Table 1.
Comparison of the nucleotide and deduced amino acid sequences of S genes of PEDV (porcine epidemic diarrhea virus) reference strains and PEDV outbreak in Gansu, China.
| Virus strian | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 JY5C | 100.0 | 100.0 | 99.3 | 99.3 | 97.6 | 95.1 | 93.4 | 93.4 | 95.1 | 95.2 | 94.4 | 98.4 | 97.7 | 94.6 | 95.3 | 97.5 | 95.0 | 93.3 | 94.9 | 95.7 | 93.4 | 95.1 | 97.1 | 95.9 | 95.0 | 95.8 | 94.7 | 96.5 | 93.8 | 93.2 | 93.6 | 93.2 | 94.5 | 94.3 | 93.8 | 93.7 | |
| 2 JY6C | 100.0 | 100.0 | 99.3 | 99.3 | 97.6 | 95.1 | 93.4 | 93.4 | 95.1 | 95.2 | 94.4 | 98.4 | 97.7 | 94.6 | 95.3 | 97.5 | 95.0 | 93.3 | 94.9 | 95.7 | 93.4 | 95.1 | 97.1 | 95.9 | 95.0 | 95.8 | 94.7 | 96.5 | 93.8 | 93.2 | 93.6 | 93.2 | 94.5 | 94.3 | 93.8 | 93.7 | |
| 3 JY7C | 100.0 | 100.0 | 99.3 | 99.3 | 97.6 | 95.1 | 93.4 | 93.4 | 95.1 | 95.2 | 94.4 | 98.4 | 97.7 | 94.6 | 95.3 | 97.5 | 95.0 | 93.3 | 94.9 | 95.7 | 93.4 | 95.1 | 97.1 | 95.9 | 95.0 | 95.8 | 94.7 | 96.5 | 93.8 | 93.2 | 93.6 | 93.2 | 94.5 | 94.3 | 93.8 | 93.7 | |
| 4 YJ3F | 99.0 | 99.0 | 99.0 | 100.0 | 97.6 | 95.1 | 93.5 | 93.5 | 95.1 | 95.2 | 94.4 | 98.4 | 97.7 | 94.7 | 95.3 | 97.5 | 95.0 | 93.3 | 94.9 | 95.6 | 93.5 | 95.2 | 97.0 | 95.8 | 94.9 | 95.7 | 94.7 | 96.7 | 93.8 | 93.3 | 93.7 | 93.2 | 94.6 | 94.2 | 93.8 | 93.8 | |
| 5 YJ7C | 99.0 | 99.0 | 99.0 | 99.9 | 97.6 | 95.1 | 93.6 | 93.5 | 95.1 | 95.2 | 94.4 | 98.4 | 97.7 | 94.7 | 95.4 | 97.6 | 95.0 | 93.4 | 94.9 | 95.6 | 93.6 | 95.2 | 97.0 | 95.9 | 95.0 | 95.8 | 94.8 | 96.7 | 93.9 | 93.4 | 93.7 | 93.2 | 94.6 | 94.3 | 93.9 | 93.8 | |
| 6 CH1 | 97.9 | 97.9 | 97.9 | 97.6 | 97.6 | 94.5 | 93.4 | 93.3 | 94.5 | 94.6 | 95.8 | 98.4 | 98.5 | 94.2 | 94.9 | 97.1 | 94.6 | 92.9 | 94.5 | 94.9 | 93.0 | 94.8 | 96.5 | 95.4 | 94.8 | 95.3 | 94.5 | 96.2 | 93.5 | 93.2 | 93.3 | 93.1 | 94.3 | 94.1 | 93.4 | 93.4 | |
| 7 CH2 | 95.1 | 95.1 | 95.1 | 94.9 | 94.9 | 94.6 | 95.8 | 95.8 | 99.5 | 99.6 | 97.6 | 95.3 | 94.0 | 96.8 | 95.9 | 94.4 | 97.3 | 95.2 | 97.2 | 98.4 | 95.6 | 93.1 | 93.9 | 93.8 | 92.9 | 93.8 | 92.8 | 93.6 | 95.8 | 95.6 | 92.6 | 95.2 | 93.0 | 92.7 | 95.7 | 95.6 | |
| 8 CH3 | 92.8 | 92.8 | 92.8 | 92.8 | 93.0 | 92.9 | 95.3 | 99.7 | 95.8 | 96.0 | 95.8 | 93.7 | 93.1 | 97.6 | 96.6 | 94.4 | 96.0 | 96.2 | 95.9 | 96.3 | 96.6 | 94.0 | 93.4 | 93.5 | 93.0 | 93.4 | 94.2 | 93.6 | 96.8 | 99.5 | 93.8 | 97.6 | 94.2 | 94.2 | 96.8 | 96.7 | |
| 9 CH4 | 92.8 | 92.8 | 92.8 | 92.8 | 93.0 | 92.9 | 95.3 | 99.4 | 95.8 | 95.9 | 95.7 | 93.6 | 93.0 | 97.5 | 96.6 | 94.3 | 95.9 | 96.2 | 95.8 | 96.2 | 96.6 | 94.0 | 93.3 | 93.4 | 92.9 | 93.3 | 94.1 | 93.5 | 96.8 | 99.4 | 93.7 | 97.5 | 94.2 | 94.1 | 96.8 | 96.7 | |
| 10 CH5 | 94.6 | 94.6 | 94.6 | 94.5 | 94.5 | 94.1 | 99.1 | 94.9 | 94.9 | 99.6 | 97.6 | 95.3 | 94.0 | 96.7 | 95.9 | 94.3 | 97.3 | 95.2 | 97.2 | 98.4 | 95.6 | 93.1 | 93.9 | 93.8 | 92.9 | 93.8 | 92.8 | 93.6 | 95.8 | 95.6 | 92.6 | 95.2 | 93.0 | 92.7 | 95.7 | 95.6 | |
| 11 CH6 | 95.1 | 95.1 | 95.1 | 94.9 | 94.9 | 94.6 | 99.6 | 95.4 | 95.4 | 99.1 | 97.7 | 95.4 | 94.1 | 96.9 | 96.1 | 94.5 | 97.4 | 95.4 | 97.3 | 98.5 | 95.7 | 93.3 | 94.0 | 93.9 | 93.0 | 93.9 | 93.0 | 93.8 | 96.0 | 95.7 | 92.8 | 95.3 | 93.2 | 92.9 | 95.9 | 95.8 | |
| 12 CH7 | 94.6 | 94.6 | 94.6 | 94.3 | 94.3 | 95.6 | 97.5 | 95.3 | 95.3 | 97.0 | 97.5 | 94.7 | 95.1 | 96.5 | 95.6 | 94.0 | 97.2 | 94.9 | 97.0 | 97.8 | 95.3 | 92.8 | 93.5 | 93.5 | 92.9 | 93.5 | 92.6 | 93.4 | 95.4 | 95.5 | 92.3 | 95.1 | 92.7 | 92.4 | 95.4 | 95.3 | |
| 13 CH8 | 98.1 | 98.1 | 98.1 | 98.0 | 98.0 | 98.6 | 95.0 | 92.9 | 92.9 | 94.6 | 95.0 | 94.6 | 97.5 | 94.6 | 95.3 | 97.4 | 94.9 | 93.3 | 94.8 | 95.6 | 93.4 | 95.2 | 96.9 | 95.8 | 95.0 | 95.7 | 94.8 | 96.5 | 93.8 | 93.5 | 93.5 | 93.4 | 94.7 | 94.5 | 93.8 | 93.7 | |
| 14 CHGD01 | 98.1 | 98.1 | 98.1 | 97.9 | 97.9 | 98.2 | 93.9 | 92.7 | 92.7 | 93.5 | 93.9 | 94.6 | 97.4 | 94.3 | 95.0 | 97.1 | 94.4 | 92.9 | 94.4 | 94.7 | 92.9 | 94.6 | 96.5 | 95.3 | 94.5 | 95.3 | 94.4 | 96.3 | 93.4 | 92.9 | 93.4 | 92.9 | 94.2 | 93.9 | 93.4 | 93.4 | |
| 15 CH-FJND-1-2011 | 93.8 | 93.8 | 93.8 | 94.0 | 94.1 | 93.6 | 96.0 | 97.3 | 97.2 | 95.6 | 96.1 | 95.7 | 93.8 | 93.7 | 98.9 | 96.7 | 96.8 | 95.9 | 96.7 | 97.3 | 96.0 | 93.2 | 94.2 | 94.2 | 93.2 | 94.1 | 93.3 | 94.1 | 96.4 | 97.3 | 93.1 | 96.1 | 93.4 | 93.3 | 96.4 | 96.3 | |
| 16 CH-FJND-2-2011 | 95.1 | 95.1 | 95.1 | 95.2 | 95.4 | 94.9 | 95.0 | 96.1 | 96.0 | 94.6 | 95.1 | 94.7 | 94.8 | 94.9 | 98.6 | 97.5 | 96.1 | 95.2 | 96.0 | 96.5 | 95.3 | 93.6 | 94.9 | 94.5 | 93.6 | 94.5 | 93.7 | 94.7 | 95.7 | 96.4 | 93.4 | 95.3 | 93.8 | 93.5 | 95.8 | 95.7 | |
| 17 CH-FJND-3-2011 | 97.0 | 97.0 | 97.0 | 97.1 | 97.3 | 96.8 | 93.8 | 93.8 | 93.8 | 93.3 | 93.8 | 93.4 | 96.7 | 96.6 | 96.3 | 97.5 | 94.5 | 93.6 | 94.5 | 94.9 | 93.7 | 95.1 | 96.9 | 95.9 | 95.0 | 95.8 | 95.1 | 96.5 | 94.1 | 94.2 | 93.9 | 93.7 | 94.9 | 94.8 | 94.1 | 94.1 | |
| 18 DX | 95.3 | 95.3 | 95.3 | 95.2 | 95.2 | 94.8 | 97.2 | 95.4 | 95.4 | 96.9 | 97.2 | 97.0 | 95.0 | 94.6 | 96.5 | 95.5 | 94.4 | 95.5 | 99.1 | 98.1 | 95.9 | 93.2 | 94.2 | 94.3 | 93.4 | 94.2 | 93.1 | 94.0 | 96.0 | 95.7 | 93.0 | 95.3 | 93.2 | 93.0 | 96.0 | 95.9 | |
| 19 LZC | 92.8 | 92.8 | 92.8 | 92.6 | 92.8 | 92.3 | 94.8 | 94.9 | 94.9 | 94.4 | 95.0 | 94.6 | 92.3 | 92.6 | 94.9 | 94.2 | 92.7 | 94.8 | 95.4 | 95.9 | 95.8 | 93.4 | 93.1 | 93.2 | 93.0 | 93.2 | 93.5 | 93.5 | 99.4 | 96.0 | 93.8 | 95.5 | 93.7 | 93.3 | 99.5 | 99.4 | |
| 20 LJB-03 | 94.9 | 94.9 | 94.9 | 94.8 | 94.8 | 94.4 | 96.9 | 95.2 | 95.2 | 96.6 | 96.9 | 96.7 | 94.6 | 94.3 | 96.0 | 95.0 | 93.8 | 98.6 | 94.5 | 98.0 | 95.8 | 93.2 | 94.2 | 94.1 | 93.3 | 94.1 | 93.1 | 93.9 | 96.0 | 95.6 | 92.9 | 95.2 | 93.1 | 92.9 | 96.0 | 95.9 | |
| 21 JS-2004-2 | 95.7 | 95.7 | 95.7 | 95.5 | 95.5 | 94.9 | 98.0 | 95.8 | 95.8 | 97.6 | 98.0 | 97.6 | 95.3 | 94.7 | 96.7 | 95.7 | 94.4 | 98.0 | 95.4 | 97.8 | 96.2 | 93.6 | 94.7 | 94.6 | 93.7 | 94.6 | 93.3 | 94.4 | 96.4 | 96.1 | 93.1 | 95.7 | 93.4 | 93.2 | 96.4 | 96.3 | |
| 22 CHS | 93.3 | 93.3 | 93.3 | 93.3 | 93.5 | 93.0 | 95.4 | 96.1 | 96.1 | 95.2 | 95.5 | 95.2 | 93.1 | 93.0 | 95.6 | 94.6 | 93.3 | 95.7 | 95.2 | 95.4 | 96.1 | 94.0 | 93.9 | 93.9 | 93.4 | 93.8 | 93.7 | 93.7 | 96.3 | 96.3 | 93.5 | 95.8 | 94.0 | 93.4 | 96.4 | 96.3 | |
| 23 KUN-0901 | 94.7 | 94.7 | 94.7 | 94.7 | 94.8 | 94.4 | 92.9 | 93.4 | 93.3 | 92.5 | 93.1 | 92.5 | 94.7 | 94.4 | 92.7 | 93.5 | 94.5 | 93.0 | 92.8 | 92.7 | 93.3 | 93.6 | 95.4 | 95.5 | 95.7 | 95.4 | 97.9 | 95.8 | 93.9 | 93.7 | 96.0 | 93.4 | 96.7 | 94.7 | 93.9 | 93.9 | |
| 24 KUN-0902 | 96.4 | 96.4 | 96.4 | 96.1 | 96.3 | 95.9 | 93.1 | 92.4 | 92.4 | 92.9 | 93.1 | 92.8 | 96.0 | 95.9 | 93.0 | 94.2 | 96.0 | 93.6 | 92.3 | 93.2 | 94.1 | 93.5 | 94.5 | 97.8 | 95.3 | 97.6 | 94.9 | 96.5 | 93.6 | 93.1 | 93.8 | 92.9 | 94.6 | 94.3 | 93.6 | 93.6 | |
| 25 KUN-0903 | 95.0 | 95.0 | 95.0 | 94.8 | 95.0 | 94.4 | 93.1 | 92.6 | 92.5 | 92.8 | 93.3 | 93.1 | 94.7 | 94.4 | 93.1 | 94.1 | 94.8 | 93.6 | 92.3 | 93.1 | 94.1 | 93.5 | 95.1 | 96.5 | 96.8 | 99.8 | 95.1 | 95.8 | 93.7 | 93.2 | 94.1 | 92.9 | 95.1 | 94.6 | 93.8 | 93.7 | |
| 26 KUN-0904 | 94.1 | 94.1 | 94.1 | 94.0 | 94.2 | 93.9 | 92.5 | 92.0 | 92.0 | 92.1 | 92.8 | 92.4 | 93.9 | 93.8 | 92.3 | 93.3 | 93.9 | 92.8 | 91.9 | 92.5 | 93.1 | 92.8 | 95.3 | 94.0 | 96.5 | 96.7 | 95.1 | 96.2 | 93.5 | 92.7 | 93.9 | 92.3 | 95.0 | 94.2 | 93.5 | 93.5 | |
| 27 KUN-0905 | 94.7 | 94.7 | 94.7 | 94.6 | 94.7 | 94.2 | 93.1 | 92.4 | 92.3 | 92.8 | 93.2 | 93.0 | 94.4 | 94.2 | 92.9 | 93.8 | 94.6 | 93.4 | 92.2 | 92.9 | 94.0 | 93.3 | 95.0 | 96.2 | 99.6 | 96.4 | 95.0 | 95.7 | 93.6 | 93.1 | 94.0 | 92.9 | 94.9 | 94.5 | 93.7 | 93.6 | |
| 28 KUN-0801 | 94.1 | 94.1 | 94.1 | 94.1 | 94.2 | 94.2 | 92.3 | 93.6 | 93.5 | 91.9 | 92.5 | 92.2 | 94.2 | 94.2 | 92.8 | 93.6 | 94.5 | 92.8 | 92.7 | 92.4 | 93.0 | 93.3 | 97.9 | 94.1 | 94.7 | 94.5 | 94.4 | 95.4 | 94.1 | 93.9 | 97.8 | 93.6 | 97.9 | 95.0 | 94.1 | 94.0 | |
| 29 KUN-0802 | 96.6 | 96.6 | 96.6 | 96.6 | 96.8 | 96.2 | 93.5 | 92.8 | 92.8 | 93.1 | 93.6 | 93.2 | 96.3 | 96.5 | 93.6 | 94.7 | 96.2 | 93.8 | 92.7 | 93.4 | 94.2 | 93.4 | 95.4 | 96.4 | 95.5 | 94.9 | 95.2 | 95.5 | 94.0 | 93.3 | 94.2 | 93.0 | 95.1 | 94.6 | 94.1 | 94.0 | |
| 30 Parent DR13 | 93.7 | 93.7 | 93.7 | 93.6 | 93.7 | 93.3 | 95.7 | 95.9 | 95.9 | 95.4 | 96.0 | 95.4 | 93.3 | 93.5 | 95.7 | 95.0 | 93.5 | 95.7 | 98.9 | 95.4 | 96.2 | 96.0 | 93.6 | 93.1 | 93.1 | 92.7 | 93.0 | 93.6 | 93.5 | 96.6 | 94.3 | 96.0 | 94.2 | 93.9 | 99.9 | 99.8 | |
| 31 Attenuated DR13 | 92.8 | 92.8 | 92.8 | 92.8 | 93.0 | 92.8 | 95.2 | 99.2 | 99.1 | 94.8 | 95.3 | 95.2 | 92.8 | 92.6 | 97.0 | 95.9 | 93.7 | 95.3 | 94.8 | 95.0 | 95.7 | 95.8 | 93.1 | 92.3 | 92.5 | 92.0 | 92.3 | 93.3 | 92.8 | 95.7 | 93.5 | 97.3 | 94.0 | 93.9 | 96.5 | 96.4 | |
| 32 Chinju99 | 92.5 | 92.5 | 92.5 | 92.5 | 92.6 | 92.3 | 90.9 | 92.0 | 92.0 | 90.5 | 91.2 | 90.9 | 92.3 | 92.5 | 91.6 | 92.2 | 92.8 | 91.5 | 92.0 | 91.2 | 91.8 | 92.0 | 95.4 | 92.5 | 92.8 | 92.7 | 92.6 | 97.3 | 93.6 | 92.8 | 91.9 | 93.3 | 96.3 | 93.8 | 94.4 | 94.4 | |
| 33 MK | 93.4 | 93.4 | 93.4 | 93.1 | 93.3 | 93.5 | 94.9 | 96.6 | 96.5 | 94.5 | 94.9 | 95.1 | 93.3 | 93.3 | 95.4 | 94.7 | 93.5 | 95.2 | 94.8 | 94.9 | 95.5 | 95.5 | 93.3 | 93.1 | 92.9 | 92.2 | 92.7 | 93.8 | 93.4 | 95.6 | 96.3 | 92.5 | 93.8 | 93.7 | 96.1 | 96.0 | |
| 34 NK | 93.9 | 93.9 | 93.9 | 94.1 | 94.2 | 93.9 | 92.8 | 93.7 | 93.6 | 92.3 | 93.0 | 92.6 | 94.0 | 93.8 | 93.0 | 93.7 | 94.2 | 93.1 | 92.9 | 92.7 | 93.5 | 93.8 | 96.3 | 93.7 | 94.4 | 94.2 | 94.2 | 97.5 | 94.7 | 93.8 | 93.5 | 95.5 | 94.1 | 95.2 | 94.2 | 94.2 | |
| 35 KH | 93.9 | 93.9 | 93.9 | 93.7 | 93.9 | 93.8 | 92.7 | 93.1 | 93.0 | 92.3 | 92.8 | 92.3 | 94.0 | 93.7 | 92.3 | 93.2 | 93.8 | 92.7 | 92.3 | 92.3 | 92.9 | 93.1 | 94.2 | 93.4 | 94.1 | 93.4 | 93.9 | 94.6 | 94.1 | 93.3 | 92.9 | 92.8 | 93.7 | 94.9 | 93.8 | 93.8 | |
| 36 CV777 | 93.7 | 93.7 | 93.7 | 93.6 | 93.7 | 93.3 | 95.7 | 95.9 | 95.9 | 95.3 | 95.9 | 95.4 | 93.3 | 93.6 | 95.9 | 95.2 | 93.6 | 95.7 | 99.1 | 95.4 | 96.2 | 96.2 | 93.7 | 93.2 | 93.2 | 92.8 | 93.1 | 93.6 | 93.6 | 99.7 | 95.7 | 93.0 | 95.7 | 93.8 | 93.2 | 99.9 | |
| 37 Br1-87 | 93.6 | 93.6 | 93.6 | 93.4 | 93.6 | 93.1 | 95.4 | 95.6 | 95.6 | 95.1 | 95.6 | 95.2 | 93.1 | 93.4 | 95.6 | 94.9 | 93.5 | 95.4 | 98.8 | 95.2 | 96.0 | 95.9 | 93.6 | 93.1 | 93.1 | 92.7 | 93.0 | 93.5 | 93.5 | 99.4 | 95.4 | 93.0 | 95.4 | 93.8 | 93.1 | 99.7 |
Nucleotide identity (%) in upper triangle; Deduced amino acid identity (%) in lower triangle.