A score method for comparison of partial genomic regions in their representatives of full-length genome of hepatitis E virus for genotyping.

In this article, a statistical score method for comparison of partial genomic regions in their representatives of full-length genome of hepatitis E virus (HEV) for genotyping was developed. The critical values of the statistics for hypothesis testing were generated through Monte Carlo simulations. It was found that fragment III might be a statistically representative region for the whole genome of HEV for genotyping. Based on both the full-length sequence and fragment III, the same four genotypes were identified by the subsequent phylogenetic analysis, and similar ranges of mean nucleotide difference were also observed to differentiate HEV sequences at the three levels genotype, subtype and isolate, which further verified the statistical results. It may be concluded from this study that the score method is effective for comparing partial genomic regions with full-length genome of HEV strains for genotyping. (c) 2007 S. Karger AG, Basel.