TABLE 3.
Virus | Mutation no.a | Mutationb | Amino acid changec | Locationd |
---|---|---|---|---|
VUSS3p5c2 | 1 | C21149A | Pro102Thr | nsp16 CDS |
VUSS3p5c4 | 2 | A4608G | Asn635Asp | nsp3 CDS |
VUSS3p5c5 | 3 | C21149A | Pro102Thr | nsp16 CDS |
VUSS3p5c6 | 4 | A21515C | Met224Leu | nsp16 CDS |
rExoN1p5c1 | 5 | U150C | Silent | 5′ UTR |
6 | G1092A | Val48Ile | nsp2 CDS | |
7 | G17723A | Val455Ile | nsp13 CDS | |
8 | A21069U | Asp75Val | nsp16 CDS | |
9 | U24030C | None | S gene | |
10 | U25845C | None | S gene | |
11 | U28207C | None | ORF4b | |
rExoN1p5c2 | 12 | U694A | Leu162Gln | nsp1 CDS |
13 | U14122C | None | nsp12 CDS | |
14 | G15133A | None | nsp12 CDS | |
15 | A15706G | None | nsp12 CDS | |
16 | A17747G | Lys463Glu | nsp13 CDS | |
17 | A18802U | None | nsp14 CDS | |
18 | G19115A | Ala319Thr | nsp14 CDS | |
19 | U23407A | Silent | HE | |
20 | U25783A | Phe619Ile | S gene | |
21 | U26721C | None | S gene | |
22 | C28194U | Thr46Met | ORF4b | |
rExoN3p5c1 | 23 | G812U | None | nsp1 CDS |
24 | U2144A | None | nsp2 CDS | |
25 | U4081G | Ile459Ser | nsp3 CDS | |
26 | U13481C | None | nsp10 CDS | |
27 | G15375A | Arg600His | nsp12 CDS | |
28 | G17711A | Val451Met | nsp13 CDS | |
29 | U18772C | None | nsp14 CDS | |
30 | C27928A | Silent | IGR | |
31 | G27930U | Silent | IGR | |
32 | A27931C | Silent | IGR | |
33 | U insertione | Multiple | ORF4b | |
rExoN3p5c2 | 34 | A1342G | Glu131Gly | nsp2 CDS |
35 | C3337U | Ala211Val | nsp3 CDS | |
36 | U17227A | His289Gln | nsp13 CDS | |
37 | G17452A | None | nsp13 CDS | |
38 | A23139G | Silent | HE | |
39 | U24188C | Val87Ala | S gene |
Numbers refer to secondary mutations depicted in Fig. 5.
Nucleotide positions refer to the MHV-A59 complete genome sequence (GenBank accession no. AY910861).
Amino acid positions in nsps refer to residues in mature, processed nsps (i.e., the first residue after each viral proteinase cleavage site is renumbered as 1).
CDS, coding sequence; UTR, untranslated region; ORF4b, putative 11.7-kDa protein; HE, hemagglutinin-esterase pseudogene (not expressed) in MHV-A59; IGR, intergenic region between spike gene and ORF4.
A single U insertion was identified in a run of five consecutive U residues (nt 28104 to 28108) and is predicted to result in a frameshift relative to WT sequence and, consequently, in substitutions of His18Ser and Val19Cys and early termination after amino acid residue 19 in ORF4b.