenty-five intergenotypes, including 171 genomes, were revealed from the potential intergenotype recombinants by phylogenetic analysis of the precisely derived mosaic fragments. Among these, four new intergenotypes were discovered. Many genomes were revealed as putative intergenotype recombinants for the first time. About 87 % of the putative recombinants were B/C (120) and A/D (29) hybrids. The other recombinants comprised A/B/C, A/C, A/E, A/G, C/D, C/F, C/G, C/U (U for unknown genotype) and B/C/U hybrids. Genotypes A and C showed a higher recombination tendency than did other genotypes. The results also demonstrated region priority and breakpoint hot spots in the intergenotype recombination. Recombination breakpoints were found to be concentrated mainly in the vicinity of the DR1 region (nt 1640-1900), the pre S1/S2 region (nt 3150-100), the 3'-end of the C gene (nt 2330-2450) and the 3'-end of the S gene (nt 650-830). These results support the suggestion that intergenotype recombinants may result from co-infection with different genotypes.

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    • "Phylogenetic analysis against representative sequences of genotypes A–H was performed. A total of 34 sequences were selected at random from HBV full-length sequences of authentic genotypes A–H, four to five sequences for each genotype, according to Norder et al [12] and Yang et al [31]. The genome of woolly monkey hepadnavirus was used as outgroup control in the analysis. "
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