When Should “I” Consider a New Hepatitis B Virus Genotype?

Kurbanov, Fuat; Tanaka, Yasuhito; Kramvis, Anna; Simmonds, Peter; Mizokami, Masashi

doi:10.1128/jvi.00793-08

Cited by 61 publications

(52 citation statements)

References 13 publications

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“…2B). To further test the possibility of recombination between the ancestors of the rat TLVs and SAFVs, the grouping scan analysis test for recombination (29,43) was also used. This method failed to find evidence for recombination between TLV of rats and SAFV above the threshold grouping score of 0.5 (data not shown).…”

Section: Resultsmentioning

confidence: 99%

Cardioviruses Are Genetically Diverse and Cause Common Enteric Infections in South Asian Children

Blinkova

Kapoor

Victoria

et al. 2009

J Virol

125

161

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Section: Resultsmentioning

confidence: 99%

Cardioviruses Are Genetically Diverse and Cause Common Enteric Infections in South Asian Children

Blinkova

Kapoor

Victoria

et al. 2009

J Virol

125

161

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“…Likewise, the C/D recombinant prevails in Tibet and northern China (50). To avoid assigning a new genotype for every newly discovered sporadic recombinant HBV variant, evidence of intergenotypic recombination should be carefully eliminated (14). However, in some cases, designation of a new genotype is proposed by a potential epidemiological significance of a novel genetic variant.…”

Section: Discussionmentioning

confidence: 99%

A Genetic Variant of Hepatitis B Virus Divergent from Known Human and Ape Genotypes Isolated from a Japanese Patient and Provisionally Assigned to New Genotype J

Tatematsu¹,

Tanaka²,

Kurbanov³

et al. 2009

J Virol

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390

306

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Hepatitis B virus (HBV) of a novel genotype (J) was recovered from an 88-year-old Japanese patient with hepatocellular carcinoma who had a history of residing in Borneo during the World War II. It was divergent from eight human (A to H) and four ape (chimpanzee, gorilla, gibbon, and orangutan) HBV genotypes, as well as from a recently proposed ninth human genotype I, by 9.9 to 16.5% of the entire genomic sequence and did not have evidence of recombination with any of the nine human genotypes and four nonhuman genotypes. Based on a comparison of the entire nucleotide sequence against 1,440 HBV isolates reported, HBV/J was nearest to the gibbon and orangutan genotypes (mean divergences of 10.9 and 10.7%, respectively). Based on a comparison of four open reading frames, HBV/J was closer to gibbon/orangutan genotypes than to human genotypes in the P and large S genes and closest to Australian aboriginal strains (HBV/C4) and orangutan-derived strains in the S gene, whereas it was closer to human than ape genotypes in the C gene. HBV/J shared a deletion of 33 nucleotides at the start of preS1 region with C4 and gibbon genotypes, had an S-gene sequence similar to that of C4, and expressed the ayw subtype. Efficient infection, replication, and antigen expression by HBV/J were experimentally established in two chimeric mice with the liver repopulated for human hepatocytes. The HBV DNA sequence recovered from infected mice was identical to that in the inoculum. Since HBV/J is positioned phylogenetically in between human and ape genotypes, it may help to trace the origin of HBV and merits further epidemiological surveys.Worldwide, an estimated 400 million people are infected with hepatitis B virus (HBV) persistently, of whom three quarters live in the Southeast and Far East Asia, and one million die of decompensated cirrhosis and/or hepatocellular carcinoma (HCC) annually (8,15). HBV is the smallest animal DNA virus and has a genome made of approximately 3,200 nucleotides (nt) that contains four open reading frames for P, C, S, and X genes; they code for DNA polymerase/reversetranscriptase, core protein, surface protein, and X protein, respectively (49). The S gene is divided into preS1 and preS2 regions and the small S gene, and the C gene splits into PreC and C.Eight genotypes of HBV have been recognized by a sequence divergence of Ͼ8% in the entire genome and named by capital alphabet letters (A to H) in the order of discovery (3,26,29,42). HBV genotypes are further classified into subgenotypes, such as B1/Bj and B2-5/Ba (44), as well as C1/Cs, C2/Ce, and C3-5 (36). A systematic nomenclature is proposed for designating HBV subgenotypes using Arabic numbers, such as A1, A2, and A3 (25). HBV genotypes have distinct geographical distribution (16,23). Genotype A is prevalent in Africa, Europe and India, genotypes B and C are common in Asia, and genotype E is common in sub-Saharan Africa. Genotypes F and H are restricted to Central and South American continents, whereas genotype D is distributed all over the world. HBV genot...

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“…To date, eight genotypes (A-H) have been established based on intergroup divergence of .7.5 % in the complete nucleotide sequence (Arauz-Ruiz et al, 2002;Kramvis et al, 2008;Norder et al, 1994;Okamoto et al, 1988;Stuyver et al, 2000). Recently, a ninth genotype isolated in Laos (Olinger et al, 2008a) and Vietnam (Hannoun et al, 2000;Olinger et al, 2008b;Tran et al, 2008) and tentatively termed 'I' was proposed, although it is still subject to debate (Kurbanov, 2008). In addition, a tenth genotype provisionally termed genotype 'J' was isolated from a Japanese patient (Tatematsu et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

A novel hepatitis B virus (HBV) subgenotype D (D8) strain, resulting from recombination between genotypes D and E, is circulating in Niger along with HBV/E strains

Chekaraou

Brichler

Mansour

et al. 2010

Journal of General Virology

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Niger is a west African country that is highly endemic for hepatitis B virus (HBV) infection. The seroprevalence for HBV surface antigen (HBsAg) is about 20 %; however, there are no reports on the molecular epidemiology of HBV strains spreading in Niger. In the present study, HBV isolates from the sera of 58 consecutive, asymptomatic, HBsAg-positive blood donors were characterized. Genotype affiliation was determined by amplification, sequencing and phylogenetic analysis of the preS1, polymerase/reverse transcriptase (RT/Pol) and precore (preC)/C regions. The first series of results revealed that different genomic fragments clustered with different genotypes on phylogenetic trees, suggesting recombination events. Twenty-four complete genomic sequences were obtained by amplification and sequencing of seven overlapping regions covering the whole genome, and were studied by extensive phylogenetic analysis. Among them, 20 (83.3 %) were classified unequivocally as genotype E (HBV/E). The remaining four (16.7%) clustered on a distinct branch within HBV/D with strong bootstrap and posterior probability values. Complete molecular characterization of these four strains was achieved by the Simplot program, bootscanning analysis and cloning experiments, and enabled us to identify an HBV/D-E recombinant that formed a new HBV/D subgenotype spreading in Niger, tentatively named D8. Moreover, 20 new complete HBV/E nucleotide sequences were determined that exhibited higher genetic variability than is generally described in Africa. One was found to be a recombinant containing HBV/D sequences in the preS2 and RT/Pol regions. Taken together, these data suggest that, in Niger, genetic variability of HBV strains is still evolving, probably reflecting ancient endemic HBV infection. INTRODUCTIONHepatitis B virus (HBV) infection remains a major public health problem, particularly in Africa, although data for precisely estimating the burden of HBV infection are lacking. It is estimated that 2 billion people worldwide are or have been infected with HBV (WHO: http://www.who. int/csr/disease/hepatitis/HepatitisB_whocdscsrlyo2002_2.pdf), among whom over 360 million are in a chronic carrier state with a high risk of developing cirrhosis and hepatocellular carcinoma (Ganem & Prince, 2004;Lee et al., 1997;Lok, 2004). About 70-140 million of these carriers live in Africa, and about 250 000 of the 1.3 million HBV-related deaths recorded each year throughout the world occur in Africa (Andernach et al., 2009;Hubschen et al., 2008;Kramvis & Kew, 2007;Kramvis et al., 2002;Mulders et al., 2004). HBV belongs to the family Hepadnaviridae and is characterized by a partially double-stranded circular DNA genome of 3These authors contributed equally to this work.The GenBank/EMBL/DDBJ accession numbers for the sequences determined in this study are FN594748-FN594771.A supplementary list of additional GenBank sequences used in this study is available with the online version of this paper. RESULTS Nucleotide sequences and phylogenetic analysesSeveral nucleot...

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When Should “I” Consider a New Hepatitis B Virus Genotype?

Cited by 61 publications

References 13 publications

Cardioviruses Are Genetically Diverse and Cause Common Enteric Infections in South Asian Children

Cardioviruses Are Genetically Diverse and Cause Common Enteric Infections in South Asian Children

A Genetic Variant of Hepatitis B Virus Divergent from Known Human and Ape Genotypes Isolated from a Japanese Patient and Provisionally Assigned to New Genotype J

A novel hepatitis B virus (HBV) subgenotype D (D8) strain, resulting from recombination between genotypes D and E, is circulating in Niger along with HBV/E strains

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