Table 3.
Sequence analysis of Asibi and Asibi-derived re-encoded viruses.
| Strain name | Re-encoded region | Position (nt) | Protein | Consensus mutation | Expected sequence (nt) | Observed sequence (first variant (nt)) | Observed sequence (second variant (nt)) | First variant proportion (per cent) | Second variant proportion (per cent) |
|---|---|---|---|---|---|---|---|---|---|
| Asibi | – | – | – | – | – | – | – | – | – |
| rTs1 | 3,927–6,753 | – | – | – | – | – | – | – | – |
| rTs2 | 3,927–6,753 | 5,430 | – | – | C | T | C | 77.5 | 22.3 |
| 5,442 | – | – | C | T | C | 82.0 | 18.0 | ||
| rTs3 | 3,927–6,753 | 4,357 | NS2B | M99V | A | G | A | 78.3 | 21.7 |
| 9,150 | – | – | A | G | A | 78.5 | 21.5 | ||
| rUA | 3,927–6,753 | – | – | – | – | – | – | – | – |
| rCG | 3,924–6,750 | 4,396 | NS2B | F112L | T | C | T | 88.2 | 11.8 |
| 5,430 | – | – | C | T | – | >95 | – | ||
| 5,667 | – | – | A | G | – | >95 | – | ||
| 6,082 | NS3 | C544R | T | C | – | >95 | – | ||
| rSS | 3,939–6,759 | 561 | – | – | T | C | – | >95 | – |
| 3,190 | NS1 | I286V | A | G | – | >95 | – | ||
| 4,308 | – | – | G | T | – | >95 | – | ||
| 4,623 | – | – | A | G | – | >95 | – | ||
| 6,012 | – | – | A | G | – | >95 | – | ||
| rN | 3,924–6,750 | – | – | – | – | – | – | – | – |
| rTCG | 3,939–6,759 | 2,468 | NS1 | I44T | T | C | – | >95 | – |
| 2,795 | NS1 | Q154R | A | G | – | >95 | – | ||
| 7,629 | – | – | T | C | – | >95 | – | ||
| 8,565 | – | – | T | C | – | >95 | – | ||
| 8,916 | – | – | T | C | – | >95 | – | ||
| 9,297 | – | – | T | C | – | >95 | – | ||
| rTs4 | 3,927–9,765 | – | – | – | – | – | – | – | – |
Note: For each virus, the consensus changes found in the CDS from the viral stock are detailed above. The expected sequence refers to that of plasmids that served for subgenomic fragment amplification while producing viruses using the ISA method. Only consensus mutations associated with major variants (CNP>75%) are described. Amino Acid (AA) positions are given with reference to the beginning of mature protein sequence (i.e., AA position 107 in prM, written prM 107, corresponds to AA position 228 within the precursor polyprotein). A detailed map of protein positions within the YFV polyprotein sequence is provided in the supplementary Table S11.