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.

You can ask for more help

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 (may need revision!!) 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).

• FJ426403 swKOR-1 (3a) - Hepatitis E virus. South Korea, pig, 2007. Have a very similar regions 1-2778 and 7404-7520 (of the alignment) like FJ426403 swKOR-1 (3a).

• DQ450072 __ (4i) - Hepatitis E virus . , , . Similar to AB369690 __ (4i) but with the region 2034-2726 (of the alignment) more like GU188851 __ (4h) and the region 4988-5428 (of the alignment) more like FJ527832 __ (3b).

• KF303499 __ (3a) - Hepatitis E virus . , , . Similar to AY753648 __ (3a) but with a very different region 6570-6768 (of the alignment).

• DQ079631 __ (4i) - Hepatitis E virus . , , . Similar to DQ079628 __ ( ) but with the region - (of the alignment) more like AJ272108 __ (4d).

• __ ( ) - Hepatitis E virus . , , . Similar to __ ( ) but with the region 1054-2014 (of the alignment) more like __ ( ).