Table 1.
SARS-CoV-2 polymorphic sites under the study
Twenty-six polymorphic sites with <50 % ambiguous bases and aggregated minor allele frequencies of >5 % of the collected sequences were analysed in our analyses. Sites with co-occurring variants, i.e. those with pairwise uncertainty coefficients of >0.90 (Table S5), were grouped together for analysis.
|
Nucleotide position* |
Nucleotide grouping* |
Reference variant [frequency (%)]* |
Alternative variant [frequency (%)] |
Gene location |
Substitution type |
Amino acid change† |
|---|---|---|---|---|---|---|
|
313 |
313 |
C(70.18) |
T(29.66), N(0.1), –(0.03), Y(0.03) |
ORF1ab:NSP1 |
Synonymous |
L16 |
|
1059 |
1059 |
C(91.43) |
T(8.47), Y(0.07), N(0.03) |
ORF1ab:NSP2 |
Non-synonymous |
T85I |
|
3037 |
3037 |
C(17.71) |
T(82.16), N(0.07), Y(0.07) |
ORF1ab:NSP3 |
Synonymous |
F106 |
|
11 083 |
11 083 |
G(92.62) |
T(6.79), N(0.56), K(0.03) |
ORF1ab:NSP6 |
Non-synonymous |
L37F |
|
18 877 |
18 877 |
C(94.21) |
T(5.76), N(0.03) |
ORF1ab:NSP14 |
Synonymous |
L280 |
|
20 268 |
20 268 |
A(93.02) |
G(6.59), N(0.4) |
ORF1ab:NSP15 |
Synonymous |
L216 |
|
23 403 |
23 403 |
A(18.21) |
G(81.53), N(0.2), R(0.07) |
S |
Non-synonymous |
D614G |
|
25 563 |
25 563 |
G(83.88) |
T(14.96), C(1.06), N(0.1) |
ORF3a |
Non-synonymous |
Q57H |
|
26 730 |
26 730 |
G(94.64) |
A(5.1), T(0.13), C(0.07), N(0.07) |
M |
Non-synonymous |
V70I, V70F, V70L |
|
26 735 |
26 735 |
C(94.87) |
T(5.06), N(0.07) |
M |
Synonymous |
Y71 |
|
28 975 |
28 975 |
G(92.98) |
T(6.29), C(0.53), N(0.2) |
N |
Non-synonymous |
M234I |
|
29 692 |
29 692 |
G(92.65) |
T(5.66), –(1.42), N(0.26) |
3′UTR |
Non-coding |
– |
|
241 |
241/14 408 |
C(16.95) |
T(82.75), G(0.13), A(0.07), Y(0.07), –(0.03) |
5′UTR |
Non-coding |
– |
|
14 408 |
C(17.28) |
T(82.36), Y(0.2), N(0.17) |
ORF1ab:RDRP |
Non-synonymous |
P323L |
|
|
8782 |
8782/28 144 |
C(92.98) |
T(6.92), N(0.1) |
ORF1ab:NSP4 |
Synonymous |
S76 |
|
28 144 |
T(93.25) |
C(6.75) |
ORF8 |
Non-synonymous |
L84S |
|
|
18 167 |
18167/21 518 |
C(94.14) |
T(5.79), A(0.07) |
ORF1ab:NSP14 |
Non-synonymous |
P43L, P43H |
|
21 518 |
G(93.88) |
T(5.83), N(0.3) |
ORF1ab:NSP16 |
Non-synonymous |
R287I |
|
|
28 881 |
28 881/28 882/28 883 |
G(49.75) |
A(49.85), N(0.3), R(0.1) |
N |
Non-synonymous |
R203K, K204R |
|
28 882 |
G(49.95) |
A(49.65), N(0.26), R(0.1), T(0.03) |
||||
|
28 883 |
G(50.05) |
C(49.59), N(0.26), S(0.1) |
||||
|
4346 |
4346/9286/10 376/14 708/28 725 |
T(94.24) |
C(5.76) |
ORF1ab:NSP3 |
Non-synonymous |
S543P |
|
9286 |
C(94.11) |
T(5.79), N(0.1) |
ORF1ab:NSP4 |
Synonymous |
N244 |
|
|
10 376 |
C(93.88) |
T(6.06), N(0.07) |
ORF1ab:NSP5 |
Non-synonymous |
P108S |
|
|
14 708 |
C(94.17) |
T(5.79), N(0.03) |
ORF1ab:RDRP |
Non-synonymous |
A423V |
|
|
28 725 |
C(94.11) |
T(5.86), N(0.03) |
N |
Non-synonymous |
P151L |
*With respect to the reference SARS-CoV-2 genome (RefSeq accession number: NC_045512.2).
†Reported for non-ambiguous base changes only.