Variability of the E2/NS1 region of Swedish hepatitis C virus strains and its correlation to genotypes.
Serum RNA was extracted from 5 Swedish patients infected with hepatitis C virus (HCV). The N-terminal part of the genomic region coding for the gp70 (E2/NS1), including the hypervariable domain of the E2 protein, was reverse transcribed and amplified by the polymerase chain reaction (PCR) using biotinylated primers. The amplicon was immobilized on magnetic polystyrene beads coated with streptavidine. Solid-state sequencing was carried out on the bound single-stranded DNA, after denaturation. The results of phylogenetic sequence analysis and calculated ratios of transition and transversion mutations showed that 4 of the strains clustered together with the USA prototype strains HCV-1 and HCV-H (genotype I), while 1 strain was close to the Japanese isolate HCV-J, and particularly to isolate HCV-BK (genotype II). Possible antigenic epitopes in the Swedish strains were mapped in the HVR region.
Johansson
B
B
Department of Virology, Stockholm County Council, Sweden.
Yun
Z B
ZB
Sönnerborg
A
A
D000595:Amino Acid Sequence; D001483:Base Sequence; D014644:Genetic Variation; D005838:Genotype; D016174:Hepacivirus / Q000235:genetics* / Q000276:immunology; D006801:Humans; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D012367:RNA, Viral / Q000097:blood / Q000235:genetics; D017422:Sequence Analysis, DNA; D013548:Sweden; D014764:Viral Proteins / Q000235:genetics*
D012367:RNA, Viral; D014764:Viral Proteins