Novel Subgenotypes of Hepatitis B Virus Genotypes C and D in Papua, Indonesia

Lusida, Maria Inge; Nugrahaputra, Victor Eka; Soetjipto,; Handajani, Retno; Nagano-Fujii, Motoko; Sasayama, Mikiko; Utsumi, Takako; Hotta, Hak

doi:10.1128/jcm.01681-07

Cited by 89 publications

(111 citation statements)

References 34 publications

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“…Phylogenetic analysis of 15present isolates were demonstrating that HBV/D (73%) is most predominant HBV genotype, followed by HBV/C (27%) genotype C among HBV Saudi chronic Patients. This result is consistent with many previous observations postulated that genotype D appears to be predominating in the Mediterranean basin and the Middle East countries (Saudy et al, 2003;Norder et al, 2004;Zekri et al, 2007;El Hadad et al, 2013), whereas HBV/C is predominant in Southeast Asia countries (Lusida et al, 2008).…”

Section: Discussionsupporting

confidence: 82%

“…Previously, analysis of the whole HBsAg gene sequence of some HBV strain alone might be insufficient to classify HBV/D into sub genotypes (Norder et al, 2004). Recently, new HBV subgenotype has been classified and designated as HBV/B3 using the partial sequence of the S gene (Lusida et al, 2008). Also the novel HBV/D9 have been classified from isolates showed recombination between genotype D and C in the pre core/core region, although the pre-S/S ORF didn't possess any unique motif that can distinguish HBV/D9 isolates from the other eight subgenotypes of D. Moreover, the sequencing of only the pre-S/S region that is frequently practiced for defining genotype/subgenotype will lead to their improper classification as subgenotype D3 or D2 (Ghosh et al, 2013).…”

Section: Discussionmentioning

confidence: 99%

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Identification of Novel D11 Hepatitis B Surface Antigen Subgenotype in Jeddah, Kingdom of Saudi Arabia

Hadad¹,

Alakilli²,

Rabah³

et al. 2015

Biotechnology

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A B S T R A C T Hepatitis B virus (HBV) infection remains to be a worldwide health problem. In Saudi Arabia, HBV is the most predominant type of hepatitis followed by hepatitis C and hepatitis A while little is known about the molecular epidemiology of the prevalence of HBV genotype/subgenotype particularly in Jeddah. Serum samples were collected from HBV chronic patients and subjected to HBsAg gene amplification. Sequencing and phylogenetic analysis of the entire HBsAg gene sequences revealed that 11 isolates belonged to HBV/D while 4 isolates were associated with HBV/C. Interestingly, HBV/D subgenotypes identified eight HBV/D present isolates belonged to HBV/D1 while three isolates showed a new cluster supporting by a branch with 99% bootstrap value and 4.3-5.8% nucleotide divergence over the entire HBsAg gene from other known subgenotypes D1 to D10, despite they were appearing more related to HBV/D5. The three strains of the new D subgenotype showed unique amino acid sequences consisting of Thr7non, 75Pro in the preS1 gene, 112Ile, 161Gly in the preS2 gene and 196Glu, 197Ala, 238Ser, 259Cys in the S gene. In addition to three amino acid residues in the S gene (373Ile, 374Ala and 381Thr) were specified S118S isolate. Subsequently, it have been verified that HBV/D1 is the most prevalent HBV subgenotype in Jeddah as well as we proposed a novel subgenotype designated HBV/D11. The identification of HBV/D11 novel subgenotypes in the present study suggested that further studies with a large number of subjects in previously examined and unexamined areas may lead to discovering new HBV strain genotypes and/or subgenotypes circulating in Saudi Arabia.

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Section: Discussionsupporting

confidence: 82%

Section: Discussionmentioning

confidence: 99%

Identification of Novel D11 Hepatitis B Surface Antigen Subgenotype in Jeddah, Kingdom of Saudi Arabia

Hadad¹,

Alakilli²,

Rabah³

et al. 2015

Biotechnology

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“…Further extensive phylogenetic analyses of HBV genotypes in different studies worldwide have resulted in recognition of several subgenotypes within genotypes, A (A1-A5), B (B1-B8), C (C1-C7), D (D1-D7) and F (F1-F4), defined by . 4 % intra-genotypic divergence but , 7.5 % (Cavinta et al, 2009;Hubschen et al, 2009;Kramvis et al, 2008;Lusida et al, 2008;Meldal et al, 2009;Mulyanto et al, 2009;Norder et al, 2004;Nurainy et al, 2008;Schaefer, 2007). Several large-scale studies carried out in a number of African countries have disclosed the emergence of a trend in the distribution of genotypes.…”

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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“…HBV isolates of different genotypes and subtypes show different geographical distributions, virological characteristics, and possibly, clinical outcomes (9,10). Genotypes B and C (HBV/B and HBV/C, respectively) are predominant in Asia and particularly, in Indonesia (11,12).…”

Section: Introductionmentioning

confidence: 99%

High Rates of Hepatitis B Virus (HBV), Hepatitis C Virus (HCV), and Human Immunodeficiency Virus Infections and Uncommon HBV Genotype/Subtype and HCV Subtype Distributions among Transgender Individuals in Surabaya, Indonesia

et al. 2016

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SUMMARY:Transgender people are at a high risk for sexually transmitted viruses such as hepatitis B virus (HBV) and human immunodeficiency virus (HIV). Moreover, Indonesia has a moderate-to-high rate of HBV infection and rapid epidemic growth of HIV infection; hepatitis C virus (HCV) infection can co-occur with HBV and HIV infections. In this study, 10 of 107 individuals (9.3z) were positive for HBV surface antigen (HBsAg) and/or HBV DNA, whereas 19 of 101 individuals (18.8z) with negative results for HBsAg were positive for HBV core antibody (anti-HBc). Seven of the 107 individuals (6.5z) were anti-HCV positive, and 16 of the 100 tested samples (16.0z) were HIV positive. Genotype and subtype analyses of all 10 HBV DNA (6 HBsAg positive and 4 anti-HBc positive) strains showed that 3 were of the HBV genotype/HBsAg subtype C/adrq ＋ , one was of C/adw2, and 5 were of B/adw2. The HCV subtype distribution showed that 33.3z were of HCV-1b, and 66.7z were of HCV-3k (n ＝ 6). These distributions differed from those found in the general population of Surabaya, Indonesia. Interestingly, HIV subtype analysis showed a high prevalence of HIV, with possible recombinants of CRF01_AE and subtype B.

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Novel Subgenotypes of Hepatitis B Virus Genotypes C and D in Papua, Indonesia

Cited by 89 publications

References 34 publications

Identification of Novel D11 Hepatitis B Surface Antigen Subgenotype in Jeddah, Kingdom of Saudi Arabia

Identification of Novel D11 Hepatitis B Surface Antigen Subgenotype in Jeddah, Kingdom of Saudi Arabia

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

High Rates of Hepatitis B Virus (HBV), Hepatitis C Virus (HCV), and Human Immunodeficiency Virus Infections and Uncommon HBV Genotype/Subtype and HCV Subtype Distributions among Transgender Individuals in Surabaya, Indonesia

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