Table 2.
Identification of 31 potential recombination events in the complete genome of PDCoVs isolated during 2004–2020. The genogroups were defined based on the phylogenetic tree of PDCoV full-length genome ine in this study (see Fig. 1). The P values for each detection method are shown in Supplementary Table 1
| Event serial number | Recombinant | Minor parent | Major parent | |||
|---|---|---|---|---|---|---|
| GenBank ID: Virus name/Country-Year | Genogroup | GenBank ID: Virus name/Country-Year | Genogroup | GenBank ID: Virus name/Country-Year | Genogroup | |
| 1 | KY363867.1:CHN-GD16–03(China-2016) | GI-d | MN025260.1:CH/GX/1468B/2017 (China-2017) | GII-a | MF280390.1:CHN-GD-2016(China-2016) | GI-d |
| 2 | MN781985.1:CHzmd2019(China-2019) | GI-a | KX361344.1:P2_13_ST2_0313/PDCoV/0213/Thailand (Thailand-2013) | GII-a | MZ802955.1:CH-HLJ-20(China-2020) | GI-a |
| 3 | KX998969.1:P29_15_VN_1215(Viet_Nam-2015) | GII-a | KR265859.1:USA/Minnesota159/2014(USA-2014) | GI-a | KX834351.1:PDCoV/Swine/Vietnam/HaNoi6/2015(Viet_Nam-2015) | GII-a |
| 4 | KT266822.1:CH/Sichuan/S27/2012(China-2012) | GI-g | KX361344.1:P2_13_ST2_0313/PDCoV/0213/Thailand(Thailand-2013) | GII-a | KP757891.1:CHN-HB-2014(China-2014) | GI-b |
| 5 | *MN173781.1:CHN-GX81–2018(China-2018) | GII-b | KX834351.1:PDCoV/Swine/Vietnam/HaNoi6/2015(Viet_Nam-2015) | GII-a | MN173779.1:CHN-GX11–2018(China-2018) | GII-b |
| 6 | *MK572803.1:SCNC201705(China-2017) | GI-f | KX998969.1:P29_15_VN_1215(Viet_Nam-2015) | GII-a | MK211169.1:CHN/Sichuan/2017(China-2017) | GI-f |
| 7 | *MF642325.1:CHN/QH/2017/1(China-2017) | GI-b | KX834351.1:PDCoV/Swine/Vietnam/HaNoi6/2015(Viet_Nam-2015) | GII-a | MN520196.1:SD2018–306(China-2018) | GI-g |
| 8 | KY065120.1:CHN/Tianjin/2016(China-2016) | GI-d | MN025260.1:CH/GX/1468B/2017 (China-2017) | GII-a | MH715491.1:PDCoV/CHGD/2016(China-2016) | GI-d |
| 9 | MN520209.1:JS2019-A1414(China-2019) | GI-d | KX998969.1:P29_15_VN_1215(Viet_Nam-2015) | GII-a | MW854634.1:104–553(Taiwan-2015) | GI-d |
| 10 | MN520209.1:JS2019-A1414(China-2019) | GI-d | MN025260.1:CH/GX/1468B/2017 (China-2017) | GII-a | KT021234.1:CH/SXD1/2015(China-2015) | GI-d |
| 11 | KT021234.1:CH/SXD1/2015(China-2015) | GI-d | MZ802774.1:PDCoV/CBR-3/2016/Thailand(Thailand-2016) | GII-a | KU665558.1:CHN-LYG-2014(China-2014) | GI-d |
| 12 | *MN520196.1:SD2018–306(China-2018) | GI-g | MT260149.1:HNZK-04-P5(China-2018) | GI-d | MG242062.1:CHN-HeB1–2017(China-2017) | GI-e |
| 13 | *KT021234.1:CH/SXD1/2015(China-2015) | GI-d | MN781985.1:CHzmd2019(China-2019) | GI-a | MH715491.1:PDCoV/CHGD/2016(China-2016) | GI-d |
| 14 | *MK993519.1:CHN/Sichuan/2019(China-2019) | GI-f | MN025260.1:CH/GX/1468B/2017 (China-2017) | GII-a | MN173781.1:CHN-GX81–2018(China-2018) | GII-b |
| 15 | MF095123.1:CHN-HG-2017(China-2017) | GI-d | KX998969.1:P29_15_VN_1215(Viet_Nam-2015) | GII-a | KR265849.1:USA/Michigan447/2014(USA-2014) | GI-a |
| 16 | KX443143.2:CH-01(China-2016) | GI-g | KX361344.1:P2_13_ST2_0313/PDCoV/0213/Thailand(Thailand-2013) | GII-a | LC260043.1:OKN/JPN/2014(Japan-2014) | GI-a |
| 17 | *MF280390.1:CHN-GD-2016(China-2016) | GI-d | KX443143.2:CH-01(China-2016) | GI-g | MH715491.1:PDCoV/CHGD/2016(China-2016) | GI-d |
| 18 | MK355396.1:CHN-SC2015(China-2016) | GI-f | MT260149.1:HNZK-04-P5(China-2018) | GI-d | MK211169.1:CHN/Sichuan/2017(China-2017) | GI-f |
| 19 | MK211169.1:CHN/Sichuan/2017(China-2017) | GI-f | MN520206.1:HN2019-C132(China-2019) | GI-d | MN520207.1:JS2018-QF49(China-2018) | GI-f |
| 20 | *MW685623.1:PDCoV/Haiti/Human/0256–1/2015(Haiti-2015) | GI-a | KR150443.1:USA/Arkansas61/2015(USA-2015) | GI-a | MN520198.1:AH2019-H(China-2019) | GI-a |
| 21 | *MN520207.1:JS2018-QF49(China-2018) | GI-f | MK005882.1:Swine/CHN/SC/2018/1(China-2018) | GI-f | KU665558.1:CHN-LYG-2014(China-2014) | GI-d |
| 22 | MT663769.1:CHN-TS1–2019(China-2019) | GI-c | MK211169.1:CHN/Sichuan/2017(China-2017) | GI-f | MF041982.1:SHJS/SL/2016(China-2016) | GI-e |
| 23 | *MN520206.1:HN2019-C132(China-2019) | GI-d | MK211169.1:CHN/Sichuan/2017(China-2017) | GI-f | KU665558.1:CHN-LYG-2014(China-2014) | GI-d |
| 24 | *MF041982.1:SHJS/SL/2016(China-2016) | GI-e | KP757892.1:CHN-JS-2014(China-2014) | GI-d | MG242062.1:CHN-HeB1–2017(China-2017) | GI-e |
| 25 | MN173781.1:CHN-GX81–2018(China-2018) | GII-b | MN025260.1:CH/GX/1468B/2017 (China-2017) | GII-a | MN520199.1:AH2018–93(China-2018) | GII-b |
| 26 | MN520206.1:HN2019-C132(China-2019) | GI-d | MK572803.1:SCNC201705(China-2017) | GI-f | MN520190.1:AH2018–322(China-2018) | GI-d |
| 27 | MN520204.1:HN2018-LH2(China-2018) | GI-f | MN520190.1:AH2018–322(China-2018) | GI-d | MK572803.1:SCNC201705(China-2017) | GI-f |
| 28 | *KY363868.1:CHN-GD16–05(China-2016) | GI-a | KX443143.2:CH-01(China-2016) | GI-g | MN520198.1:AH2019-H(China-2019) | GI-a |
| 29 | *MK993519.1:CHN/Sichuan/2019(China-2019) | GI-f | MN025260.1:CH/GX/1468B/2017 (China-2017) | GII-a | MN520199.1:AH2018–93(China-2018) | GII-b |
| 30 | *MT263013.1:CHN-HN-17(China-2017) | GI-g | MK572803.1:SCNC201705(China-2017) | GI-f | MK005882.1:Swine/CHN/SC/2018/1(China-2018) | GI-f |
| 31 | MN520194.1:SD2018–10(China-2018) | GI-c | LC260043.1:OKN/JPN/2014(Japan-2014) | GI-a | MH025764.1:CH/JXJGS01/P50(China-2016) | GI-c |
* The major or minor parent may be the actual recombinant due to the possibility of misidentification