Genomic typing of hepatitis C viruses from Korean patients : implications of genome variation in the E2/NS1 region

Abstract

Comparative nucleotide sequence studies of a 2.4-kb cDNA fragment (nt -49 to 2361) of Korean-type hepatitis C virus (HCV) were carried out. The nt sequences of the Korean HCV isolates have stronger sequence homologies with type II HCV (Japanese HCV-BK) than with types I (HCV-1) or III (HCV-6). In addition, the nt sequences of a part of the core region of ten different samples confirmed that prevalent HCV in Korea belongs to type II with the exception of one sample which belongs to type III. The nt sequence of a cDNA fragment of E2/NS1 region of HCV, from six different serum samples, which comprises the hypervariable regions-1 (HVR-1) and -2 (HVR-2), revealed sequence heterogeneity with type II HCV (75.4 to 80.7% nt homology and 75.5 to 79.7% amino acid homology). However, it was relatively well conserved among the Korean isolates, in fact, aa sequences of HVR-2 as well as HVR-1, converged into two groups. Also we found consensus sequences (T.V.G..AGRTT.G..SLE......K) in HVR-1. Thus, we propose that the conserved patterns in HVR-1 and -2 are characteristics of the six different Korean isolates.