Comparison of hepatitis C virus genotyping by 5' noncoding region- and core-based reverse transcriptase PCR assay with sequencing and use of the assay for determining subtype distribution in India.

Phylogenetic analysis of the sequences of the 5' noncoding regions (5'NCR) of 149 samples from hepatitis C virus (HCV) RNA-positive chronic carriers representing northern, southern, eastern, and western India showed that type 3 and type 1 are the predominant genotypes circulating in India, with an overall prevalence of 53.69 and 38.25%, respectively. Type 4 viruses (6.04%) were seen only in southern India. Sequence analysis of the core region of 51 of the above isolates enabled us to classify them further into subtypes as 1b (number of isolates [n] = 10), 1a (n = 6), 3a (n = 9), 3g (n = 14), 3f (n = 1), and 4d (n = 3). Three new subtypes were identified for the first time and designated as 3i (n = 5), 3j (n = 2), and 6l (n = 1). Sequencing the 5'NCR could differentiate HCV types, whereas classification at the level of subtype was possible with sequence analysis of the core region.