Full genomic analysis of hepatitis delta virus prevalent on Miyako Island, Japan

The aims of this study were to determine the full-length genome sequences of hepatitis delta virus (HDV) in HDV RNA-positive subjects, and to elucidate the molecular specificity of the HDVs that are clustered on a distant island in Japan. This study included 3 subjects with chronic hepatitis who were positive for hepatitis B surface (HBs) antigen and HDV RNA, and who were admitted to the Okinawa Prefectural Miyako Hospital in 1998. The full-length genome sequence of HDV was determined by nested polymerase chain reaction (PCR) using four kinds of primer sets. The genomic length of HDV was 1,675, 1,679 and 1,681 base pairs, respectively. There was 90-92% nucleotide homology between each pair of isolates. In comparison with HDV isolates in geographically neighboring regions, the nucleotide homology of the 3 HDV isolates were 73-75% with the China isolate of genotype I; 77-78% with the Taiwan isolate of genotype I; 83-84% with a Japan isolate of genotype IIa; 85-87% with the Taiwan isolate of genotype IIa, and 87-88% with the Taiwan isolates of genotype IIb. Therefore, the Miyako Island isolates had high homology with the Taiwan isolate of genotype IIa and IIb. Phylogenetic analysis of the full-length genome sequences of HDV revealed that the two Miyako Island isolates were classified into a genotype IIb'. The other one was classified as genotype IIb. In conclusion, the HDV of Miyako Island isolates can be classified as a novel subgroup of genotype IIb, designated type IIb', and genotype IIb.     

应用型特异性引物巢式PCR分析温州地区乙型肝炎病毒基因型及其临床意义

目的了解温州地区乙型肝炎病毒（HBV）基因型的分布及其与临床的相关性。方法选取温州地区HBVDNA阳性的慢性HBV感染者202例,其中慢性无症状乙型肝炎表面抗原携带者52例,慢性乙型肝炎103例,肝硬化27例,肝细胞癌20例,应用型特异性引物巢式PCR检测HBV的基因型。结果202例HBVDNA阳性血清标本中,B型37例（18．3％）,C型123例（60．9％）,B／C混合型41例（20．3％）,D型1例（0．5％）,未发现A、E、F和G型;与B基因型、B／C混合型相比,C基因型在慢性乙型肝炎和肝细胞癌中明显升高,分别为56．1％和14．6％（P〈0．05）;C基因型感染者血清丙氨酸氨基转移酶水平（226±268）U／L高于B基因型的（114±183）U／L和B／C混合型的（130±222）U／L,差异有统计学意义（P〈0．05）;C基因型感染者HBeAg阳性率和HBVDNA含量明显高于B基因型和BC混合型感染者相比,差异有统计学意义（P〈0．05）。结论温州地区存在HBV的B、C、D和B／C混合基因型,C型为本地区的优势基因型．并且C型HBV感染易引起较重肝脏损伤。     

Chronic hepatitis B in patients coinfected with human immunodeficiency virus in Japan: a retrospective multicenter analysis

A nationwide survey in Japan revealed that about 6 % of human immunodeficiency virus (HIV)-positive patients are coinfected with hepatitis B virus (HBV). To further analyze the features of liver disease in HIV/HBV-coinfected patients, we analyzed 252 patients from six hospitals in the HIV/AIDS (acquired immunodeficiency syndrome) Network of Japan. The mean age was 39.5 years, and the proportion of male patients was very high (243 of 252; 96 %). The main transmission route was male homosexual contact (186 of 252; 74 %), followed by heterosexual contact. The HBV genotype was determined in 77 patients. Among them, genotype A HBV was the most frequent (58 of 77; 75 %) and was detected almost exclusively in homosexual patients. Acute hepatitis B was documented in 21 patients (8 %). Three of the 252 HIV/HBV-coinfected patients developed advanced liver disease with the complication of ascites, hepatic encephalopathy, or hepatocellular carcinoma. A comparison between patients not treated and those treated with antiretroviral drugs including anti-HBV drugs revealed that the baseline liver function was worse in treated patients. However, the serum albumin levels and platelet counts in both groups increased after treatment and were similar. Liver disease-associated death was not observed. Here, we characterize the clinical features of liver disease in HIV/HBV-coinfected patients in Japan for the first time. The findings suggest that antiretroviral therapy with anti-HBV drugs may retard the progression of a liver disease and prevent liver disease-associated death in such patients.     

型特异性引物巢式PCR快速检测HBV基因型及其临床意义

目的　应用型特异性引物巢式PCR检测HBV基因型并初步了解山东地区HBV基因型的分布状况。方法　随机选择山东地区HBVDNA阳性患者共 178例 ,其中无症状携带者 (ASC) 5 3例 ,慢性活动性肝炎 (CH) (包括轻、中、重度 ) 87例 ,肝硬化(LC) 38例 ,先通过外引物进行第一轮PCR ,然后 ,将 6对型特异性引物分到两个反应体系 (MixA和MixB)中分别对第一轮扩增产物进行第二轮PCR ,根据阳性结果判断出样本的基因型。结果　C基因型 85例 (47.8% ) ,B基因型 6 3例 (35 .4 % ) ,B C混合基因型 30例 (16 .8% )。C基因型在活动性肝病 (CH及LC)中占优势 ,而ASC组则是以B基因型为主 ,差异有显著性 (P <0 .0 1)。C基因组中HBeAg阳性率、HBVDNA定量及ALT水平均较B基因组为高 (P <0 .0 0 1或P <0 .0 0 5 ) ,而抗HBe阳性率则在B基因型组显著升高 (P <0 .0 0 5 )。结论　山东地区存在C、B及B C混合基因型 ,并以C基因型为主。型特异性引物巢式PCR敏感性高 ,特异性强 ,可以快捷准确地检测HBV基因型。     

Heterogeneity of hepatitis B virus genotype D in Japan

OBJECTIVE: Hepatitis B virus (HBV) genotypes B and C are predominant in Japan. Previously, we reported that approximately 9% of HBV carriers in the Ehime area of western Japan were infected with genotype D (HBV/D) and their sequences closely related. Recently, serum samples from 3 patients with chronic HBV/D infections living in Tokyo and the surrounding area became available for testing. The purpose of this study was to determine whether the HBV/D isolates from these different areas of Japan are closely related. METHODS: Of the 3 Tokyo area patients infected with HBV/D, 2 had chronic hepatitis, and 1 had hemophilia with a history of frequent coagulation factor injections. The complete HBV/D genome sequences of each were determined, and compared with those of subjects from the Ehime area. RESULTS: All 3 HBV/D sequences had a genomic length of 3,182 bases, and the hepatitis B surface antigen subtype was ayw3. Phylogenetic analysis revealed that the 1 of the HBV/D isolates was closely related to the isolates from Ehime Prefecture, while 1 was similar and 1 was clearly distinct. CONCLUSION: Our results indicate that HBV/D infections in Japan are heterogeneous.     

实时荧光定量PCR方法检测乙型肝炎病毒基因型

目的建立一种快速准确的实时荧光PCR方法检测乙型肝炎病毒基因型。用此方法对安徽地区乙肝患者进行检测,了解该地区HBV基因型分布情况。方法首先用实时荧光定量PCR方法对150例安徽地区乙肝患者进行HBVDNA定量检测和分型检测,然后对其中载毒量大于5000IU/mL的113例标本和1例1000IU/mL≤载毒量<5000IU/mL进行测序分型检测,验证所建立方法的准确性,了解安徽地区HBV基因型分布情况。结果150例HBV样本中HBVDNA含量<1000IU/mL30例,分型检测结果均为阴性,对载毒量≥5000IU/mL的样本检出率为97.35%(110/113);对1000IU/mL≤载毒量<5000IU/mL的样本检出率为14.29%(1/7);对全部DNA阳性样本的检出率为92.5%(111/120)。HBV分型检测与HBVDNA测序检测的114例样本中,只要是HBVB基因型、C基因型或B/C混合型,乙型肝炎病毒基因分型检测都能检出来(共111例),其中部分样本经分型检测属于B/C混合基因型,测序结果都是混合基因型中占优势的基因型结果,总体符合率为100%。未能被本法检出的样本共3例,3例样本经测序分型均为D型。120例病毒载毒量≥1000IU/mL乙肝患者中B型病例占51.67%(62/120);C型占29.17%(35/120);B/C混合型占11.67%(14/120)。PCR测序检出为D型3例,占2.5%(3/120)。结论应用TaqMan探针的实时荧光定量PCR方法能快速对我国HBV主要基因型B基因型、C基因型进行检测,结果准确可靠,特异性高。安徽地区的HBV基因型以B型为主,C型次之,亦存在着D型的少数感染病例和B/C的混合感染。     

多对型特异性引物巢式PCR检测乙型肝炎病毒基因型分析

目的采用多对型特异性引物通过巢式PCR法检测HBeAg阳性患者血清中乙肝病毒(HBV)基因型的分布情况。方法根据从前S1基因到S基因中的保守序列设计出10条内外引物,并将其中8条内引物分成A、B两组分别扩增A、B、C和D、E、F型HBV,然后将第2轮PCR的两组产物分别用3%琼脂糖进行电泳,根据PCR产物片段大小直接判定HBV基因型。用该法检测15例慢性乙肝患者血清中HBV基因型,了解HBV基因型分布情况。结果 HBV基因分型结果为B型7例(46.7%)、C型4例(26.7%)、B+C型2例(13.3%),另有2例未能分型。结论人群HBV优势基因型以B型为主,C型次之。     

Co-infection with hepatitis B virus genotype D and other genotypes in Western Japan

OBJECTIVE: Genotypes B and C are the prevalent hepatitis B virus (HBV) genotypes in eastern Asia. Although very rare in this region of the world, genotype D was found to be prevalent in a small area of western Japan. In this study, we confirm the frequency and clinical significance of co-infection with different genotypes among patients from that area infected with genotype D. METHODS: Twenty-three patients from the same area of western Japan infected with HBV genotype D, determined using a genotyping enzyme immunoassay, were studied. Cloning was done using DNA extracted from serum samples, and polymerase chain reaction assays with the restriction fragment length polymorphism for HBV genotyping were performed with 10 clones from each patient. RESULTS: Four (17.4%) of the 23 patients were found to be co-infected with HBV genotype C, and the HB surface antigen subtype was ayw in both mono- and co-infected patients. No clinical differences were found between mono-infected and co-infected patients carrying genotype D. CONCLUSION: A significant number of patients from the study area found to be infected with HBV genotype D were co-infected with genotype C. Additional study with a larger number of patients is needed to elucidate the possible clinical significance.     

A long-term follow-up of five patients with hepatitis delta virus in Japan.

From 1973 to 1989 five patients with hepatitis delta virus having anti-hepatitis delta antibodies continuously in the serum for more than 5 years were identified among 1019 hepatitis B virus carriers who were being followed-up for more than 3 years (mean 8.9 years). Of the five patients with antibodies, three had a history of blood transfusion, in two cases the transfusion was massive, and one patient had been addicted to narcotics given intravenously 35 years before. In the remaining patient, the route of superinfection could not be determined. Hepatitis delta antigen was detected in hepatocyte nuclei of one of the three patients in whom liver biopsies were performed and there was chronic persistent hepatitis detected by an indirect immunoperoxidase technique. During the follow-up, hepatocellular carcinoma developed in one case but the clinical prognosis was favourable in the remaining four cases.     

浙江省义乌地区病毒性乙型肝炎病毒基因型分布

目的了解浙江省义乌地区病毒性乙型肝炎（乙肝）病毒（HBV）基因型分布特点,为乙肝的流行病学研究、临床诊治提供参考资料。方法用HBV基因分型（B、C基因型）荧光PCR法直接检测,或用HBV基因型特异引物经聚合酶链反应扩增乙肝患者血清HBV,将目的条带切下,经纯化后测序。测序得到的结果用CLUSTALX及Mega软件进行HBV分型分析。结果该地区基因分型结果,其中B型61.76% (63／102)、C型29.41％(30／102),B/C混合型8.82％ (9／102);男、女感染者中B型、C型基因型的构成比较,结果显示差异无统计学意义 (x2 =0.03,P＞0.05)。B/C混合基因型性别间差异有统计学意义 (x2=4.25,P＜0.05);对B基因型和C基因型感染者血清HBV-DNA定量检测结果比较,差异无统计学意义（Uc=1.1213,P＞0.05）,B基因型和C基因型感染者血清中HBeAg的阳性率分别是33.33%、20.00%,差异无统计学意义（x2 =1.75,P＞0.05）。结论浙江义乌HBV基因型为B型、C型和B/C混合型,以B型为主,且具有一定的地域特征。     

Rapid identification of Pseudomonas aeruginosa from ocular isolates by PCR using exotoxin A-specific primers

The purpose of this research was to evaluate the use of PCR for the identification of ocular isolates of Pseudomonas aeruginosa by using primers specific to the exotoxin A gene of the bacteria. Genomic DNA was obtained from ocular microbial isolates of keratitis patients. Primers were designed based on the published sequence of the exotoxin A gene of P. aeruginosa. Using the primers designed, PCR reactions were performed on the DNA samples. The PCR was also examined for its specificity and sensitivity. In addition, a direct PCR using heating method was attempted on P. aeruginosa with no separate DNA extraction step. ATCC strains of P. aeruginosa were included as positive controls. The rest of the bacteria other than P. aeruginosa served as negative controls. A single band was obtained when analysed on agarose gel electrophoresis only from samples that contained genomic DNA of P. aeruginosa. The direct PCR method was also successful with the same band produced from the amplification. The whole process was completed within 4 h. The direct PCR amplification targeting at the exotoxin A gene of P. aeruginosa is potentially a rapid, specific, sensitive and relatively simple method for the identification of ocular isolates of P. aeruginosa.     

HBV基因型、基因亚型及基因变异与原发性肝癌的关系

目的探讨乙型肝炎病毒（HBV）不同基因型、基因亚型及基因变异与原发性肝癌（PHC）的关系,为制定PHC的预防和治疗措施提供科学依据。 方法收集新疆生产建设兵团医院2013年3月至2016年3月共4例感染HBV基础上的PHC患者,利用荧光定量PCR法检测HBV DNA,酶联免疫法检测HBeAg。应用PCR方法检测患者HBV基因型、基因亚型分布特征,检测HBV基因变异情况。 结果此4例感染HBV基础上的PHC患者中,3例患者HBeAg（＋）,HBeAg阳性率为75%。4例患者中3例HBV DNA（＋）,定量检测结果分别为2.03×10⁵ IU/ml、2.56×10⁶ IU/ml、3.12×10⁵ IU/ml;1例患者HBV DNA（-）。检测患者基因型为B型1例（B2亚型）,C型3例（C1亚型1例,C2亚型2例）。HBV B2亚型、C1亚型和1例C2亚型患者,分别在APC、CTNNB1、IGF2R基因处出现基因变异;1例C2亚型患者（80岁）,在UGT1A5、ZFYVE16、MALRD1基因的外显子序列检测中发现移码变异。 结论HBV基因型,尤其是C型可能是PHC发生的危险因素。基因变异与PHC的发生发展可能也存在密切关系。     

Full-length sequences of six hepatitis E virus isolates of genotypes III and IV from patients with sporadic acute or fulminant hepatitis in Japan

OBJECTIVE: Ranges of variation and conservation in sequence need to be defined for detecting and genotyping hepatitis E virus (HEV). METHODS: Six HEV isolates from Japanese patients were sequenced over the entire genome and compared phylogenetically along with 16 reported HEV isolates, including two from pigs. RESULTS: Three of the six HEV isolates were of genotype III, and the remaining three were of genotype IV. Local clusterings of Japanese HEV isolates were observed in the phylogenetic analyses, including a swine HEV isolate reported previously (swJ570). All six HEV isolates possessed three open reading frames (ORFs). The ORF3 in the three isolates of genotype III were in a different reading frame, while that in the three isolates of genotype IV were in the same reading frame as ORF1. A stretch of 46-96 nucleotides was identified, point mutations and deletions in which were specific for the four genotypes (I-IV). A polymerase chain reaction method was developed with 9 nested universal primers, deduced from conserved regions in the 5'-terminal sequences of the 22 HEV genomes. CONCLUSIONS: Conserved and genotype-specific variation in HEV sequences, identified in the comparison of 22 full-length genomes, would be useful in designing primers for sensitive detection and specific genotyping of HEV RNA.     

乙型肝炎病毒基因型与血清病毒量及纤维化的关系

目的研究乙型肝炎病毒基因型与血清病毒量及纤维化的关系。方法采用聚合酶链式反应结合Taqm anMGB探针技术对我院191例患者进行HBV基因分型。结果 191例中单B型72例(37.7%),C型108例(56.5%),BC型6例(3.1%),非B非C型5例(2.6%)。C型HBV DNA值明显高于B型(P0.01)。肝纤维化四项及F ibroscan检查C型高于B型,两组比较差异有统计学意义(P均0.01)。结论江苏地区HBV基因型以C型为主,B型次之,发现少数BC型及非B非C型。C型病毒复制活跃,纤维化程度明显。     

Differences of hepatocellular carcinoma patients with hepatitis B virus genotypes of Ba, Bj or C in Japan

Hepatitis B virus (HBV) genotypes B (HBV/B) and C (HBV/C) are prevalent in Asia. Recently HBV/B has been classified into two subtypes, HBV/Ba which is ubiquitously found in Asia, and HBV/Bj which is specific in Japan. In addition, the frequency of positive HBeAg has been reported to be higher in patients with HBV/Ba than those with HBV/Bj. However, little is known about the differences between patients with various genotypes who developed hepatocellular carcinoma (HCC). In 296 serum samples of HCC patients collected from all over Japan, HBV genotypes were determined with the restriction fragment length polymorphism. HBV/A was detected in 1.0%, HBV/Ba in 4.4%, HBV/Bj in 7.4%, and HBV/C in 86.5%. In the Tohoku district and Okinawa, HBV/Ba, HBV/Bj and HBV/C were found in 6.7, 40.0 and 48.9%, compared to 4.0, 1.6 and 93.2% in the other districts in Japan. HBV/Bj patients were more frequently found in the group older than 65 years while HBV/Ba patients were found in all age groups. The frequency of positive HBeAg in HBV/Bj patients was significantly low compared to that in the other patients. More than 60% of the patients with HCC had cirrhosis as the underlying liver diseases. However, in HBV/Ba patients aged 50 years or younger, 80% of them had chronic hepatitis, while 87.5% of those aged older than 50 years had cirrhosis. These data suggest that great differences exist among patients with HCC infected with different genotypes.     

A TaqMan PCR assay using degenerate primers for the quantitative detection of woodchuck hepatitis virus DNA of multiple genotypes

Woodchuck hepatitis virus (WHV) is a valuable animal model system for studies of hepatitis B virus infection and accurate assessments of WHV viral load are necessary in these studies. Wild-captured woodchucks that are naturally infected with WHV are sometimes used in these studies, however, the sequence variation in WHV isolates generally precludes the use of TaqMan PCR. To facilitate this, we have created a real-time TaqMan PCR assay for WHV using degenerate primers with inosine residues employed at the locations of known sequence heterogeneity. This TaqMan assay has a dynamic range of 10-10(8) genomic equivalents (ge) of WHV DNA per reaction and the assay is robust and reproducible in the 10(2)-10(7) ge WHV DNA per reaction range (intra-assay coefficient of variation (CV) <2.1%, inter-assay CV <2.9%). During our assay validation, we cloned and analyzed a series of six naturally occurring virus variants that contained sequence heterogeneity in the TaqMan primer sequence region. We showed that the presence of some of these sequence variations prevented the PCR amplification of the target when regular primer sequences were used, while degenerate primer sequences were able to efficiently amplify all tested sequences equally well.     

荧光PCR法检测乙型肝炎病毒YMDD基因变异的研究

目的探讨荧光PCR法在检测酪氨酸-蛋氨酸-天门冬氨酸-天门冬氨酸(YMDD)基因变异上的临床应用价值及其拉米夫定治疗一年慢性乙型肝炎(CHB)患者发生YMDD基因变异的情况。方法61例HBsAg(+)HBeAg(+)HBcAb(+)HBVDNA(+)CHB患者接受拉米夫定治疗一年,采用荧光定量PCR法检测其血清HBVDNA含量,ELISA法检测血清乙肝五项标志物,动力学法检测血清谷丙转氨酶(ALT)含量。HBVYMDD基因变异采用荧光PCR法进行检测。结果61例CHB患者经拉米夫定治疗一年后HBV-DNA阳性率降至34.4%(21/61),YMDD基因变异发生率18.0%(11/61),分析YMDD基因变异类型:4例为混合变异,其中3例为YMDD+YIDD,1例为YMDD+YVDD;7例为完全变异,其中5例为YIDD,2例为YVDD。变异患者组无1例出现HBeAb血清学转换,血清HBVDNA含量106.6±0.8(copies/ml),明显高于HBVDNA(+)无变异组(P<0.05),ALT含量123.8±53.8(U/L),明显高于HBVDNA(-)无变异组(P<0.01)。结论YMDD基因变异CHB患者HBVDNA均反跳,伴有ALT升高,及时了解CHB患者有无YMDD基因变异对避免造成患者不必要的经济负担、指导临床合理用药具有重要意义。荧光PCR法用于检测YMDD基因变异,具有经济实用、自动化程度高、简便快捷的优点。     

荧光PCR法检测乙型肝炎病毒YMDD基因变异的研究

目的探讨荧光PCR法在检测酪氨酸-蛋氨酸-天门冬氨酸-天门冬氨酸(YMDD)基因变异上的临床应用价值及其拉米夫定治疗一年慢性乙型肝炎(CHB)患者发生YMDD基因变异的情况.方法61例HBsAg(+)HBeAg(+)HBcAb(+)HBVDNA(+)CHB患者接受拉米夫定治疗一年,采用荧光定量PCR法检测其血清HBVDNA含量,ELISA法检测血清乙肝五项标志物,动力学法检测血清谷丙转氨酶(ALT)含量.HBV YMDD基因变异采用荧光PCR法进行检测.结果61例CHB患者经拉米夫定治疗一年后HBV-DNA阳性率降至34.4%(21/61),YMDD基因变异发生率18.0%(11/61),分析YMDD基因变异类型:4例为混合变异,其中3例为YMDD+YIDD,1例为YMDD+YVDD;7例为完全变异,其中5例为YIDD,2例为YVDD.变异患者组无1例出现HBeAb血清学转换,血清HBVDNA含量1066±0.8(copies/mi),明显高于HBVDNA(+)无变异组(P＜0.05),ALT含量123.8±53.8(U/L),明显高于HBVDNA(-)无变异组(P＜0.01).结论YMDD基因变异CHB患者HBVDNA均反跳,伴有ALT升高,及时了解CHB患者有无YMDD基因变异对避免造成患者不必要的经济负担、指导临床合理用药具有重要意义.荧光PCR法用于检测YMDD基因变异,具有经济实用、自动化程度高、简便快捷的优点.