Genotyping HCV isolates from Italy by type-specific PCR assay in the core region

Res Virol. Jul-Aug 1998;149(4):209-18. doi: 10.1016/s0923-2516(98)80002-2.

Abstract

A revision of the polymerase chain reaction (PCR) core procedure was performed for genotyping hepatitis C virus (HCV) in 139 patients from Italy. This procedure, developed prior to the identification of new genotypes, may be inadequate in several geographical areas. We proposed a new typing mixture in which primers for types 2c and 4, that are reported to be circulating in Italy, were added and a primer for type 2b was substituted. Using the modified procedure, 139 HCV-positive patients were analysed. The HCV genotype was identified in 96.4% of the cases. We observed double infections and unclassified genotypes in 5 (3.6%) and 5 (3.6%) patients, respectively. The classification of isolates into genotypes and subtypes 2b, 2c and 4 was confirmed by sequence analysis. Furthermore, the efficiency and accuracy of the modified core procedure were evaluated by parallel testing of 107 out of 139 samples using the line probe assay, and demonstrated a 98.9% degree of concordance. The results demonstrated the specificity of the selected primers for type 2c, 2b and 4 and confirmed the circulation of types 2c and 4 in Italy. In conclusion, the proposed modified PCR procedure is the only primer-specific PCR genotyping method available for identification of the 2c and 4 genotypes reported to be circulated in Italy and other European countries.

MeSH terms

  • 5' Untranslated Regions / genetics
  • Adult
  • Base Sequence
  • DNA Primers
  • Female
  • Genotype
  • Hepacivirus / classification*
  • Hepacivirus / genetics*
  • Hepacivirus / isolation & purification
  • Hepatitis C / epidemiology
  • Hepatitis C / virology*
  • Humans
  • Italy / epidemiology
  • Male
  • Molecular Sequence Data
  • Polymerase Chain Reaction / methods*
  • Retrospective Studies
  • Sequence Analysis, DNA
  • Species Specificity
  • Viral Core Proteins / genetics*

Substances

  • 5' Untranslated Regions
  • DNA Primers
  • Viral Core Proteins
  • nucleocapsid protein, Hepatitis C virus

Associated data

  • GENBANK/AJ222665
  • GENBANK/AJ222666
  • GENBANK/AJ222668
  • GENBANK/AJ222669
  • GENBANK/AJ222670
  • GENBANK/AJ222671
  • GENBANK/AJ222672
  • GENBANK/AJ222673
  • GENBANK/AJ222674
  • GENBANK/AJ222675
  • GENBANK/AJ222676
  • GENBANK/AJ222677
  • GENBANK/D31974
  • GENBANK/D31994
  • GENBANK/L38319
  • GENBANK/L38321
  • GENBANK/L38322
  • GENBANK/L38324
  • GENBANK/L38325
  • GENBANK/L38326
  • GENBANK/L38328
  • GENBANK/L38329
  • GENBANK/L38330
  • GENBANK/V10211
  • GENBANK/Y09368
  • GENBANK/Y09369
  • GENBANK/Y09370