Table 3.
Sequence and intra-population diversity from viral culture supernatant and hamster liver samples for mutant strains Asibi E/Q27H, E/D155A, E/Q27H-D155A, E/Q27H-D28G-D155A, Ap7m E/Q27A, E/Q27N, E/T154A
| Strain name | Position (nt) | Protein | Mutation | Expected sequence (nt) | Observed sequence (nt) | Observed sequence (2nd variant) (nt) | AA change | Inoculum | Hamster | |||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1st variant proportion | 2nd variant proportion | Hamster no | 1st variant proportion | 2nd variant proportion | ||||||||
| Asibi E/Q27H | 59 | C | V20A | T | C | T | V→A | - | - | 4/5 | 70.8% | 29.1% |
| 1041 | 347 | N62K | T | G | T | N→K | - | - | 4/5 | 68.9% | 31.1% | |
| 3019 | NS1 | T229A | A | G | A | T→A | - | - | 1/5 | 70.4% | 29.6% | |
| Asibi E/D155A | 239 | C | V80A | T | C | T | V→A | 79.7% | 20.3% | 5/5 | 86.8% | 13.2% |
| 3863 | NS2A | V158A | T | C | T | V→A | 81.3% | 18.7% | - | - | - | |
| Asibi E/Q27H-D155A | 760 | prM | V133M | G | A | G | V→M | 74.0% | 25.7% | 4/5* | 91.1% | 8.8% |
| 2151 | E | - | A | G | A | - | 69.8% | 30.2% | 4/5* | 87.7% | 12.3% | |
| 3042 | NS1 | - | T | C | T | - | 70.2% | 29.8% | 4/5* | 89.8% | 10.2% | |
| 6717 | NS4A | - | A | G | A | - | 68.9% | 31.1% | - | - | - | |
| 7866 | NS5 | - | G | A | G | - | 68.9% | 30.1% | - | - | - | |
| 9883 | NS5 | T789A | A | G | A | T→A | 67.8% | 32.2% | - | - | - | |
| Asibi E/Q27H-D28G-D155A | 788 | prM | V142A | T | C | - | V→A | > 95% | - | 5/5 | > 95% | - |
| 936 | E | - | C | T | - | - | > 95% | - | 5/5 | > 95% | - | |
| 1305 | E | - | A | G | - | - | > 95% | - | 5/5 | > 95% | - | |
| 2065 | E | M404V | A | G | - | M→V | > 95% | - | 4/5* | > 95% | - | |
| 2661 | NS1 | - | T | C | T | - | - | - | 1/5 | 80.9% | 19.1% | |
| 3703 | NS2A | T105A | A | G | A | T→A | - | - | 1/5 | 80.3% | 19.7% | |
| 6195 | - | - | T | C | - | - | > 95% | - | - | - | - | |
| 7735 | NS5 | - | C | T | - | - | > 95% | - | - | - | - | |
| Ap7M E/Q27A | 360 | - | - | T | C | - | - | > 95% | - | - | - | - |
| 1697 | E | V281A | T | C | - | V→A | > 95% | - | - | - | - | |
| 2644 | NS1 | F104L | T | C | - | F→L | > 95% | - | - | - | - | |
| 4683 | - | - | C | T | - | - | > 95% | - | - | - | - | |
| 6824 | NS4B | L19S | T | C | - | L→S | > 95% | - | - | - | - | |
| Ap7M E/Q27N | 1455 | E | K200N | A | T | A | K→N | 61.7% | 38.2% | - | - | - |
| 2911 | NS1 | S192G | A | G | - | S→G | > 95% | - | - | - | - | |
| 6050 | - | - | A | G | - | - | > 95% | - | - | - | - | |
| Ap7M E/T154A | 3446 | NS2A | V19A | T | C | - | V→A | > 95% | - | 5/5 | > 95% | - |
For each reversion mutant, the changes found either in the complete coding sequence from the viral stock or in partial sequences from infected hamster liver homogenates are detailed above. For mutations identified in more than one sequence from hamster liver, 1st and 2nd variant proportions are given as means unless no 2nd variant was detected ( > 95%). Expected sequence refers either to that of plasmids or to that of primers (used for mutation introduction) that served for subgenomic fragment amplification. For Asibi E/Q27H-D155A and Asibi E/Q27H-D28G-D155A mutants, some mutations were found to be reverted in one out of the five hamsters as indicated by the asterisk (*). In this case, the 1st and 2nd variants proportions were not included for means’ calculation.