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Hudu SA, Niazlin MT, Nordin SA, Tan SS, Omar H, Shahar H, Mutalib NA, Sekawi Z. Genetic diversity of hepatitis B co-infection with hepatitis C, D and E viruses among Malaysian chronic hepatitis B patients. Afr Health Sci 2018; 18:1117-1133. [PMID: 30766578 PMCID: PMC6354894 DOI: 10.4314/ahs.v18i4.33] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Hepatitis B virus co-infection with other strains of viral hepatitis is associated with increased risk of liver cirrhosis and hepatic decompensation. OBJECTIVES This is a prevalence study that assessed the genetic diversity of chronic hepatitis B patients and coinfection. METHODS Chronic hepatitis B patients enrolled in this study were tested for antibodies of other hepatitis viruses using ELISA kits. Patient clinical profiles were collected and partial genes of HBV, HCV, and HEV were amplified, sequenced, and analyzed using phylogenetic analysis. The associations between variables were determined using the chi-squared test. RESULTS Of the 82 patients recruited for this study, 53.7% were non-cirrhotic, 22.0% cirrhotic, 20.7% acute flare and 3.7% hepatocellular carcinoma. Majority (58%) of patients had a high level of ALT (≥34 U/L). Sequence analysis showed HBV (63.9%) belonged to genotype B, HEV belonged to genotype 4 while HCV belonged to genotype 3a and the genotypes were found to be significantly associated with the clinical stage of the patients (χ2=56.632; p<0.01). Similarly, Hepatitis B e antigen was also found to be significantly associated with the clinical stage of infection (χ2=51.952; p<0.01). CONCLUSION This study revealed that genetic diversity was found to have a significant impact on the severity of infection.
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Affiliation(s)
- Shuaibu Abdullahi Hudu
- Department of Medical Microbiology and Parasitology, Faculty of Basic Medical Sciences, College of Health Sciences, Usmanu Danfodiyo University Sokoto, 840232 Sokoto State, Nigeria
| | - Mohd Taib Niazlin
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, University Putra Malaysia
| | - Syafinaz Amin Nordin
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, University Putra Malaysia
| | - Soek Siam Tan
- Department of Hepatology, Selayang Hospital, Lebuh Selayang Batu Cave Selangor, Malaysia
| | - Haniza Omar
- Department of Hepatology, Selayang Hospital, Lebuh Selayang Batu Cave Selangor, Malaysia
| | - Hamiza Shahar
- Department of Hepatology, Selayang Hospital, Lebuh Selayang Batu Cave Selangor, Malaysia
| | - Noor Aliza Mutalib
- Department of Hepatology, Selayang Hospital, Lebuh Selayang Batu Cave Selangor, Malaysia
| | - Zamberi Sekawi
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, University Putra Malaysia
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Hepatitis B virus subgenotyping: history, effects of recombination, misclassifications, and corrections. INFECTION GENETICS AND EVOLUTION 2013; 16:355-61. [PMID: 23538336 DOI: 10.1016/j.meegid.2013.03.021] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 03/15/2013] [Accepted: 03/16/2013] [Indexed: 12/23/2022]
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.
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Shi W, Zhu C, Zheng W, Zheng W, Ling C, Carr MJ, Higgins DG, Zhang Z. Subgenotyping of genotype C hepatitis B virus: correcting misclassifications and identifying a novel subgenotype. PLoS One 2012; 7:e47271. [PMID: 23077582 PMCID: PMC3471840 DOI: 10.1371/journal.pone.0047271] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Accepted: 09/10/2012] [Indexed: 12/23/2022] Open
Abstract
Background More than ten subgenotypes of genotype C Hepatitis B virus (HBV) have been reported, including C1 to C16 and two C/D recombinant subgenotypes (CD1 and CD2), however, inconsistent designations of these subgenotypes still exist. Methodology/Principal Findings We performed a phylogenetic analysis of all full-length genotype C HBV genome sequences to correct the misclassifications of HBV subgenotypes and to study the influence of recombination on HBV subgenotyping. Our results showed that although inclusion of the recombinant sequences changed the topology of the phylogenetic tree, it did not affect the subgenotyping of the non-recombinant sequences, except subgenotype C2. In addition, most of the subgenotypes have been properly designated. However, several misclassifications of HBV subgenotypes have been identified and corrected. For example, C11 proposed by Utsumi and colleagues in 2011 was found to be grouped with C12 proposed by Mulyanto and colleagues. Two sequences, GQ358157 and GU721029, previously designated as C6 have been re-designated as C12 and C7, respectively. Moreover, a quasi-subgenotype C2 was proposed, which included the old C2, several previously unclassified sequences and previously designated C14. In particular, we identified a novel subgenotype, tentative C14, which was well supported by phylogenetic analysis and sequence divergence of >4%. Conclusions/Significance A number of misclassifications in the subgenotyping of genotype C HBV have been identified in this study. After correcting the misclassifications, we proposed a better classification for the subgenotyping of genotype C HBV, in which a novel quasi-subgenotype C2 and a novel subgenotype, tentative C14, were described. Based on this large-scale analysis, we propose that a novel subgenotype should only be reported after a complete comparison of all relevant sequences rather than a few representative sequences only.
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Affiliation(s)
- Weifeng Shi
- Guangzhou Institute of Advanced Technology, Chinese Academy of Sciences, Guangzhou, China
- * E-mail: (WS); (ZZ)
| | - Chaodong Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Weimin Zheng
- Guangzhou Institute of Advanced Technology, Chinese Academy of Sciences, Guangzhou, China
| | - Wei Zheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Cheng Ling
- Guangzhou Institute of Advanced Technology, Chinese Academy of Sciences, Guangzhou, China
| | - Michael J. Carr
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Desmond G. Higgins
- The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Zhong Zhang
- Department of Basic Medicine, Taishan Medical College, Taian, Shandong, China
- * E-mail: (WS); (ZZ)
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Mulyanto, Pancawardani P, Depamede SN, Wahyono A, Jirintai S, Nagashima S, Takahashi M, Nishizawa T, Okamoto H. Identification of four novel subgenotypes (C13-C16) and two inter-genotypic recombinants (C12/G and C13/B3) of hepatitis B virus in Papua province, Indonesia. Virus Res 2011; 163:129-40. [PMID: 21925554 DOI: 10.1016/j.virusres.2011.09.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Revised: 09/02/2011] [Accepted: 09/02/2011] [Indexed: 02/07/2023]
Abstract
Four novel subgenotypes (C6, C11, C12, and D6) of hepatitis B virus (HBV) were identified in Papua, a multiethnic province of Indonesia. To characterize the HBV strains in Papua, serum samples collected from 515 indigenous inhabitants (mean age: 26.6±9.6 years) in a previously unexamined area, Nabire, located in northern Papua, were used in the present study. Among 46 samples whose 1.6-kilobase (kb) HBV DNA sequence was amplified, 38 (83%) were typeable into known subgenotypes [B3 (n=4), C1 (n=2), C5, (n=1), C6 (n=5), C12 (n=13), and D6 (n=13)]. An analysis of the full-length sequence of the eight remaining HBV/C isolates whose sequence was either unclassifiable or uncertain within the 1.6-kb sequence showed no significant evidence of recombination in six isolates, and inter-genotypic recombination in two isolates (NAB20 and NAB46). By pairwise comparisons and a maximum-likelihood phylogenetic analysis, six non-recombinant isolates were considered significantly remote from known HBV/C isolates of subgenotypes C1-C12, and were classifiable into four novel subgenotypes (tentatively designated C13-C16). NAB20 and NAB46 were hybrids of C13/B3 and C12/G, respectively, displaying recombination breakpoints in the 5'-terminus of the P gene. Notably, the distribution of presumably indigenous subgenotypes C11-C16 was associated with particular language speakers in Papua.
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Affiliation(s)
- Mulyanto
- Immunobiology Laboratory, Faculty of Medicine, University of Mataram, Mataram, Indonesia
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Mulyanto, Depamede SN, Wahyono A, Jirintai, Nagashima S, Takahashi M, Okamoto H. Analysis of the full-length genomes of novel hepatitis B virus subgenotypes C11 and C12 in Papua, Indonesia. J Med Virol 2011; 83:54-64. [PMID: 21108339 DOI: 10.1002/jmv.21931] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Two novel subgenotypes (C6 and D6) of hepatitis B virus (HBV) were identified recently in Papua, a multiethnic area of Indonesia. To characterize further the HBV strains in Papua, serum samples collected from 59 viremic subjects (44 males and 15 females; mean age: 30.0 ± 15.5 years) among indigenous inhabitants in Papua, were subjected to phylogenetic analysis of an 1.6-kb partial sequence. Forty-five samples (76%) had genotype C HBV (HBV/C) [C5 (n = 1), C6 (n = 40), and unclassifiable (n = 4)], while seven samples (12%) were HBV/D [D1 (n = 1) and D6 (n = 6)] and six samples (10%) were HBV/B [B2 (n = 1), B3 (n = 3), B7 (n = 1), and B8 (n = 1)]; the remaining sample possessed B3 and C6. An analysis of the full-length sequence of the four HBV/C isolates (NMB09122, NMB09124, NMB09075, and MRK89073) that were unclassifiable into any of the 10 known HBV/C subgenotypes (C1-C10) showed no significant evidence of recombination. Over the entire genome, the NMB09122 and NMB09124 isolates shared 99.8% identity and segregated into a cluster with a bootstrap value of 100%, differing from HBV/C1-HBV/C10 by 3.8-6.9% (mean, ≥4.0%), indicating that NMB09122 and NMB09124 can be classified into a novel subgenotype within genotype C (tentatively designated C11). The NMB09075 and MRK89073 isolates were 97.4% identical to each other and differed from known HBV/C isolates, including the C11 strains, by 4.0-7.2% (mean, ≥4.5%) over the entire genome, indicating that NMB09075 and MRK89703 can be classified into another novel HBV/C subgenotype (C12). The distribution of C11 and C12 seemed to be associated with particular language speakers in Papua.
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Affiliation(s)
- Mulyanto
- Immunobiology Laboratory, Faculty of Medicine, University of Mataram, Mataram, Indonesia
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Mulyanto, Depamede SN, Surayah K, Tjahyono AAH, Jirintai, Nagashima S, Takahashi M, Okamoto H. Identification and characterization of novel hepatitis B virus subgenotype C10 in Nusa Tenggara, Indonesia. Arch Virol 2010; 155:705-15. [DOI: 10.1007/s00705-010-0628-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Accepted: 02/07/2010] [Indexed: 01/01/2023]
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Yin J, Zhang H, He Y, Xie J, Liu S, Chang W, Tan X, Gu C, Lu W, Wang H, Bi S, Cui F, Liang X, Schaefer S, Cao G. Distribution and hepatocellular carcinoma-related viral properties of hepatitis B virus genotypes in Mainland China: a community-based study. Cancer Epidemiol Biomarkers Prev 2010; 19:777-86. [PMID: 20160279 DOI: 10.1158/1055-9965.epi-09-1001] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
INTRODUCTION Hepatitis B virus (HBV) genotypes, replication status, and mutations have been associated with the risk of hepatocellular carcinoma (HCC). Our aim was to study the distribution and HCC-related viral properties of HBV genotypes/subgenotypes in Mainland China. METHODS A multistage cluster probability sampling method was applied to select 81,775 participants between 1 and 59 years at 160 national disease surveillance points. We examined hepatitis B surface antigen, HBV genotypes and subgenotypes, hepatitis B e antigen, viral load, and mutations in the PreS and core promoter regions of HBV genome. RESULTS HBV subgenotypes B2 (27.3%), C1 (10.7%), and C2 (58.0%) were predominant. Genotype D (D1, 80.8%) was frequent in the Uygur. We identified a new subgenotype, C9, mainly in Tibetans. Compositions of subgenotypes B2 and C1 and genotype mixture increased from the North to Central South, which was consistently associated with the increasing prevalence of hepatitis B surface antigen. Hepatitis B e antigen positivity and viral loads were higher in the young with genotype B and declined more rapidly with increasing age than those with genotype C. In contrast to G1896A, PreS deletion, T31C, T1753V, and A1762T/G1764A were more frequent in subgenotype C2 than in subgenotype B2. A1762T/G1764A, T1753V, C1653T, and G1896A, except PreS deletion, consecutively increased with increasing age. CONCLUSION HBV subgenotypes B2, C1, and C2 are endemic in Mainland China. HBV genotype C exhibits less replication activity in the young and harbors higher frequencies of the HCC-associated mutations than genotype B. IMPACT These basic data could help evaluate the association of HBV variations with HCC.
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Affiliation(s)
- Jianhua Yin
- Department of Epidemiology, 3rd Hospital, Second Military Medical University, Shanghai, China
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Cao GW. Clinical relevance and public health significance of hepatitis B virus genomic variations. World J Gastroenterol 2010. [PMID: 19998495 DOI: 10.3748/wjg.15.5761.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/29/2022] Open
Abstract
Ten hepatitis B virus (HBV) genotypes (A-J) and 34 HBV subgenotypes have been identified so far. HBV genotypes and subgenotypes have distinct geographical distributions, and have been shown to differ with regard to clinical outcome, prognosis, and response to interferon treatment. Infection with subgenotype A2 is frequently associated with high viral load, resulting in acute infection via horizontal transmission. Genotypes A and B are more sensitive to interferon treatment than genotypes D and C, respectively. Genotype B is more frequent in acute hepatitis than genotype C, whereas genotype C (C2) is more frequently associated with an increased risk of hepatocellular carcinoma (HCC), mostly cirrhotic, as compared with genotype B (B2). Genotype mixture is associated with high viral load and worse outcome of HBV infection. HBV mutations in the S genes, especially amino acids substitution at position 145 (G145R), are associated with immune escape, whereas mutations in the PreS or S genes which impair HBsAg secretion could present a risk to blood safety. HBV variants harboring mutations in the viral polymerase gene that confer resistance to nucleoside analogs may be selected during antiviral therapy. Different genotypes have distinct mutation patterns in the PreS and EnhII/BCP/Precore regions. PreS deletions, C1653T, T1753V, and A1762T/G1764A are associated with an increased risk of HCC. HCC-associated HBV mutants may not transmit via mother-to-child transmission, and are likely generated during HBV-induced pathogenesis. Examination of HBV mutations alone or in combination and host genetic susceptibility will be helpful in classifying the HBV-infected subjects who will develop HCC and need active anti-viral treatments.
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Abstract
Ten hepatitis B virus (HBV) genotypes (A-J) and 34 HBV subgenotypes have been identified so far. HBV genotypes and subgenotypes have distinct geographical distributions, and have been shown to differ with regard to clinical outcome, prognosis, and response to interferon treatment. Infection with subgenotype A2 is frequently associated with high viral load, resulting in acute infection via horizontal transmission. Genotypes A and B are more sensitive to interferon treatment than genotypes D and C, respectively. Genotype B is more frequent in acute hepatitis than genotype C, whereas genotype C (C2) is more frequently associated with an increased risk of hepatocellular carcinoma (HCC), mostly cirrhotic, as compared with genotype B (B2). Genotype mixture is associated with high viral load and worse outcome of HBV infection. HBV mutations in the S genes, especially amino acids substitution at position 145 (G145R), are associated with immune escape, whereas mutations in the PreS or S genes which impair HBsAg secretion could present a risk to blood safety. HBV variants harboring mutations in the viral polymerase gene that confer resistance to nucleoside analogs may be selected during antiviral therapy. Different genotypes have distinct mutation patterns in the PreS and EnhII/BCP/Precore regions. PreS deletions, C1653T, T1753V, and A1762T/G1764A are associated with an increased risk of HCC. HCC-associated HBV mutants may not transmit via mother-to-child transmission, and are likely generated during HBV-induced pathogenesis. Examination of HBV mutations alone or in combination and host genetic susceptibility will be helpful in classifying the HBV-infected subjects who will develop HCC and need active anti-viral treatments.
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