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The ORF structure analysis as a novel genotyping tool for HEV and the subsequent discovery of an inter-genotype recombinant

Rothamsted Research

¹ E-mail: jun.fan-rres{at}bbsrc.ac.uk

Accurate viral genotyping is important. Here we investigate genotypes in Hepatitis E Virus (HEV) and find that the ORF structure (the lengths of three ORFs and the overlapping relationships among the ORFs) can be a good criterion for genotyping HEV. An inter-genotype recombinant DQ450072 [GenBank] was revealed by analyzing the ORF structure and confirmed by the phylogenetic analyses. This discovery of the inter-genotype recombinant indicates that genotyping in HEV should be based on full length sequences. The Mexican strain which is currently classified as a genotype 2 strain also demonstrated the mosaic sequence pattern though without statistical support.

Received 5 December 2008; accepted 17 February 2009.