Recommended links

For fast genotyping:

NCBI BLAST based genotyping: http://www.ncbi.nlm.nih.gov/projects/genotyping/formpage.cgi

Press button Advanced and select Clear all - the last item - from the Select drop list.

If you want to use the sequences recommended in Proposed reference sequences for hepatitis E virus subtypes. Smith, Simmonds et al, 2016, copy the following list and paste it into the Add/remove reference sequences as Accession|subtype text box:

M73218|1a D11092|1b X98292|1c AY230202|1d AY204877|1e JF443721|1f M74506|2a AF082843|3a AP003430|3b FJ705359|3c AB248521|3e AB369687|3f AF455784|3g JQ013794|3h FJ998008|3i AY115488|3j AB290312|3 JQ953664|3 AB369689|3 AB290313|3 EU360977|3 KJ873911|3 EU723513|3 FJ906895|3ra KJ013415|3 JQ013791|3 AB197673|4a DQ279091|4b AB074915|4c AJ272108|4d AY723745|4e AB220974|4f AB108537|4g GU119961|4h DQ450072|4i AB369688|4 AB573435|5a AB602441|6a AB856243|6 KJ496143|7a KJ496144|7 AF173231|2b AF173232|2b AY903950|2b AF296165|3d AF296166|3d AF296167|3d

The last 6 sequences are partial and in some situations you may want to exclude it.

Now paste the sequence you want to subtype in FASTA format (or the Acc. Number) in the Enter your query sequence as Accession/GI or FASTA text box and hit Subtype.

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Find recombinants

Using RDP4: Detection and analysis of recombination patterns in virus genomes. Darren et al, 2015. Donwload and install RDP4, read the manual.

Open RDP4, load your fasta alignment and hit Run for a first automatic exploratory analysis of possible recombinants. This fast way I have found the following:

-D11093 Uigh179 (1b) - Hepatitis E virus genomic RNA, complete genome. China, human, 1987. Similar to M80581 SAR-55 (1b) but with the region 1054-2014 (of the alignment) more like D10330 Burma (1a).