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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Available from: Ke Xing, Sep 04, 2014
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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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    ABSTRACT: Hepatitis B virus (HBV) genotypes and subgenotypes may vary in geographical distribution and virological features. Previous investigations, including ours, showed that HBV genotypes B and C were respectively predominant in South and North China, while genotypes A and D were infrequently detected and genotype G was not found. In this study, a novel A/C/G intergenotype was identified in patients with chronic HBV infection in Guilin, a city in southern China. Initial phylogenetic analysis based on the S gene suggested the HBV recombinant to be genotype G. However, extended genotyping based on the entire HBV genome indicated it to be an A/C/G intergenotype with a closer relation to genotype C. Breakpoint analysis using the SIMPLOT program revealed that the recombinant had a recombination with a arrangement of genotypes A, G, A and C fragments. Compared with the HBV recombinants harboring one or two genotype G fragments found in Asian countries, this Guilin recombinant was highly similar to the Vietnam (98-99%) and Long An recombinants (96-99%), but had a relatively low similarity to the Thailand one (89%). Unlike those with the typical genotype G of HBV, the patients with the Guilin recombinant were seropositive for HBeAg. Moreover, a relatively high HBV DNA viral load (>2×10(6) IU/ml) was detected in the patients, and the analysis of viral replication capacity showed that the Guilin recombinant strains had a competent replication capacity similar to genotypes B and C strains. These findings can aid in not only the clarification of the phylogenetic origin of the HBV recombinants with the genotype G fragment found in Asian countries, but also the understanding of the virological properties of these complicated HBV recombinants.
    PLoS ONE 01/2014; 9(1):e84005. DOI:10.1371/journal.pone.0084005 · 3.23 Impact Factor
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    • "We considered all possible pairs of the involving sequences of genotypes A and C to simulate the occurrence of recombination between the two genotypes. When a recombination occurred between a pair of sequences with probability p, location of the recombinant fragment was randomly chosen on the HBV genome, and length of the recombinant fragment was determined by the empirical length distribution of recombinants from Yang et al’s study [15]. Because HBV genome is a circular molecular, we allowed recombinant fragment cover the junction of sequence end and start. "
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    ABSTRACT: Background Hepatitis B virus (HBV) is an important infectious agent that causes widespread concern because billions of people are infected by at least 8 different HBV genotypes worldwide. However, reconstruction of the phylogenetic relationship between HBV genotypes is difficult. Specifically, the phylogenetic relationships among genotypes A, B, and C are not clear from previous studies because of the confounding effects of genotype recombination. In order to clarify the evolutionary relationships, a rigorous approach is required that can effectively explore genetic sequences with recombination. Result In the present study, phylogenetic relationship of the HBV genotypes was reconstructed using a consensus phylogeny of phylogenetic trees of HBV genome segments. Reliability of the reconstructed phylogeny was extensively evaluated in agreements of local phylogenies of genome segments. The reconstructed phylogenetic tree revealed that HBV genotypes B and C had a closer phylogenetic relationship than genotypes A and B or A and C. Evaluations showed the consensus method was capable to reconstruct reliable phylogenetic relationship in the presence of recombinants. Conclusion The consensus method implemented in this study provides an alternative approach for reconstructing reliable phylogenetic relationships for viruses with possible genetic recombination. Our approach revealed the phylogenetic relationships of genotypes A, B, and C of HBV.
    BMC Evolutionary Biology 06/2013; 13(1):120. DOI:10.1186/1471-2148-13-120 · 3.37 Impact Factor
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    • "The 3.2 kb circular genome of HBV comprises two partially overlapping double-stranded DNA strands and is highly heterogeneous . Two principal reasons account for the high level of HBV genetic diversity: firstly, the virally-encoded reverse transcriptase (RT) lacks proof-reading ability (Duffy et al., 2008), and secondly, HBV genomes undergo frequent recombination (Shi et al., 2012a; Simmonds and Midgley, 2005; Yang et al., 2006; Ye et al., 2010). HBV has been divided into various genotypes based on the recommendation that different genotypes should diverge by at least 8% over the entire genome (Kramvis et al., 2005; Schaefer, 2007). "
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    ABSTRACT: Hepatitis B virus (HBV) has evolved into phylogenetically separable genotypes and subgenotypes. Accurately assigning the subgenotype for an HBV strain is of clinical and epidemiological significance. In this paper, we review the recommendations currently employed for HBV subgenotyping, the history of HBV subgenotyping, the effects of recombination on HBV subgenotyping, misclassifications in HBV subgenotyping, and suggestions are made to correct the misclassifications. Finally, proposals are made to guide future HBV subgenotyping.
    Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases 03/2013; 16. DOI:10.1016/j.meegid.2013.03.021 · 3.02 Impact Factor
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