Table 3.
Sequence analyses of CH6aORF_22m virus after the first and second passages.
| HCV | Passage (day) | E2 | NS3 | NS3 | NS5B | NS5B | NS5B |
|---|---|---|---|---|---|---|---|
| Nucleotide position | |||||||
| Recombinant specific | 1582 | 3698 | 5282 | 7997 | 8099 | 9162 | |
| H77 reference (AF009606) | 1578 | 3684 | 5268 | 7974 | 8076 | 9138 | |
| Recombinant nucleotide | T | C | A | G | C | G | |
| CH6aORF_22m recombinanta | |||||||
| First (10) | C/t | A | C | ⋅ | T | T | |
| Second (7) | C | A | C | A/G | T | T | |
| CH6aORF_26m | Second (5) | C | A | C | ⋅ | ⋅ | T |
| Amino acid position | |||||||
| Recombinant specific | 413 | 1120 | 1648 | 2553 | 2587 | 2941 | |
| H77 reference (AF009606) | 414 | 1115 | 1643 | 2545 | 2579 | 2933 | |
| Amino acid change | I-T | Q-K | K-Q | D-N | L | A-V |
Culture supernatant from CH6aORF_22m (Figure 4A) transfected Huh7.5.1-VISI-mCherry cells was passaged to naïve cells. The first- and second-passage viruses were sequenced for the ORF. Mutations identified in the viruses are listed. Two capital letter separated by a slash indicates a nucleotide quasispecies of 50/50 in sequencing reads. Dot (⋅), indicates no change for the original nucleotide. Nucleotides in shading indicate that these nucleotides were engineered into the recombinant plasmid. Sequence analysis of CH6aORF_26m revealed that no additional mutations were identified. aFour complete coding changes (I413T/Q1120K/K1648Q/A2941V) were engineered into Ch6aORF_22m to make CH6aORF_26m (Figure 4A).