Table 2 Nucleotide similarities (%) of S and N genes of our five PDCoV isolates and other reported PDCoVs and coronaviruses
From: Occurrence and sequence analysis of porcine deltacoronaviruses in southern China
S gene | N gene | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
GenBank No. | KU204694 | KU204695 | KU204696 | KU204697 | KX534090 | KU204698 | KU204699 | KU204700 | KU204701 | KX534091 | |
Strain | CH/GD01/2015 | CH/GD02/2015 | CH/HN01/2015 | CH/GX01/2015 | CH/GD03/2015 | CH/GD01/2015 | CH/GD02/2015 | CH/HN01/2015 | CH/GX01/2015 | CH/GD03/2015 | |
KR131621 | PDCoV/CHJXNI2/2015 | 99.5 | 98.9 | 98.9 | 99.1 | 99.2 | 99.7 | 99.1 | 99.1 | 99.3 | 99.4 |
KP757892 | CHN-JS-2014 | 99.1 | 98.5 | 98.5 | 98.7 | 98.7 | 99.3 | 99.3 | 99.3 | 99.5 | 99.0 |
KP757891 | CHN-HB-2014 | 98.9 | 98.4 | 98.4 | 98.7 | 98.5 | 98.8 | 98.6 | 98.6 | 98.8 | 98.5 |
JQ065042 | HKU15-44 | 98.6 | 98.2 | 98.2 | 98.5 | 98.3 | 98.7 | 98.5 | 98.5 | 98.7 | 98.4 |
JQ065043 | HKU15-155 | 98.5 | 98.2 | 98.2 | 98.4 | 98.2 | 98.7 | 98.5 | 98.5 | 98.7 | 98.4 |
KT021234 | CH/SXD1/2015 | 98.4 | 97.9 | 97.9 | 98.1 | 98.0 | 99.0 | 98.8 | 98.8 | 99.0 | 98.7 |
KT266822 | CH/Sichuan/S27/2012 | 98.4 | 98.0 | 98.0 | 98.2 | 98.0 | 99.2 | 99.0 | 99.0 | 99.2 | 98.9 |
KM820765 | KNU14-04 | 98.4 | 97.9 | 97.9 | 98.2 | 98.1 | 98.8 | 98.6 | 98.6 | 98.8 | 98.5 |
KJ620016 | MI6148 | 98.4 | 97.9 | 97.9 | 98.1 | 98.0 | 98.8 | 98.6 | 98.6 | 98.8 | 98.5 |
KJ584360 | MN3092 | -a | -a | -a | -a | -a | 98.8 | 98.6 | 98.6 | 98.8 | 98.5 |
KJ584358 | PA3148 | 98.4 | 98.0 | 98.0 | 98.2 | 98.0 | 98.8 | 98.6 | 98.6 | 98.8 | 98.5 |
KJ584357 | KY4813 | 98.4 | 97.9 | 97.9 | 98.1 | 98.0 | 98.8 | 98.6 | 98.6 | 98.8 | 98.5 |
KJ584355 | IL2768 | 98.4 | 97.9 | 97.9 | 98.1 | 98.0 | 98.8 | 98.6 | 98.6 | 98.8 | 98.5 |
KT381613 | OH11846 | 98.4 | 97.9 | 97.9 | 98.1 | 98.0 | 98.8 | 98.6 | 98.6 | 98.8 | 98.5 |
KJ601779 | PDCoV/USA/Illinois136/2014 | 98.4 | 97.9 | 97.9 | 98.1 | 98.0 | 98.5 | 98.3 | 98.3 | 98.5 | 98.3 |
KJ481931 | PDCoV/USA/Illinois121/2014 | 98.4 | 97.9 | 97.9 | 98.1 | 98.0 | 98.5 | 98.3 | 98.3 | 98.5 | 98.3 |
KJ769231 | OhioCVM1/2014 | 98.4 | 97.8 | 97.8 | 98.1 | 98.0 | 98.3 | 98.2 | 98.2 | 98.3 | 98.1 |
KJ601777 | PDCoV/USA/Illinois133/2014 | 98.4 | 97.8 | 97.8 | 98.1 | 98.0 | 98.7 | 98.5 | 98.5 | 98.7 | 98.4 |
KJ584359 | NE3579 | 98.4 | 97.8 | 97.8 | 98.1 | 98.0 | 98.7 | 98.5 | 98.5 | 98.7 | 98.4 |
KJ584356 | SD3424 | 98.4 | 97.8 | 97.8 | 98.1 | 98.0 | 98.5 | 98.3 | 98.4 | 98.5 | 98.3 |
KJ462462 | OH1987 | 98.4 | 97.8 | 97.8 | 98.1 | 98.0 | 98.7 | 98.5 | 98.5 | 98.7 | 98.4 |
KJ601778 | PDCoV/USA/Illinois134/2014 | 98.3 | 97.8 | 97.8 | 98.0 | 98.0 | 98.7 | 98.5 | 98.5 | 98.7 | 98.4 |
KP995358 | OH-FD22 | 98.3 | 97.8 | 97.8 | 98.0 | 98.0 | -b | -b | -b | -b | -b |
KJ601780 | PDCoV/USA/Ohio137/2014 | 98.3 | 97.8 | 97.8 | 98.0 | 98.0 | 98.7 | 98.5 | 98.5 | 98.7 | 98.4 |
KJ569769 | IN2847 | 98.3 | 97.8 | 97.8 | 98.1 | 98.0 | 98.8 | 98.6 | 98.6 | 98.8 | 98.5 |
KJ567050 | 8734/USA-IA/2014 | 98.3 | 97.9 | 97.9 | 98.1 | 98.0 | 98.7 | 98.5 | 98.5 | 98.7 | 98.4 |
KP981395 | USA/IL/2014/026PDV_P11 | 98.3 | 97.8 | 97.8 | 98.0 | 97.9 | 98.7 | 98.5 | 98.5 | 98.7 | 98.4 |
KM012168 | Michigan/8977/2014 | 98.3 | 97.8 | 97.8 | 98.0 | 97.9 | 98.7 | 98.5 | 98.5 | 98.7 | 98.4 |
KP757890 | CHN-AH-2004 | 98.0 | 97.5 | 97.5 | 97.8 | 97.7 | 98.1 | 97.9 | 97.9 | 98.1 | 97.8 |
KU051641 | PDCoV/Swine/Thailand/S5011/2015 | 95.8 | 95.6 | 95.6 | 95.9 | 95.4 | 97.1 | 96.9 | 96.9 | 97.1 | 96.8 |
KU051649 | PDCoV/Swine/Thailand/S5015L/2015 | 95.8 | 95.5 | 95.5 | 95.9 | 95.4 | 97.1 | 96.9 | 96.9 | 97.1 | 96.8 |
KU984334 | P23_15_TT_1115 | 95.9 | 95.8 | 95.6 | 95.9 | 95.5 | 97.8 | 97.8 | 97.8 | 98.0 | 97.5 |
EF584908 | Guangxi/F230/2006 | 97.5 | 97.1 | 97.1 | 97.3 | 97.0 | 98.0 | 97.8 | 97.8 | 98.0 | 97.7 |
JQ065045 | HKU17-6124 | 40.9 | 40.8 | 40.8 | 40.7 | 40.7 | 92.9 | 92.6 | 92.8 | 92.9 | 92.6 |
FJ376621 | HKU12-600 | 40.7 | 41.1 | 41.1 | 41.0 | 40.6 | 76.4 | 75.7 | 76.2 | 76.3 | 76.3 |
JQ065044 | HKU16-6847 | 57.0 | 56.9 | 56.9 | 57.0 | 57.2 | 75.1 | 75.3 | 75.2 | 75.4 | 75.1 |
FJ376619 | HKU11-934 | 65.9 | 68.9 | 68.9 | 66.1 | 65.8 | 74.4 | 74.3 | 74.5 | 74.4 | 74.2 |
FJ376620 | HKU11-796 | 65.3 | 65.6 | 65.7 | 65.6 | 65.1 | 74.4 | 74.6 | 74.5 | 74.4 | 74.2 |
KJ408801 | OH1414 (PEDV) | 38.2 | 38.3 | 38.3 | 38.1 | 37.8 | 3.6 | 3.5 | 3.5 | 3.6 | 3.6 |
FJ755618 | H16(TGEV) | 38.1 | 38.1 | 38.1 | 38.0 | 37.9 | 2.8 | 4.9 | 7.5 | 5.0 | 2.8 |
DQ811787 | ISU-1(PRCV) | 37.4 | 25.7 | 25.7 | 25.7 | 37.3 | 7.3 | 7.4 | 7.5 | 7.4 | 7.4 |
BCU00735 | Mebus(bovine) | 12.4 | 12.5 | 12.5 | 12.4 | 7.1 | 2.1 | 2.1 | 2.1 | 2.1 | 2.1 |
AY654624 | TJF(SARS) | 6.8 | 6.9 | 6.9 | 6.8 | 6.9 | 8.8 | 8.8 | 2.4 | 8.8 | 8.1 |
DQ011855 | VW572(PHEV) | 21.9 | 21.9 | 21.9 | 21.9 | 21.8 | 2.1 | 2.1 | 2.1 | 2.1 | 2.1 |
JF893452 | YN(CIBV) | 22.0 | 22.1 | 22.1 | 22.3 | 22.0 | 12.5 | 12.5 | 12.5 | 12.6 | 12.4 |
NC_010800 | MG10 (Turkey) | 24.1 | 23.5 | 23.5 | 23.3 | 24.0 | 14.0 | 14.0 | 14.0 | 14.1 | 14.1 |
NC_010646 | SW1 (whale) | 15.0 | 13.7 | 13.7 | 13.8 | 14.8 | 7.7 | 7.7 | 7.7 | 7.7 | 7.7 |