Table 2.
Missense variants annotated by SNPeff within DWV-A and DWV-B quasispecies populations across all samples
|
Annotated variants | |||||||
|---|---|---|---|---|---|---|---|
|
DWV-A | |||||||
|
Putative region |
Position |
Nucleotide change |
AA change |
P0 Allele frequency |
P1 Allele frequency |
P5 Allele frequency |
Additional characteristics |
|
LP |
1319 |
G>A |
Ala59Thr |
0 |
0.125 |
0.1087 |
L specific, minor variant by Passage 5 (P5) |
|
LP |
1412 |
A>G |
Thr90Ala |
0 |
0.25 |
0.2935 |
Sole variant in C lineage, minor variant in other lines |
|
LP |
1521 |
A>G |
Lys126Arg |
0 |
0 |
0.0870 |
P5 specific; Minor variant throughout |
|
LP / structural |
1765 |
G>T |
Gln207His |
0 |
0.125 |
0.0978 |
In VP2, possibly interacting with RNA genome; M lineage specific, minor variant by P5 |
|
Structural |
3405 |
C>T |
Ala754Val |
0 |
0.125 |
0.0761 |
In capsid protein spike; M lineage specific, minor variant by P5 |
|
Structural |
3638 |
A>G |
Asn832Asp |
0 |
0.125 |
0.1087 |
In capsid protein spike; L lineage specific, minor variant by P5 |
|
Structural |
3794 |
G>T |
Ala884Ser |
0 |
0.1875 |
0.0761 |
In capsid protein spike; in J lineage in Passage 1 (P1) but not P5, minor variant by P5 for M lineage |
|
Structural |
4490 |
T>G |
Ser1116Ala |
0 |
0.0625 |
0.0761 |
In VP3; Minor variant in P1 and P5 |
|
Non-structural |
6323 |
G>T |
Gly1727Cys |
0 |
0.125 |
0.1087 |
L lineage specific, minor variant by P5 |
|
Non-structural |
6398 |
G>A |
Val1752Ile |
0 |
0.1875 |
0.3804 |
Sole variant in C lineage, minor variant in other lines |
|
Non-structural |
6527 |
G>A |
Ala1795Thr |
0.5 |
0.1875 |
0.1304 |
Sole variant in N lineage, minor variant in others |
|
Non-structural |
6702 |
C>T |
Thr1853Ile |
0 |
0.0625 |
0.0761 |
Minor variant in M lineage |
|
Non-structural |
7713 |
A>T |
His2190Leu |
0 |
0 |
0.0870 |
Variant in a highly conserved residue in 3C protease - P5 specific in K lineage |
|
Non-structural |
8330 |
T>A |
Ser2396Thr |
0 |
0.125 |
0.0761 |
M specific; sole variant in P1, minor variant in Passage 5 |
|
Non-structural |
9181 |
G>A |
Met2679Ile |
0 |
0.1875 |
0.3804 |
In P1, only present in C lineage, then present in C,K,L, and M lineages by P5 |
|
Non-structural |
9561 |
A>G |
Lys2806Arg |
0 |
0.0625 |
0.0761 |
Variant in a highly conserved aa in motif VII of RDRP; M specific minor variant throughout |
|
DWV-B | |||||||
|
Putative region |
Location |
Nucleotide change |
AA change |
P0 Allele frequency |
P1 Allele frequency |
P5 Allele frequency |
Lineage or passage specific? |
|
LP |
1433 |
T>C |
Tyr106His |
0 |
0.3125 |
0.1196 |
Specific to C and E lineages (except for one P1 N) |
|
Structural |
2275 |
T>C |
Leu386Phe |
0 |
0.3125 |
0.0652 |
Only maintained in C lineage |
|
Non-structural |
8530 |
C>T |
Lys2471Asn |
0 |
0.125 |
0.0870 |
P lineage specific |
|
Non-structural |
9109 |
C>T |
Leu2664Phe |
0 |
0.25 |
0.1522 |
E and N lineage specific |
|
Non-structural |
9163 |
C>T |
Met2682Ile |
0 |
0.25 |
0.1522 |
E and N lineage specific |