TABLE 1.
Nucleotide changes in K33S-GPC rCan upon serial passage in the presence and absence of 1 mM AmCl
| Nucleotide(s) (nt) | Stock |
p11 no AmCl |
p21 AmCl |
|||
|---|---|---|---|---|---|---|
| nt changea (% reads) | Amino acid change | nt change (% reads) | Amino acid change | nt change (% reads) | Amino acid change | |
| S RNA | ||||||
| 5′ end | 1–8 missing | 1–8 missing | 1–8 missing | |||
| 186–202; 217 | K33S oligonucleotideb (≥98) | K33S oligonucleotide (≥98) | K33S oligonucleotide (≥98) | |||
| 590 | G→A (55) | GP1 A168T | ||||
| 863–883 | Delete codons T259DSSGKD265 | GP2 ΔFP | ||||
| 1127 | A→T (88) | GP2 I347F | ||||
| 1146 | T→C (39) | GP2 V353A | ||||
| 1401 | T→C (19) | GP2 F438S | ||||
| 1535 | A→G (35) | GP2 R483G | ||||
| 1655 | G→A (51) | NP A560T | ||||
| 2382 | T→C (40) | NP S317 silent | ||||
| 3406 (3′-UTR) | A→T (56) | A→T (38) | ||||
| 3′ end | 3407–3413 missing | 3411–3413 missing | ||||
| L RNA | ||||||
| 5′ end | 1–4 missing | 1–5 missing | ||||
| 150 | G→A (90) | Z A23T | ||||
| 4687 | A→G (49) | L N800D | ||||
| 3′ end | 7111–7114 missing | 7111–7114 missing | ||||
a
Changes present in ≥10% of reads relative to the sequence of reverse genetics plasmids used to construct rCan viruses (28). The raw RNA-Seq data originally were aligned to Candid#1 S and L RNA reference genomes (AY746353.1 and AY746354.1, respectively).
b
In addition to the K33S mutation, the mutagenic oligonucleotide introduced 4 synonymous nucleotide changes and an I35V change (see Materials and Methods and the text).