Variable and hypervariable domains are found in the regions of HCV corresponding to the flavivirus envelope and NS1 proteins and the pestivirus envelope glycoproteins

Importance of primer selection for the detection of hepatitis C virus RNA with the polymerase chain reaction assay

We compared four primer sets from conserved regions of the hepatitis C virus (HCV) genome for their ability to detect HCV RNA in a "nested" cDNA polymerase chain reaction assay on sera from 114 anti-HCV antibody-positive individuals from around the world. The different primer sets had equivalent sensitivity, detecting less than 1 chimpanzee ID50 (dose that infects 50%) when tested against reference strain H of HCV. We tested equal amounts of RNA extracted from the serum of each individual with the four primer sets. The set derived from two highly conserved domains within the 5' noncoding (NC) region of the HCV genome, which also share significant similarity with Pestivirus 5' NC sequences, was the most effective at detecting HCV RNA. All samples positive for HCV RNA with any other primer set were also positive with the primer set from the 5' NC region, and the latter was at least 3 times more likely to detect HCV infection than a primer set from within the nonstructural protein 3-like gene region (P less than 0.001). We had no false positive results in greater than 500 negative controls interspersed among the test samples. The 5' NC region primer set detected HCV-specific RNA, verified by high-stringency Southern blot hybridization and DNA sequencing, in 100% of 15 acute and 33 chronic non-A, non-B hepatitis patients from the United States, Europe, and Asia and 10 hepatocellular carcinoma patients from Africa and Asia that tested negative for the hepatitis B virus-encoded surface antigen. In conclusion, use of an appropriate primer set is crucial for detecting HCV RNA in the serum of infected individuals.

New developments in hepatitis C

Since the detection of hepatitis B virus (HBV) in the 1960s and hepatitis A virus in the 1970s, a considerable proportion of infections of (probably viral) hepatitis could not be classified. About 90% of transfusion-related hepatitis was identified as non-A/non-B. In 1988 investigators from the Chiron Company (USA) detected the non-A, non-B agent and named it hepatitis C virus (HCV). An anti-HCV antibody assay (ELISA) and subsequently confirmation tests (immunoblot and polymerase chain reaction) were developed. HCV infection results in a chronic carrier state of the virus in about 80%. Almost all HCV carriers have, irrespective of their liver function tests, histologic signs of chronic hepatitis and/or liver cirrhosis. Chronic HCV infection is, like HBV, also associated with the development of hepatocellular carcinoma. Most HCV carriers are infected by parenteral routes (intravenous drug use, blood transfusion, tattooing). Intravenous drug users and haemophilia patients have the highest risk (80-90%) of becoming infected. Sexual and perinatal transmission does not play an important role in spreading the infection. Antiviral therapy (alpha-interferon) in patients with chronic hepatitis C will normalize liver function tests in about 25% of the cases, but it is unclear if the HCV carrier state will disappear and if liver cirrhosis will be prevented. At present no specific immunoglobulin or vaccine preparations are available to prevent the HCV infection.

Discrimination of hepatitis C virus in liver tissues from different patients with hepatocellular carcinomas by direct nucleotide sequencing of amplified cDNA of the viral genome

We investigated the presence of the hepatitis C virus (HCV) genome in liver tissues of eight different patients with hepatocellular carcinoma by using the reverse transcriptase polymerase chain reaction (PCR) method. RNA was extracted separately from cancerous and peripheral noncancerous portions of the liver tissues of each patient. For reverse transcriptase PCR, we used sets of primers derived either from nonstructural region 3 (the NS3 region) or from the nucleocapsid-envelope (C/E) region of the HCV genome. The nucleotide sequences of the amplimers were directly determined without subcloning. Of 16 samples tested, cDNA of the HCV genome was detected in 2 cancerous tissues and in 4 noncancerous tissues by either pair of primers. Nucleotide sequences of HCV cDNA fragments amplified from cancerous and peripheral noncancerous tissues from the same patients were identical. However, 4.4 to 6.3% and 7.5 to 11.3% sequence variation was observed in NS3 and C/E regions, respectively, among cDNA fragments from different patients. The result indicated that the HCV genome detected in a given patient is distinguishable from that in others by a simple direct nucleotide sequencing of the reverse transcriptase PCR products.

Distribution of plural HCV types in Japan

A detection system was developed to distinguish the four different HCV genomes [HCV-J, HCV-US, HCV-K2 and group II HCV (HCV-GII)], involving reverse transcription followed by a nested polymerase chain reaction using specific primers for each HCV type. The putative non-structural (NS) 5 regions of HCV-J, HCV-US and HCV-K2 and the putative NS3 region of HCV-GII were amplified. Of 95 specimens from patients with acute hepatitis, chronic hepatitis, liver cirrhosis or hepatocellular carcinoma, 67 specimens were positive for HCV-J, 2 for HCV-US, 23 for HCV-K2 and 11 for HCV-GII. About half the specimens that were positive for HCV-K2 or HCV-GII were coinfected with HCV-J and all those that were positive for HCV-GII were also positive for HCV-K2. Nucleotide sequence analysis of several amplified cDNA products revealed that HCV-K2 and HCV-GII could each be classified into two groups, and the pattern of classification of HCV-K2 was identical with that of HCV-GII. Therefore, our results strongly suggest that HCV-K2 is the same as HCV-GII.

Genomic structure of the human prototype strain H of hepatitis C virus: comparison with American and Japanese isolates

Genomic RNA from the human prototype strain H of the hepatitis C virus (HCV-H) has been molecularly cloned and sequenced. The HCV-H sequence reported consists of 9416 nucleotides including the 5' and 3' untranslated regions. HCV-H shows 96% amino acid identity with the American isolate HCV-1 but only 84.9% with the Japanese isolates HCV-J and HCV-BK. In addition to the hypervariable region (region V) previously identified in the putative E2 domain, three other variable domains were identified: region V1 (putative E1), region V2 (putative E2), and region V3 (putative NS5). These regions appear rather conserved (86-100%) among the American isolates (HCV-1 and HC-J1) or among various Japanese isolates (HCV-J, HCV-BK, HCV-JH, and HC-J4) but show striking heterogeneity when the two subgroups are compared (42-87.5% amino acid difference). A structural similarity between the 5'-terminal hairpin structure of HCV and of poliovirus was observed. This study further suggests the existence of at least two genomic subtypes of HCV and confirms a distant relationship between HCV and pestiviruses.

Use of a signature nucleotide sequence of hepatitis C virus for detection of viral RNA in human serum and plasma

The nucleic acid sequence of the putative 5'-untranslated (5PUT) region of hepatitis C virus (HCV), determined for samples obtained from a variety of geographic origins, was found to be over 98% conserved among all isolates. On the basis of this signature sequence for HCV, a viral RNA assay was developed by using cDNA synthesis with reverse transcriptase, followed by polymerase chain reaction (PCR). The new assay was compared with the Ortho-Chiron C100-3 HCV enzyme-linked immunosorbent assay to research radioimmunoassays for antibodies to the C33c and C22 HCV antigens and to the first reported set of HCV PCR primers designed from the NS3 domain. Plasma samples from 16 Japanese patients with non-A, non-B hepatitis (NANBH) and 16 immunoassay-positive blood donors from the United States were investigated. The 5PUT PCR primers were found to be superior to the NS3 primers in sensitivity and specificity (15 of 25 versus 3 of 25 of the C100 enzyme-linked immunosorbent assay-positive samples, respectively). Samples from two C100-negative patients with acute NANBH were found to react with the 5PUT primers but not with the NS3 primers. Also, two of three patients with chronic NANBH converted from reverse transcriptase PCR positive to negative after interferon treatment. Although the clinical significance of the presence or absence of HCV RNA in samples from patients is not fully understood, the use of probes and primers from the 5PUT region (as opposed to primers from other segments) should not lead to false-negative results due to nucleic acid sequence variations in viral isolates.

Two French genotypes of hepatitis C virus: homology of the predominant genotype with the prototype American strain

A hepatitis C virus (HCV) cDNA covering part of the nonstructural region, NS3, was amplified from the serum of 50 out of 76 French non-A, non-B hepatitis patients by the nested polymerase chain reaction (PCR). Determination of a 407-bp sequence from four such cases revealed the presence of two different virus genotypes, F1 and F2, which exhibited 19-20% sequence divergence. F1 was represented by three of the four isolates and showed a sequence homology of about 97.5% to the prototype American HCV isolate, but of only 79% to a reported Japanese isolate. In contrast, F2 had 91.6% homology to the Japanese isolate, but only 81% homology to the prototype American HCV. PCR products from the 50 samples were hybridized with labeled F1 and F2 fragments under stringent conditions; results indicated the F1-related strain(s) as the major HCV genotype. Furthermore, a total of 1477 bp of sequence has been determined for one of the isolates belonging to the F1 category. These results will have implications for the PCR detection of HCV infection and production of HCV vaccines, especially for European countries.

Isolation of a complementary DNA fragment of hepatitis C virus in Taiwan revealed significant sequence variations compared with other isolates

To clone and characterize hepatitis C virus strains present in Taiwan, RNA was extracted from liver tissue collected from a patient during the acute phase of posttransfusion non-A, non-B hepatitis. RNA was then subjected to complementary DNA synthesis and the polymerase chain reaction, using primers derived from the original nucleotide sequence of the United States hepatitis C virus strain. A complementary DNA clone, HCV-T3, containing 552 base pairs of hepatitis C virus complementary DNA sequences was isolated and characterized. The homologies in nucleotide sequence between the Taiwan isolate and either the United States or Japan isolate were 80.1% and 91.5%, respectively. However, most of the nucleotide changes occurred in the third base positions, resulting in much higher homologies in amino acid sequence of 91.8% and 97.3%, respectively. Amplification of the less conserved region of hepatitis C virus genome with the polymerase chain reaction was improved by use of primers with nucleotides matched to the local strain. Finally, in addition to the liver and serum, the viral genome was also demonstrated in the spleen tissue by similar methods, suggesting another possible target for hepatitis C viral infection. These findings indicate that there is considerable heterogeneity in hepatitis C virus genomes isolated from different areas of the world.

Gene mapping of the putative structural region of the hepatitis C virus genome by in vitro processing analysis

Processing of the putative structural proteins of hepatitis C virus was examined by using an in vitro expression system. An RNA transcript for cell-free translation was prepared from a cDNA construct that encompasses the region encoding the 980 amino-terminal residues of the viral polyprotein precursor. Processing of the in vitro translation product proceeded cotranslationally in the presence of microsomal membranes and generated four major membrane-associated products. Two of these four major products, named gp35 and gp70, were shown to be transported into microsomes and heavily glycosylated, suggesting that the processing events are partly mediated by the signal peptidase of the endoplasmic reticulum. The other two products, p19 and p21, were probably associated with the outer surface of the microsomal membrane. Analysis of processed proteins translated from a series of truncated forms of the cDNA construct as well as determination of amino-terminal amino acid sequences of gp35 and gp70 indicated that these four products are arranged from the amino-terminal end of the polyprotein precursor in the order: NH2-p22-gp35-gp70-p19. Both gp35 and gp70 could be candidates of initially processed forms of envelope proteins of the hepatitis C virus.

Hepatitis C virus (HCV)-RNA in non-A, non-B chronic hepatitis in France. Nucleotide sequence of a French HCV isolate

The sera of 36 French patients with post-transfusional and sporadic non-A, non-B (NANB) chronic hepatitis were investigated, with a combination of serological and polymerase chain reaction (PCR) assays, for HBV and HCV infections. Eighty-nine percent of the patients were found positive with serological and/or molecular tests. Among the positive patients, 68% (22/32) were found positive for both anti-HCV and HCV-RNA, 16% (5/32) and 16% (5/32) were found positive only for anti-HCV or HCV-RNA, respectively. HBV-DNA sequences were detected in two patients associated to the HCV viraemia. This study confirms the extremely high prevalence of HCV infection in NANB chronic hepatitis in France. It also shows the possible co-infection by HCV and HBV in NANB hepatitis. We have also determined the nucleotide sequence of the 5' non-coding, E1, E2/NS1 and NS3/NS4 regions of a French isolate using the polymerase chain reaction. Comparison of these nucleotide sequences with those available from American and Japanese isolates showed a significant genetic variability. The genetic variability is higher in the E2/NS1 (13 to 33% and 12 to 30% at the nucleic acid and amino acid level, respectively) than in the E1 (10 to 28% and 7 to 21%) and NS3/NS4 (5 to 21% and 2 to 7%) regions. The sequence of the French isolate is more closely related to that of the American HCV prototype than to the Japanese HCV isolates. This study confirms the extent of HCV genetic variability.

Sequence analysis of the putative structural genes of hepatitis C virus from Japanese and European origin

cDNA fragments encoding the putative structural genes of the hepatitis C genome were isolated from a plasma pool of Japanese non-A, non-B hepatitis patients and from sera of individual Spanish patients. From the Japanese plasma pool a series of E1 clones was obtained that showed 88-98% homology among each other, both at the nucleotide and amino acid level. Compared to the sequences published by the Chiron Corporation and Takeuchi et al., the amino acid homology was 75-79% and 91-94%, respectively. Analysis of the core and E2/NS1 genes showed a high conservation of the core sequence and a high sequence variation in the 5' end of the E2/NS1 gene. The E1 gene of one Spanish isolate showed greater homology to the Chiron than to the Japanese sequence. Another Spanish isolate was more homologous to the Japanese sequence indicating that both hepatitis C genotypes are present in Europe. Analysis of the E1 gene of an isolate derived from a single patient with a 5-year interval revealed nine nucleotide and five amino acid changes.

Hepatitis C virus

HepCV is the major cause of NANB PT hepatitis and is also implicated as the cause in a large proportion of sporadic cases of NANBH. Chronic infection with HepCV has also been linked to the development of hepatocellular carcinoma. Chimpanzees and marmosets are the only animals found to be experimentally infectable and the virus has not been propagated in any cell culture system. HepCV is an enveloped virus with a diameter of 30-60 nm and a 10-kb positive-stranded RNA genome. Its genome organization resembles that of the flaviviruses and pestiviruses. A 5'-untranslated segment of 341 nucleotides precedes a continuous ORF of 9030/9033 nucleotides which is followed by a 54 nucleotides long 3'-non-coding segment. Further work is required to resolve the question of whether the genomic RNA possesses a 3'-poly(U) or poly(A) tail. The genome also carries an internal poly(A) segment towards the 5'-end of its ORF. Genomic RNA is probably translated into a single polyprotein of 3010/3011 amino acids which is processed into functional proteins. The viral proteins have not been identified, but on the basis of the predicted amino acid sequences, hydrophobicity plots, location of potential glycosylation sites and similarities of these properties to those of pesti- and flaviviruses, the following genome organization has been predicted. The predicted viral structural proteins, a nucleocapsid protein and two envelope glycoproteins are located at the amino-terminal end of the polyprotein. They are followed by a highly hydrophobic protein and proteins that exhibit proteinase, helicase and replicase domains and thus are probably involved in RNA replication and protein processing. The replicase domain is located close to the carboxy terminus of the polyprotein. Although the overall nucleotide and amino acid homologies between HepCV and pestiviruses are low, a number of similarities exist that point to a closer ancestral relationship to the latter than the flaviviruses. First, the 5'-untranslated segment of the HepCV genome resembles that of the pestivirus genomes in size and presence of several short ORFs and it contains several segments with high nucleotide homology. Second, the two putative envelope glycoproteins of HepCV resemble two of the three putative envelope glycoproteins of the pestiviruses. Because its genome organization and predicted virion structure closely resemble those of the flaviviruses and pestiviruses, HepCV has been proposed to be placed in the family Flaviviridae.(ABSTRACT TRUNCATED AT 400 WORDS)