Table 2.
Nucleotide and amino acid sequence identity (%) of different regions of the SHQP/YM/2013 genome compared with those of the other viruses (values in bold show highest identities)
| Strain | 5′UTR | ORF1a | ORF1b | S | ORF3 | E | M | N | 3′UTR |
|---|---|---|---|---|---|---|---|---|---|
| Virulent DR13 | 98.0(−) | 98.0(98.6) | 98.8(99.6) | 95.1(94.5) | 98.4(99.1) | 97.8(98.7) | 98.2(98.2) | 96.9(96.8) | 98.2(−) |
| Attenuated DR13 | 98.0(−) | 97.9(98.4) | 97.8(99.4) | 94.1(93.2) | 92.8(91.3) | 97.1(95.7) | 97.8(97.4) | 96.1(96.8) | 98.8(−) |
| SM98 | 96.9(−) | 96.9(97.4) | 97.7(99.0) | 93.9(92.7) | 96.8(95.5) | 95.7(94.8) | 97.9(97.4) | 95.2(96.2) | 97.6(−) |
| CV777 | 98.3(−) | 97.1(97.7) | 97.8(99.2) | 94.2(93.6) | 97.0(96.0) | 96.5(97.4) | 98.1(98.2) | 95.4(96.4) | 97.9(−) |
| CH/S | 98.6(−) | 97.9(97.9) | 98.5(99.0) | 94.0(93.5) | 98.4(99.6) | 96.1(96.1) | 97.9(98.2) | 96.0(96.6) | 98.5(−) |
| LZC | 96.6(−) | 97.0(97.4) | 97.7(99.1) | 93.7(92.6) | 95.7(94.2) | 95.7(94.8) | 97.1(96.5) | 95.2(95.9) | 97.3(−) |
| JS2008 | 97.9(−) | 98.0(98.4) | 98.2(99.4) | 94.4(93.5) | 92.8(91.3) | 95.7(93.5) | 97.7(96.9) | 96.1(96.8) | 98.8(−) |
| LC | 98.3(−) | 99.4(99.3) | 99.0(99.7) | 97.9(98.3) | 96.1(96.9) | 98.7(98.7) | 98.5(98.2) | 96.2(96.8) | 99.4(−) |
| GD-1 | 98.3(−) | 98.2(98.8) | 99.0(99.6) | 97.8(97.8) | 95.4(96.0) | 98.3(97.4) | 98.5(98.2) | 96.3(97.1) | 99.1(−) |
| GD-A | 98.3(−) | 98.3(98.8) | 99.0(99.6) | 97.8(98.0) | 95.7(96.0) | 98.7(98.7) | 98.4(97.4) | 96.1(96.8) | 99.4(−) |
| GD-B | 98.3(−) | 99.8(99.8) | 99.8(99.8) | 99.4(98.9) | 99.6(99.6) | 99.1(98.7) | 99.9(99.6) | 99.2(99.1) | 99.8(−) |
| AJ1102 | 99.0(−) | 99.4(99.4) | 99.0(99.7) | 97.9(98.3) | 96.1(96.9) | 98.7(98.7) | 98.5(98.2) | 96.2(97.1) | 99.4(−) |
| SD-M | 98.0(−) | 97.9(98.4) | 97.8(99.4) | 94.0(92.9) | 92.8(91.3) | 96.1(94.8) | 97.9(97.8) | 95.9(96.6) | 98.5(−) |
| BJ-2011-1 | 99.3(−) | 99.7(99.6) | 99.6(99.7) | 99.4(99.1) | 98.8(99.1) | 98.7(98.7) | 99.6(98.7) | 99.3(99.3) | 99.4(−) |
| ZJCZ4 | 98.6(−) | 98.1(98.7) | 99.6(99.8) | 98.4(98.7) | 96.0(96.4) | 98.7(98.7) | 98.2(98.2) | 96.2(97.3) | 99.4(−) |
| CH/FJND-3/2011 | 99.0(−) | 99.3(99.2) | 99.1(99.6) | 97.4(97.1) | 99.1(99.1) | 98.3(98.7) | 99.4(99.6) | 99.0(99.1) | 99.1(−) |
| CH/FJZZ-9/2012 | 98.6(−) | 99.2(99.2) | 98.7(99.3) | 98.0(98.4) | 97.9(99.1) | 97.8(98.7) | 99.4(99.6) | 99.2(99.3) | 98.8(−) |
| CH/ZMDZY/11 | 98.3(−) | 99.4(99.5) | 98.5(99.7) | 98.8(98.6) | 98.8(99.1) | 97.0(96.1) | 99.7(99.1) | 98.6(98.9) | 98.8(−) |
| AH2012 | 99.0(−) | 99.5(99.6) | 99.2(99.3) | 99.3(99.1) | 98.8(99.1) | 98.7(98.7) | 99.6(99.6) | 98.9(98.6) | 98.5(−) |
| JS-HZ2012 | 99.3(−) | 99.9(99.8) | 99.9(99.9) | 99.5(99.3) | 99.6(99.6) | 99.1(98.7) | 99.9(99.6) | 99.2(99.3) | 98.5(−) |
| CH/GDGZ/2012 | 98.3(−) | 98.1(98.5) | 98.8(99.2) | 97.5(97.4) | 95.9(96.4) | 98.3(98.7) | 98.2(98.2) | 94.5(93.2) | 99.1(−) |
| CHGD-01 | 96.6(−) | 98.4(98.8) | 98.9(99.4) | 97.8(98.1) | 96.1(96.9) | 98.3(97.4) | 98.2(97.8) | 96.2(96.8) | 98.5(−) |
| 13-019349 | 99.0(−) | 99.2(99.4) | 99.2(99.4) | 99.0(99.0) | 99.0(99.6) | 98.7(98.7) | 99.9(99.6) | 99.1(99.1) | 99.4(−) |
| IA1 | 99.3(−) | 99.2(99.4) | 99.2(99.6) | 99.1(99.4) | 99.0(99.6) | 98.7(98.7) | 99.7(99.6) | 99.1(99.1) | 99.4(−) |
| IA2 | 99.3(−) | 99.2(99.4) | 99.2(99.7) | 99.1(99.3) | 99.0(99.6) | 98.7(98.7) | 99.9(99.6) | 99.0(98.1) | 99.4(−) |
| MN | 99.3(−) | 99.2(99.4) | 99.2(99.7) | 99.1(99.2) | 99.0(99.6) | 98.7(98.7) | 99.9(99.6) | 99.1(99.1) | 98.8(−) |
| USA/Colorado/2013 | 99.0(−) | 99.3(99.5) | 99.2(99.7) | 99.2(99.4) | 98.8(99.1) | 98.7(98.7) | 99.9(99.6) | 99.1(99.1) | 99.4(−) |
| USA/Indiana/17846/2013 | 99.0(−) | 99.2(99.4) | 99.2(99.3) | 99.1(99.4) | 98.7(99.1) | 98.7(98.7) | 99.9(99.6) | 99.1(99.1) | 99.4(−) |
| USA/Iowa/16465/2013 | 99.0(−) | 99.2(99.4) | 99.1(99.3) | 98.8(99.4) | 99.0(99.6) | 98.7(98.7) | 99.9(99.6) | 99.1(99.1) | 99.4(−) |
| USA/Iowa/18984/2013 | 99.3(−) | 99.2(99.4) | 99.2(99.4) | 99.1(99.4) | 99.0(99.6) | 98.7(98.7) | 99.9(99.6) | 99.1(99.1) | 99.4(−) |
| ISU13-19338E-IN-homogenate | 99.3(−) | 99.2(99.4) | 99.2(99.7) | 99.1(99.4) | 98.7(99.1) | 98.7(98.7) | 99.9(99.6) | 99.1(99.1) | 99.4(−) |
| ISU13-22038-IA-homogenate | 99.3(−) | 99.2(99.4) | 99.2(99.7) | 99.1(99.3) | 99.0(99.6) | 98.7(98.7) | 99.9(99.6) | 99.1(99.1) | 99.4(−) |