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Tables of mutating sites in Spike, updated daily

Last update: May 19, 2022

Dates of current data


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Collection dates: 2021-11-20 - 2022-05-17

Table 1A. Table of sites with common mutations, found with a frequency of >0.003. (Within the ACE2 contact region, the frequency threshold for inclusion is lower, >0.001.)

Note: The mutation D614G is not included in this summary; it is now the globally dominant form and can be readily tracked using many other tools at this site.

# of seqs: 2,817,963

oriposmutcountfrequency
L5#1130.0000401
-490.0000174
F329660.0116985
I740.0000263
P10.0000004
S10.0000004
V10.0000004
X16640.0005905
Y10.0000004
L18-160.0000057
F73040.0025919
H70.0000025
I950.0000337
K20.0000007
P11690.0004148
R160.0000057
S50.0000018
T10.0000004
V520.0000185
X2570.0000912
T19#20.0000007
-140.0000050
A130.0000046
G430.0000153
I9783580.3471862
K1530.0000543
L4280.0001519
P10.0000004
R7069470.2508716
S240.0000085
V10.0000004
X42630.0015128
L24$30.0000011
-9440960.3350278
F6860.0002434
I170.0000060
M10.0000004
S8650.0003070
V280.0000099
X47320.0016792
Y10.0000004
P25#30.0000011
-9451820.3354132
A30.0000011
H180.0000064
L2990.0001061
R50.0000018
S6020.0002136
T5610.0001991
X49860.0017694
P26#32900.0011675
$30.0000011
-9411800.3339930
A10.0000004
C10.0000004
D10.0000004
F50.0000018
H1840.0000653
I6630.0002353
L12660.0004493
N220.0000078
Q410.0000145
R500.0000177
S22200.0007878
T280.0000099
V10.0000004
X54370.0019294
A27#120.0000043
-10530.0003737
D120.0000043
E120.0000043
G100.0000035
I40.0000014
K320.0000114
P120.0000043
S9428120.3345722
T1470.0000522
V8410.0002984
X80990.0028741
Y10.0000004
V36#40.0000014
-50.0000018
A40.0000014
F103360.0036679
I1070.0000380
L50.0000018
X1070.0000380
A67#40.0000014
-2000.0000710
D250.0000089
F860.0000305
G150.0000053
I10.0000004
L30.0000011
P20.0000007
S12210.0004333
T210.0000075
V11200110.3974541
X19480.0006913
H69#2320.0000823
-11143090.3954307
D50.0000018
F20.0000007
I50.0000018
L1160.0000412
N2050.0000727
P30.0000011
Q20.0000007
R730.0000259
S20.0000007
T1170.0000415
X97460.0034585
Y16330.0005795
V70#33700.0011959
-11105380.3940925
A3280.0001164
D20.0000007
F14860.0005273
G320.0000114
I38180.0013549
K110.0000039
L1230.0000436
T120.0000043
X96600.0034280
T95#10.0000004
-50.0000018
A770.0000273
F50.0000018
I14771130.5241776
L180.0000064
M110.0000039
N1750.0000621
P30.0000011
S810.0000287
V1370.0000486
X81670.0028982
S112-20.0000007
A660.0000234
F110.0000039
L102280.0036296
M20.0000007
P790.0000280
T40.0000014
W20.0000007
X2890.0001026
G142#280.0000099
-13570.0004816
A110.0000039
D27052090.9599874
E540.0000192
H130.0000046
I10.0000004
L10.0000004
N410.0000145
P10.0000004
R10.0000004
S20.0000007
T370.0000131
V470.0000167
X462620.0164168
Y520.0000185
V143#260.0000092
-11115570.3944541
A340.0000121
D780.0000277
F2570.0000912
G30.0000011
H10.0000004
I1360.0000483
K10.0000004
L30.0000011
P4170.0001480
S10.0000004
T120.0000043
X89790.0031863
Y144#1710.0000607
$20.0000007
-11137620.3952366
C50.0000018
D10.0000004
F240.0000085
H340.0000121
I10.0000004
K10.0000004
L110.0000039
N40.0000014
P6190.0002197
Q1160.0000412
R150.0000053
S170.0000060
T30.0000011
W20.0000007
X86220.0030597
Y145#810.0000287
-11105380.3940925
C60.0000021
D4350.0001544
F10.0000004
H655040.0232452
K20.0000007
N3050.0001082
P20.0000007
Q10.0000004
T10.0000004
V10.0000004
W10.0000004
X81360.0028872
E156#6070.0002154
-2650.0000940
A1640.0000582
D690.0000245
F10.0000004
G6970120.2473460
K200.0000071
Q760.0000270
V510.0000181
X78230.0027761
F157#340.0000121
-6982960.2478017
C20.0000007
G10.0000004
L19130.0006789
S7630.0002708
V10.0000004
X86090.0030550
Y50.0000018
R158#4270.0001515
$110.0000039
-6971480.2473943
F10.0000004
G2810.0000997
I120.0000043
K120.0000043
M10.0000004
S280.0000099
T60.0000021
X92310.0032758
Y50.0000018
G181#20.0000007
-30.0000011
A7620.0002704
E4540.0001611
L70.0000025
R6690.0002374
V73020.0025912
X2280.0000809
N211#2130.0000756
-10965200.3891180
A10.0000004
D300.0000106
E780.0000277
G860.0000305
H270.0000096
I5590.0001984
K4150.0001473
R10.0000004
S1720.0000610
T70.0000025
V10.0000004
X126790.0044993
Y160.0000057
L212$800.0000284
-86910.0030841
A20.0000007
C4410.0001565
F630.0000224
G10.0000004
I10919650.3875015
K50.0000018
M20.0000007
N10.0000004
P60.0000021
R70.0000025
S29030.0010302
T620.0000220
V710.0000252
X90660.0032172
V213#70.0000025
$10.0000004
-4510.0001600
A6800.0002413
D190.0000067
E4130.0001466
F60.0000021
G9819450.3484592
L6550.0002324
M970.0000344
R70.0000025
S40580.0014400
T10.0000004
X18840.0006686
A222#10.0000004
-10.0000004
F40.0000014
I170.0000060
L10.0000004
P550.0000195
S10840.0003847
T610.0000216
V882670.0313230
X5230.0001856
G339-10.0000004
A300.0000106
C110.0000039
D21003770.7453529
E140.0000050
H80.0000028
K90.0000032
N4030.0001430
P10.0000004
S1150.0000408
T10.0000004
V320.0000114
X12560.0004457
Y340.0000121
R346-110.0000039
A10.0000004
E80.0000028
G1320.0000468
I2390.0000848
K6410720.2274948
N30.0000011
Q10.0000004
S3820.0001356
T9990.0003545
V10.0000004
X45780.0016246
S371#40.0000014
-20.0000007
A80.0000028
F9675600.3433544
H10.0000004
I460.0000163
L11095980.3937589
N10.0000004
P1810.0000642
R10.0000004
T40.0000014
X193830.0068784
Y3260.0001157
S373#10.0000004
-10.0000004
A70.0000025
L1530.0000543
P20968910.7441159
Q50.0000018
T20.0000007
X16780.0005955
S375#20.0000007
-90.0000032
A310.0000110
C30.0000011
F20954610.7436084
I10.0000004
L20.0000007
N10.0000004
P70.0000025
V30.0000011
X24420.0008666
Y180.0000064
T376#20.0000007
-50.0000018
A9785180.3472430
I5010.0001778
K20.0000007
N280.0000099
S610.0000216
V50.0000018
X25260.0008964
D405#10.0000004
-20.0000007
A30.0000011
E40.0000014
G170.0000060
H70.0000025
N9808850.3480830
S30.0000011
V10.0000004
X20670.0007335
Y110.0000039
R408G90.0000032
I1000.0000355
K110.0000039
N10.0000004
S9585820.3401684
T80.0000028
X167150.0059316
K417#30.0000011
E50.0000018
H270.0000096
I2130.0000756
M20.0000007
N20082250.7126513
Q10.0000004
R170.0000060
S110.0000039
T45610.0016185
X300920.0106786
Y50.0000018
N440#20.0000007
-10.0000004
D80.0000028
H10.0000004
I250.0000089
K19949220.7079305
R120.0000043
S20.0000007
T90.0000032
X441930.0156826
Y610.0000216
G446-30.0000011
A90.0000032
D720.0000256
F10.0000004
I200.0000071
N1250.0000444
R2450.0000869
S10843800.3848099
T190.0000067
V25380.0009007
X41660.0014784
L452#10.0000004
-10.0000004
M22220.0007885
P20.0000007
Q239970.0085157
R7169150.2544089
W490.0000174
X19630.0006966
S477-10.0000004
D610.0000216
G970.0000344
I13450.0004773
K490.0000174
N20957530.7437120
R620.0000220
T240.0000085
X16470.0005845
T478#20.0000007
$10.0000004
-10.0000004
E1020.0000362
G10.0000004
I100.0000035
K28072840.9962104
N110.0000039
Q140.0000050
R2090.0000742
X8120.0002882
E484-20.0000007
A20938570.7430392
D560.0000199
G570.0000202
H10.0000004
K6550.0002324
P1230.0000436
Q41770.0014823
R60.0000021
S1230.0000436
T990.0000351
V10860.0003854
X16420.0005827
Q493#30.0000011
-10.0000004
E180.0000064
G20.0000007
H450.0000160
K150.0000053
L550.0000195
P30.0000011
R20915640.7422255
V10.0000004
X17890.0006349
G496-30.0000011
C20.0000007
D10.0000004
I40.0000014
N1590.0000564
S11126560.3948441
T290.0000103
V70.0000025
X20020.0007104
Q498#20.0000007
$20.0000007
-80.0000028
D20.0000007
H30.0000011
I10.0000004
K10.0000004
L60.0000021
P10.0000004
R20912140.7421013
S10.0000004
X38370.0013616
Y110.0000039
N501#20.0000007
$10.0000004
-170.0000060
C40.0000014
D10.0000004
F70.0000025
G10.0000004
H40.0000014
I290.0000103
K50.0000018
L10.0000004
M10.0000004
Q40.0000014
R10.0000004
S2360.0000837
T3110.0001104
W10.0000004
X9120.0003236
Y20949670.7434331
Y505#40.0000014
-220.0000078
F20.0000007
H20929700.7427244
X11830.0004198
T547#10.0000004
A290.0000103
E10.0000004
I10880.0003861
K11208130.3977387
R140.0000050
S20.0000007
X13740.0004876
Q613$10.0000004
-10.0000004
E7070.0002509
H105420.0037410
K60.0000021
L40.0000014
P10.0000004
R210.0000075
X900.0000319
H655#10.0000004
F480.0000170
L60.0000021
N10.0000004
P10.0000004
Q10.0000004
R400.0000142
X6890.0002445
Y21052250.7470733
Q677$20.0000007
-200.0000071
E11490.0004077
G10.0000004
H94710.0033609
K290.0000103
L610.0000216
P360.0000128
R780.0000277
X1250.0000444
Y40.0000014
N679-140.0000050
D40.0000014
H20.0000007
I1740.0000617
K21039380.7466166
M70.0000025
Q40.0000014
R260.0000092
S1070.0000380
T1980.0000703
V10.0000004
X9280.0003293
Y800.0000284
P681#20.0000007
-50.0000018
C30.0000011
G10.0000004
H20973060.7442631
L630.0000224
N180.0000064
Q40.0000014
R7099350.2519320
S30.0000011
X25010.0008875
Y3250.0001153
A701E240.0000085
G10.0000004
P280.0000099
S4580.0001625
T830.0000295
V873200.0309869
X10260.0003641
S704#20.0000007
$10.0000004
A340.0000121
L304030.0107890
P2070.0000735
T80.0000028
X2650.0000940
Y10.0000004
N764D10.0000004
E210.0000075
F10.0000004
H30.0000011
I90.0000032
K20804640.7382865
Q40.0000014
R190.0000067
S10.0000004
T10.0000004
X125030.0044369
Y60.0000021
D796-10.0000004
A30.0000011
C50.0000018
F30.0000011
G1270.0000451
H3420.0001214
I20.0000007
N480.0000170
V40.0000014
X25450.0009031
Y21007250.7454764
I850-10.0000004
F160.0000057
L109690.0038925
M50.0000018
N30.0000011
S60.0000021
T490.0000174
V1220.0000433
X1250.0000444
N856#40.0000014
$30.0000011
-10.0000004
G10.0000004
I10.0000004
K11198030.3973803
L10.0000004
R20.0000007
S810.0000287
X21090.0007484
Y10.0000004
D950#40.0000014
-10.0000004
A40.0000014
E10.0000004
G130.0000046
H910.0000323
I10.0000004
N6878060.2440791
S220.0000078
T160.0000057
V10.0000004
X190030.0067435
Y120.0000043
Q954D10.0000004
H21038740.7465939
K140.0000050
L370.0000131
N80.0000028
R80.0000028
X11060.0003925
Y1560.0000554
N969#50.0000018
-20.0000007
K21041490.7466915
R150.0000053
S50.0000018
T40.0000014
X8780.0003116
L981#20.0000007
-10.0000004
F11195200.3972799
I790.0000280
P10.0000004
S370.0000131
V10.0000004
X17790.0006313
I1081F310.0000110
L220.0000078
M20.0000007
T90.0000032
V167160.0059319
X2280.0000809
V1104$10.0000004
A210.0000075
I1060.0000376
L105370.0037392
X1420.0000504
P1162#10.0000004
-20.0000007
A2250.0000798
L52010.0018457
Q890.0000316
R1320.0000468
S45240.0016054
T470.0000167
X2780.0000987
V1264#20.0000007
-10.0000004
A2090.0000742
E60.0000021
F250.0000089
G100.0000035
I60.0000021
L253620.0090001
M16290.0005781
X2750.0000976


Table 1B. Details regarding common mutations listed in A and their geographic locations.


oriposmutcodonmutcovariationslocation# of occurrences#seqs from local#seqs from state/province#seqs from country#seqs from continent
L5#CTT-TTA67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F,D614GAustralia_New-South-Wales_Sydney28589858939384Oceania 47974
L5#CTT-TTA67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F,D614GAustralia_Queensland3957239384Oceania 47974
L5#CTT-TTT19I,L24-,P25-,P26-,A27S,G142D,V213G,G339D,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,S477N,T478K,E484A,Q493R,Q498R,N501Y,Y505H,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K,D614GAustralia_Queensland11957239384Oceania 47974
L5#CTT-TTT19I,L24-,P25-,P26-,A27S,G142D,V213G,G339D,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,S477N,T478K,E484A,Q493R,Q498R,N501Y,Y505H,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K,D614GBelgium_Beveren11920763Europe 1758058
L5#CTT-TTT19R,G142D,E156G,F157-,R158-,L452R,T478K,P681R,D950N,D614GBelgium_Ghent1109120763Europe 1758058
L5#CTT-TTT19I,L24-,P25-,P26-,A27S,G142D,V213G,G339D,R346X,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,S477N,T478K,E484A,Q493R,Q498R,N501Y,Y505H,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K,D614GCzech-Republic_Prague_Praha117711595855Europe 1758058
L5#CTT-TTT19R,T95X,Y144X,E156G,F157-,R158-,L452R,T478K,P681R,N856X,D950N,D614GEcuador_Pichincha_Quito119116512South-America 33683
L5#CTT-TTL18F,T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,P681R,D950N,D614GFrance_Normandie1178874553Europe 1758058
L5#CTT-TTT19R,G142D,E156G,F157-,R158-,L452R,T478K,P681R,D950N,D614GFrance_Normandie3178874553Europe 1758058
L5#CTT-TTT19R,G142D,E156G,F157-,R158-,L452R,T478K,P681R,D950N,D614GIndonesia_Banten14918623Asia 165567
L5#CTT--TT19R,G142D,E156G,F157-,R158-,L452R,T478K,P681R,D950N,D614GKosovo_Peje114122Europe 1758058
L5#CTT-TTT19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,P681R,D950N,D614GLebanon_Nabatieh_Bint-Jbeil11453Asia 165567
L5#CTT--TT19R,G142D,E156G,F157-,R158-,L452R,T478K,P681R,D950N,D614GMontenegro_Bar119232Europe 1758058
L5#CTT-TTA67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F,D614GNew-Zealand_Auckland18015174Oceania 47974
L5#CTT-TTA67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,H655Y,N679K,P681H,A701V,N764K,D796Y,N856K,Q954H,N969K,L981F,D614GNew-Zealand_Canterbury17335174Oceania 47974
L5#CTT-TTA67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F,D614GNew-Zealand_Canterbury47335174Oceania 47974
L5#CTT-TTA67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F,D614GNew-Zealand_Counties-Manukau28175174Oceania 47974
L5#CTT-TTT19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,P681R,D950N,D614GNew-Zealand_Nelson-Marlborough1715174Oceania 47974
L5#CTT-TTT19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,P681R,D950N,D614GNew-Zealand_Waitemata53835174Oceania 47974
L5#CTT-TTA67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F,D614GSwitzerland_Bern3453027553Europe 1758058
L5#CTT-TTT19R,G142D,E156G,F157-,R158-,L452R,T478K,P681R,D950N,D614GUSA_California_Butte216996670688156North-America 798475
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L5FCTTTTTT19R,G142X,E156G,F157-,R158-,L452R,T478K,P681R,D950N,D614GArgentina12200South-America 33683
L5FCTTTTTT95I,E484K,A701V,D614GArgentina_Alberti112200South-America 33683
L5FCTTTTTL5F,A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,G339D,R346K,S371L,S373P,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F,D614GArgentina_Buenos-Aires18792200South-America 33683
L5FCTTTTTT19R,A67V,G142D,E156G,F157-,R158-,A222V,L452R,T478K,P681R,D950N,D614GArgentina_Buenos-Aires18792200South-America 33683
L5FCTTTTTT19R,A67V,G142X,E156G,F157-,R158-,A222V,L452R,T478K,P681R,D950N,D614GArgentina_Buenos-Aires38792200South-America 33683
L5FCTTTTTT19R,G142D,E156G,F157-,R158-,L452R,T478K,P681R,D950N,D614GArgentina_Buenos-Aires68792200South-America 33683
L5FCTTTTTT19R,G142X,E156G,F157-,R158-,L452R,T478K,P681R,D950N,D614GArgentina_Buenos-Aires248792200South-America 33683
L5FCTTTTTT19R,G142X,E156G,F157-,R158-,L452R,T478K,P681R,D950N,V1264L,D614GArgentina_Buenos-Aires18792200South-America 33683
L5FCTTTTTT19R,G142X,E156G,F157-,R158-,L452R,T478K,P681R,D950X,V1264L,D614GArgentina_Buenos-Aires18792200South-America 33683
.....
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