Quantitative detection of hepatitis C virus RNA by polymerase chain reaction and dot blot hybridization

We have developed a new technique to quantify hepatitis C virus (HCV)-RNA using polymerase chain reaction (PCR) and dot blot hybridization. PCR was performed on 10-fold dilutions of an HCV-cDNA fragment for various numbers of cycles and on various serum volumes for 30 cycles. The resulting PCR products were spotted onto nitrocellulose filters and hybridized with a³²P-labelled internal probe. The intensity of the hybridization signal was proportional to the quantity of template cDNA and increased in proportion to the number of PCR cycles. Clear signals were detected after 30 cycles of PCR using an original serum volume of greater than 250 pl. Thus, this new technique allows the quantitation of HCV-RNA, and as it is simple and cost-effective, it promises to have many clinical applications.     

Mother-to-child transmission of hepatitis C virus detected by nested polymerase chain reaction.

Serum samples from eight pregnant women and their offspring were studied by nested polymerase chain reaction (PCR) for detection of hepatitis C virus (HCV) RNA to evaluate mother-to-child transmission of this virus. The mothers were all infected with human immunodeficiency virus (HIV); none showed symptoms of HCV infection. Anti-HCV antibodies were tested for by recombinant immunoblot assay. HCV viral sequences were found in five of the mothers and four of eight children, three of them at birth. Viremia was persistent in one infant who had chronic transaminase elevation and persistently remained anti-HCV-positive. The other three babies had intermittent viremia; all were asymptomatic and lost anti-HCV antibodies during follow-up. This loss of antibodies was also observed in PCR-negative infants. Thus, these results demonstrate transmission of HCV from mother to child by women coinfected with HCV and HIV. They indicate the usefulness of PCR for direct and early detection of HCV viremia in neonates.     

应用竞争性荧光定量聚合酶链反应检测乙型肝炎病毒DNA

目的:建立竞争性荧光定量聚合酶链反应(CFQ-PCR),并探讨CFQ-PCR在乙型肝炎病毒(HBV)临床检测中的意义.方法:根据HBV病毒adr亚型基因组序列合成一对HBV特异的引物,和一条特异的TaqMan探针;根据上述引物序列,采用分子克隆技术制备内对照DNA;再根据内对照序列合成一条内对照DNA特异的与上述TaqMan探针不同标记的TaqMan探针;将适量的内对照DNA加入到PCR反应体系中,使其与HBV靶序列共扩增.结果:在30μL CFQ-PCR反应体系中,加入约20拷贝内对照DNA能够稳定地获得共扩增曲线;经琼脂糖凝胶电泳分析,加入约100-500拷贝内对照DNA能够有效地获得共扩增产物条带信号;在210个临床HBsAg阳性血清标本的CFQ-PCR扩增中识别出8个未能有效扩增的标本,60份HBsAg阴性血清标本中识别出2个内对照未能有效扩增的标本,后经DNA纯化处理,上述全部标本的内对照均获得阳性扩增结果,其中有7个HBsAg阳性血清标本获得HBV DNA扩增阳性结果.结论:CFQ-PCR能够有效地提示临床标本HBV DNA体外扩增时由于扩增失败导致的假阴性,适合临床推广应用.     

Hepatitis C virus genotypes and hepatic fibrosis regulate 24-h decline of serum hepatitis C virus RNA during interferon therapy in patients with chronic hepatitis C

BACKGROUND AND AIMS: Recently, hepatitis C virus (HCV) dynamics during interferon (IFN) therapy have been studied in detail. We examined factors that regulate the viral kinetics and the relationship between the viral kinetics and clinical effect of IFN therapy. METHODS: Eighty-eight patients with chronic hepatitis C entered this study. All patients had been treated with 3 MU of IFN-beta twice a day for the first 2-4 weeks, then IFN-alpha for the next 20-22 weeks (three injections per week). The levels of serum HCV RNA were determined by Amplicor HCV Monitor version 1.0, before and 24 h after the first injection of IFN; then the decline of HCV was calculated. Liver inflammation and fibrosis were scored as 0 (none), 1 (mild), 2 (moderate) or 3 (severe) using biopsy specimens. RESULTS: The decline of serum HCV RNA was 1.42 +/- 0.65 log copies/mL in genotype 1b and 1.83 +/- 0.72 in genotype 2a or 2b (P < 0.01). By a logistic regression model, genotype (1b, 2a or 2b) and hepatic fibrosis (0 or 1, 2 or 3) associated with 24-h decline of serum HCV RNA, independently. As the predictor of IFN therapy, the decline of serum HCV RNA and serum HCV RNA levels before IFN therapy were the independent significant factors (P < 0.001). CONCLUSIONS: The decline of serum HCV RNA during the first 24 h of IFN therapy was regulated by genotypes and hepatic fibrosis. The decline of serum HCV RNA and initial HCV load were independent factors that can be the predictor of the subsequent sustained viral response to IFN therapy.     

Factors useful in predicting the response to interferon therapy in chronic hepatitis C

To determine how various factors influence the response to interferon (IFN) therapy, we retrospectively studied 157 consecutive Japanese patients with chronic hepatitis C who received various treatment schedules of IFN. They were divided into two groups on the bases of outcome. One group was comprised of 65 patients who achieved a sustained normalization of serum alanine aminotransferase (ALT) levels for at least 6 months after treatment, while the other group was comprised of 84 patients with persistent elevation of serum ALT levels, despite treatment. Genotyping of hepatitis C virus (HCV) was done by polymerase chain reaction (PCR) with genotype specific primers, analysing the variations in nucleotide sequence within the NS 5 region of the HCV genome, namely genotypes PT, K1, K2a and K2b. We then used a multivariate analysis to determine the factors related to mode of treatment, patient characteristics and HCV genotype in relation to the response to IFN therapy. Of the 16 factors analysed, the HCV genotype (genotype K2a or K2b, P < 0.0008), treatment schedule (intermittent administration following a daily schedule, designated as combined schedule, P > 0.0014) and liver histology just before treatment (chronic persistent hepatitis or mild chronic aggressive hepatitis, P < 0.0324) were the most strongly correlated with a normalizing response to IFN therapy. These results suggest that not only are the IFN treatment schedule and patient profile significant, but the properties of the virus also influences the response. However, as the IFN treatment schedule is the only changeable factor, it should be designed to maximize the benefit of IFN therapy.     

Comparison of real-time quantitative polymerase chain reaction with three other assays for quantitation of hepatitis C virus

BACKGROUND AND AIMS: Evaluation of serum levels of hepatitis C virus (HCV) is important for predicting the response to interferon treatment and monitoring its therapeutic efficacy. The aim of this study was to evaluate real-time quantitative polymerase chain reaction (PCR) as a method for the measurement of HCV-RNA. METHODS: The subjects were 50 patients with chronic hepatitis C: 36 with genotype 1b, eight with genotype 2a, and six with genotype 2b. Samples were tested for HCV-RNA by using real-time quantitative PCR with the ABI Prism 7700 sequence detection system, a branched DNA signal amplification assay, and an Amplicor monitor test; and for HCV core protein by using a fluorescent enzyme immunoassay. RESULTS: The detection range of the real-time quantitative PCR was between 10(1)-10(8) copies/mL of HCV-RNA. Hepatitis C virus RNA was detectable in all 50 samples by the use of real-time quantitative PCR, but was undetectable in 14 samples by the use of a branched DNA assay and in two samples by using the Amplicor monitor test; HCV core protein was undetectable in three samples. A significant correlation was found between the results of real-time quantitative PCR and those of the three other assays: branched DNA assay (r = 0.837, P < 0.0001), Amplicor monitor test (r = 0.853, P < 0.0001), and HCV core protein concentrations (r = 0.549, P < 0.0001). CONCLUSIONS: Our results showed that the real-time quantitative PCR was a highly sensitive assay for the measurement of HCV-RNA.     

Detection of hepatitis C virus RNA by nested polymerase chain reaction in sera of patients with chronic non-A, non-B hepatitis treated with interferon.

To evaluate the effect of interferon-alpha treatment on the levels of serum aminotransferase (sALT) and of hepatitis C virus (HCV)-RNA, we studied 19 patients with chronic non-A, non-B (NANB) hepatitis. Before therapy, 14 patients were positive by nested polymerase chain reaction (PCR) with primers deduced from the 5'-non-coding region of the HCV genome. Serum HCV-RNA had disappeared in 12 (85.7%) of them by the end of therapy, but then reappeared 6 months later in 4 of these 12 patients. A marked improvement in sALT was seen in 5 of the 8 patients with sustained HCV-RNA disappearance, but not in the 4 patients with only transient HCV-RNA negativity. Pre-treatment levels of hepatitis C viremia, analyzed by single PCR and dot blot hybridization, ranged from 2 x 10(3) to 2 x 10(8) copies/ml, and were below 2 x 10(5) copies/ml in patients with a complete response to interferon therapy. These results suggest that this HCV-RNA assay, combined with sALT testing, may be useful for estimation of the long-term efficacy of interferon therapy in hepatitis C.     

Evaluation of multiplex nested polymerase chain reaction for routine hepatitis C virus genotyping in egyptian patients

Background

At least six HCV (hepatitis C virus) genotypes are unequally distributed worldwide. HCV genotyping guides the selection of treatment regimens and provides important epidemiological markers that enable the outbreak source to be traced and the spread of disease to be controlled. In Egypt, there is an increasing need for cost-effective, fast, and easily performable HCV genotyping assays.Recently, a multiplex PCR assay was developed to determine HCV genotypes. It employs genotype-specific primers, based on sequences of the entire core region and part of the 5’UTR of the genome.

Objectives

In this study, we compared a simple, new, modified multiplex PCR system for HCV genotyping with a commercially available line probe assay (INNO-LiPA) that is based on reverse hybridization.

Patients and Methods

Serum samples from chronic HCV Egyptian patients (n = 73) were genotyped using the modified multiplex PCR assay, and genotypes were verified using the INNO-LiPA HCV II assay.

Results

The modified multiplex PCR method was able to type HCV-4 in 65 of 70 typeable samples (92.86%) and had 100% concordance with the INNO-LiPA assay.

Conclusions

Genotype 4 was the most prevalent genotype in our study. Based on our results, the modified multiplex nested PCR assay is a sensitive and inexpensive alternative for HCV genotyping and can be used in routine diagnostic laboratories. INNO-LiPA may be useful as a second-line assay for genotyping samples that are indeterminate by multiplex PCR. This approach will effect better treatment optimization and a reduction of the spread of HCV.     

Predicting interferon therapy efficacy from hepatitis C virus genotype and RNA titer

We classified 53 Japanese patients with chronic hepatitis C who were treated with natural interferon- into genotypes and also tested the amounts of hepatitis C virus (HCV) RNA. The rate of the long-term complete response group, whose alanine aminotransferase levels remained within the normal range during the six months after therapy, was significantly higher (P<0.01) in the type-III patients (4/5, 80.0%) than in type-II patients (4/43, 9.3%). For these long-term complete responders, the amounts of HCV RNA was less than 10⁷ copies/ml serum in type-II patients, whereas two type-III patients with relatively high amounts of HCV RNA responded completely. These results confirm that the genotype of HCV is an important factor for predicting the response to interferon therapy. The amounts of HCV RNA can also predict its efficacy in type-II patients.This work was supported by a Grant-in-Aid from the Ministry of Education, Science and Culture, Japan, and the Research Group of Intractable Hepatitis sponsored by the Ministry of Health and Welfare of Japan.     

Screening blood donations for hepatitis C virus by polymerase chain reaction

BACKGROUND AND OBJECTIVES: The contamination of blood components by bacteria is an adverse event, which, although very uncommon, has an exceptionally high mortality rate. CASE REPORT: A patient suffering from terminal adenocarcinoma of the ovary received a red blood cell unit. During the transfusion, the patient developed fever. Cultures of both the patient's blood and the blood unit were done, and she was treated with antibiotics. Forty-eight and seventy-two hours after the transfusion, Candida parapsilosis grew in the blood cultures of the red blood cell bag and of the patient. The infection was controlled with amphotericin. The patient died from cancer progression. CONCLUSIONS We describe the first case of transfusion-associated sepsis caused by C. parapsilosis.     

丙型肝炎病毒聚合酶链反应直接序列分析方法的建立及应用(英文)

目的探讨快速完成丙型肝炎病毒ｃＤＮＡ（ＨＣＶｃＤＮＡ）序列分析的方法．方法将聚合酶链反应（ＰＣＲ）扩增与核酸序列分析技术相结合，以ＰＣＲ产物为测序模板，以ｒ３２ＰＡＴＰ标记ＰＣＲ扩增引物为测序引物，用ｔａｑＤＮＡ聚合酶直接测序．结果以琼脂糖或聚丙烯酰胺凝胶电泳回收ＰＣＲ产物制备测序模板可获得最佳测序效果．在需要测定大量标本时，为进一步简化操作步骤，可降低套式ＰＣＲ中第一次扩增反应的ｄＮＴＰ与引物浓度，以第一次ＰＣＲ扩增产物为模板，也可得到较好的测序结果。ＰＥＧ沉淀回收法不能去除非特异性ＰＣＲ产物，对ＰＣＲ直接测序有一定影响．采用此方法首次在一株ＨＣＶＮＳ５ｂ区发现一个新的缺失突变．结论ＰＣＲ直接序列分析是一种简便，快速，经济有效的核酸序列分析方法，适用于丙型肝炎病毒基因组的分析研究．     

乙型肝炎病毒共价闭合环状DNA套式-实时荧光定量聚合酶链反应的建立

目的 建立检测HBV共价闭合环状DNA(cccDNA)的套式一实时荧光定量PCR法.方法 根据HBV cccDNA与松环DNA(rcDNA)结构上的差异,设计2对跨缺口的特异引物及1条位于负链缺口下游的特异TaqMan荧光探针.根据Plasmid-SafeTM ATP-Dependent Dnasc(PSAD)对rcDNA与cccDNA作用的不同,对模板DNA进行酶切纯化,降解reDNA,再进行套式PCR扩增,先用外引物和模板进行第一轮常规PCR,再用内引物、荧光探针和第一轮PCR产物进行实时荧光定量PCR,根据阳性参照标准品,得出待检标本定量值.结果 检测阳性参照标准品.得出该方法灵敏度可达2 lg拷贝/mL.用上述方法检测34份乙型肝炎患者血清HBV DNA阳性标本,25份血清HBVcccDNA阳性,28份外周血单个核细胞HBV cccDNA阳性.27份健康对照者血清HBV DNA阴性标本,6份HBV cccDNA阳性.对5份HBV cccDNA阳性标本扩增产物进行克隆测序,无碱基缺失、突变.与HBV不同基因型序列(A～G)比较,同源性为90.6%～99.1%,其中,与B、C基因型同源性为95.3%～99.1%,验证了方法的特异度.结论 套式-实时定量PCR法可检测乙型肝炎患者血清、PBMC中的HBV CCCDNA,且具有敏感、特异性.     

Biochemical and structural analysis of the NS5B RNA-dependent RNA polymerase of the hepatitis C virus

Hepatitis C virus (HCV), the major causative agent of chronic and sporadic non-A, non-B hepatitis worldwide, is a distinct member of the Flaviviridae virus family. These viruses have in common a plus-strand RNA genome that is replicated in the cytoplasm of the infected cell via minus-strand RNA intermediates. Owing to the lack of reliable cell culture systems and convenient animal models for HCV, the mechanisms governing RNA replication are not known. As a first step towards the development of appropriate in vitro systems, we expressed the NS5B RNA-dependent RNA polymerase (RdRp) in insect cells, purified the protein to near homogeneity and studied its biochemical properties. It is a primer- and RNA template-dependent RNA polymerase able to copy long heteropolymeric templates without additional viral or cellular cofactors. We determined the optimal reaction parameters, the kinetic constants and the substrate specificity of the enzyme, which turned out to be similar to those described for the 3D polymerase of poliovirus. By analysing a series of nucleosidic and non-nucleosidic compounds for their effect on RdRp activity, we found that ribavirin triphosphates have no inhibitory effect, providing direct experimental proof that the therapeutic effect observed in patients is not related to a direct inhibition of the viral polymerase. Finally, mutation analysis was performed to map the minimal NS5B sequence required for enzymatic activity and to identify the 'classical' polymerase motifs important for template and NTP binding and catalysis.