Complete genome sequence and phylogenetic analysis of hepatitis B virus (HBV) isolates from patients with chronic HBV infection in Korea

Although there is a report of high rate of hepatitis B virus (HBV) infection in South Korea, only a few entire genome sequences of HBV isolates from Korea have been reported. To obtain the complete nucleotide sequence of the Korean HBV, viral DNA was extracted from sera of Korean patients with chronic HBV infection who have not been exposed to any antiviral treatment. Complete genomic sequences were determined on three Korean HBV isolates. The entire genomic length of Korean HBV isolates, designated as KUHB84, KUHB81, and KUHB95, was 3,215 base pairs. No deletions and insertions were observed. Core promoter mutations (T1762/A1764) were detected in two isolates, KUHB84 and KUHB95. Phylogenetic analysis based on the entire genomic sequences showed that the Korean HBV isolates were genotype C and related closely to the Japanese HBV.     

Molecular virology of hepatitis E virus

This review details the molecular virology of the hepatitis E virus (HEV). While replicons and in vitro infection systems have recently become available, a lot of information on HEV has been generated through comparisons with better-studied positive-strand RNA viruses and through subgenomic expression of viral open reading frames. These models are now being verified with replicon and infection systems. We provide here the current knowledge on the HEV genome and its constituent proteins - ORF1, ORF2 and ORF3. Based on the available information, we also modify the existing model of the HEV life cycle.     

中国人丙型肝炎病毒基因组3′端非编码区的研究

目的分析中国丙型肝炎病人ＨＣＶ基因组３′端非编码区（３′ＮＣＲ）,以促进对ＨＣＶ基因组复制机制的研究。方法采用两种方法,从上海地区感染ＨＣＶ的病人血清中,扩增获得ＨＣＶ基因组３′端非编码区：一是用套式ＰＣＲ直接扩增,二是先分别获得ＨＣＶ３′ＮＣＲ的前半部分和后半部分,再将两片段进行融合ＰＣＲ。ＰＣＲ产物进行测序后作同源性分析。在此基础上,建立了针对３′端非编码区的ＲＴＰＣＲ方法,并与基于５′端非编码区的ＲＴＰＣＲ方法检测ＨＣＶＲＮＡ的特异性和灵敏度比较。结果序列分析表明,中国丙型肝炎病人ＨＣＶ基因组３′非编码区由４部分组成：高度变异区、Ｐｏｌｙ（Ｕ）区、Ｐｏｌｙ（Ｕ／Ｃ）区和９８碱基区。同源性分析显示,９８碱基区在不同分离株间高度保守并与国外报道株一致,而Ｐｏｌｙ（ＵＵＣ）区存在较大差异。３′端非编码区和５′非编码区ＲＴＰＣＲ检测血清ＨＣＶＲＮＡ有较高符合率（９５％）。结论ＨＣＶ基因组３′端非编码区的３′末端（９８碱基）,在不同分离株间的高度保守性提示,该区在ＨＣＶ基因复制中起重要作用。基于３′非编码区的ＲＴＰＣＲ方法,将有助于ＨＣＶ感染的诊断。     

Failure to detect hepatitis C virus (HCV) genome by polymerase chain reaction in human anti-HCV-positive intravenous immunoglobulins

The prevalence of HCV antibodies was determined by a second-generation ELISA and a four-antigen rccombinant immunoblot assay in nine intravenous immunoglobulin (IVIG) preparations commercially available in Italy. In addition, the clinical safety of six of them was ascertained by polymerase chain reaction (PCR) of HCV RNA and a prospective study in 14 patients with immunodeficiency disorders. Results indicated that all IVIG preparations were anti-HCV-positive. However, there were substantial variations in their anti-HCV antibody titres. The preparations retained IgG subelass reactivilies to HCV-associated structural (C223) and non-structural (C33c, C100-3) proteins. Our sensitive and specific PCR assay was unable to detect HCV RNA in the six preparations tested. Clinical surveillance of IVIG-trcated patients prospectivcly evaluated over a mean period of 83 months failed to delect clinical and/or biochemical evidence of hepatitis.     

Distribution of hepatitis B virus (HBV) genotypes among HBV carriers in the Cote d'Ivoire: complete genome sequence and phylogenetic relatedness of HBV genotype E

The characteristics of hepatitis B virus (HBV) genotype E are not well known because only a few studies have been carried out by complete genome analysis. The aim of this study was to elucidate the distribution of HBV genotypes in Cote d'Ivoire, and to clarify the genotype-related characteristics of genotype E. The distribution of HBV genotypes among 48 HBV carriers in Cote d'Ivoire was determined using serological and genetic methods. The characteristics of genotype E were evaluated by complete genome sequences, and further investigations of small S gene, basic core promoter (BCP) mutation, and precore mutation were undertaken. HBV genotype distribution among the 48 carriers was 6.3% for genotype A, 6.3% for genotype D, and 87.4% for genotype E. Complete genomes of two genotype E strains were sequenced, and found to have 98.2% to 99.2% homology at the nucleotide level when compared with genotype E strains reported previously. In 24 genotype E carriers, the precore mutation was detected in 75% of the patients without HBeAg, in contrast to only 25% of the patients with HBeAg (P < 0.05). All 24 strains have T at nucleotide 1858 in the precore region. In contrast, BCP double mutation was detected in 17% of the patients with HBeAg, and 33% of the patients without HBeAg. These results indicated as the following: (1) genotypes A, D, and E of HBV exist in Cote d'Ivoire and genotype E is the most prevalent; (2) genotype E spread with low genetic diversity over the complete genome in West Africa; (3) HBV precore and/or BCP double variants were common among the patients with genotype E infections.     

Genotype,serotype, and phylogenetic characterization of the complete genome sequence of hepatitis B virus isolates from Malawian chronic carriers of the virus

Hepatitis B virus (HBV) genotypes have distinct geographical distribution. HBV sequences among hepatitis B carriers in Malawi have not been evaluated thus far. HBsAg serotype and genotype of HBV was determined in 20 serum samples from Malawian chronic HBV carriers, and two complete genomes and 13 entire pre-S2/S genes were sequenced directly. Genotype A HBV isolates were found in all of the samples, and serotype with adw2 and ayw2 were detected in three and 17 samples, respectively. In phylogenetic analyses, two complete genomes were classified into a subgroup A' that was described previously in South African isolates of the virus, and were separated from HBV isolates in Western countries with nucleotide differences ranging from 4.1-6.2%. The separation of subgroup A' was also evident in the tree topology of the entire pre-S1/S2, X and precore/core region, but not evident in the small-S region. The nucleotide divergences in subgroup A' were higher than those among genotype A without subgroup A' in the complete genomes as well as each of four open reading frames. All of the 13 pre-S2/S sequences were classified into the subgroup A', and clustered with known HBV isolates with ayw2 in carriers from South Africa and Zimbabwe. Three amino acids in the pre-S2/S gene were characteristic of subgroup A' with ayw2. In conclusion, unique HBV isolates of subgroup A' with ayw2 are prevalent in Malawi, and subgroup A' with a relatively higher nucleotide diversity may be a HBV isolate characteristic of the indigenous population of some African countries.     

丙型肝炎病毒全长cDNA模板的构建及鉴定

目的 构建具有功能的丙型肝炎病毒(HCV)全长cDNA克隆。方法 应用长模板RTPCR法扩增1份上海地区HCV感染者血清的RNA(基因型为1b)，分段扩增、融合拼接成9．2kb的基因片段，克隆人含有HCV基因两端非编码区序列的载体作为模板。为检测此过程是否发生对特定变异株的选择，分析4个独立克隆的HVRl序列。对原核细胞中表达的HCV核心蛋白、NS3蛋白酶及解旋酶，以蛋白印迹实验确证其免疫反应性。并构建NS3／4A-SEAP表达系统检验NS3的蛋白酶活性。结果 获得丙型肝炎病毒全长cDNA模板。不同克隆间HVR1序列存在较大差异，提示长模板RT-PCR所制备HCVcDNA具有HCV基因准种(quasispecies)的特性。该模板编码基因在原核细胞内得到高效表达，并具有良好的免疫反应性。在NS3／4A-SEAP表达系统内，NS3可切割、释放其下游的SEAP，具有蛋白酶活性。结论 本工作为构建全长功能性HCV cDNA模板及感染性克隆奠定了基础。     

I. hepatitis E virus (87A strain) propagated in A549 cells

A strain of hepatitis E virus (HEV), the 87A strain isolated in 2BS cells from the feces of a patient with hepatitis E, has been reported previously. In this study, the 87A strain was propagated in A549 cells, and the marked cytopathic effect (CPE) appeared in the infected monolayer cells. The size of this virus is about 30 nm in diameter. Furthermore, HEV-RNAfrom the supernatants of the virus of different passages was detected by polymerase chain reaction (PCR) amplification using ET1 .1 HEV primers. A band of HEV for 239 bp from PCR products was revealed by electro-phoresis. PCR products of the fourth passage were sequenced. These results show that the 87A virus replicates in the A549 cell line. © Wiley-Liss, Inc.     

Complete genome sequence and phylogenetic analysis of hepatitis B virus (HBV) isolated from Mongolian patients with chronic HBV infection

Although there is a report of a high rate of hepatitis B virus (HBV) infection in Mongolia, the entire nucleotide sequence of HBV circulating among Mongolian patients has not been reported. To obtain the complete nucleotide sequence of the Mongolian HBV, viral DNA was extracted from sera of patients with HBV infection. Six Mongolian HBV strains were amplified by PCR. Complete genomic sequences were determined for two Mongolian HBV isolates, MBT181 and MMU36. The entire genome of Mongolian HBV isolates was 3,182 bp long and genetic distance between Mongolian HBV isolates was 3.2%. Precore stop codon resulting from a guanine to adenine mutation at nucleotide 1,896 was detected in MBT181 strain. Based on phylogenetic analysis, the six Mongolian isolates were classified as genotype D.     

Subcellular localization of hepatitis E virus (HEV) replicase

Hepatitis E virus (HEV) is a hepatotropic virus with a single sense-strand RNA genome of approximately 7.2 kb in length. Details of the intracellular site of HEV replication can pave further understanding of HEV biology. In-frame fusion construct of functionally active replicase-enhanced green fluorescent protein (EGFP) gene was made in eukaryotic expression vector. The functionality of replicase-EGFP fusion protein was established by its ability to synthesize negative-strand viral RNA in vivo, by strand-specific anchored RT-PCR and molecular beacon binding. Subcellular co-localization was carried out using organelle specific fluorophores and by immuno-electron microscopy. Fluorescence Resonance Energy Transfer (FRET) demonstrated the interaction of this protein with the 3' end of HEV genome. The results show localization of replicase on the endoplasmic reticulum membranes. The protein regions responsible for membrane localization was predicted and identified by use of deletion mutants. Endoplasmic reticulum was identified as the site of replicase localization and possible site of replication.     

戊型肝炎病毒TaqMan Real-time RT-PCR法的建立及应用

目的 建立灵敏、特异、稳定的戊型肝炎病毒(HEV) TaqMan Real-time PCR检测方法.方法 根据GenBank中的HEV相关序列,选取HEV基因组ORF2的保守区域设计合成特异性引物和探针,建立TaqMan HEV Real-time RT-PCR检测体系,评价体系的特异性、敏感度和稳定性,并应用于临床样本的检测.结果 本研究建立的HEV Real-time RT-PCR检测体系最低检测极限达到10个拷贝/反应,重复性实验Ct值的变异系数(CV)最大为1.53％,并且该体系能特异检测出戊肝临床样本中的HEV,其拷贝数从1.87×104拷贝/ml到8.12×106拷贝/ml不等.结论 成功建立特异性强、灵敏度高的HEV Real-time RT-PCR检测方法,应用于临床样本检测时取得了良好效果,为HEV分子病原学诊断打下基础.     

Full genomic sequence analysis of swine genotype 3 hepatitis E virus isolated from Shanghai

The full genomic nucleotide sequence of a previously identified genotype 3 hepatitis E virus (HEV), strain SAAS-JDY5, was obtained using RT-PCR and rapid amplification of cDNA ends (RACE). The genome consisted of 7225 nucleotides, excluding a poly-A tail at the 3′ terminus, and contained three open reading frames (ORFs), ORF-1, ORF-2 and ORF-3, encoding 1702, 660 and 113 amino acids, respectively. Phylogenetic analysis confirmed that SAAS-JDY5 belonged to genotype 3 HEV and was most closely related to the Japanese isolate wbJYG1 (AB222184). SAAS-JDY5 shared approximately 87% nucleotide similarity to human and swine strains from the United States, compared with 74–75% similarity to Asian (genotype 4) and Mexican strains (genotype 2). Alignment of the SAAS-JDY5 genomic sequence with reference sequences of the same genotype revealed one nucleotide substitution and one deletion at positions 5145 and 7189 (3′ UTR), respectively. Moreover, SAAS-JDY5 contained two additional nucleotides (AC) at the very end of the 3′-terminus preceding the poly-A tail of the genome. Comparison of the putative amino acid sequence encoded by the SAAS-JDY5 genome with sequences of other genotype 3 isolates revealed 15 unique amino acid substitutions and one deletion in ORF-1, and three substitutions in ORF-2.     

Novel hepatitis E virus (HEV) isolates from Europe: evidence for additional genotypes of HEV

Hepatitis E infection is associated with areas in which hepatitis E virus (HEV) infection is endemic. Acute infections in industrialized nations are usually linked to travel to endemic areas. Recently, an acute hepatitis infection in a patient from the United States (US), with no recent foreign travel history, was linked to a novel strain of HEV. Although a few additional cases have been reported from patients who have not traveled to endemic areas, the source of these infections has not been determined. The objective of this study was to identify additional HEV isolates from patients with acute infection who had no recent history of travel to areas where HEV is considered endemic, and to determine the genetic relationship between these and other HEV isolates. Viral RNA was isolated from serum and polymerase chain reaction (PCR) was performed using consensus primers based on a number of HEV isolates. HEV sequence in open reading frame (ORF) 1 and ORF2 was identified in three patients from nonendemic areas, one from Italy and two from Greece. Comparative and phylogenetic analyses were performed. The Greek and Italian isolates were significantly divergent from two isolates from the US and isolates identified previously from HEV-endemic regions. The Italian isolate was distinct from the two Greek isolates. In addition, the two Greek isolates were significantly divergent from each other. Phylogenetic analysis indicated that the Italian and two Greek isolates represent three new genotypes of HEV, distinct from the Burmese, Mexican, and US genotypes.     

Complete sequence of a Kyrgyzstan swine hepatitis E virus (HEV) isolated from a piglet thought to be experimentally infected with human HEV

Hepatitis E virus (HEV) was identified by RT-PCR amplification with degenerate ORF2 primers in the stool of a piglet experimentally inoculated with a stool suspension from a patient with acute hepatitis during an outbreak of non-A, non-B hepatitis in Kyrgyzstan. Further characterization by sequencing of the complete genome and phylogenetic analysis showed that the piglet isolate was most closely related to HEV genotype 3. Because the original human stool specimen used to inoculate the piglet was no longer available, stool samples from three patients obtained during the same outbreak were sequenced and found to be HEV genotype 1. These findings suggest that the HEV isolated from the swine stool was probably an HEV enzootic in Kyrgyzstan and not the virus inoculated from the human stool.     

Genomic full-length sequence of HLA-Cw*140201, identified by cloning and sequencing

Genomic full-length sequence of HLA-Cw*140201, differing from Cw*1403 by four nucleotide exchanges in exon 2 and intron 5, was identified by cloning and sequencing from a male Chinese donor.     

中国南京庚型肝炎病毒部分基因的克隆及cDNA序列分析

采用反转录聚合酶链反应（ＲＴＰＣＲ）从南京地区某输血后丙型肝炎患者血清中克隆出庚型肝炎病毒（ＨＧＶ）非结构区部分基因。序列分析结果表明：该序列与国外发表的庚型肝炎病毒ＨＧＵ４４４０２，ＨＧＵ４５９６６，ＨＧＵ３６３８０（ＧＢＶＣ）对应位置核苷酸序列同源性分别为８９０９％，９２１２％，８７２７％，与已报道的ＨＧＶ河北株序列同源性为９３９４％。对４０份输血后丙型肝炎血清和３０份非甲非乙非丙非丁非戊型肝炎血清进行了检测，ＨＧＶＲＮＡ阳性率分别为１０００％和６６７％。     

非霍奇金淋巴瘤EB病毒特异DNA序列的检测

目的　探讨EB病毒 (EBV)与中国南方地区非霍奇金淋巴瘤 (NHL)的相关性 ,以及EBV与不同类型NHL的关系。方法　采用PCR技术 ,检测 2 0 6例石蜡包埋的NHL组织及 2 3例反应性增生的淋巴组织中的EBV特异DNA序列。结果　(1 ) 2 0 6例NHL组织中 ,94例PCR扩增出EBV特异的DNA序列 ,阳性率 4 5 6 % ;对照组反应性增生的淋巴组织 2 3例中 ,5例阳性 ,阳性率 2 1 7% ;两者差异有显著性 (P <0 0 5 )。 (2 ) 2 0 6例NHL中B NHL 1 2 8例 ,EBV阳性者 4 8例 ,阳性率 37 5 % ;T NHL 78例 ,EBV阳性者 4 6例 ,阳性率 5 9 0 %。两者差异有显著性 (P <0 0 5 )。结论　EBV与中国南方地区NHL ,特别是T NHL有一定的相关性     

广州地区肝炎患者血清中庚型肝炎病毒核酸检测和病毒核苷酸测序

目的 了解广州地区肝炎患者中庚型肝炎病毒（HGV）的感染情况及基因型特点。方法 采用逆转录－套式聚合酶链反应（RT－nested PCR)方法检测出肝炎患者血清中HGV RNA,引物位于HGV基因组的非编码区,并对扩增产物进行直接测序。结果 251例急慢性肝炎血清中共检出25例HGV RNA阳性,总阳性率为9．96％,其中56例非甲－戊型肝炎中要出4例阳性（7．14％）,77例乙型肝炎（HB）中检出8例阳性（10．39％）,118例丙型肝炎（HC）中检出13例阳性（11．17％）;2株HGV广州核苷酸之间的同源性为98．0％,与非洲洲的同源性分别为81．7％和84．2％,与美国株的同源性均为91．1％。结论 广州地区肝炎患者中存在HGV感染,2株HGV广州株可能为同一基因型,且与HGV美国株具有较高的同源性。     

TT病毒的检测及部分核苷酸序列比较

目的 为阐明ＴＴ病毒（ＴＴＶ）流行病学特征和基因级异质性以及血清学诊断试剂的研制提供资料。方法 从健康查体者的血清中提取ＤＮＡ，设计一套引物，采用套式聚合酶链反应（ｎｅｓｔｅｌ－ＰＣＲ）检测ＴＴＶ，对其中７例阳性标本进行了克隆测序，并与２株ＴＴＶ的核苷酸序列作了比较。结果 １１１例正常人中ＴＴＶ的感染率为１２．６％。７株中国株ＴＴＶ间的核苷酸同源性为９０．６％～９５．４％，与日本株ＴＸ０１１（Ｏ）