A second-generation method of genotyping hepatitis C virus by the polymerase chain reaction with sense and antisense primers deduced from the core gene

Virology of hepatitis C virus

Advances in molecular biology techniques have allowed the cloning of HCV and the characterization of this virus. This article provides a short summary of our current knowledge on the genomic organization of HCV, the implications of its genetic heterogeneous nature, and the probable replication strategy of this virus.

Genotyping of hepatitis C virus isolates from Saudi patients by analysis of sequences from PCR-amplified core region of the virus genome

We investigated the genotype distribution of hepatitis C virus (HCV) among Saudi patients with chronic hepatitis C. Serum specimens from 119 native Saudi Arabian patients with chronic hepatitis C, as documented by serology and polymerase chain reaction (PCR) for HCV RNA, were used. Genotyping was performed by reverse transcription-PCR, using specific primers at the core region of HCV genome, and DNA sequencing of the resultant amplicons. It was found that the majority of samples (47.9%) belong to genotype 4, followed by subtype 1b (16.8%), and subtype 1a (10.1%). Twenty samples (16.8%) were not able to be typed by our method. We confirmed the results by cloning at least one PCR amplicon from each genotype, and determining the nucleotide sequence of the clones. Our findings suggest that genotype 4 is the most common among native Saudi Arabian patients with chronic hepatitis C infection. Genotypes 1b and 1a were also prevalent.

Infection with GB virus C and hepatitis C virus in drug addicts, patients on maintenance hemodialysis, or with chronic liver disease in Nepal

Infection with GB virus C (GBV-C) and hepatitis C virus (HCV) was surveyed in various populations in Kathmandu, Nepal. GBV-C RNA and HCV RNA were detected in four (2%) and none, respectively, of 181 normal controls. Viral RNAs were detected significantly more frequently (P < 0.001) in 32 (44%) and 43 (60%), respectively, of 72 users of illicit intravenous drug, and in three (14%) and one (5%) of 22 patients on maintenance hemodialysis. The three hemodialysis patients with GBV-C RNA had been transfused with more blood units than the 19 without GBV-C RNA (51 +/- 21 vs. 5 +/- 3 units, P < 0.01), and one was co-infected with HCV. Of 145 patients with chronic liver disease, GBV-C RNA was detected in four (3%) and HCV RNA in 12 (8%); only one patient with GBV-C RNA was without markers of HCV or hepatitis B virus infection. In the 32 drug addicts infected with GBV-C, genotypes were G1 in two (6%), G2 in 26 (81%), G3 in three (9%), and the remaining one (3%) was coinfected with G2 and G3. GBV-C genotypes in the 13 individuals in the populations other than drug addicts were G2 in 11 (85%) and G3 in two (15%). HCV genotypes in the 43 drug addicts with viremia were l/1a in 21 (49%), V/3a in 19 (44%) and l/1a plus V/3a in two (5%); these genotypes were not prevalent in normal controls and patients with chronic liver disease in Nepal. These results indicate that GBV-C infection is prevalent in healthy subjects in Nepal at a frequency (2%) comparable with those in the other countries and that GBV-C transmits efficiently by intravenous drug abuse among drug addicts and by transfusion in hemodialysis patients.

Comparative evaluation of five rapid methods for identifying subtype 1b and 2c hepatitis C virus isolates

A panel of 61 HCV isolates belonging to five different subtypes were used to evaluate five methods for rapid typing of HCV RNA: an in-house type-specific polymerase chain reaction based on the core region (type-specific PCR), a commercial amplification of the core region followed by hybridisation to probe coated wells (DEIA), a commercial amplification of the 5'-UTR region followed by hybridisation to probes immobilised on strips (LiPA), an in-house restriction fragment polymorphism analysis of the 5'UTR (RFLP), and a commercial serological method using synthetic peptides from the NS4 region (serotyping). The correct viral type was identified in 90% of cases by DEIA, in 82% of cases by type-specific PCR, in 80% of cases by LiPA and RFLP, and in 67% of cases by serotyping. Correct identification of the virus subtype was much less frequent and was beyond the performance characteristics of some assays. Major problems were found in the identification of isolates belonging to type 2. This was probably at least partly due to the fact that all type 2 isolates in the viral panel were of subtype 2c, which has been considered rare until recently.

Infection with GB virus C and hepatitis C virus in hemodialysis patients and blood donors in Beijing

RNAs of GB virus C (GBV-C) and hepatitis C virus (HCV) were sought by reverse-transcription polymerase chain reaction with nested primers deduced from the 5' untranslated region: 79 patients on maintenance hemodialysis, 205 commercial blood donors, and 205 voluntary donors in Beijing were studied. GBV-C RNA was detected in 43 (54%) patients and 17 (8%) commercial donors, and HCV RNA in 43 (54%) patients and 13 (6%) commercial donors, respectively. By contrast, GBV-C RNA was detected only in 2 (1%) and HCV RNA in none among 205 volunteer blood donors serving as controls. Thus both patients and commercial blood donors were at higher risk for infection with GBV-C (P < 0.001) than controls. HCV RNA was detected more often in patients with GBV-C RNA than without (29/43 or 67%, vs. 14/36 or 39%, P < 0.05) as well as in commercial donors with GBV-C RNA than without (5/17 or 29% vs. 8/188 or 4%, P < 0.01). A phylogenetic tree constructed on a sequence of 100 base pairs in the helicase region indicated that GBV-C isolates from Beijing are more similar to Japanese isolates than to isolates from the United States and Africa. Sequences from certain hemodialysis patients and those from some commercial donors were similar, suggesting nosocomial infection and spread among restricted groups.

Genotyping hepatitis C virus isolates from Spain, Brazil, China, and Macau by a simplified PCR method

An improved and simplified method of genotyping was developed for classifying hepatitis C virus (HCV) isolates into the five common genotypes, i.e., I/1a, II/1b, III/2a, IV/2b, and V/3a, by PCR with genotype-specific primers deduced from the core gene. Sense and antisense primers, specific for each of the five common genotypes, were designed by comparison of 319 core gene sequences from HCV isolates of various genotypes from genetic groups 1 to 9. In the first round of PCR, a sequence of 433 bp representing nucleotides 319 to 751 was amplified with universal primers. The second round of PCR was performed with respective sense and antisense primers in two separate reactions, one for the amplification of genotypes I/1a and II/1b and the other for the amplification of genotypes III/2a, IV/2b, and V/3a. The specificity of genotyping was confirmed with a panel of 191 serum samples containing HCV isolates whose core gene sequences were known: 110 serum samples infected with HCV of the five common genotypes and 81 serum samples infected with HCV of other genotypes. The use of sense and antisense primers for genotype II/1b (primers 389 and 492) abolished the cross-reaction of the antisense primer for genotype II/1b (primer 133) with some HCV isolates of genotype I/1a found by our original method. The new method was used for genotyping 130 HCV isolates from Spain, 53 from Brazil, 106 from China, and 30 from Macau. A total of 329 bp of the NS5b region (nucleotides 8279 to 8607) of five isolates from Spain and five isolates from Macau which could not be classified as any of the five common HCV genotypes or genotype 2c were sequenced, and the sequences were compared with those of HCV isolates of known genotypes; two isolates from Spain were deduced to be of genotype 4d and one was deduced to be of genotype 1d, while the remaining two isolates from Spain had novel genotypes in genetic group 2; however, all five isolates from Macau were of genotype 6a.

Prevalence of hepatitis C virus and distribution of its genotypes in Northern Eurasia

We tested hepatitis C virus (HCV) antibody in 4216 sera collected from healthy people living in European part of Russia (including Northern, North-Western, Central, Central-Blacksoil, Volga-Vyatka, Volga, and North-Caucasian regions), non-European part of Russia (the Urals, East-Siberia, and the Far-East regions) and Mongolia. Prevalence of HCV antibody varied significantly by regions, ranging from 0.7% in Central region of European part of Russia to 10.7% in Mongolia. Genotyping of HCV (into 1a, 1b, 2a, 2b, and 3a) was performed on 469 sera from blood donors and patients (in Russia, Moldova, Turkmenistan, and Mongolia) who were positive for both HCV antibody and RNA. Genotype 1b was the most dominant genotype irrespective of regions (68.9%), with the highest rate in Moldova (96%). HCV unclassifiable into genotypes 1a-to-3a was found in 28 (6.0%) samples: particularly 4 of 10 samples from Lipetzk were untypable. Overall, HCV genotypes in European part of Russia were more similar to those in European countries, while those in Eastern part of Russia more similar to China or Japan. Genotype distribution was not associated with the clinical expression of HCV disease: acute hepatitis, chronic hepatitis or liver cirrhosis.

Full-length genomic sequence of a hepatitis C virus genotype 2c isolate (BEBE1) and the 2c-specific PCR primers

We sequenced the entire genome of an Italian isolate of hepatitis C virus: the first full-length sequence for the genotype 2c. We report hereby its characteristics and differential detection of 2c isolates using PCR.