Skip to main content

Table 1 Identification of 28 potential recombination events in the spike gene of PEDVs isolated in China during 2007–2019 using RDP4 software package [61]

From: The spike glycoprotein genes of porcine epidemic diarrhea viruses isolated in China

Recombination Event serial number Recombinant Major parent Minor parent Detection methods
GenBank ID: Virus name/Country-Year Geno-group GenBank ID: Virus name/Country-Year Geno-group GenBank ID: Virus name/Country-Year Geno-group R G B M C S T
1 MH061336.1:CH/SCGA/2017/China-2017 GI-c MH726406.1:GDS49/China-2017 GII-C5 MF375374.1:CH/JXJA/2017/China-2017 GII-C9  +   +   +   +   +   +   + 
2 MN486588.1:Ah2016f2/China-2016 GI-c KF761675.1:CH/YNKM-8/China-2013 GII-C3 KX839247.1:85–7-mutant1/China-2015 GI-a  +   +   +   +   +   +   + 
3 MK673545.1:TW/Yunlin550/China-2018 GI-c KU558702.1:CO/P14/IC/China-2013 GII-C1 MH726401.1:GDS41/China-2011 GII-C9  +   +   +   +   +   +   + 
4 MK140813.1:CH/TP-4–3/2018/China-2018 GI-c MH061337.1:CH/SCZG/China-2017* GII-C1 KM609203.1:PEDV-1C/China-2012* GII-C9  +   +   +   +   +   +   + 
5 MK138516.1:V7-HB2018/China-2018 GI-c MK606368.1:CH-HB1-2018/China-2018 GII-C5 MN315264.1:AH-2018-HF1/China-2018 GI-b  +   +   +   +   +   +   + 
6 KM609211.1:PEDV-LS/China-2014 GII-C3 MH726371.1:GDS21/China-2014* GII-C5 MH726406.1:GDS49/China-2017* GII-C9  +   +   +   +   +   + 
7 MF346935.1:CH/JLDH/2016/China-2016 GII-C9 KM609209.1:PEDV-CHZ/China-2013 GII-C1 MH726406.1:GDS49/China-2017 GII-C9  +   +   +   +   +   +   + 
8 KM609204.1:PEDV-7C/China-2011 GII-C1 MH726374.1:GDS11/China-2014* GII-C6 MN486588.1:Ah2016f2/China-2016* GI-c  +   +   +   +   +   + 
9 KU380331.1:CH-SD01/China-2015 GII-C8 KM609209.1:PEDV-CHZ/China-2013 GII-C1 MK138353.1:G2/China-2016* GII-C9  +   +   +   +   +   +   + 
10 MH726374.1:GDS11/China-2014 GII-C6 KM609204.1:PEDV-7C/China-2011 GII-C1 MH056657.1:JSX2014/ATT/China-2018 GII-C1  +   +   +   +   +   +   + 
11 MK140813.1:CH/TP-4–3/China-2018 GI-c KM609209.1:PEDV-CHZ/China-2013 GII-C1 MK644601.1:G2-HE2017/China-2017* GII-C9  +   +   +   +   +   +   + 
12 MH726384.1:GDS06/China-2011 GII-C8 KM609204.1:PEDV-7C/China-2011 GII-C1 MH056657.1:JSX2014/ATT/China-2018 GII-C1  +   +   +   +   +   +   + 
13 KM609204.1:PEDV-7C/China-2011 GII-C1 MH726406.1:GDS49/China-2017 GII-C9 MH061337.1:CH/SCZG/China-2017* GII-C1  +   +   +   +   +   +   + 
14 KM609209.1:PEDV-CHZ/China-2013 GII-C1 MH726363.1:GDS20/China-2012* GII-C1 MN486588.1:Ah2016f2/China-2016* GI-c  +   +   +   +   + 
15 MK644601.1:G2-HE2017/China-2017 GII-C9 MH581489.1:CH/HBTS/2017/China-2017* GII-C9 MK138516.1:V7-HB2018/China-2018* GI-c  +   +   +   +   +   + 
16 MH726402.1:GDS46/China-2016 GII-C9 MH726406.1:GDS49/China-2017* GII-C9 MK409659.1:ZJ15XS0101-P120/China-2016* GII-C1  +   +   +   +   + 
17 KM609203.1:PEDV-1C/China-2012 GII-C1 MH726369.1:GDS30/China-2014* GII-C6 MH726379.1:GDS33/China-2014* GII-C2  +   +   +   +   +   +   + 
18 MH726366.1:GDS24/China-2012 GII-C4 MH726365.1:GDS25/China-2013* GII-C2 KM609208.1:PEDV-15F/China-2012* GII-C3  +   +   +   + 
19 MN037494.1:WHLL/China-2017 GII-C8 KM609208.1:PEDV-15F/China-2012 GII-C3 KT021233.1:YN200/China-2014 GII-C8  +   +   +   + 
20 KR818832.1:XY2013/China-2013 GII-C4 MK392335.1:LW/L/China-2010* GII-C8 KX812523.1:XM1-2/China-2016* GII-C1  +   +   +   +   +   + 
21 MH581489.1:CH/HBTS/2017/China-2017 GII-C9 KX058033.1:CH/JX/01/P30/China-2014 GII-C1 MN037494.1:WHLL/China-2017 GII-C8  + 
22 KR095279.1:CH/HNQX-3/14/China-2015 GII-C10 MH726401.1:GDS41/China-2011* GII-C9 KC196276.1:CH/ZMDZY/11/China-2011* GII-C2  +   +   +   + 
23 KF761675.1:CH/YNKM-8/China-2013 GII-C3 MH726398.1:GDS37/China-2011 GII-C9 KX812523.1:XM1-2/China-2016 GII-C1  +   +   + 
24 JQ023161.1:Virulent DR13/South Korea-2009 GI-a EF185992.1:LZC/China-2007* GI-a KC109141.1:JS2008-2/China-2012* GI-b  + 
25 MK644604.1:N7-GD2017/China-2017 GII-C6 MH726392.1:GDS44/China-2013 GII-C8 MK796238.1:CN/Liaoning25/2018/China-2018 GII-C3  + 
26 MH061342.1:CH/SCZJ/2018/China-2018 GII-C3 MH107321.1:GDS10/China-2013* GII-C2 MK409659.1:ZJ15XS0101-P120/China-2016* GII-C1  + 
27 KM609208.1:PEDV-15F/China-2012 GII-C3 MH061342.1:CH/SCZJ/2018/China-2018 GII-C3 MK409659.1:ZJ15XS0101-P120/China-2016 GII-C1  + 
28 MK644605.1:T10-HB2018/China-2018 GII-C9 MH061341.1:CH/SCLS/2018/China-2018 GII-C9 KM609212.1:PEDV-LYG/China-2014 GII-C1  +   
  1. The potential recombination events were identified by each of 7 algorithms (RDP, GENECONV, Bootscan, MaxChi, Chimaera, SiScan, and PhylPro) embedded in the RDP4 package. Genogroup was defined based on the phylogenetic tree of full-length spike gene of the PEDVs in this study (see Figure 1).
  2. R: RDP; G: GENECONV; B: BootScan; M: MaxChi; C: Chimaera; S: SiScan; T: Phylpro. +: verified; −: not verified.
  3. * The major or minor parent may be the actual recombinant due to the possibility of misidentification.