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Abstract
Sequence heterogeneity is a feature of hepatitis B virus (HBV), the prototype member of the family Hepadnaviridae. Based on an intergroup divergence of greater than 7.5% across the complete genome, HBV has been classified phylogenetically into 9 genotypes, A-I, with a putative 10th genotype 'J', isolated from a single individual. With between approximately 4 and 8% intergroup nucleotide divergence across the complete genome and good bootstrap support, genotypes A-D, F, H, and I are classified further into subgenotypes. There is a broad and highly statistically significant correlation between serological subtypes and genotypes, and in some cases, serological subtypes can be used to differentiate subgenotypes. The genotypes, and certain subgenotypes, have distinct geographical distributions and are important in both the clinical manifestation of infection and response to antiviral therapy. HBV genotypes/subgenotypes and genetic variability of HBV are useful in epidemiological and transmission studies, tracing human migrations, and in predicting the risk for the development of severe liver disease and response to antiviral therapy. Moreover, knowledge of the genotype/subgenotype is important in implementing preventative strategies. Thus, it is crucial that new strains are correctly assigned to their respective genotype/subgenotype and consistent, unambiguous, and generally accepted nomenclature is utilized.
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Affiliation(s)
- Anna Kramvis
- Hepatitis Virus Diversity Research Programme (HVDRP), Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Wang B, Feng Y, Li Z, Duan H, Zhao T, Zhang A, Liu L, Baloch Z, Xia X. Distribution and diversity of hepatitis B virus genotypes in Yunnan, China. J Med Virol 2014; 86:1675-82. [PMID: 24992445 PMCID: PMC4255792 DOI: 10.1002/jmv.24002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2014] [Indexed: 12/17/2022]
Abstract
Hepatitis B virus (HBV) is one of the most prevalent pathogens in the world, and infection with this virus is a serious threat for public health. Yunnan is considered as an important endemic center for blood-borne viruses such as human immunodeficiency virus and hepatitis C virus, in China. However, the distribution and diversity of HBV subgenotypes remain unclear in Yunnan province. In the current study, HBV positive samples were collected from different prefectures of Yunnan province and their molecular epidemiological characters were determined. Phylogenetic analysis on the pre-S/S gene (865 bps) showed the prevalence of four HBV genotypes, including genotype B (24 cases, 33.3%), genotype C (45 cases, 62.5%), genotype I (two cases, 2.78%) and C/D recombinants (one case, 1.39%). The most prevalent genotypes B and C could be sub classified into subgenotype B2 and C1, C2, C5, and C7, respectively. Clusters of subgenotype B2 and C2 consisted of strains from China and other East Asian countries, while subgenotype C1, C5, and C7 and genotype I formed a cluster together with strains from Southeast Asia. Using Bayesian inference from phylogenetic, HBV genotypes B and C were estimated to have originated in 1860s and 1910s with an evolutionary rate of 3.26 and 8.01 × 10(-4) substitutions/site/year, respectively. These findings indicate that the distribution of HBV genotypes in Yunnan was influenced by strains from the rest of China and the neighboring countries.
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Affiliation(s)
- Binghui Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
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53
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Zehender G, Ebranati E, Gabanelli E, Sorrentino C, Lo Presti A, Tanzi E, Ciccozzi M, Galli M. Enigmatic origin of hepatitis B virus: An ancient travelling companion or a recent encounter? World J Gastroenterol 2014; 20:7622-7634. [PMID: 24976700 PMCID: PMC4069291 DOI: 10.3748/wjg.v20.i24.7622] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 01/08/2014] [Accepted: 03/13/2014] [Indexed: 02/06/2023] Open
Abstract
Hepatitis B virus (HBV) is the leading cause of liver disease and infects an estimated 240 million people worldwide. It is characterised by a high degree of genetic heterogeneity because of the use of a reverse transcriptase during viral replication. The ten genotypes (A-J) that have been described so far further segregate into a number of subgenotypes which have distinct ethno-geographic distribution. Genotypes A and D are ubiquitous and the most prevalent genotypes in Europe (mainly represented by subgenotypes D1-3 and A2); genotypes B and C are restricted to eastern Asia and Oceania; genotype E to central and western Africa; and genotypes H and F (classified into 4 subgenotypes) to Latin America and Alaska. This review summarises the data obtained by studying the global phylodynamics and phylogeography of HBV genotypes, particularly those concerning the origin and dispersion histories of genotypes A, D, E and F and their subgenotypes. The lack of any consensus concerning the HBV substitution rate and the conflicting data obtained using different calibration approaches make the time of origin and divergence of the various genotypes and subgenotypes largely uncertain. It is hypothesised that HBV evolutionary rates are time dependent, and that the changes depend on the main transmission routes of the genotypes and the dynamics of the infected populations.
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54
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Bonvicino CR, Moreira MA, Soares MA. Hepatitis B virus lineages in mammalian hosts: Potential for bidirectional cross-species transmission. World J Gastroenterol 2014; 20:7665-7674. [PMID: 24976704 PMCID: PMC4069295 DOI: 10.3748/wjg.v20.i24.7665] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 12/30/2013] [Accepted: 03/13/2014] [Indexed: 02/06/2023] Open
Abstract
The hepatitis B virus (HBV) is a cosmopolitan infectious agent currently affecting over 350 million people worldwide, presently accounting for more than two billion infections. In addition to man, other hepatitis virus strains infect species of several mammalian families of the Primates, Rodentia and Chiroptera orders, in addition to birds. The mounting evidence of HBV infection in African, Asian and neotropical primates draws attention to the potential cross-species, zoonotic transmission of these viruses to man. Moreover, recent evidence also suggests the humans may also function as a source of viral infection to other mammals, particularly to domestic animals like poultry and swine. In this review, we list all evidence of HBV and HBV-like infection of nonhuman mammals and discuss their potential roles as donors or recipients of these viruses to humans and to other closely-related species.
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Utsumi T, Yano Y, Hotta H. Molecular epidemiology of hepatitis B virus in Asia. World J Med Genet 2014; 4:19-26. [DOI: 10.5496/wjmg.v4.i2.19] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Revised: 02/25/2014] [Accepted: 03/17/2014] [Indexed: 02/05/2023] Open
Abstract
Although safe and effective vaccines against hepatitis B virus (HBV) have been available for three decades, HBV infection remains the leading cause of chronic hepatitis, cirrhosis and hepatocellular carcinoma (HCC) worldwide, especially in Asian countries. HBV has been classified into at least 9 genotypes according to the molecular evolutionary analysis of the genomic DNA sequence and shown to have a distinct geographical distribution. Novel HBV genotypes/subgenotypes have been reported, especially from Southeast Asian countries. The clinical characteristics and therapeutic effectiveness of interferon (IFN) and nucleos(t)ide analogues vary among different HBV genotypes. Mutations at T1653C in subgenotype C2 from Japan and South Korea, C/A1753T and C1858T in subgenotype C1 from Vietnam, and C1638T and T1753V in subgenotype B3 from Indonesia were reported to be associated with advanced liver diseases including HCC. Genotype distribution in Japan has been changed by an increasing ratio of subgenotype A2 in chronic hepatitis B. While a large number of epidemiological and clinical studies have been reported from Asian countries, most of the studies were conducted in developed countries such as Taiwan, China, South Korea and Japan. In this review, the most recent publications on the geographical distribution of genetic variants of HBV and related issues such as disease progression and therapy in Asia are updated and summarized.
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Bao H, Zhao W, Ruan B, Wang Q, Zhao J, Lei X, Wang W, Liu Y, Sun J, Xiang A, Guo Y, Yan Z. Rapid high-throughput genotyping of HBV DNA using a modified hybridization-extension technique. Phys Chem Chem Phys 2014; 15:18179-84. [PMID: 24065125 DOI: 10.1039/c3cp51971f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
China has the highest incidence of hepatitis B virus (HBV) infection worldwide. HBV genotypes have variable impacts on disease pathogenesis and drug tolerance. We have developed a technically simple and accurate method for HBV genotyping that will be applicable to pre-treatment diagnosis and individualized treatment. Multiple sequence alignments of HBV genomes from GenBank were used to design primers and probes for genotyping of HBV A through H. The hybridization was carried out on nitrocellulose (NC) membranes with probes fixed in an array format, which was followed by hybrid amplification by an extension step with DNA polymerase to reinforce the double-stranded DNA hybrids on the NC membrane and subsequent visualization using an avidin-biotin system. Genotyping results were confirmed by DNA sequencing and bioinformatics analysis using the National Center for Biotechnology Information genotyping database, and compared with results from the line probe assay. The data show that multiple sequence alignment defined a 630 bp region in the HBV PreS and S regions that was suitable for genotyping. All genotyping significant single nucleotides in the region were defined. Two-hundred-and-ninety-one HBV-positive serum samples from Northwest Chinese patients were genotyped, and the genotyping rate from the new modified hybridization-extension method was 100% compared with direct sequencing. Compared with line probe assay, the newly developed method is superior, featuring reduced reaction time, lower risk of contamination, and increased accuracy for detecting single nucleotide mutation. In conclusion, a novel hybridization-extension method for HBV genotyping was established, which represents a new tool for accurate and rapid SNP detection that will benefit clinical testing.
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Affiliation(s)
- Han Bao
- The State Key Laboratory of Cancer Biology, Department of Pharmacogenomics, School of Pharmacy, The Fourth Military Medical University, 169 Changle West Road, Xi'an 710032, China.
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Bajrai LH, Kumosani T, El-Kafrawy S, El-Daly M, Hindawi S, Ashshi A, Azhar EI. Distribution of HBV genotypes from two blood transfusion centers in western Saudi Arabia. Future Virol 2014. [DOI: 10.2217/fvl.14.29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: To determine the distribution of HBV genotypes among HBsAg-positive blood donors in Makkah and Jeddah. Materials & methods: A total of 158 volunteered HBsAg-positive male blood donors donated blood samples at two transfusion centers in western Saudi Arabia. RFLP digestion was performed on 83 PCR products of the S gene. A subset of 77 positive samples were sequenced and aligned with reference Genbank sequences. Results: RFLP showed the following genotype distribution: 71 (85.6%) D; two (2.4%) E; one (1.2%) A; one (1.2%) B; one (1.2%) C; five (6.0%) untypable; one (1.2%) mixed genotypes D+A; and one (1.2%) mixed genotype D+C. Seventy-seven samples were genotyped by sequencing as follows: 73 (94.8%) D, three (3.9%) E; and one (1.3%) A. The study showed that there is concordance in the results of RFLP and sequencing in 67 samples and discrepancy in ten samples: genotypes B, genotype C, one of genotype E and dual genotypes by RFLP could only been detected as genotype D by sequencing. Sequencing showed the RFLP untypable samples as genotypes D and E. Conclusion: HBV type D is the most prevalent genotype in western Saudi Arabia. RFLP is a reliable tool for predicting genotype D in Saudi population.
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Affiliation(s)
- Leena H Bajrai
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Taha Kumosani
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Experimental Biochemistry Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sherif El-Kafrawy
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mai El-Daly
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Salwa Hindawi
- Blood Transfusion Services, King Abdulaziz University Hospital, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed Ashshi
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Esam I Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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Saeed U, Waheed Y, Ashraf M. Hepatitis B and hepatitis C viruses: a review of viral genomes, viral induced host immune responses, genotypic distributions and worldwide epidemiology. ASIAN PACIFIC JOURNAL OF TROPICAL DISEASE 2014; 4. [PMCID: PMC4032054 DOI: 10.1016/s2222-1808(14)60322-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Hepatitis B and hepatitis C viruses (HCV) are frequently propagating blood borne pathogens in global community. Viral hepatitis is primarily associated with severe health complications, such as liver cirrhosis, hepatocellular carcinoma, hepatic fibrosis and steatosis. A literature review was conducted on hepatitis B virus (HBV), HBV genome, genotypic distribution and global epidemiology of HBV, HCV, HCV genome, HCV and host immune responses, HCV genotypic distribution and global epidemiology. The valued information was subjected for review. HBV has strict tissue tropism to liver. The virus infecting hepatocytes produces large amount of hepatitis B surface antigen particles which lack the DNA. It has capability to integrate into host genome. It has been found that genotype C is most emerging genotype associated with more severe liver diseases (cirrhosis). The approximate prevalence rate of genotype C is 27.7% which represents a major threat to future generations. Approximately 8% of population is chronic carrier of HBV in developing countries. The chronic carrier rate of HBV is 2%-7% in Middle East, Eastern and Southern Europe, South America and Japan. Among HCV infected individuals, 15% usually have natural tendency to overcome acute viral infection, where as 85% of individuals were unable to control HCV infection. The internal ribosomal entry site contains highly conserved structures important for binding and appropriate positioning of viral genome inside the host cell. HCV infects only in 1%-10% of hepatocytes, but production of tumor necrosis factor alpha (from CD8+ cells) and interferon-gamma cause destruction of both infected cells and non-infected surrounding cells. Almost 11 genotypes and above 100 subtypes of HCV exists worldwide with different geographical distribution. Many efforts are still needed to minimize global burden of these infections. For the complete eradication of HBV (just like small pox and polio) via vaccination strategies, sincere efforts would be required from government and nongovernmental organizations.
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Affiliation(s)
- Umar Saeed
- *Corresponding author: Umar Saeed, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad (44000) Pakistan. Tel: +92-323-5338544. E-mail:
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59
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Construction of replication competent plasmids of hepatitis B virus subgenotypes A1, A2 and D3 with authentic endogenous promoters. J Virol Methods 2014; 203:54-64. [PMID: 24681050 DOI: 10.1016/j.jviromet.2014.03.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 03/14/2014] [Accepted: 03/18/2014] [Indexed: 12/13/2022]
Abstract
Hepatitis B virus (HBV) is hyperendemic to southern Africa, with genotype A of HBV being the predominant genotype, and subgenotype A1 prevailing. Infection with this subgenotype is associated with rapid disease progression, and high frequency of hepatocellular carcinoma development. The objectives of our study was to construct recombinant 1.28 mer replication competent HBV DNA plasmids of subgenotypes A1, A2 and D3 containing authentic endogenous HBV promoters and to follow their replication in vitro after transfection of Huh7 cells. We found that subgenotype D3 replicated at a lower level, as measured by HBsAg and HBV DNA levels, when compared to cells transfected with genotype A. There was no difference in the intracellular and extracellular HBsAg between cells transfected with subgenotypes A1 or A2. Cells transfected with subgenotype A1 had higher levels of intracellular replicative intermediates and HBcAg, and lower extracellular expression of HBeAg from days 1 to 3, when compared to cells transfected with subgenotype A2. In conclusion, the generation of these replication competent clones is an important step in the functional characterization of subgenotypes of HBV circulating in Africa and their comparison to strains circulating in other geographical regions of the world.
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Tuteja A, Siddiqui AB, Madan K, Goyal R, Shalimar, Sreenivas V, Kaur N, Panda SK, Narayanasamy K, Subodh S, Acharya SK. Mutation profiling of the hepatitis B virus strains circulating in North Indian population. PLoS One 2014; 9:e91150. [PMID: 24637457 PMCID: PMC3956465 DOI: 10.1371/journal.pone.0091150] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 02/07/2014] [Indexed: 12/11/2022] Open
Abstract
AIMS The aim of this study was to investigate the genomic mutations in the circulating Hepatitis B virus strains causing infection in the Indian population. Further, we wanted to analyze the biological significance of these mutations in HBV mediated disease. METHODS 222 HBsAg positive patients were enrolled in the study. The genotype and mutation profile was determined for the infecting HBV isolate by sequencing overlapping fragments. These sequences were analyzed by using different tools and compared with previously available HBV sequence information. Mutation Frequency Index (MFI) for the Genes and Diagnosis group was also calculated. RESULTS HBV Genotype D was found in 55% (n = 121) of the patient group and genotype A was found in 30% (n = 66) of samples. The majority (52%) of the HBV-infected individuals in the present study were HBeAg-negative in all the age groups studied. Spontaneous drug associated mutations implicated in resistance to antiviral therapy were also identified in about quarter of our patients, which is of therapeutic concern. The MFI approach used in the study indicated that Core peptide was the most conserved region in both genotypes and Surface peptide had highest mutation frequency. Few mutations in X gene (T36A and G50R) showed high frequency of association with HCC. A rare recombinant strain of HBV genotype A and D was also identified in the patient group. CONCLUSIONS HBV genotype D was found out to be most prevalent. More than half of the patients studied had HBeAg negative disease. Core region was found to be most conserved. Drug Associated mutations were detected in 22% of the patient group and T36A and G50R mutations in X gene were found to be associated with HCC.
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Affiliation(s)
- Amit Tuteja
- Institute of Molecular Medicine, New Delhi, India
- Amity Institute of Biotechnology, Amity University, Noida, India
| | | | - Kaushal Madan
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Rohit Goyal
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Shalimar
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | | | - Navkiran Kaur
- Amity Institute of Biotechnology, Amity University, Noida, India
| | - Subrat K. Panda
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | | | - Swati Subodh
- Institute of Molecular Medicine, New Delhi, India
- Open Source Drug Discovery Unit, Council of Scientific & Industrial Research, New Delhi, India
| | - Subrat K. Acharya
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
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61
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Chen QY, Harrison TJ, Sabin CA, Li GJ, Huang GM, Yang JY, Wang XY, Li H, Liu MH, Fang ZL. The Effect of HBV Genotype C on the Development of HCC Differs Between Wild-Type Viruses and Those With BCP Double Mutations (T(1762)A(1764)). HEPATITIS MONTHLY 2014; 14:e16214. [PMID: 24693312 PMCID: PMC3950570 DOI: 10.5812/hepatmon.16214] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Revised: 12/17/2013] [Accepted: 12/27/2013] [Indexed: 12/11/2022]
Abstract
BACKGROUND Association of hepatitis B virus (HBV) genotype C with hepatocellular carcinoma (HCC) development remains controversial. HBV basal core promoter (BCP) double mutations (T(1762)A(1764)) are very strong confounding factors of genotypes B and C in HCC development. OBJECTIVES To investigate the association of HBV genotype C with HCC development after controlling for BCP double mutations. MATERIALS AND METHODS Four hundred and two serum samples from patients with HCC, liver cirrhosis (LC) and chronic hepatitis (CH) and also from asymptomatic HBsAg carriers were analyzed. RESULTS Genotypes B (31.1%), C (62.8%), and I (6.1%) were detected. With the severity of liver disease the prevalence of genotype B decreased, but genotype C increased. No trend was found for genotype I. The prevalence of BCP double mutations in genotypes C and I viruses was significantly higher than genotype B. BCP double mutations are risk factors for CH, LC and HCC. Genotype C was not identified as a particular risk factor for HCC prior to the stratification analysis but after that genotype C viruses with BCP double mutations were found to be a particular risk factor for HCC (P = 0.008, OR = 17.19 [95% CI: 2.10 - 140.41]), but those with the wild-type BCP were not. In the interaction analysis, genotype C and BCP double mutations were found to have a synergistic effect on HCC development (P < 0.0001, OR = 52.56 [95% CI: 11.49-240.52]). CONCLUSIONS The effect of HBV genotype C on the development of HCC differs between wild-type viruses and those with BCP double mutations, suggesting that not all individuals infected with genotype C HBV are at increased risk of HCC.
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Affiliation(s)
- Qin-Yan Chen
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, China
| | - Tim J Harrison
- Division of Medicine, Faculty of Medical Sciences, University College London, London, UK
| | - Caroline A Sabin
- Research Department of Infection and Population Health, UCL Medical School, London, UK
| | - Guo-Jian Li
- Department of Public Health of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Gao-Ming Huang
- School of Public Health, Guangxi Medical University, Nanning, China
| | - Jin-Ye Yang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, China
| | - Xue-Yan Wang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, China
| | - Hai Li
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, China
| | - Mo-Han Liu
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, China
- School of Preclinical Medicine, Guangxi Medical University, Nanning, China
| | - Zhong-Liao Fang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, China
- School of Preclinical Medicine, Guangxi Medical University, Nanning, China
- Corresponding Author: Zhong-Liao Fang, Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, 18 Jin Zhou Road, Nanning, Guangxi, China. Tel: +86-7712518306, Fax: +86-7712518678, E-mail:
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Andernach IE, Hunewald OE, Muller CP. Bayesian inference of the evolution of HBV/E. PLoS One 2013; 8:e81690. [PMID: 24312336 PMCID: PMC3843692 DOI: 10.1371/journal.pone.0081690] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 10/21/2013] [Indexed: 12/16/2022] Open
Abstract
Despite its wide spread and high prevalence in sub-Saharan Africa, hepatitis B virus genotype E (HBV/E) has a surprisingly low genetic diversity, indicating an only recent emergence of this genotype in the general African population. Here, we performed extensive phylogeographic analyses, including Bayesian MCMC modeling. Our results indicate a mutation rate of 1.9×10−4 substitutions per site and year (s/s/y) and confirm a recent emergence of HBV/E, most likely within the last 130 years, and only after the transatlantic slave-trade had come to an end. Our analyses suggest that HBV/E originated from the area of Nigeria, before rapidly spreading throughout sub-Saharan Africa. Interestingly, viral strains found in Haiti seem to be the result of multiple introductions only in the second half of the 20th century, corroborating an absence of a significant number of HBV/E strains in West Africa several centuries ago. Our results confirm that the hyperendemicity of HBV(E) in today's Africa is a recent phenomenon and likely the result of dramatic changes in the routes of viral transmission in a relatively recent past.
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Affiliation(s)
- Iris E. Andernach
- Institute of Immunology, Centre de Recherche Public de la Santé/Laboratoire National de Santé, Luxembourg, Luxembourg
| | - Oliver E. Hunewald
- Institute of Immunology, Centre de Recherche Public de la Santé/Laboratoire National de Santé, Luxembourg, Luxembourg
| | - Claude P. Muller
- Institute of Immunology, Centre de Recherche Public de la Santé/Laboratoire National de Santé, Luxembourg, Luxembourg
- * E-mail:
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Zhi X, Deng M, Yang H, Gao G, Wang K, Fu H, Zhang Y, Chen D, Cui D. A novel HBV genotypes detecting system combined with microfluidic chip, loop-mediated isothermal amplification and GMR sensors. Biosens Bioelectron 2013; 54:372-7. [PMID: 24292142 DOI: 10.1016/j.bios.2013.11.025] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 10/28/2013] [Accepted: 11/06/2013] [Indexed: 02/08/2023]
Abstract
Genotyping of hepatitis B virus (HBV) can be used for clinical effective therapeutic drug-selection. A novel microfluidic biochip for HBV genotyping has been fabricated, for the first time, integrating loop-mediated isothermal amplification (LAMP), line probes assay (LiPA) and giant magnetoresistive (GMR) sensors. Coupling LAMP with LiPA in microfluidic chip shortened reaction time substantially, and combining LAMP with GMR sensor enabled limit of detection to attain 10 copies mL(-1) target HBV DNA molecules in 1 h. Furthermore, the independent designed GMR sensors and microfluidic chip can decrease manufacturing cost and patient's test-cost, and facilitate GMR detector repeating use for signal detection. In addition, the detection system has a lower background signal owing to application of superparamagnetic nanoclusters. And it can be expected to use for multiple target molecules synchronous detection in microfluidic chip based on a characteristic of stationary reaction temperature of LAMP. In conclusion, the neoteric detecting system is well suitable for quick genotyping diagnosis of clinical HBV and other homothetic biomolecule detection in biological and medical fields.
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Affiliation(s)
- Xiao Zhi
- (a)National Key Laboratory of Nano/Micro Fabrication Technology, Key Laboratory for Thin Film and Microfabrication of Ministry of Education, Institute of Micro/Nano Science and Technology, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, People's Republic of China
| | - Min Deng
- (a)National Key Laboratory of Nano/Micro Fabrication Technology, Key Laboratory for Thin Film and Microfabrication of Ministry of Education, Institute of Micro/Nano Science and Technology, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, People's Republic of China
| | - Hao Yang
- (b)Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, No. 20 Dongda Street, Fengtai, Beijing 100071, P.R. China
| | - Guo Gao
- (b)Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, No. 20 Dongda Street, Fengtai, Beijing 100071, P.R. China
| | - Kan Wang
- (a)National Key Laboratory of Nano/Micro Fabrication Technology, Key Laboratory for Thin Film and Microfabrication of Ministry of Education, Institute of Micro/Nano Science and Technology, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, People's Republic of China
| | - Hualin Fu
- (a)National Key Laboratory of Nano/Micro Fabrication Technology, Key Laboratory for Thin Film and Microfabrication of Ministry of Education, Institute of Micro/Nano Science and Technology, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, People's Republic of China
| | - Yixia Zhang
- (a)National Key Laboratory of Nano/Micro Fabrication Technology, Key Laboratory for Thin Film and Microfabrication of Ministry of Education, Institute of Micro/Nano Science and Technology, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, People's Republic of China
| | - Di Chen
- (a)National Key Laboratory of Nano/Micro Fabrication Technology, Key Laboratory for Thin Film and Microfabrication of Ministry of Education, Institute of Micro/Nano Science and Technology, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, People's Republic of China
| | - Daxiang Cui
- (a)National Key Laboratory of Nano/Micro Fabrication Technology, Key Laboratory for Thin Film and Microfabrication of Ministry of Education, Institute of Micro/Nano Science and Technology, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, People's Republic of China.
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Characterization of the occult hepatitis B virus variants circulating among the blood donors from eastern India. ScientificWorldJournal 2013; 2013:212704. [PMID: 24302857 PMCID: PMC3834618 DOI: 10.1155/2013/212704] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 09/23/2013] [Indexed: 12/18/2022] Open
Abstract
A previous study from West Bengal documented very high rate of occult HBV infection (OBI) among the HBsAg negative blood donors. This study was aimed to characterize the OBI strains circulating among the blood donors and to estimate the risk associated with the prevailing viral variants/mutants. Blood samples from 2195 voluntary blood donors were included in the study. HBsAg, HBeAg, anti-HBc, and anti-HBs statuses of the samples were done by ELISA based detection. PCR amplification and sequencing were done to determine HBV genotypes, basal core promoter (BCP), and precore (Pre-C) mutations. Among the study samples, 268 were anti-HBc positive/HBsAg negative, among which 65 (24.25%) were HBV DNA positive. Phylogenetic analysis revealed the presence of HBV/D (87.23%), HBV/A (8.51%), and HBV/C (4.26%) (P < 0.0001). HBV/D3 (65.85%) was the significantly prevalent subgenotype over HBV/D2 (26.83%) and HBV/D1 (7.31%) (P = 0.0003). Considerable prevalence of differential BCP (1752C, 1753C, 1762T/1764A, 1753C+1762T/1764A, 1773C, and 1814C) and reverse transcriptase (rt) gene (rtI91L, rtL93P, rtS106C, rtR110G, rtN118T, rtS119T, rtY126H, rtG127W/R, rtC136R, and rtY158H) mutations was identified. Association of specific HBV subgenotypes with OBI was interesting and needs further study. Clinically relevant mutations were prevalent among the OBI strains which are of serious concern.
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Inoue H, Motani-Saitoh H, Sakurada K, Ikegaya H, Yajima D, Nagasawa S, Iwase H. Genotypic polymorphisms of hepatitis B virus provide useful information for estimating geographical origin or place of long-term residence of unidentified cadavers. J Forensic Sci 2013; 59:236-41. [PMID: 24020429 DOI: 10.1111/1556-4029.12257] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Revised: 10/01/2012] [Accepted: 10/13/2012] [Indexed: 02/06/2023]
Abstract
Increasing numbers of unidentified cadavers are a major problem. We have developed a new method for providing identification information that can determine the geographical origin or place of long-term residence of unidentified cadavers based on genotypic polymorphisms of hepatitis B virus (HBV) known to correlate with their geographical distribution. PCR of serum samples detected HBV DNA from 4 (3.9%) of 102 randomly selected Japanese forensic cadavers. Multiplex PCR did not detect multiple HBV genotypes from any single cadaver, confirming the absence of coinfection. Phylogenetic tree analysis based on a 485-bp mutant region of the HBV S gene successfully classified the HBV genotypes into A to J. Among 10 HBV-infected cadavers, 8 had genotype Ce/C2, a genotype prevalent in East Asia, and 2 had genotype Bj/B1, a Japanese-specific genotype. HBV genotypic polymorphisms correlate with the geographical distribution of the virus and thus provide important information for identifying unidentified cadavers infected with HBV.
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Affiliation(s)
- Hiroyuki Inoue
- Department of Legal Medicine, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan; Forensic Science Laboratory, Chiba Prefectural Police Headquarters', 1-71-1 Chuo-minato, Chuo-ku, Chiba, 260-0024, Japan
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Li GJ, Hue S, Harrison TJ, Yang JY, Chen QY, Wang XY, Fang ZL. Hepatitis B virus candidate subgenotype I1 varies in distribution throughout Guangxi, China and may have originated in Long An county, Guangxi. J Med Virol 2013; 85:799-807. [PMID: 23508905 DOI: 10.1002/jmv.23533] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2013] [Indexed: 12/13/2022]
Abstract
Sequencing of the complete hepatitis B virus (HBV) genomes from Vietnam, China and Laos led to the identification of a complex recombinant, referred to initially as an aberrant genotype and later proposed to be a new genotype, I. However, epidemiological data regarding this new genotype are lacking. A cross-sectional study was carried out to investigate the epidemiology of HBV candidate genotype I in Guangxi, China using stratified, random cluster sampling. Four thousand five hundred thirteen subjects were recruited from five counties within Guangxi. Three genotypes, B, C, and I, were identified with a prevalence of 32.6% (114/350), 64% (224/350), and 3.4% (12/350), respectively. All the genotype I isolates belong to candidate subgenotype I1 and were found in Bing Yang (15.3%, 9/59) and Na Po (5.0%, 3/60) counties only. The prevalence of this subgenotype is significantly higher in males (5.1%, 10/195) than in females (1.3%, 2/155; X(2) = 3.959, P < 0.05) but does not differ significantly with age. It was found in the Han (4.5%, 9/201) and Zhuang (3.1%, 3/97) ethnic populations only. There is no significant difference from other genotypes in the prevalence of HBV serological markers. Phylogeographic analysis revealed that genotype I1 likely arose in Long An county, then spread later to Bing Yang, Na Po counties and elsewhere in southeast Asia. In conclusion, the distribution of candidate genotype I within Guangxi is not even and it is highly endemic in some counties. Its prevalence is associated with gender and ethnicity. Subgenotype I1 likely originated in Long An county.
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Affiliation(s)
- Guo-Jian Li
- Department of Public Health, Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China
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Locarnini S, Littlejohn M, Aziz MN, Yuen L. Possible origins and evolution of the hepatitis B virus (HBV). Semin Cancer Biol 2013; 23:561-75. [PMID: 24013024 DOI: 10.1016/j.semcancer.2013.08.006] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 08/27/2013] [Indexed: 02/06/2023]
Abstract
All members of the family Hepadnaviridae are primarily viruses which contain double-stranded DNA genomes that are replicated via reverse transcription of a pregenomic RNA template. There are two subgroups within this family: mammalian and avian. The avian member's include the duck hepatitis B virus (DHBV), heron hepatitis B virus, Ross goose hepatitis B virus, stork hepatitis B virus and the recently identified parrot hepatitis B virus. More recently, the detection of endogenous avian hepadnavirus DNA integrated into the genomes of zebra finches has revealed a deep evolutionary origin of hepadnaviruses that was not previously recognised, dating back over 40 million years ago. The non-primate mammalian members of the Hepadnaviridae include the woodchuck hepatitis virus (WHV), the ground squirrel hepatitis virus and arctic squirrel virus, as well as the recently described bat hepatitis virus. The identification of hepatitis B virus (HBV) in higher primates such as chimpanzee, gorilla, orangutan, and gibbons that cluster with the human genotypes further implies a more complex origin of this virus. By studying the molecular epidemiology of HBV in indigenous and relict populations in Asia-Pacific we propose a model for the origin and evolution of HBV that involves multiple cross-species transmissions and subsequent recombination events on a background of genotype C HBV infection.
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Affiliation(s)
- Stephen Locarnini
- Research & Molecular Development, Victorian Infectious Diseases Reference Laboratory, Melbourne, Australia.
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68
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Martinez AA, Zaldivar Y, Hong CC, Alvarado-Mora MV, Smith R, Ortiz AY, Pinho JRR, Cristina J, Pascale JM. Molecular characterisation of hepatitis B virus in the resident Chinese population in Panama City. Mem Inst Oswaldo Cruz 2013; 108:541-7. [PMID: 23903967 PMCID: PMC3970604 DOI: 10.1590/s0074-02762013000500002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 04/26/2013] [Indexed: 02/06/2023] Open
Abstract
Despite the effectiveness of current hepatitis B virus (HBV) vaccines, it is estimated that 350 million individuals suffer from chronic HBV infection and more than 50% of these affected individuals live on the Asian continent. Panama is a country with a great diversity of foreign groups; the Chinese community is a large example of this phenomenon. There is an urgent need to perform studies that evaluate the prevalence and the genetic diversity of HBV in this community. This study aimed to evaluate the prevalence of HBV and its genotypes and mutant variants in the Chinese population residing in Panama. In total, 320 subjects were enrolled in the study. Forty-two subjects (13.1%) were positive for HBsAg and HBV-DNA from 18 subjects revealed the presence of genotypes B2 and C1. Secondary mutations associated with drug resistance at positions rtV207L and rtN239T of the reverse transcriptase gene were identified. Additionally, the mutation pair A1762T/G1764A was found in three samples and the mutation G1896A was detected in an HBeAg-negative subject. In conclusion, to our knowledge, this is the first study to report high HBV prevalence rates in resident ethnic Chinese in Central America and the presence of genotypes B2 and C1 in this region.
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Affiliation(s)
- Alexander Augusto Martinez
- Gorgas Memorial Institute for Health Studies, Panama, Panama
- Department of Biotechnology, Acharya Nagarjuna University, Guntur,
India
- Instituto de Investigaciones Científicas y Servicios de Alta
Tecnología-AIP, Ciudad del Saber, Clayton, Panama
| | | | - Chen Ch Hong
- Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Monica Viviana Alvarado-Mora
- Laboratório de Gastroenterologia e Hepatologia Tropical,
Departamento de Gastroenterologia, Instituto de Medicina Tropical, Faculdade de
Medicina, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Rebecca Smith
- Gorgas Memorial Institute for Health Studies, Panama, Panama
| | - Alma Y Ortiz
- Gorgas Memorial Institute for Health Studies, Panama, Panama
| | - João Renato Rebello Pinho
- Laboratório de Gastroenterologia e Hepatologia Tropical,
Departamento de Gastroenterologia, Instituto de Medicina Tropical, Faculdade de
Medicina, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Juan Cristina
- Laboratorio de Virología Molecular, Centro de Investigaciones
Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Juan Miguel Pascale
- Gorgas Memorial Institute for Health Studies, Panama, Panama
- School of Medicine, University of Panama, Panama, Panama
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69
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Martinez AA, Zaldivar Y, Hong CC, Alvarado-Mora MV, Smith R, Ortiz AY, Pinho JRR, Cristina J, Pascale JM. Molecular characterisation of hepatitis B virus in the resident Chinese population in Panama City. Mem Inst Oswaldo Cruz 2013; 108. [PMID: 23903967 PMCID: PMC3970604 DOI: 10.1590/0074-0276108052013002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Despite the effectiveness of current hepatitis B virus (HBV) vaccines, it is estimated that 350 million individuals suffer from chronic HBV infection and more than 50% of these affected individuals live on the Asian continent. Panama is a country with a great diversity of foreign groups; the Chinese community is a large example of this phenomenon. There is an urgent need to perform studies that evaluate the prevalence and the genetic diversity of HBV in this community. This study aimed to evaluate the prevalence of HBV and its genotypes and mutant variants in the Chinese population residing in Panama. In total, 320 subjects were enrolled in the study. Forty-two subjects (13.1%) were positive for HBsAg and HBV-DNA from 18 subjects revealed the presence of genotypes B2 and C1. Secondary mutations associated with drug resistance at positions rtV207L and rtN239T of the reverse transcriptase gene were identified. Additionally, the mutation pair A1762T/G1764A was found in three samples and the mutation G1896A was detected in an HBeAg-negative subject. In conclusion, to our knowledge, this is the first study to report high HBV prevalence rates in resident ethnic Chinese in Central America and the presence of genotypes B2 and C1 in this region.
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Affiliation(s)
- Alexander Augusto Martinez
- Gorgas Memorial Institute for Health Studies, Panama, Panama , Department of Biotechnology, Acharya Nagarjuna University, Guntur,
India , Instituto de Investigaciones Científicas y Servicios de Alta
Tecnología-AIP, Ciudad del Saber, Clayton, Panama
| | | | - Chen Ch Hong
- Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Monica Viviana Alvarado-Mora
- Laboratório de Gastroenterologia e Hepatologia Tropical,
Departamento de Gastroenterologia, Instituto de Medicina Tropical, Faculdade de
Medicina, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Rebecca Smith
- Gorgas Memorial Institute for Health Studies, Panama, Panama
| | - Alma Y Ortiz
- Gorgas Memorial Institute for Health Studies, Panama, Panama
| | - João Renato Rebello Pinho
- Laboratório de Gastroenterologia e Hepatologia Tropical,
Departamento de Gastroenterologia, Instituto de Medicina Tropical, Faculdade de
Medicina, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Juan Cristina
- Laboratorio de Virología Molecular, Centro de Investigaciones
Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Juan Miguel Pascale
- Gorgas Memorial Institute for Health Studies, Panama, Panama , School of Medicine, University of Panama, Panama, Panama , Corresponding author:
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70
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Forbi JC, Ben-Ayed Y, Xia GL, Vaughan G, Drobeniuc J, Switzer WM, Khudyakov YE. Disparate distribution of hepatitis B virus genotypes in four sub-Saharan African countries. J Clin Virol 2013; 58:59-66. [PMID: 23871163 DOI: 10.1016/j.jcv.2013.06.028] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 05/23/2013] [Accepted: 06/21/2013] [Indexed: 12/12/2022]
Abstract
BACKGROUND Hepatitis B virus (HBV) places a substantial health burden on Africa. Here, we investigated genetic diversity of HBV variants circulating in 4 countries of sub-Saharan Africa using archived samples. In total, 1492 plasma samples were tested from HIV-infected individuals and pregnant women, among which 143 (9.6%) were PCR-positive for HBV DNA (Côte d'Ivoire, 70/608 [11.5%]; Ghana, 13/444 [2.9%]; Cameroon, 33/303 [10.9%]; and Uganda, 27/137 [19.7%]). STUDY DESIGN/RESULTS Phylogenetic analysis of the S-gene sequences identified HBV genotypes E (HBV/E, n=96) and A (HBV/A, n=47) distributed as follows: 87% of HBV/E and 13% of HBV/A in Côte d'Ivoire; 100% of HBV/E in Ghana; 67% of HBV/E and 33% of HBV/A in Cameroon; and 100% of HBV/A in Uganda. The average and maximal nucleotide distances among HBV/E sequences were 1.9% and 6.4%, respectively, suggesting a greater genetic diversity for this genotype than previously reported (p<0.001). HBV/A strains were classified into subgenotypes HBV/A1, HBV/A2 and HBV/A3. In Uganda, 93% of HBV/A strains belonged to HBV/A1 whereas HBV/A3 was the only subgenotype of HBV/A found in Cameroon. In Côte d'Ivoire, HBV/A strains were classified as HBV/A1 (11.1%), HBV/A2 (33.3%) and HBV/A3 (55.6%). Phylogeographic analysis of the sequences available from Africa supported earlier suggestions on the origin of HBV/A1, HBV/A2 and HBV/A3 in East, South and West/Central Africa, respectively. Using predicted amino acid sequences, hepatitis B surface antigen (HBsAg) was classified into serotype ayw4 in 93% of HBV/E strains and adw2 in 68% of HBV/A strains. Also, 7.7% of the sequences carried substitutions in HBsAg associated with immune escape. CONCLUSIONS The observations of pan-African and global dissemination of HBV/A1 and HBV/A2, and the circulation of HBV/E and HBV/A3 almost exclusively in West and Central Africa suggest a more recent increase in prevalence in Africa of HBV/E and HBV/A3 compared to HBV/A1 and HBV/A2. The broad genetic heterogeneity of HBsAg detected here may impact the efficacy of prevention and control efforts in sub-Saharan Africa.
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Affiliation(s)
- Joseph C Forbi
- Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Rd NE, Atlanta, GA 30333, USA.
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71
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Mello FCA, Araujo OC, Lago BV, Motta-Castro ARC, Moraes MTB, Gomes SA, Bello G, Araujo NM. Phylogeography and evolutionary history of hepatitis B virus genotype F in Brazil. Virol J 2013; 10:236. [PMID: 23855930 PMCID: PMC3751091 DOI: 10.1186/1743-422x-10-236] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 07/11/2013] [Indexed: 02/08/2023] Open
Abstract
Background Hepatitis B virus (HBV) genotype F (HBV/F) is considered to be indigenous to the Americas, but its emergence and spread in the continent remain unknown. Previously, only two HBV/F complete genome sequences from Brazil were available, limiting the contribution of Brazilian isolates to the phylogenetic studies of HBV/F. The present study was carried out to assess the proportion and geographic distributions of HBV/F subgenotypes in Brazil, to determine the full-length genomic sequences of HBV/F isolates from different Brazilian geographic regions, and to investigate the detailed evolutionary history and phylogeography of HBV/F in Brazil. Methods Complete HBV/F genomes isolated from 12 Brazilian patients, representing the HBV/F subgenotypes circulating in Brazil, were sequenced and analyzed together with sequences retrieved from GenBank, using the Bayesian coalescent and phylogeographic framework. Results Phylogenetic analysis using all Brazilian HBV/F S-gene sequences available in GenBank showed that HBV/F2a is found at higher frequencies countrywide and corresponds to all sequences isolated in the Brazilian Amazon Basin. In addition, the evolutionary analysis using complete genome sequences estimated an older median ancestral age for the Brazilian HBV/F2a compared to the Brazilian HBV/F1b and HBV/F4 subgenotypes, suggesting that HBV/F2a represents the original native HBV of Brazil. The phylogeographic patterns suggested a north-to-south flow of HBV/F2a from Venezuela to Brazil, whereas HBV/F1b and HBV/F4 strains appeared to have spread from Argentina to Brazil. Conclusions This study suggests a plausible route of introduction of HBV/F subgenotypes in Brazil and demonstrates the usefulness of recently developed computational tools for investigating the evolutionary history of HBV.
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Affiliation(s)
- Francisco C A Mello
- Laboratory of Molecular Virology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, RJ, Brazil
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72
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Ezzikouri S, Pineau P, Benjelloun S. Hepatitis B virus in the Maghreb region: from epidemiology to prospective research. Liver Int 2013; 33:811-9. [PMID: 23530901 DOI: 10.1111/liv.12135] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 01/28/2013] [Indexed: 12/21/2022]
Abstract
Hepatitis B virus (HBV) represents an important health problem in the Maghreb countries, Algeria, Libya, Mauritania, Morocco and Tunisia, but no detailed synthesis of its epidemiology is available. In this review, we systematically searched for data about HBV in the Maghreb in peer-reviewed databases and included in our analysis works written in English and French, as well as institutional reports and regional conference meeting abstracts. We estimated national and regional prevalence of chronic HBV infection. In addition, we discuss molecular features of the viral strains circulating in the region. Data analysis suggests that in the Maghreb region HBs antigen carriage concerns 1.8-4.9% of the population for an estimated number of 2.7 million persons. Genotype D, subtype D7, is predominant and mutations in the precore region of HBV genome are highly prevalent. This epidemiological situation requires obviously widespread active interventions for prevention and control. In addition, anti-hepatitis B vaccination programme should be applied with the utmost discipline in the five countries considered in this present review. This systematic review will, hopefully, increase knowledge at disposal of Public Health authorities, enabling better resource allocation and healthcare delivery. The present synthesis intends to stimulate policies aiming at preventing the spread of HBV, keeping in mind that eradication of the virus from Maghrebi populations should be the ultimate objective of Public Health authorities.
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Affiliation(s)
- Sayeh Ezzikouri
- Virology Unit, Viral Hepatitis Laboratory, Pasteur Institute of Morocco, Casablanca, Morocco.
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73
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Komas NP, Vickos U, Hübschen JM, Béré A, Manirakiza A, Muller CP, Le Faou A. Cross-sectional study of hepatitis B virus infection in rural communities, Central African Republic. BMC Infect Dis 2013; 13:286. [PMID: 23800310 PMCID: PMC3694350 DOI: 10.1186/1471-2334-13-286] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 06/18/2013] [Indexed: 12/11/2022] Open
Abstract
Background As most data on hepatitis in resource-poor countries relate to urban communities, surveys in the rural environment are necessary to determine the ‘true’ prevalence of these viral infections. We undertook a survey to determine the prevalence of hepatitis B virus (HBV) infection in an apparently healthy rural population in the Central African Republic (CAR). Methods The cross-sectional study was based on dried blood spots (DBS) from 273 people recruited in four prefectures (Lobaye, Nana-Mambéré, Ouham and Ouaka). Eluates from DBS were tested with commercial ELISA kits to detect markers of HBV infection. DBS were directly used for DNA extraction, followed by PCR and genotyping based on preS/S gene sequences. Results The overall prevalence of HBc antibodies was 27.1% (Lobaye 29%, Nana-Mambéré 28%, Ouaka 29% and Ouham 23%) and that of HBsAg was 10.6% (Lobaye 9%, Nana-Mambéré 9%, Ouaka 19% and Ouham 8%), with no statistically significant difference among the surveyed communities. Nineteen sequences obtained from 74 anti-HBc-positive patients all belonged to genotype E. Risk factor analysis of HBV infection pointed to sexual transmission of the virus. Conclusion The prevalence of HBV is high in rural communities in the CAR and comparable to that observed in urban areas. In addition, genotype E is prevalent in these areas. These findings underline the importance of instituting a programme of active HBV surveillance and vaccination of the population.
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Affiliation(s)
- Narcisse P Komas
- Viral Hepatitis Laboratory, Institut Pasteur de Bangui, PO Box 923, Bangui, Central African Republic.
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74
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Development of a highly sensitive bioluminescent enzyme immunoassay for hepatitis B virus surface antigen capable of detecting divergent mutants. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2013; 20:1255-65. [PMID: 23761660 DOI: 10.1128/cvi.00186-13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Hepatitis B virus (HBV) infections are sometimes overlooked when using commercial kits to measure hepatitis B virus surface antigen (HBsAg) due to their low sensitivities and reactivities to mutant strains of various genotypes. We developed an ultrasensitive bioluminescent enzyme immunoassay (BLEIA) for HBsAg using firefly luciferase, which is adaptable to a variety of HBsAg mutants, by combining four monoclonal antibodies with a polyclonal antibody against HBsAg. The measurement of seroconversion panels showed trace amounts of HBsAg during the early infection phase by the BLEIA because of its high sensitivity of 5 mIU/ml. The BLEIA detected HBsAg as early as did PCR in five of seven series and from 2.1 to 9.4 days earlier than commercial immunoassay methods. During the late infection phase, the BLEIA successfully detected HBsAg even 40 days after the disappearance of HBV DNA and the emergence of antibodies against HBsAg. The HBsAg BLEIA successfully detected all 13 recombinant HBsAg and 45 types of HBsAg mutants with various mutations within amino acids 90 to 164 in the S gene product. Some specimens had higher values determined by the BLEIA than those by a commercial chemiluminescent immunoassay; this suggests that such discrepancies were caused by the dissociation of preS1/preS2 peptides from the particle surface. With its highly sensitive detection of low-titer HBsAg, including various mutants, the HBsAg BLEIA is considered to be useful for the early diagnosis and prevention of HBV infection because of the shorter window of infection prior to detection, which facilitates early prediction of recurrence in HBV-infected individuals.
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75
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Ismail AM, Goel A, Kannangai R, Abraham P. Further evidence of hepatitis B virus genotype I circulation in Northeast India. INFECTION GENETICS AND EVOLUTION 2013; 18:60-5. [PMID: 23665463 DOI: 10.1016/j.meegid.2013.04.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 04/26/2013] [Accepted: 04/29/2013] [Indexed: 12/18/2022]
Abstract
Hepatitis B virus (HBV) genotypes have known to show a geographical pattern in their distribution and have been used to trace the migration of populations from geographically distant regions. Novel recombinants between HBV genotypes A, G and C referred as genotype I has been recently reported from Eastern India. In our investigation to characterise antiviral resistance mutations, we identified a rare case of HBV genotype I infection in chronic hepatitis B subject. We encountered confounding results of this emerging genotype 'designated as genotype G' in three widely used HBV sequence database for genotype determination. The recombinant fragment of genotype G largely occupies the surface gene sequence of the newly identified genotype I and could hence lead to misclassification of genotype I. Additionally, recombination analysis of the generated sequences in Simplot and jpHMM model showed two different patterns of recombination events. In conclusion, the increasing recognition of genotype I in this population suggests that further studies may reveal uncommon genotypes from other geographically distant regions. Our observation of potential genotype I misclassification despite the use of public HBV sequence database and other recombination analysis tools highlights the need for updating and validating public sequence domains of diagnostic importance.
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Highly sensitive detection of hepatitis B virus surface antigen by use of a semiautomated immune complex transfer chemiluminescence enzyme immunoassay. J Clin Microbiol 2013; 51:2238-44. [PMID: 23658266 DOI: 10.1128/jcm.00324-13] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The performance of hepatitis B surface antigen (HBsAg) screening assays is continuously improved to reduce the risk of transfusion-associated hepatitis B. In this study, a semiautomated immune complex transfer chemiluminescence enzyme immunoassay (ICT-CLEIA) for the detection of HBsAg, which is as sensitive as hepatitis B virus (HBV) DNA PCR, was developed; the ICT-CLEIA assay performance was compared with the performance of the Architect HBsAg QT assay and HBV DNA PCR. The specificities in the initial assay and after retesting were 99.50% (1,988/1,998 samples) and 99.95% (1,997/1,998 samples), respectively. The analytical detection limit was determined to be 0.2 mIU/ml using the 2nd International WHO HBsAg standard, and the cutoff value (0.5 mIU/ml) of the ICT-CLEIA assay was 8.0 standard deviations (SD) above the mean of the HBsAg-negative specimens. The ICT-CLEIA assay could detect HBsAg even in the presence of anti-HBs antibodies and demonstrated a 23.6-day-shorter window period using commercially available HBsAg seroconversion panels than the Architect HBsAg QT assay. Furthermore, the monitoring of the viral kinetics by the ICT-CLEIA assay and the HBV DNA PCR produced very similarly shaped curves during both the HBsAg seroconversion and reverse seroconversion periods. Therefore, the ICT-CLEIA assay may be useful not only for an earlier detection of HBV reactivation but also for the monitoring of hepatitis B patients.
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77
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Chen X, He JM, Ding LS, Zhang GQ, Zou XB, Zheng J. Prevalence of hepatitis B virus and hepatitis C virus in patients with human immunodeficiency virus infection in Central China. Arch Virol 2013; 158:1889-94. [PMID: 23553454 DOI: 10.1007/s00705-013-1681-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Accepted: 02/19/2013] [Indexed: 12/18/2022]
Abstract
Co-infection of hepatitis B virus (HBV) and/or hepatitis C virus (HCV) with human immunodeficiency virus (HIV) has an adverse effect on liver disease progression. This study investigated the prevalence of HBV and/or HCV co-infection in HIV-infected patients in Central China. A total of 978 HIV-infected patients from Hunan Province were enrolled. HBV serum markers, anti-hepatitis-C-virus antibody (anti-HCV), HBV DNA, and HBV genotypes were analyzed. The prevalence of hepatitis B surface antigen (HBsAg) and anti-HCV in HIV-infected patients was 19.4 % and 62.4 %, respectively. The prevalence of anti-HCV in HIV-positive intravenous drug users was 93.6 %. Among HBsAg-positive patients, 88.1 % were found to have at least one HBV serum marker. The rates of HIV mono-infection, HBV/HIV dual infection, HCV/HIV dual infection, and HBV/HCV/HIV triple infection were 30.4 %, 7.2 %, 50.2 %, and 12.2 %, respectively. Antibody to HBsAg (Anti-HBs) was more common in anti-HCV-positive than anti-HCV-negative patients (53.3 % vs 40.2 %, P = 0.000), but isolated hepatitis B core antibody (anti-HBc) was more common in anti-HCV-negative than anti-HCV-positive patients (24.2 % vs 12.3 %, P = 0.000). Hepatitis B e antigen (HBeAg) and sexual transmission were independent risk factors for active HBV replication. Intravenous drug use and male sex were independent risk factors, but old age and presence of HBeAg were independent protective factors for anti-HCV. Co-infection of HBV and/or HCV with HIV infection is common in central China. HCV status is associated with anti-HBs and isolated anti-HBc in co-infected patients.
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Affiliation(s)
- Xi Chen
- Hunan Provincial Center for Diseases Control and Prevention, 450 Furongzhong Rd. sec 1, Changsha 410005, China.
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78
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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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79
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Bell TG, Kramvis A. Mutation Reporter Tool: an online tool to interrogate loci of interest, with its utility demonstrated using hepatitis B virus. Virol J 2013; 10:62. [PMID: 23433201 PMCID: PMC3749809 DOI: 10.1186/1743-422x-10-62] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 01/28/2013] [Indexed: 12/23/2022] Open
Abstract
Background An online tool, which extracts and summarises nucleotide or amino acid sequence data at specified loci of interest, was developed and tested using the basic core promoter/precore (BCP/PC) region of the hepatitis B virus (HBV). The tool is aimed at researchers without specialist computer skills. Methods The tool consists of a web-based front-end, with a CGI script, which runs Python code to generate an output web-page. The Python code searches the input sequence data for a specified anchor motif, after which it generates summary tables and graphs of residue and motif distributions. Results After the user provides an input file in FASTA format containing aligned sequence data (nucleotides or amino acids) and specifies an anchor motif at a known coordinate, the tool summarizes the nucleotides or amino acids at the specified loci, their frequency and analyzes motif patterns of the loci.The tool can output a graph that displays the frequency of mutations relative to a reference sequence. The tool was used to analyze the BCP/PC region of HBV belonging to subgenotypes A1, A2 and subgenotype D and to serotype HBV. The “Discovery Mode” ignores conserved loci and assists in identifying potential loci of interest. Conclusions Although HBV was used to demonstrate the utility of the Mutation Reporter Tool, the tool has wide application as it is genome-agnostic: nucleotide or amino acid sequence data from any organism can be processed. Rapid characterisation of many sequences can be achieved easily when the loci of interest are known. The tool is available online, without charge, at http://hvdr.bioinf.wits.ac.za/tools
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Affiliation(s)
- Trevor G Bell
- Hepatitis B Virus Diversity Research Programme, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Parktown, Johannesburg 2193, South Africa
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80
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Zhang Y, Li C, Zhang Y, Zhu H, Kang Y, Liu H, Wang J, Qin Y, Mao R, Xie Y, Huang Y, Zhang J. Comparative analysis of CpG islands among HBV genotypes. PLoS One 2013; 8:e56711. [PMID: 23451072 PMCID: PMC3579858 DOI: 10.1371/journal.pone.0056711] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 01/14/2013] [Indexed: 12/18/2022] Open
Abstract
DNA methylation is being increasingly recognized to play a role in regulation of hepatitis B virus (HBV) gene expression. The aim of this study was to compare the CpG island distribution among different HBV genotypes. We analyzed 176 full-length HBV genomic sequences obtained from the GenBank database, belonging to genotypes A through J, to identify the CpG islands in the HBV genomes. Our results showed that while 79 out of 176 sequences contained three conventional CpG islands (I–III) as previously described, 83 HBV sequences harbored only two of the three known islands. Novel CpG islands were identified in the remaining 14 HBV isolates and named as CpG island IV, V, and VI. Among the eight known HBV genotypes and two putative genotypes, while HBV genomes containing three CpG islands were predominant in genotypes A, B, D, E, and I; genotypes C, F, G, and H tended to contain only two CpG islands (II and III). In conclusion, the CpG islands, which are potential targets for DNA methylation mediated by the host functions, differ among HBV genotypes, and these genotype-specific differences in CpG island distribution could provide new insights into the understanding of epigenetic regulation of HBV gene expression and hepatitis B disease outcome.
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Affiliation(s)
- Yongmei Zhang
- Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chenxiao Li
- Department of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yijun Zhang
- Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Haoxiang Zhu
- Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yaoyue Kang
- Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hongyan Liu
- Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jinyu Wang
- Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yanli Qin
- Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Richeng Mao
- Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yi Xie
- Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yuxian Huang
- Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- * E-mail: (JZ) (YH); (YH) (JZ)
| | - Jiming Zhang
- Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Key Laboratory of Medical Molecular Virology (MOH & MOE), Shanghai Medical College, Fudan University, Shanghai, China
- * E-mail: (JZ) (YH); (YH) (JZ)
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81
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Siburian MD, Utama A, Dhenni R, Arnelis N, Fanany I, Intan MDB, Kurniasih TS, Andriani F, Afadlal S, Julianto EB, Rasman WS, Zubir N, Mathew G. High prevalence of hepatitis B virus genotype C/C1 in the Minangkabau ethnic group in Indonesia. Virol J 2013; 10:27. [PMID: 23336976 PMCID: PMC3583810 DOI: 10.1186/1743-422x-10-27] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Accepted: 01/15/2013] [Indexed: 12/13/2022] Open
Abstract
Background The Minangkabau is one of the major ethnic groups in Indonesia. Previous studies with a limited number of samples have shown a different prevalence of HBV/C in the Minangkabau compared to the Indonesian population in general. The aim of this study was to assess the HBV genotype distribution pattern and the prevalence of pre-S, T1753V and A1762T/G1764A mutations among the Minangkabau HBV carriers. The samples were collected from Padang, West Sumatera and from western Java. Mixed primers for specific genotypes were used to determine the HBV genotype. Pre-S or S genes were amplified, sequenced and aligned with reference sequences from GenBank to derive a phylogenetic tree for subgenotyping. Pre-S genes were also analyzed for mutations. The basal core promoter (BCP) region was amplified and directly sequenced to analyze T1753V and A1762T/G1764A mutations. Results The predominant HBV genotype among the Minangkabau HBV carriers (n=117) was C (72.6%) followed by B (24.8%) and co-infection with B and C (2.6%). The prevalence of pre-S mutations, including both the pre-S deletion and pre-S2 start codon mutation, was 41.0%, and the T1753V and A1762T/G1764A mutations were found in 51.9% and 71.2% respectively. HBV/C1 was the predominant HBV subgenotype in the Minangkabau HBV carriers, and was found in 66.2%, followed by B3, B7, C8, B2, B9, C2, and C10 (18.3%, 7.0%, 2.8%, 1.4%, 1.4%, 1.4%, and 1.4% respectively). From samples that were found to be co-infected with HBV B and C, two samples were successfully cloned and subgenotyped, including one with mixed subgenotypes of B3 and C1, and another one with mixed subgenotypes of B7, C1, putative intergenotypic of B/A, and C/A. Furthermore, three samples from donors of non-Minangkabau ethnicity from Padang were found to be infected with an intragenotypic recombination form, including a putative recombinant of B8/B3 and B9/B7. Conclusion HBV/C with subgenotype C1 was the predominant HBV genotype among HBV carriers of Minangkabau ethnicity. The prevalence of pre-S, A1762T/G1764A, and T1753V mutations was higher among the Minangkabau compared to Indonesian HBV carriers in general.
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Affiliation(s)
- Marlinang D Siburian
- Molecular Epidemiology Division, Mochtar Riady Institute for Nanotechnology, Universitas Pelita Harapan, Lippo Karawaci, Tangerang, Indonesia
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82
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Louisirirotchanakul S, Olinger CM, Arunkaewchaemsri P, Poovorawan Y, Kanoksinsombat C, Thongme C, Sa-Nguanmoo P, Krasae S, Theamboonlert A, Oota S, Fongsatitkul L, Puapairoj C, Promwong C, Weber B. The distribution of hepatitis B virus genotypes in Thailand. J Med Virol 2013; 84:1541-7. [PMID: 22930500 DOI: 10.1002/jmv.23363] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Phylogenetic analysis was performed on hepatitis B virus (HBV) strains obtained from 86 hepatitis B surface antigen (HBsAg) positive donors from Thailand originating throughout the country. Based on the S gene, 87.5% of strains were of genotype C while 10.5% were of genotype B, with all genotype B strains obtained from patients originating from the central or the south Thailand. No genotype B strains were found in the north of Thailand. Surprisingly, one patient was infected with a genotype H strain while another patient was infected with a genotype G strain. Complete genome sequencing and recombination analysis identified the latter as being a genotype G and C2 recombinant with the breakpoint around nucleotide position 700. The origin of the genotype G fragment was not identifiable while the genotype C2 fragment most likely came from strains circulating in Laos or Malaysia. The performance of different HBsAg diagnostic kits and HBV nucleic acid amplification technology (NAT) was evaluated. The genotype H and G/C2 recombination did not interfere with HBV detection.
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83
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Zhang Y, Wu Y, Ye S, Wang T, Zhao R, Chen F, Abe K, Jin X. The response to interferon is influenced by hepatitis B virus genotype in vitro and in vivo. Virus Res 2013; 171:65-70. [DOI: 10.1016/j.virusres.2012.10.027] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 10/18/2012] [Accepted: 10/23/2012] [Indexed: 02/07/2023]
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84
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Araujo NM, Araujo OC, Silva EM, Villela-Nogueira CA, Nabuco LC, Parana R, Bessone F, Gomes SA, Trepo C, Kay A. Identification of novel recombinants of hepatitis B virus genotypes F and G in human immunodeficiency virus-positive patients from Argentina and Brazil. J Gen Virol 2012; 94:150-158. [PMID: 23079380 DOI: 10.1099/vir.0.047324-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Hepatitis B virus (HBV) genotype G (HBV/G) infection is almost always detected along with a co-infecting HBV strain that can supply HBeAg, typically HBV/A2. In this study we describe, in two human immunodeficiency virus (HIV)-positive patients from Argentina and Brazil, the first report of HBV/G infection in Argentina and co-circulation of HBV/G, HBV/F and G/F recombinants in the American continent. HBV isolates carrying the 36 bp insertion of HBV/G were the most prevalent in both patients, with >99 % of colonies hybridizing to a probe specific for this insertion. Phylogenetic analyses of full-length genomes and precore/core fragments revealed that F4 and F1b were the co-infecting subgenotypes in the Brazilian and Argentinian patients, respectively. Bootscanning analysis provided evidence of recombination in several clones from both patients, with recombination breakpoints located mainly at the precore/core region. These data should encourage further investigations on the clinical implications of HBV/G recombinants in HBV/HIV co-infected patients.
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Affiliation(s)
- Natalia M Araujo
- Laboratory of Molecular Virology, Oswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro 21040-360, Brazil
| | - Oscar C Araujo
- Laboratory of Molecular Virology, Oswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro 21040-360, Brazil
| | - Edinete M Silva
- Centre de Recherche en Cancérologie de Lyon - INSERM U 1052/CNRS UMR 5286, 69424 Lyon Cedex 03, France
| | - Cristiane A Villela-Nogueira
- Hepatology Division, Clementino Fraga Filho University Hospital, Federal University of Rio de Janeiro, Rio de Janeiro 21941-970, Brazil
| | - Letícia C Nabuco
- Hepatology Division, Clementino Fraga Filho University Hospital, Federal University of Rio de Janeiro, Rio de Janeiro 21941-970, Brazil
| | - Raymundo Parana
- Department of Hepato-Gastroenterology, Prof. Edgard Santos University Hospital, Federal University of Bahia, Salvador 40110-060, Brazil
| | - Fernando Bessone
- Department of Gastroenterology and Hepatology, University of Rosario School of Medicine, Rosario 2000, Argentina
| | - Selma A Gomes
- Laboratory of Molecular Virology, Oswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro 21040-360, Brazil
| | - Christian Trepo
- Centre de Recherche en Cancérologie de Lyon - INSERM U 1052/CNRS UMR 5286, 69424 Lyon Cedex 03, France
| | - Alan Kay
- Centre de Recherche en Cancérologie de Lyon - INSERM U 1052/CNRS UMR 5286, 69424 Lyon Cedex 03, France
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85
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Makondo E, Bell TG, Kramvis A. Genotyping and molecular characterization of hepatitis B virus from human immunodeficiency virus-infected individuals in southern Africa. PLoS One 2012; 7:e46345. [PMID: 23029487 PMCID: PMC3460816 DOI: 10.1371/journal.pone.0046345] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 08/30/2012] [Indexed: 12/12/2022] Open
Abstract
Hepatitis B virus (HBV) and human immunodeficiency virus (HIV) are hyperendemic in sub-Saharan Africa. The HBV genotypes prevailing in HIV-infected Africans are unknown. Our aim was to determine the HBV genotypes in HIV-infected participants and to identify clinically significant HBV mutations. From 71 HBV DNA+ve HIV-infected participants, 49 basic core promoter/precore (BCP/PC) and 29 complete S regions were successfully sequenced. Following phylogenetic analysis of 29 specimens in the complete S region, 28 belonged to subgenotype A1 and one to D3. Mutations affecting HBeAg expression at the transcriptional (1762T1764A), translational (Kozak 1809–1812, initiation 1814–1816, G1896A with C1858T), or post translational levels (G1862T), were responsible for the high HBeAg-negativity observed. The G1862T mutation occurred only in subgenotype A1 isolates, which were found in one third (7/21) of HBsAg−ve participants, but in none of the 18 HBsAg+ve participants (p<0.05). Pre-S deletion mutants were detected in four HBsAg+ve and one HBsAg−ve participant/s. The following mutations occurred significantly more frequently in HBV isolated in this study than in strains of the same cluster of the phylogenetic tree: ps1F25L, ps1V88L/A; ps2Q10R, ps2 R48K/T, ps2A53V and sQ129R/H, sQ164A/V/G/D, sV168A and sS174N (p<0.05). ps1I48V/T occurred more frequently in females than males (p<0.05). Isolates with sV168A occurred more frequently in participants with viral loads >200 IU per ml (p<0.05) and only sS174N occurred more frequently in HBsAg−ve than in HBsAg+ve individuals (p<0.05). Prior to initiation of ART, ten percent, 3 of 29 isolates sequenced, had drug resistance mutations rtV173L, rtL180M+rtM204V and rtV214A, respectively. This study has provided important information on the molecular characteristics of HBV in HIV-infected southern Africans prior to ART initiation, which has important clinical relevance in the management of HBV/HIV co-infection in our unique setting.
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Affiliation(s)
| | | | - Anna Kramvis
- Hepatitis Virus Diversity Research Programme, Department of Internal Medicine, University of the Witwatersrand, Johannesburg, South Africa
- * E-mail:
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86
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Agrawal S, Dhiman RK. Hepatobiliary quiz-3 (2012). J Clin Exp Hepatol 2012; 2:297-302. [PMID: 25755450 PMCID: PMC3940521 DOI: 10.1016/j.jceh.2012.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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87
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Tong W, He J, Sun L, He S, Qi Q. Hepatitis B virus with a proposed genotype I was found in Sichuan Province, China. J Med Virol 2012; 84:866-70. [PMID: 22499007 DOI: 10.1002/jmv.23279] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
To date, eight hepatitis B virus (HBV) genotypes, A-H, have been designated, and two additional genotypes, I and J, have also been proposed. A serological survey targeting children in difficult-to-reach vaccination areas was carried out in remote counties of Sichuan Province, China. HBV genotypes and serotypes were also determined from HBsAg-positive serum samples by direct sequencing. Phylogenetic analysis showed two strains isolated from the Yi ethnic children clustered with the proposed genotype I. The pairwise genome genetic distance was 7.5% between genotypes I and C, and ranged from 8.4% to 15.2% between genotype I and other genotypes, except genotype C. Grouping Scan analyses of the two strains revealed apparent recombination events between an unknown genotype and genotype C. Two out of four HBV strains isolated from the Yi ethnic children were confirmed to be genotype I, suggesting widespread circulation and common infection with genotype I HBV in the local Yi population. High prevalence of HBsAg and low hepatitis B vaccination coverage indicated that additional efforts are needed to control HBV infection in those areas.
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Affiliation(s)
- Wenbin Tong
- Institute of Microbiological Detection, Sichuan Center for Disease Control and Prevention, Chengdu, China.
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88
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Inoue J, Ueno Y, Kawamura K, Yamamoto T, Mano Y, Miura M, Kobayashi T, Niitsuma H, Kondo Y, Kakazu E, Ninomiya M, Kimura O, Obara N, Kawagishi N, Kinouchi Y, Shimosegawa T. Association between S21 substitution in the core protein of hepatitis B virus and fulminant hepatitis. J Clin Virol 2012; 55:147-52. [PMID: 22795596 DOI: 10.1016/j.jcv.2012.06.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Revised: 06/11/2012] [Accepted: 06/20/2012] [Indexed: 02/07/2023]
Abstract
BACKGROUND The viral factors of hepatitis B virus (HBV), such as genotypes and mutations, were reported to affect the development of fulminant hepatitis B (FHB), but the mechanism is still unclear. OBJECTIVES To investigate HBV mutations associated with FHB, especially in the subgenotype B1/Bj HBV (HBV/B1), which are known to cause FHB frequently in Japan. STUDY DESIGN A total of 96 serum samples from acute self-limited hepatitis B (AHB) patients and 13 samples from FHB patients were used for full-genome/partial sequencing. A total of 107 chronic infection patients with HBV were also examined for the distribution of mutants. RESULTS In the analysis of full-genome sequences of HBV/B1 (FHB, n=11; non-FHB, n=35) including those from the databases, mutations at nt 1961 [T1961V (not T)] and nt 1962 [C1962D (not C)], which change S21 in the core protein, were found more frequently in FHB than in non-FHB (100% vs. 20%, 55% vs. 3%, respectively). When our FHB and AHB samples were compared, T1961V and C1962D were significantly more frequent in FHB than in AHB, both in the overall analysis (46% vs. 6%, 39% vs. 3%, respectively) and in HBV/B1 (100% vs. 29%, 100% vs. 14%, respectively). A newly developed PCR system detecting T1961V showed that HBV/B1 and low viral load were independent factors for the mutation among chronic infection patients. CONCLUSIONS T1961V/C1962D mutations were found frequently in FHB, especially in HBV/B1. The resulting S21 substitution in the core protein may play important roles in the development of FHB.
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Affiliation(s)
- Jun Inoue
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
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89
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Parusu T, Ponneri V. RP-HPLC method for simultaneous determination of atenolol and indapamide in pharmaceutical dosage forms, human blood and milk. ACTA ACUST UNITED AC 2012. [DOI: 10.5155/eurjchem.3.2.138-142.537] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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90
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Dunford L, Carr MJ, Dean J, Nguyen LT, Ta Thi TH, Nguyen BT, Connell J, Coughlan S, Nguyen HT, Hall WW, Thi LAN. A multicentre molecular analysis of hepatitis B and blood-borne virus coinfections in Viet Nam. PLoS One 2012; 7:e39027. [PMID: 22720022 PMCID: PMC3374772 DOI: 10.1371/journal.pone.0039027] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 05/15/2012] [Indexed: 02/06/2023] Open
Abstract
Hepatitis B (HBV) infection is endemic in Viet Nam, with up to 8.4 million individuals estimated to be chronically infected. We describe results of a large, multicentre seroepidemiological and molecular study of the prevalence of HBV infection and blood-borne viral coinfections in Viet Nam. Individuals with varying risk factors for infection (n = 8654) were recruited from five centres; Ha Noi, Hai Phong, Da Nang, Khanh Hoa and Can Tho. A mean prevalence rate of 10.7% was observed and levels of HBsAg were significantly higher in injecting drug users (IDUs) (17.4%, n = 174/1000) and dialysis patients (14.3%, n = 82/575) than in lower-risk groups (9.4%; p<0.001). Coinfection with HIV was seen in 28% of HBV-infected IDUs (n = 49/174) and 15.2% of commercial sex workers (CSWs; n = 15/99). HCV infection was present in 89.8% of the HBV-HIV coinfected IDUs (n = 44/49) and 40% of HBV-HIV coinfected CSWs (n = 16/40). Anti-HDV was detected in 10.7% (n = 34/318) of HBsAg positive individuals. Phylogenetic analysis of HBV S gene (n = 187) showed a predominance of genotype B4 (82.6%); genotypes C1 (14.6%), B2 (2.7%) and C5 (0.5%) were also identified. The precore mutation G1896A was identified in 35% of all specimens, and was more frequently observed in genotype B (41%) than genotype C (3%; p<0.0001). In the immunodominant 'a' region of the surface gene, point mutations were identified in 31% (n = 58/187) of sequences, and 2.2% (n = 4/187) and 5.3% (n = 10/187) specimens contained the major vaccine escape mutations G145A/R and P120L/Q/S/T, respectively. 368 HBsAg positive individuals were genotyped for the IL28B SNP rs12979860 and no significant association between the IL28B SNP and clearance of HBsAg, HBV viral load or HBeAg was observed. This study confirms the high prevalence of HBV infection in Viet Nam and also highlights the significant levels of blood-borne virus coinfections, which have important implications for hepatitis-related morbidity and development of effective management strategies.
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Affiliation(s)
- Linda Dunford
- Ireland Viet Nam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi, Viet Nam
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Michael J. Carr
- Ireland Viet Nam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi, Viet Nam
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Jonathan Dean
- Ireland Viet Nam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi, Viet Nam
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Linh Thuy Nguyen
- Ireland Viet Nam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi, Viet Nam
- Laboratory for Molecular Diagnostics, National Institute of Hygiene and Epidemiology, Ha Noi, Viet Nam
| | - Thu Hong Ta Thi
- Ireland Viet Nam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi, Viet Nam
- Laboratory for Molecular Diagnostics, National Institute of Hygiene and Epidemiology, Ha Noi, Viet Nam
| | - Binh Thanh Nguyen
- Ireland Viet Nam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi, Viet Nam
- Laboratory for Molecular Diagnostics, National Institute of Hygiene and Epidemiology, Ha Noi, Viet Nam
| | - Jeff Connell
- Ireland Viet Nam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi, Viet Nam
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Suzie Coughlan
- Ireland Viet Nam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi, Viet Nam
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Hien Tran Nguyen
- Ireland Viet Nam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi, Viet Nam
- Laboratory for Molecular Diagnostics, National Institute of Hygiene and Epidemiology, Ha Noi, Viet Nam
| | - William W. Hall
- Ireland Viet Nam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi, Viet Nam
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- * E-mail: (LANT); (WWH)
| | - Lan Anh Nguyen Thi
- Ireland Viet Nam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Ha Noi, Viet Nam
- Laboratory for Molecular Diagnostics, National Institute of Hygiene and Epidemiology, Ha Noi, Viet Nam
- * E-mail: (LANT); (WWH)
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91
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Beggel B, Neumann-Fraune M, Döring M, Lawyer G, Kaiser R, Verheyen J, Lengauer T. Genotyping hepatitis B virus dual infections using population-based sequence data. J Gen Virol 2012; 93:1899-1907. [PMID: 22694900 DOI: 10.1099/vir.0.043042-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The hepatitis B virus (HBV) is classified into distinct genotypes A-H that are characterized by different progression of hepatitis B and sensitivity to interferon treatment. Previous computational genotyping methods are not robust enough regarding HBV dual infections with different genotypes. The correct classification of HBV sequences into the present genotypes is impaired due to multiple ambiguous sequence positions. We present a computational model that is able to identify and genotype inter- and intragenotype dual infections using population-based sequencing data. Model verification on synthetic data showed 100 % accuracy for intergenotype dual infections and 36.4 % sensitivity in intragenotype dual infections. Screening patient sera (n = 241) revealed eight putative cases of intergenotype dual infection (one A-D, six A-G and one D-G) and four putative cases of intragenotype dual infection (one A-A, two D-D and one E-E). Clonal experiments from the original patient material confirmed three out of three of our predictions. The method has been integrated into geno2pheno([hbv]), an established web-service in clinical use for analysing HBV sequence data. It offers exact and detailed identification of HBV genotypes in patients with dual infections that helps to optimize antiviral therapy regimens. geno2pheno([hbv]) is available under http://www.genafor.org/g2p_hbv/index.php.
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Affiliation(s)
- Bastian Beggel
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
| | | | - Matthias Döring
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Glenn Lawyer
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Rolf Kaiser
- Institute of Virology, University of Cologne, Cologne, Germany
| | - Jens Verheyen
- Institute of Virology, University of Cologne, Cologne, Germany
| | - Thomas Lengauer
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
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92
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Madan K, Tyagi P. Hepatitis B virus genotyping: is the time ripe for routine clinical use? J Clin Exp Hepatol 2012; 2:174-80. [PMID: 25755425 PMCID: PMC3940128 DOI: 10.1016/s0973-6883(12)60105-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 06/17/2012] [Indexed: 12/12/2022] Open
Abstract
Hepatitis B is one of the major causes of end-stage liver disease and liver cancer worldwide. A number of host and viral factors influence the disease course and outcomes. One such viral factor is hepatitis B virus (HBV) genotypes. There are eight major HBV genotypes described from various geographic regions of the world. Although direct sequencing appears to be the gold standard for HBV genotyping, it is expensive and laborintensive and therefore cannot be applied for routine clinical use. The newer molecular methods including serotyping have made genotyping easier and simple to apply to large number of samples rapidly. The data collected mainly over the last decade have suggested that HBV genotypes may have a bearing over the natural course of the disease and its response to therapy. This review summarizes the available literature and highlights how genotyping could be incorporated into routine clinical practice in order to improve delivery of care to HBV-infected individuals.
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Key Words
- CHB, chronic hepatitis B
- CLD, chronic liver diseases
- DNA, deoxyribonucleic acid
- Diagnosis
- ELISA, enzyme-linked immunosorbent assay
- GC, guanine-cytosine
- HAI, histological activity index
- HBV, hepatitis B virus
- HBsAg, hepatitis B surface antigen
- HCC, hepatocellular carcinoma
- IFN, interferon
- LC, liver cirrhosis
- PCR, polymerase chain reaction
- RFLP, restriction fragment length polymorphism
- SNP, single nucleotide polymorphism
- SVR, sustained viral response
- genotype
- hepatitis B
- natural history
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Affiliation(s)
- Kaushal Madan
- Medanta Institute of Digestive and Hepatobiliary Sciences, Medanta-The Medicity Hospital, Gurgaon, Haryana,Address for correspondence: Kaushal Madan, Medanta Institute of Digestive and Hepatobiliary Sciences, Medanta-The Medicity, Sector 38, Gurgaon, Haryana, India
| | - Pankaj Tyagi
- Department of Gastroenterology and Hepatology, Sir Ganga Ram Hospital, New Delhi, India
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93
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Chakravarty R. Role of molecular diagnostics in the management of viral hepatitis B. ACTA ACUST UNITED AC 2012; 6:395-406. [PMID: 23480805 DOI: 10.1517/17530059.2012.690391] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Despite the availability of a safe and effective vaccine, chronic hepatitis B virus (HBV) infection continues to be a global health concern with an estimated 350 - 400 million people infected worldwide. Globally, HBV is the leading cause of chronic liver disease that may progress to cirrhosis and hepatocellular carcinoma. Therefore, accurate diagnosis and classification of the disease are important to determine whether therapy is needed. AREAS COVERED The review contains an overview of recent data on the existing and emerging developments in the molecular diagnostic and monitoring tools for chronic liver disease. EXPERT OPINION Monitoring of HBV viral load is the most widely used method in assessing liver disease severity, predicting development of cirrhosis and hepatocellular carcinoma, deciding initiation of antiviral therapy, assessing treatment response as well as early detection of emergence of drug resistance. Some recent studies have downplayed the importance of viral load in HBV management. Phenotyping/genotyping methods can establish emergent resistance to antivirals. Increasing number of reports suggest that clinical outcome and efficacy of antiviral treatment might vary with HBV genotype and precore/core promoter mutants. The importance of covalently closed circular DNA is also becoming apparent in this regard. Further studies on the development of newer molecular methods for a better management of chronic hepatitis B (CHB) will minimize morbidity in CHB.
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Affiliation(s)
- Runu Chakravarty
- ICMR Virus Unit , GB 4, 1st Floor, ID & BG Hospital Campus, 57, Dr. Suresh Chandra Banerjee Road, Kolkata 700010 , India +91 33 2353 7425 ; +91 33 2353 7424 ;
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94
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Fan HB, Guo YB, Zhu YF, Chen AS, Zhou MX, Li Z, Xu LT, Ma XJ, Yan FM. Hepatitis B Virus Genotype B and High Expression of Interferon Alpha Receptor β Subunit are Associated With Better Response to Pegylated Interferon Alpha 2a in Chinese Patients With Chronic Hepatitis B Infection. HEPATITIS MONTHLY 2012; 12:333-8. [PMID: 22783345 PMCID: PMC3389359 DOI: 10.5812/hepatmon.6173] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Revised: 04/14/2012] [Accepted: 04/24/2012] [Indexed: 12/11/2022]
Abstract
BACKGROUND Hepatitis B virus (HBV) is one of leading causes of various hepatic diseases including acute and chronic hepatitis, cirrhosis, and hepatocellular carcinoma. Hundreds of million people worldwide are infected by HBV, chronically. OBJECTIVES This study in conducted to investigate the influence of Hepatitis B virus (HBV) genotypes and type I IFN-αreceptor β subunit (IFNAR2) expression in liver on response to treatment with pegylated IFN-α-2a (Peg-IFN-α-2a) for chronic hepatitis B infection. PATIENTS AND METHODS In this study, 65 eligible patients with chronic hepatitis B disease were enrolled. HBV genotypes of these patients were analyzed by using PCR-RFLP of the surface gene of HBV. The expression of IFNAR2 in the liver was immune histochemically investigated using anti-IFNAR2 antibody. All immune histochemical slides were read semi-quantitatively by image analysis. Chronic hepatitis B patients were treated with Peg-IFN-α2a therapy for a 48-week period and followed up for 24 weeks. Baseline characteristics and sustained viral response (SVR) to Peg-IFN-α-2a therapy were evaluated. RESULTS 55 % of patients exhibited HBV genotype B and 31.7 % patients exhibited HBV genotypes C infections. After treatment with Peg-IFN-α-2a, SVR was achieved in 66.7 % of patients with HBV genotype B and in 26.3 % of patients with HBV genotype C (P = 0.009). Semiquantitative and the image analysis indicated by gray level values revealed a higher IFNAR2 expression in the group with severe inflammation (P < 0.001). Patients' high IFNAR2 protein expression had a significant impact on SVR to Peg-IFN-α-2a therapy (P = 0.028). CONCLUSIONS HBV genotype B and high expression of IFNAR2 in the liver of chronic hepatitis B patients are closely associated with better response to Peg-IFN-α-2a therapy in chronic hepatitis B disease.
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Affiliation(s)
- He Bin Fan
- Department of Infectious Disease, The People’s Liberation Army 161 Hospital, Wuhan, China
- Corresponding author: He-Bin Fan, Department of Infectious Disease, The People’s Liberation Army 161 Hospital, Wuhan, 430010, Hubei, China. Tel.: +86-2750169074, Fax: +86-2750169007, E-mail:
| | - Ya Bin Guo
- Department of Infectious Disease, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - You Fu Zhu
- Department of Infectious Disease, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - An Shen Chen
- Department of Infectious Disease, The People’s Liberation Army 161 Hospital, Wuhan, China
| | - Mu Xiu Zhou
- Department of Pathology, The People’s Liberation Army 161 Hospital, Wuhan, China
| | - Zhi Li
- Department of Infectious Disease, The People’s Liberation Army 161 Hospital, Wuhan, China
| | - Li Tong Xu
- Department of Infectious Disease, The People’s Liberation Army 161 Hospital, Wuhan, China
| | - Xiao Ju Ma
- Department of Infectious Disease, The People’s Liberation Army 161 Hospital, Wuhan, China
| | - Fu Ming Yan
- Department of Infectious Disease, The People’s Liberation Army 161 Hospital, Wuhan, China
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95
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Firnhaber C, Chen CY, Evans D, Maskew M, Schulz D, Reyneke A, Kramvis A. Prevalence of hepatitis B virus (HBV) co-infection in HBV serologically-negative South African HIV patients and retrospective evaluation of the clinical course of mono- and co-infection. Int J Infect Dis 2012; 16:e268-72. [DOI: 10.1016/j.ijid.2011.12.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 09/20/2011] [Accepted: 12/05/2011] [Indexed: 01/05/2023] Open
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96
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Species association of hepatitis B virus (HBV) in non-human apes; evidence for recombination between gorilla and chimpanzee variants. PLoS One 2012; 7:e33430. [PMID: 22432021 PMCID: PMC3303819 DOI: 10.1371/journal.pone.0033430] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 02/08/2012] [Indexed: 01/28/2023] Open
Abstract
Hepatitis B virus (HBV) infections are widely distributed in humans, infecting approximately one third of the world's population. HBV variants have also been detected and genetically characterised from Old World apes; Gorilla gorilla (gorilla), Pan troglodytes (chimpanzee), Pongo pygmaeus (orang-utan), Nomascus nastusus and Hylobates pileatus (gibbons) and from the New World monkey, Lagothrix lagotricha (woolly monkey). To investigate species-specificity and potential for cross species transmission of HBV between sympatric species of apes (such as gorillas and chimpanzees in Central Africa) or between humans and chimpanzees or gorillas, variants of HBV infecting captive wild-born non-human primates were genetically characterised. 9 of 62 chimpanzees (11.3%) and two from 11 gorillas (18%) were HBV-infected (15% combined frequency), while other Old world monkey species were negative. Complete genome sequences were obtained from six of the infected chimpanzee and both gorillas; those from P. t .ellioti grouped with previously characterised variants from this subspecies. However, variants recovered from P. t. troglodytes HBV variants also grouped within this clade, indicative of transmission between sub-species, forming a paraphyletic clade. The two gorilla viruses were phylogenetically distinct from chimpanzee and human variants although one showed evidence for a recombination event with a P.t.e.-derived HBV variant in the partial X and core gene region. Both of these observations provide evidence for circulation of HBV between different species and sub-species of non-human primates, a conclusion that differs from the hypothesis if of strict host specificity of HBV genotypes.
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97
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98
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Shi W, Carr MJ, Dunford L, Zhu C, Hall WW, Higgins DG. Identification of novel inter-genotypic recombinants of human hepatitis B viruses by large-scale phylogenetic analysis. Virology 2012; 427:51-9. [PMID: 22374235 DOI: 10.1016/j.virol.2012.01.030] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 01/14/2012] [Accepted: 01/26/2012] [Indexed: 02/08/2023]
Abstract
Recombination plays an important role in the evolutionary history of Hepatitis B virus (HBV). We performed a phylogenetic analysis of 3403 full-length HBV genome sequences isolated from humans to define the genotype. The genome sequences were divided into 13 sub-datasets, each approximately 250 bp in length. Genotype designations obtained from the sub-datasets that differed from the genotype defined by the whole genome were assigned as putative recombinants. Our results showed that 3379 out of 3403 sequences belonged to the previously described and putative genotypes A to J respectively, with 315 sequences defined in this analysis. The remaining 24 viruses had sequence divergence of less than 8% with both genotypes B and C and were provisionally assigned genotype "BC". 1047 out of 3403 sequences were identified to be putative recombinants, of which 72 were identified to be novel recombinants. Notably, all viruses of the herein described genotype "BC" were identified to be B/C recombinants.
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Affiliation(s)
- Weifeng Shi
- The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland.
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99
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Andernach IE, Jutavijittum P, Samountry B, Yousukh A, Thammavong T, Hübschen JM, Muller CP. A high variability of mixed infections and recent recombinations of hepatitis B virus in Laos. PLoS One 2012; 7:e30245. [PMID: 22383959 PMCID: PMC3285149 DOI: 10.1371/journal.pone.0030245] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Accepted: 12/16/2011] [Indexed: 01/05/2023] Open
Abstract
In Lao PDR, where more than 8% of the population are chronic carriers of HBsAg, multiple genotypes and subgenotypes co-circulate and are prone to generate recombinant viruses. Phylogenetic analyses of multiple clones per donor revealed mixed infections of subgenotypes B1, B2, B4, C1, C5, I1 and I2 in almost 6% of HBsAg positive rejected blood donors. Recombination analyses and distance calculations furthermore showed that about 65% (17/26) of the mixed infected donors showed recombinations in the S-gene alone, involving the predominant genotypes B and C. These results suggest that, at least in Laos, hepatitis B virus (HBV) mixed infections lead to frequent recombinations. In many donors with recombinant strains, the recombinant fragment and a non-recombinant strain of the same genotype co-existed (127/185 analysed recombinant fragments). For a large proportion of these (60/127), the most closely related known virus was found, although not always exclusively, in the same donor. Recombinant virus strains are largely distinct. This is reflected in an unexpected diversity in recombination breakpoints and the relatively rare recombinations with identical recombination patterns of the same genotypes in different donors. Recent recombination events would explain the limited spread of each of the recombinants. Using a published mutation rate of 4.2×10−5 mutations per site and year, the observed minimum genetic distances of 0–0.60% between parent strain and recombinant fragment would correspond to 0–71 years of evolution from a most recent common ancestor (MRCA). Thus several lines of evidence are suggestive of recent independent recombination events, a proportion of these even occurring within the same donors. In conclusion, our analyses revealed a high variability of mixed infections as a very probable breeding ground of multiple variable recombination events in Laos that so far have not led to new dominant strains.
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Affiliation(s)
- Iris E. Andernach
- Institute of Immunology, Centre de Recherche Public-Santé/National Public Health Laboratory, Luxembourg, Luxembourg
| | | | | | - Amnat Yousukh
- Department of Pathology, Chiang Mai University, Chiang Mai, Thailand
| | - Te Thammavong
- National Blood Transfusion Centre, Lao Red Cross, Vientiane, Lao PDR
| | - Judith M. Hübschen
- Institute of Immunology, Centre de Recherche Public-Santé/National Public Health Laboratory, Luxembourg, Luxembourg
| | - Claude P. Muller
- Institute of Immunology, Centre de Recherche Public-Santé/National Public Health Laboratory, Luxembourg, Luxembourg
- * E-mail:
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100
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Zhi X, Liu Q, Zhang X, Zhang Y, Feng J, Cui D. Quick genotyping detection of HBV by giant magnetoresistive biochip combined with PCR and line probe assay. LAB ON A CHIP 2012; 12:741-5. [PMID: 22222368 DOI: 10.1039/c2lc20949g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Genotyping of human hepatitis B virus (HBV) can be used to direct clinically effective therapeutic drug-selection. Herein we report that a quick genotyping method for human HBV was established by a specially designed giant magnetoresistive (GMR) biochip combined with magnetic nanoclusters (MNCs), PCR and line probe assay. Magnetic nanoclusters of around 180 nm in diameter were prepared and modified with streptavidin, and resultant streptavidin-modified magnetic nanoclusters were used for capturing biotin-labeled hybrid products on the detection interface of the sensor. The gene fragments of HBV's B and C gene types were obtained by PCR based on a template of B- and C-type plasmids. After gene fragments were hybridized with captured probes, streptavidin-modified magnetic nanoclusters could bind with biotin-conjugated gene fragments, and the resultant hydride products could be quickly detected and distinguished by the GMR sensor, with a detection sensitivity of 200 IU mL(-1) target HBV DNA molecules. The novel method has great potential application in clinical HBV genotyping diagnosis, and can be easily extended to other biomedical applications based on molecular recognition.
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Affiliation(s)
- Xiao Zhi
- National Key Laboratory of Nano/Micro Fabrication Technology, Institute of Micro/Nano Science and Technology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
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