Table 2.
Sequence and intra-population diversity from viral culture supernatant and hamster liver samples for mutant strains Ap7M E/H27Q, E/G28D, E/A155D, E/R323K, E/R331K and NS2A/A48T
| 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 nb | 1st variant proportion | 2nd variant proportion | ||||||||
| E/H27Q | 315 | C | - | T | C | T | - | 65.0 % | 35.0 % | All | 87.1% (T) | 12.9% (C) |
| 1173 | E | - | C | T | C | - | 66.2% | 33.8% | All | 87.5% (C) | 12.4% (T) | |
| 2971 | NS1 | - | G | A | G | I→V | 60.2% | 39.7% | All | 87.7% (G) | 12.2% (A) | |
| 3270 | NS1 | - | T | C | T | - | 61.5% | 38.5% | All | 87.7% (T) | 12.3% (C) | |
| 3397 | NS2A | I3V | A | G | A | I→V | - | - | 2/5 | 60.5% | 39.5% | |
| 6880 | NS4B | A38T | G | A | G | A→T | 64.3% | 35.7% | - | - | - | |
| 7314 | NS4B | - | T | C | T | - | 60.7% | 39.3% | - | - | - | |
| E/G28D | - | - | - | - | - | - | - | - | - | - | - | - |
| E/A155D | - | - | - | - | - | - | - | - | - | - | - | - |
| E/R323K | 647 | prM | T95M | C | T | C | T→M | 64.0% | 35.9% | All | 90.1% | 9.9% |
| 965 | E | D37G | A | G | A | D→G | 89.3% | 10.6% | All | > 95% | - | |
| 2696 | NS1 | N121S | A | G | A | N→S | 89.5% | 10.5% | All | > 95% | - | |
| 4107 | NS2B | - | A | G | A | - | 87.8% | 12.2% | - | - | - | |
| 5529 | NS3 | - | C | T | C | - | 88.5% | 11.1% | - | - | - | |
| 8389 | NS5 | T291A | A | G | A | T→A | 87.4% | 12.6% | - | - | - | |
| 9798 | NS5 | - | A | G | A | - | 87.8% | 12.2% | - | - | - | |
| E/R331K | 761 | prM | A133V | T | C | T | A→V | 71.5% | 28.5% | 3/5 | 87.2% | 12.8% |
| 1275 | E | - | A | G | A | - | 75.0% | 25.0% | All | 85.0% | 15.0% | |
| NS2A/A48T | 1051 | E | T66A | A | G | A | A→T | - | - | 1/5 | 50.9% | 49% |
| 1447 | E | M198L | A | C | A | L→M | - | - | 1/5 | 51.2% | 48.7% | |
| 1653 | E | - | G | A | G | - | - | - | 1/5 | 52.3% | 47.7% | |
| 2661 | NS1 | - | C | T | C | - | > 95% | - | All | > 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 variants proportions are given as means. Expected sequence refers to that of plasmids that served as templates for subgenomic fragment amplification while producing viruses thanks to the ISA method.