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Open reading frame structure analysis as a novel genotyping tool for hepatitis E virus and the subsequent discovery of an inter-genotype recombinant

Jun Fan

Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK

Correspondence
Jun Fan
jun.fan-rres{at}bbsrc.ac.uk

Accurate viral genotyping is important. Here I investigate genotypes in hepatitis E virus (HEV) and find that the open reading frame (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 (GenBank accession no. DQ450072 [GenBank] ) was revealed by analysing the ORF structure and confirmed by 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 exhibited the mosaic sequence pattern, although without statistical support.

Present address: Centenary Building, Rothamsted Research, Harpenden AL5 2JQ, UK.

Supplementary material is available with the online version of this paper.