GENOTYPE DETERMINATION OF HEPATITIS-C VIRUS FROM NORTHERN INDIA - IDENTIFICATION OF A NEW SUBTYPE

Hepatitis C virus (HCV) shows substantial nucleotide sequence diversit y distributed throughout the viral genome, with many variants showing only 68-79% overall sequence homology. This has led to problems in dia gnosis of HCV using commercial immunoassays. Based on clustering of ho mologous sequences, various genotypes and subtypes of HCV have been de scribed from different geographical regions. In the present study, 11 isolates from India were genotyped using sequence comparison for part of the nonstructural (NS5) and structural (core) regions. Parts of the genome covering 451 bp (nt 9-459) of the core gene and a 249 bp fragm ent (nt 7959-8207) of the NS5 gene were reverse transcribed and amplif ied using nested polymerase chain reaction (RT-PCR). The amplified fra gments were cloned and sequenced. The classification into genotypes wa s done on the basis of phylogenetic analysis. Four isolates showed seq uence homology to type 1b. Two of the isolates were classified as type 3a. One isolate was classified as type 3b and the remaining four isol ates were found to be variants of type 3 but did not belong to any des ignated subtype. On the basis of phylogenetic analysis two of the uncl assified isolates were put into a new subtype of 3 named as 3g. In one of these variants, parts of a 5'-noncoding (5' NCR; 204 bp), envelope -E1 (435 bp), and NS3 (502 bp) regions were also amplified, cloned, an d sequenced. This study demonstrates the type 3 variants including a n ew subtype (3g) to be the major cause of HCV infection in India. (C) 1 996 Wiley-Liss, Inc.