COVID-19 Viral Genome Analysis Pipeline
Enabled by data from
XSPIKE
eXplore the SPIKE protein sequence in the SARS CoV-2 virus
Last update: Jul 31, 2021
Download NOTE: We are NOT tracking insertions in Spike sequences in this output; insertions are still very rare, but are found on occasion.
In particular, we have found them associated with a few rare Pango lineages including:
| B.1.621 | T95I, insert144T, Y144S, Y145N, R346K, E484K, N501Y, D614G, P681H, D950N |
| A.2.5.2 | del141-143, insert215AGG, D215Y, L452R, D614G |
| AT.1 | P9L, del136-144, D215G, H245P, E484K, D614G, N679K, insert679GIAL, E780K |
| B.1.214.2 | insert214TDR, Q414K, N450K, D614G, T716I |
Where 'insert' indicates an insertion at the given position followed by the list amino acids added, and 'del' indicates a deletion. Global
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Evaluating 222078 sequences of length 1274
Sampled from 2021-05-27 to 2021-07-26.
Specified Date Range: (datetime.date(2021, 5, 27), datetime.date(2021, 7, 26))
Highest entropy sites for: Global
Site Entropy
681 0.8315
142 0.7054
157 0.6871
950 0.6763
452 0.6747
95 0.6726
158 0.6666
156 0.6609
19 0.6584
478 0.6530
501 0.6326
70 0.6221
144 0.6084
1118 0.5920
69 0.5918
570 0.5893
716 0.5886
982 0.5875
484 0.2492
222 0.2492
138 0.2299
417 0.2044
1027 0.1944
18 0.1942
20 0.1900
26 0.1828
655 0.1771
1176 0.1758
190 0.1747
5 0.1032
152 0.0911
253 0.0723
1264 0.0615
251 0.0595
701 0.0536
936 0.0473
80 0.0455
440 0.0440
477 0.0435
859 0.0420
98 0.0414
1162 0.0408
1191 0.0405
145 0.0399
677 0.0393
490 0.0366
939 0.0354
346 0.0354
250 0.0350
67 0.0345
Most highly correlated site-pairs for: Global
cramerV mutInfo
157 156 0.5008 0.6572
157 158 0.4997 0.6544
158 156 0.5076 0.6472
158 19 0.4960 0.6335
681 19 0.4966 0.6327
157 19 0.4964 0.6319
681 157 0.5029 0.6278
681 158 0.4950 0.6265
19 478 0.5715 0.6240
156 19 0.4935 0.6220
157 950 0.7919 0.6195
158 478 0.5690 0.6188
157 478 0.5688 0.6172
681 156 0.4919 0.6156
681 478 0.5700 0.6151
20 1176 0.9842 0.1661
1176 190 0.9830 0.1654
417 1176 0.9770 0.1615
655 1176 0.9753 0.1634
26 1176 0.9668 0.1610
138 1176 0.9618 0.1576
18 1176 0.9392 0.1543
1027 26 0.9251 0.1541
1027 20 0.9201 0.1520
1027 190 0.9184 0.1509
1027 1176 0.9131 0.1491
417 1027 0.9123 0.1479
1027 655 0.9113 0.1485
138 1027 0.8987 0.1438
1027 18 0.8874 0.1436
Most common patterns for local area, where Local = Global
111111
111111111222234444444556667789999011112
1122667899344455559255541457789075780153358216796
58906790058824526780201367027840105711696902782614
LLTTPAHVDTSDGYYWEFRRATPDRKNLSTEFNAHQPATTDSDSTDPVKV Global UK Eu-UK NAmer Asia Africa SAmer Ocean Local Exact Pct [Context]
200763 90116 62264 35233 7655 1032 4102 361 200763 <----------- Totals
..R......I..D...--G........R.K......R.....N....... 67813 62017 3922 1105 573 81 8 107 67813 48468 71% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
......--.....-..................YD..H.I....A.H.... 43427 4676 26504 9825 2184 89 105 44 43427 28495 65% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
..R.........D...--G........R.K......R.....N....... 25953 12296 6194 6854 391 201 5 12 25953 17692 68% [T19R,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........D...--G.V......R.K......R.....N....... 9431 4845 3201 994 329 47 1 14 9431 6714 71% [T19R,G142D,E156-,F157-,R158G,A222V,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta+A222V
.F.NS......Y.......S.....T....K.Y.Y.........I..F.. 7689 7 1223 3817 15 0 2626 1 7689 4883 63% [L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] P.1=Gamma
..R.............--G........R.K......R.....N....... 6320 164 3514 1467 919 184 71 1 6320 4408 69% [T19R,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R......I......--G........R.K......R.....N....... 3802 455 2387 625 201 22 3 109 3802 2525 66% [T19R,T95I,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
......--.....-.R................YD..H.I....A.H.... 2248 2 2220 22 1 0 0 3 2248 1867 83% [H69-,V70-,Y144-,W152R,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] Alpha+W152R
F.....--.....-..................YD..H.I....A.H.... 1682 48 923 676 33 1 1 0 1682 1095 65% [L5F,H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
......--.....-..................YD..H.I....A.H..N. 1151 5 36 1102 5 0 1 2 1151 861 74% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H,K1191N] B.1.1.7=Alpha
..R.............--G.V......R.K......R.....N....... 1051 88 506 259 182 15 0 1 1051 711 67% [T19R,E156-,F157-,R158G,A222V,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta+A222V
..R.........D...--G........R.K......R.....N......L 868 7 36 33 786 0 0 6 868 696 80% [T19R,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N,V1264L] B.1.617.2=Delta
..........................K...K.........NF..I..... 855 0 57 2 795 1 0 0 855 760 88% [I210T,N440K,E484K,D614G,D936N,S939F,T1027I]
..R.........D...--G...L....R.K......R.....N....... 848 663 179 1 5 0 0 0 848 501 59% [T19R,G142D,E156-,F157-,R158G,P251L,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R......I.HD...--G........R.K......R.....N....... 760 751 2 5 2 0 0 0 760 570 75% [T19R,T95I,D138H,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
......--..F..-..................YD..H.I....A.H.... 698 25 519 144 6 1 3 0 698 465 66% [H69-,V70-,S98F,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
F........I.............G......K......V............ 675 0 24 536 0 0 115 0 675 499 73% [L5F,T95I,D253G,E484K,D614G,A701V] B.1.526=Iota
.............................K......H............. 601 0 2 598 1 0 0 0 601 403 67% [T478K,D614G,P681H,T732A] B.1.1.519
.....................---...Q...S.......N.......... 544 3 87 97 1 0 356 0 544 321 59% [G75V,T76I,R246N,S247-,Y248-,L249-,T250-,P251-,G252-,D253-,L452Q,F490S,D614G,T859N] C.37=Lambda
......--...H.-..................YD..H.I....A.H.... 538 6 525 5 2 0 0 0 538 333 61% [H69-,V70-,D138H,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
..R......I..D...--G........R.K......R.....N...S... 504 502 0 0 2 0 0 0 504 375 74% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N,P1162S] B.1.617.2=Delta
.................................................. 474 13 290 137 26 0 2 6 474 253 53% [D614G] G-clade
.........I...SN.........K.....K.Y...H.....N....... 464 5 192 184 3 0 80 0 464 360 77% [T95I,Y144S,Y145N,R346K,E484K,N501Y,D614G,P681H,D950N]
......--..FH.-..................YD..H.I....A.H.... 464 9 108 340 5 0 2 0 464 333 71% [H69-,V70-,S98F,D138H,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
.F.NS......Y.......S.....T....K.Y.Y.H.......I..F.. 452 1 226 12 0 0 213 0 452 394 87% [L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,P681H,T1027I,V1176F] P.1=Gamma
..R.........D...--G.V......R.K......R.....N......L 448 8 27 399 13 0 1 0 448 153 34% [T19R,G142D,E156-,F157-,R158G,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] B.1.617.2=Delta+A222V
........G....-...S.........R...........N..H....... 438 0 1 437 0 0 0 0 438 276 63% [D80G,Y144-,F157S,L452R,D614G,T859N,D950H] B.1.526.1
..R....F.I..D...--G........R.K......R.....N....... 394 392 2 0 0 0 0 0 394 280 71% [T19R,V70F,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N]
......--.....-................K.YD..H.I....A.H.... 391 9 359 14 6 1 2 0 391 223 57% [H69-,V70-,Y144-,E484K,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] Alpha+E484K
F........I.............G....N..................... 388 0 2 385 1 0 0 0 388 258 66% [L5F,T95I,D253G,S477N,D614G,Q957R] B.1.526.2
..R......I..D.H.--G.V......R.K......R.....N....... 379 378 1 0 0 0 0 0 379 299 78% [T19R,T95I,G142D,Y145H,E156-,F157-,R158G,A222V,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta+A222V
......--.....-..................YD..HVI....A.H.... 371 2 323 45 1 0 0 0 371 243 65% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,A701V,T716I,S982A,D1118H] B.1.1.7=Alpha
..R....F....D...--G.V....N.R.K......R.....N....... 351 0 0 351 0 0 0 0 351 200 56% [T19R,V70F,G142D,E156-,F157-,R158G,A222V,K417N,L452R,T478K,D614G,P681R,D950N] B.1.617.2=AY.2
F.R......I..D...--G........R.K......R.....N....... 330 299 21 7 3 0 0 0 330 233 70% [L5F,T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
...I..--.....-..................YD..H.I....A.H.... 326 38 257 30 0 1 0 0 326 264 80% [T20I,H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] Alpha+T20I
.........I...-................K.....H............. 307 22 223 48 5 7 0 2 307 210 68% [T95I,Y144-,E484K,D614G,P681H,D796H] B.1.1.318
......--.......R........S..R.......H.............. 268 11 223 28 2 0 0 4 268 155 57% [S12F,H69-,V70-,W152R,R346S,L452R,D614G,Q677H,A899S] C.36
......--.....-..................YD.HH.I....A.H.... 254 66 168 20 0 0 0 0 254 72 28% [H69-,V70-,Y144-,N501Y,A570D,D614G,Q677H,P681H,V687L,T716I,S982A,D1118H] B.1.1.7=Alpha
......--.....-............S.....YD..H.I....A.H.... 253 0 253 0 0 0 0 0 253 220 86% [H69-,V70-,Y144-,N440S,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
..R.............--G.V......R.K......R.....N......L 249 0 14 206 29 0 0 0 249 102 40% [T19R,E156-,F157-,R158G,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] B.1.617.2=Delta+A222V
.....V--.....-................K....H.............. 245 1 112 123 2 5 0 2 245 105 42% [Q52R,A67V,H69-,V70-,Y144-,E484K,D614G,Q677H,F888L] B.1.525=Eta
..R......I......--G........R.K......R............. 244 10 166 50 4 5 1 8 244 128 52% [T19R,T95I,E156-,F157-,R158G,L452R,T478K,D614G,P681R]
.F......A................N....K.Y....V............ 241 2 128 17 26 68 0 0 241 86 35% [L18F,D80A,D215G,L242-,A243-,L244-,K417N,E484K,N501Y,D614G,A701V] B.1.351=Beta
............................N..................... 239 0 161 78 0 0 0 0 239 113 47% [S477N,D614G]
......--.....-..................YD..H......A.HS..L 232 0 232 0 0 0 0 0 232 189 81% [H69-,V70-,Y144-,Y449S,N501Y,A570D,D614G,P681H,S982A,D1118H,P1162S,V1264L]
..R.............--G........R.K......R............. 219 0 155 39 3 22 0 0 219 143 65% [T19R,E156-,F157-,R158G,L452R,T478K,D614G,P681R]
......--........................YD..H.I....A.H.... 202 0 192 8 2 0 0 0 202 144 71% [H69-,V70-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H]
....S.--.....-..............N.K.....H.......IH.... 198 0 24 11 154 9 0 0 198 148 74% [P26S,H69-,V70-,V126A,Y144-,L242-,A243-,L244-,H245Y,S477N,E484K,D614G,P681H,T1027I,D1118H] B.1.620
..R.............--G...L....R.K......R.....N....... 196 13 178 3 2 0 0 0 196 176 89% [T19R,E156-,F157-,R158G,P251L,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
F.R.........D...--G........R.K......R.....N....... 187 67 55 60 3 2 0 0 187 116 62% [L5F,T19R,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..............................K.....H.I........... 177 0 177 0 0 0 0 0 177 175 98% [R102G,E484K,S494P,D614G,P681H,T716I] B.1.575
F.....--.....-.................SYD..H.I....A.H.... 172 0 170 2 0 0 0 0 172 126 73% [L5F,H69-,V70-,Y144-,F490S,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] Alpha+F490S
.F.NS......Y.......S..........K.Y.Y.........I..F.. 168 0 2 166 0 0 0 0 168 122 72% [L18F,T20N,P26S,D138Y,R190S,E484K,N501Y,D614G,H655Y,T1027I,V1176F] P.1=Gamma
......--.I...-..................YD..H.I....A.H.... 168 0 138 28 2 0 0 0 168 116 69% [H69-,V70-,T95I,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
F........I.............G....N........V............ 164 0 0 163 0 0 1 0 164 125 76% [L5F,T95I,D253G,S477N,D614G,A701V] B.1.526=Iota
......--.....-.............M....YD..H.I....A.H.... 164 0 163 1 0 0 0 0 164 144 87% [H69-,V70-,Y144-,L452M,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
.F....--.....-..................YD..H.I....A.H.... 161 1 104 55 0 0 1 0 161 92 57% [L18F,H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
..R..V...I..D...--G........R.K......R.....N....... 152 151 1 0 0 0 0 0 152 128 84% [T19R,A67V,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R..............CG........R.K......R.....N....... 151 0 0 151 0 0 0 0 151 124 82% [T19R,F157C,R158G,L452R,T478K,D614G,P681R,D950N]
..R........................R.K......R.....N....... 140 1 48 24 65 2 0 0 140 100 71% [T19R,L452R,T478K,D614G,P681R,D950N]
..R......I..D...--G....G...R.K......R.....N....... 140 140 0 0 0 0 0 0 140 87 62% [T19R,T95I,G142D,E156-,F157-,R158G,D253G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
......--.....-..................YD..H.I.Y..A.H.... 136 0 127 9 0 0 0 0 136 127 93% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,D936Y,S982A,D1118H] B.1.1.7=Alpha
......--.....-..................YD..H.I..F.A.H.... 135 0 112 20 3 0 0 0 135 64 47% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S939F,S982A,D1118H] B.1.1.7=Alpha
..R.............--G........R.K......R.....N......L 132 0 14 7 111 0 0 0 132 108 81% [T19R,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N,V1264L] B.1.617.2=Delta
........A................N....K.Y....V............ 132 1 65 11 20 32 0 3 132 49 37% [D80A,D215G,L242-,A243-,L244-,K417N,E484K,N501Y,D614G,A701V] B.1.351=Beta
......--....V-..................YD..H.I....A.H.... 127 42 77 7 0 0 1 0 127 91 71% [H69-,V70-,G142V,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
......--.....-.................SYD..H.I....A.H.... 125 19 70 35 1 0 0 0 125 85 68% [H69-,V70-,Y144-,F490S,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] Alpha+F490S
.FR......I..D...--G........R.K......R.....N....... 122 118 3 0 1 0 0 0 122 92 75% [L18F,T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
......--...Y.-..................YD..H.I....A.H.... 119 2 113 3 0 1 0 0 119 72 60% [H69-,V70-,D138Y,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
......--.....-......V...........YD..H.I....A.H.... 118 1 70 47 0 0 0 0 118 64 54% [H69-,V70-,Y144-,A222V,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
........G....-...S.........R........H..N..H....... 115 0 0 115 0 0 0 0 115 91 79% [D80G,Y144-,F157S,L452R,D614G,P681H,T859N,D950H] B.1.526.1
......--.....-..................YD..H.I....A.HS... 115 1 99 13 2 0 0 0 115 57 49% [H69-,V70-,I100T,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H,P1162S] B.1.1.7=Alpha
......--.....-..................YD..H.I....A.H...L 110 3 98 7 1 1 0 0 110 58 52% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H,V1264L] B.1.1.7=Alpha
..R.........D...--G........R.K......R............. 108 0 69 35 4 0 0 0 108 66 61% [T19R,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R]
...............C...........R...................... 103 0 1 99 0 0 3 0 103 49 47% [S13I,W152C,L452R,D614G] B.1.429/7=Epsilon
.F.NS..............S.....T....K.Y.Y.........I..F.. 102 0 20 61 0 0 21 0 102 35 34% [L18F,T20N,P26S,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F]
..R........YD...--G.V......R.K......R.....N....... 96 95 1 0 0 0 0 0 96 80 83% [T19R,D138Y,G142D,E156-,F157-,R158G,A222V,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta+A222V
............--.............R...................... 95 0 2 93 0 0 0 0 95 41 43% [L141Y,G142-,V143-,Y144-,D215Y,L452R,D614G] A.2.5.2
....................................R............. 93 0 3 1 89 0 0 0 93 51 54% [N439K,D614G,P681R]
FF.......I.............G....N..................... 82 0 0 82 0 0 0 0 82 62 75% [L5F,L18F,T95I,D253G,S477N,D614G,Q957R] B.1.526.2
..R......I..D...--G......N.R.K......R.....N....... 81 4 39 26 12 0 0 0 81 59 72% [T19R,T95I,G142D,E156-,F157-,R158G,W258L,K417N,L452R,T478K,D614G,P681R,D950N] B.1.617.2=AY.1
FF.NS......Y.......S.....T....K.Y.Y.........I..F.. 81 0 12 38 0 0 31 0 81 61 75% [L5F,L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] P.1=Gamma
.........I..D..............R..Q.....R............. 78 4 63 0 9 2 0 0 78 52 66% [T95I,G142D,E154K,L452R,E484Q,D614G,P681R,Q1071H] B.1.617.1=Kappa
..R.........D...--G.V..A...R.K......R.....N....... 77 0 74 0 3 0 0 0 77 65 84% [T19R,G142D,E156-,F157-,R158G,A222V,D253A,L452R,T478K,D614G,P681R,D950N,D979E] B.1.617.2=Delta+A222V
.....S--.....-..................YD..H.I....A.H.... 77 11 50 14 0 1 1 0 77 34 44% [A67S,H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
......--.....-..................YD..R.I....A.H.... 75 0 67 7 0 1 0 0 75 53 70% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681R,T716I,S982A,D1118H]
..R......I..D...--G..N.....R.K......R.....N....... 73 73 0 0 0 0 0 0 73 57 78% [T19R,T95I,G142D,E156-,F157-,R158G,T250N,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
......--.....-..............I...YD..H.I....A.H.... 72 0 69 3 0 0 0 0 72 62 86% [H69-,V70-,Y144-,Y449H,S477I,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
..R......I..D...--G........R.K.....HR.....N....... 71 33 30 4 4 0 0 0 71 54 76% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,Q677H,P681R,D950N] B.1.617.2=Delta
.....V--.....-..................YD..H.I....A.H.... 69 8 55 5 1 0 0 0 69 43 62% [A67V,H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
......--.....-..................YD..H.I....A.H.F.. 68 6 27 34 1 0 0 0 68 52 76% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H,V1176F] B.1.1.7=Alpha
......--.....-.................LYD..H.I....A.H.... 67 45 15 5 2 0 0 0 67 55 82% [H69-,V70-,Y144-,F490L,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H]
......--.....-..................YD....I....A.H.... 67 0 61 6 0 0 0 0 67 49 73% [H69-,V70-,Y144-,N501Y,A570D,D614G,T716I,S982A,D1118H]
.....V--..F..-..................YD..H.I.Y..A.H.... 66 0 65 0 1 0 0 0 66 65 98% [A67V,H69-,V70-,S98F,Y144-,N501Y,A570D,D614G,P681H,T716I,D936Y,S982A,D1118H] B.1.1.7=Alpha
F.R.............--G........R.K......R.....N....... 65 0 29 30 4 2 0 0 65 41 63% [L5F,T19R,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.S....I..D...--G........R.K......R.....N....... 65 65 0 0 0 0 0 0 65 46 70% [T19R,P26S,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
.R.......I........S.......K.........H.......I..... 63 0 6 57 0 0 0 0 63 49 77% [L18R,T95I,R158S,N440K,D614G,P681H,A688V,S735A,T1027I]
......--.....-H.................YD..H.I....A.H.... 63 0 63 0 0 0 0 0 63 47 74% [H69-,V70-,Y144-,Y145H,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
..R.........D...--G.V......R.K......R.....N.....N. 61 10 1 50 0 0 0 0 61 57 93% [T19R,G142D,E156-,F157-,R158G,A222V,L452R,T478K,D614G,P681R,D950N,K1191N] B.1.617.2=Delta+A222V
.R.......I........S.................H.......I..... 61 0 0 61 0 0 0 0 61 31 50% [L18R,T95I,R158S,D614G,P681H,A688V,S735A,T1027I]
..R.............--G.V......R.K......R............. 60 0 20 12 27 1 0 0 60 35 58% [T19R,E156-,F157-,R158G,A222V,L452R,T478K,D614G,P681R]
.F.NS.--...Y.......S.....T....K.Y.Y.........I..F.. 60 0 0 0 0 0 60 0 60 56 93% [L18F,T20N,P26S,H69-,V70-,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] P.1=Gamma
..R.........D...--G.V.L....R.K......R.....N....... 59 1 56 0 2 0 0 0 59 32 54% [T19R,G142D,E156-,F157-,R158G,A222V,P251L,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta+A222V
......--.....-..................YDY.H.I....A.H.... 58 3 48 2 5 0 0 0 58 30 51% [H69-,V70-,Y144-,T284I,N501Y,A570D,D614G,H655Y,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
..R.........D...--G.V......R.K......R.....N...S... 56 54 0 2 0 0 0 0 56 45 80% [T19R,G142D,E156-,F157-,R158G,A222V,L452R,T478K,D614G,P681R,D950N,P1162S] B.1.617.2=Delta+A222V
..R......I..D...--G........R.K......R...H.N....... 55 40 1 14 0 0 0 0 55 42 76% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D936H,D950N] B.1.617.2=Delta
..R.........D...--G.VS.....R.K......R.....N....... 54 3 16 4 1 25 0 5 54 26 48% [T19R,G142D,E156-,F157-,R158G,A222V,T250S,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta+A222V
..R.........D...--G..I.....R.K......R.....N....... 54 2 41 6 3 0 0 2 54 37 68% [T19R,T29A,G142D,E156-,F157-,R158G,T250I,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
................................YD..H.I....A.H.... 54 0 32 21 0 0 1 0 54 38 70% [N501Y,A570D,D614G,P681H,T716I,S982A,D1118H]
..I...--.....-..................YD..H.I....A.H.... 54 0 45 7 2 0 0 0 54 33 61% [T19I,H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
......--.....-.............R....YD..H.I....A.H.... 54 53 0 1 0 0 0 0 54 38 70% [T22I,H69-,V70-,Y144-,L452R,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
..R.........D..L--G........R.K......R.....N....... 53 1 46 6 0 0 0 0 53 48 90% [T19R,G142D,W152L,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N,L1141W] B.1.617.2=Delta
F.....--.....-..................YD..H.I....A.Y.... 53 0 39 14 0 0 0 0 53 43 81% [L5F,H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118Y]
......--.....-L.................YD..H.I....A.H.... 51 39 12 0 0 0 0 0 51 43 84% [H69-,V70-,Y144-,Y145L,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
....S.--.....-..................YD..H.I....A.H.... 51 2 39 9 1 0 0 0 51 23 45% [P26S,H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
......--.....-................Q.YD..H.I....A.H.... 50 0 41 8 1 0 0 0 50 33 66% [H69-,V70-,Y144-,E484Q,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H]
..R...--........--G........R.K......R.....N....... 50 9 24 15 1 1 0 0 50 37 74% [T19R,H69-,V70-,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N]
..R..S...I..D...--G........R.K......R.....N....... 50 46 4 0 0 0 0 0 50 41 82% [T19R,A67S,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
................................Y................. 49 0 47 1 1 0 0 0 49 43 87% [N501Y,D614G]
.FR......I..D...--G........R.K......R....FN....... 49 49 0 0 0 0 0 0 49 35 71% [L18F,T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,S939F,D950N] B.1.617.2=Delta
......--Y....-..................YD..H.I....A.H.... 48 0 24 23 1 0 0 0 48 32 66% [H69-,V70-,D80Y,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
....................V............................. 47 0 47 0 0 0 0 0 47 22 46% [A222V,D614G] GV-clade
..R......I......--G........R.K.....HR.....N....... 47 0 45 2 0 0 0 0 47 36 76% [T19R,T95I,E156-,F157-,R158G,L452R,T478K,D614G,Q677H,P681R,D950N] B.1.617.2=Delta
...S.................---...Q...S.......N.......... 47 0 0 47 0 0 0 0 47 29 61% [T20S,G75V,T76I,R246N,S247-,Y248-,L249-,T250-,P251-,G252-,D253-,L452Q,F490S,D614G,T859N] C.37=Lambda
................---...........K.............I..... 47 2 44 1 0 0 0 0 47 34 72% [E156-,F157-,R158-,F306L,E484K,S494P,D614G,E780A,D839V,T1027I] B.1.1.523
......--.....-...L..............YD..H.I....A.H.... 47 0 0 47 0 0 0 0 47 31 65% [H69-,V70-,Y144-,F157L,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
.....D--.....-.................SYD..H.I....A.H.... 47 0 0 47 0 0 0 0 47 43 91% [A67D,H69-,V70-,Y144-,F490S,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] Alpha+F490S
.F.NS......Y.......S.....T....K.Y.Y.....Y...I..F.. 46 0 6 40 0 0 0 0 46 36 78% [L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,D936Y,T1027I,V1176F] P.1=Gamma
..R......I..D...--G........R.K......R.....N....F.. 45 43 0 0 2 0 0 0 45 39 86% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N,V1176F] B.1.617.2=Delta
......--.....-..................YD.RH.I....A.H.... 45 0 43 0 2 0 0 0 45 27 60% [H69-,V70-,Y144-,N501Y,A520S,A570D,D614G,Q677R,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
..R......I..D...--G........R.K......R.I...N....... 44 44 0 0 0 0 0 0 44 36 81% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,T716I,D950N] B.1.617.2=Delta
..R.............--G..I.....R.K......R.....N....... 42 2 33 3 3 1 0 0 42 26 61% [T19R,T29A,E156-,F157-,R158G,T250I,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........D..............R.K......R.....N....... 41 0 6 2 33 0 0 0 41 30 73% [T19R,G142D,L452R,T478K,D614G,P681R,D950N]
..R......I.................R.K......R.....N....... 41 0 10 21 10 0 0 0 41 13 31% [T19R,T95I,L452R,T478K,D614G,P681R,D950N]
F.R.........D...--G.V......R.K......R.....N....... 41 24 4 9 4 0 0 0 41 36 87% [L5F,T19R,G142D,E156-,F157-,R158G,A222V,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta+A222V
......--.....-..................YD..HSI....A.H.... 41 16 17 8 0 0 0 0 41 32 78% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,A701S,T716I,S982A,D1118H] B.1.1.7=Alpha
..R.............--G.VS.....R.K......R.....N....... 40 0 4 0 0 35 0 1 40 28 70% [T19R,E156-,F157-,R158G,A222V,T250S,L452R,T478K,D614G,P681R,L752X,D950N] B.1.617.2=Delta+A222V
..R......I..D...--G........R.K......R.....N...L... 40 35 0 5 0 0 0 0 40 20 50% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N,P1162L] B.1.617.2=Delta
.F.NS......Y.-.....S.....T....K.Y.Y.........I..F.. 39 0 4 14 0 0 21 0 39 20 51% [L18F,T20N,P26S,D138Y,Y144-,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] P.1=Gamma
...I......................K...K.........NF..I..... 39 0 0 0 39 0 0 0 39 38 97% [T20I,I210T,N440K,E484K,D614G,D936N,S939F,T1027I]
..R.............--G..........K......R.....N....... 38 0 36 2 0 0 0 0 38 38 100% [T19R,E156-,F157-,R158G,T478K,D614G,P681R,D950N]
..R......I..D...--G........R.K....Y.R.....N....... 38 23 1 13 1 0 0 0 38 27 71% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,H655Y,P681R,D950N] B.1.617.2=Delta
.....V--.....-...........R....K.YD..H.I....A.H..N. 38 0 0 38 0 0 0 0 38 34 89% [A67V,H69-,V70-,Y144-,K417R,E484K,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H,K1191N] Alpha+E484K
..R...............G........R.K......R.....N....... 37 0 0 37 0 0 0 0 37 31 83% [T19R,R158G,L452R,T478K,D614G,P681R,D950N]
..R.........D...--G..........K......R.....N....... 37 0 3 34 0 0 0 0 37 26 70% [T19R,G142D,E156-,F157-,R158G,T478K,D614G,P681R,D950N]
...............L..............K................... 36 0 0 1 35 0 0 0 36 29 80% [W152L,E484K,D614G,G769V] R.1
..R.........D...--G........R.KQ.....R.....N....... 35 4 0 28 2 1 0 0 35 22 62% [T19R,K77T,G142D,E156-,F157-,R158G,L452R,T478K,E484Q,D614G,P681R,D950N] B.1.617.2=Delta
..R......I..D...--G........R.K......R...N.N....... 35 35 0 0 0 0 0 0 35 31 88% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D936N,D950N] B.1.617.2=Delta
..R......I......--G......N.R.K......R.....N....... 35 1 30 3 1 0 0 0 35 17 48% [T19R,T95I,E156-,F157-,R158G,W258L,K417N,L452R,T478K,D614G,P681R,D950N] B.1.617.2=AY.1
......--...H.-.................SYD..H.I....A.H.... 35 0 2 0 23 10 0 0 35 32 91% [H69-,V70-,D138H,Y144-,F490S,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] Alpha+F490S
..R..............CG........R.K......R............. 34 0 0 34 0 0 0 0 34 28 82% [T19R,F157C,R158G,L452R,T478K,D614G,P681R]
..R.......F.D...--G........R.K......R.....N....... 34 29 2 2 1 0 0 0 34 24 70% [T19R,S98F,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R....F........--G.V....N.R.K......R.....N....... 34 0 0 34 0 0 0 0 34 27 79% [T19R,V70F,E156-,F157-,R158G,A222V,K417N,L452R,T478K,D614G,P681R,D950N] B.1.617.2=AY.2
..R......I..D...--G........R.K......R.....N......L 34 33 1 0 0 0 0 0 34 21 61% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N,V1264L] B.1.617.2=Delta
......--.......R........S..RN......H.............. 34 0 24 10 0 0 0 0 34 16 47% [S12F,H69-,V70-,W152R,R346S,L452R,S477N,D614G,Q677H,A845S,A899S] C.36
......--.....-.........G........YD..H.I....A.H.... 34 1 25 8 0 0 0 0 34 23 67% [H69-,V70-,Y144-,D253G,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
..R.........D...--G.V......R.K......R............. 33 0 27 1 5 0 0 0 33 13 39% [T19R,G142D,E156-,F157-,R158G,A222V,L452R,T478K,D614G,P681R]
..R......I..D...--G........R.K......R..I..N....... 32 30 0 2 0 0 0 0 32 28 87% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,T859I,D950N] B.1.617.2=Delta
.........I...SN.........KN....K.Y...H.....N....... 32 13 1 16 1 0 1 0 32 25 78% [T95I,Y144S,Y145N,R346K,K417N,E484K,N501Y,D614G,P681H,D950N]
.F..S......Y.......S.....T....K.Y.Y.........I..F.. 32 0 0 12 0 0 20 0 32 20 62% [L18F,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F]
............D..............R..Q.....R............. 31 2 0 1 3 1 0 24 31 20 64% [G142D,E154K,L452R,E484Q,D614G,P681R,Q1071H,H1101Y] B.1.617.1=Kappa
..R...--.....-.............R.K......R.....N....... 31 1 18 12 0 0 0 0 31 18 58% [T19R,H69-,V70-,Y144-,L452R,T478K,D614G,P681R,D950N]
..R......I..D..............R.K......R.....N....... 31 0 1 17 13 0 0 0 31 10 32% [T19R,T95I,G142D,L452R,T478K,D614G,P681R,D950N]
......--.....-..................YD..H.I....A.HL... 31 2 20 9 0 0 0 0 31 27 87% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H,P1162L] B.1.1.7=Alpha
.R.......I........S...........Q.....H.......I..... 30 0 0 30 0 0 0 0 30 22 73% [L18R,T95I,R158S,E484Q,D614G,P681H,A688V,S735A,T1027I]
....H.--.....-..................YD..H.I....A.H.... 30 1 1 28 0 0 0 0 30 13 43% [P26H,H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,L938F,S982A,D1118H] B.1.1.7=Alpha
..R......I..D...--G........RIK......R.....N....... 29 21 0 8 0 0 0 0 29 24 82% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,S477I,T478K,D614G,P681R,D950N] B.1.617.2=Delta
......--.....-..................YD..H.I....A.Y.... 29 0 20 9 0 0 0 0 29 17 58% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118Y]
.F.NS......Y.......S.....T....K.Y.Y.R.......I..F.. 28 0 0 2 0 0 26 0 28 23 82% [L18F,T20N,P26S,D138Y,R190S,K417T,T470N,E484K,N501Y,D614G,H655Y,P681R,T1027I,V1176F,C1235F] P.1=Gamma
...........................R.......H.............. 27 0 26 0 1 0 0 0 27 13 48% [S12F,L452R,A520S,D614G,Q677H,S689I]
......--.....-..................YD..H.I.H..A.H.... 27 10 14 2 1 0 0 0 27 17 62% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,D936H,S982A,D1118H] B.1.1.7=Alpha
......--.....-..................YD..H.I....A.HQ... 27 0 27 0 0 0 0 0 27 27 100% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H,P1162Q,Q1208H] B.1.1.7=Alpha
..R.............--G.V..A...R.K......R.....N....... 26 1 24 0 1 0 0 0 26 23 88% [T19R,E156-,F157-,R158G,A222V,D253A,L452R,T478K,D614G,P681R,D950N,D979E] B.1.617.2=Delta+A222V
..R..V......D...--G.V......R.K......R.....N....... 26 1 25 0 0 0 0 0 26 26 100% [T19R,A67V,G142D,E156-,F157-,R158G,A222V,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta+A222V
..R......I..D...--G........R.K......R............. 25 0 19 3 1 0 0 2 25 17 68% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R]
..R..S......D...--G........R.K......R.....N....... 25 1 21 2 0 1 0 0 25 21 84% [T19R,A67S,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R......I..D...--G........R.K......R...Y.N....... 25 22 3 0 0 0 0 0 25 19 76% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D936Y,D950N] B.1.617.2=Delta
F........I...SN.........K.....K.Y...H.....N....... 25 0 1 1 0 0 23 0 25 25 100% [L5F,T95I,Y144S,Y145N,R346K,E484K,N501Y,D614G,P681H,D950N]
.F.NS......Y.............T....K.Y.Y.........I..F.. 25 0 5 15 0 0 5 0 25 17 68% [L18F,T20N,P26S,D138Y,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F]
......--.....F..................YD..H.I....A.H.... 25 0 17 7 1 0 0 0 25 11 44% [H69-,V70-,V143-,Y144F,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H]
......-F.....-..................YD..H.I....A.H.... 25 7 10 7 1 0 0 0 25 20 80% [H69-,V70F,S71-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H]
..R....I....D...--G........R.K......R.....N....... 24 0 0 24 0 0 0 0 24 11 45% [T19R,V70I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N]
.F...--.......................KST......N.......... 24 0 8 16 0 0 0 0 24 24 100% [L18F,A67-,I68-,H69-,G257S,E484K,F490S,N501T,D614G,T859N]
F.....--...H.-..................YD..H.I....A.H.... 24 0 24 0 0 0 0 0 24 19 79% [L5F,H69-,V70-,D138H,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
......--.....-..............R...YD..H.I....A.H.... 24 0 22 2 0 0 0 0 24 17 70% [H69-,V70-,Y144-,S477R,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
......--.....-..V...............YD..H.I....A.H.... 24 0 24 0 0 0 0 0 24 21 87% [H69-,V70-,Y144-,E156V,N501Y,A570D,D614G,S680F,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
......--.....-..................YD..H.I......H.... 23 3 15 4 1 0 0 0 23 15 65% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,D1118H]
..R.............--G........R.K..Y...R.....N....... 23 0 23 0 0 0 0 0 23 21 91% [T19R,E156-,F157-,R158G,L452R,T478K,N501Y,D614G,P681R,D950N] B.1.617.2=Delta
..R......I..D...--G........R.K......R.....N.I..... 23 23 0 0 0 0 0 0 23 13 56% [T19R,T95I,G142D,E156-,F157-,R158G,L216F,L452R,T478K,D614G,P681R,D950N,T1027I,G1124V] B.1.617.2=Delta
.F.NS......Y.......S.....T....K.Y.YH........I..F.. 23 0 4 10 0 0 9 0 23 15 65% [L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,Q677H,T1027I,V1176F] P.1=Gamma
......--.....-........T.........YD..H.I....A.H.... 23 0 23 0 0 0 0 0 23 23 100% [H69-,V70-,Y144-,P251T,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
..G......I..D...--G........R.K......R.....N....... 22 21 1 0 0 0 0 0 22 15 68% [T19G,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N]
......--.....-..................YD..H.V....A.H.... 22 1 19 2 0 0 0 0 22 10 45% [H69-,V70-,Y144-,N501Y,A570D,D614G,T632I,P681H,T716V,G932V,S982A,D1118H]
......--.....-...................D..H.I....A.H.... 21 0 14 5 1 0 1 0 21 9 42% [H69-,V70-,Y144-,A570D,D614G,P681H,T716I,S982A,D1118H]
..R.........D...--G.V......R.K......RS....N....... 21 0 1 0 20 0 0 0 21 13 61% [T19R,G142D,E156-,F157-,R158G,A222V,L452R,T478K,D614G,P681R,A701S,D950N,A1078S] B.1.617.2=Delta+A222V
..R...Y..I..D...--G........R.K......R.....N....... 21 20 1 0 0 0 0 0 21 19 90% [T19R,H69Y,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
F.R......I.HD...--G........R.K......R.....N....... 21 21 0 0 0 0 0 0 21 19 90% [L5F,T19R,T95I,D138H,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
.F.NSS.....Y.......S.....T....K.Y.Y.........I..F.. 21 0 2 12 0 0 7 0 21 20 95% [L18F,T20N,P26S,A67S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] P.1=Gamma
...............C...........R........H............. 21 0 0 21 0 0 0 0 21 13 61% [S13I,W152C,W258L,L452R,D614G,P681H] B.1.429/7=Epsilon
......--.....-...............I..YD..H.I....A.H.... 21 0 19 2 0 0 0 0 21 8 38% [H69-,V70-,Y144-,T478I,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
.............-..................YD..H.I....A.H.... 20 0 17 1 1 1 0 0 20 16 80% [Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H]
............D..............R.K......H............. 20 0 20 0 0 0 0 0 20 9 45% [G142D,K182R,L452R,T478K,D614G,P681H,D796Y,C1235F]
..R.........D...--G........R.K....Y.R.....N....... 20 4 15 1 0 0 0 0 20 12 60% [T19R,G142D,E156-,F157-,R158G,L452R,T478K,D614G,H655Y,P681R,P792S,D950N] B.1.617.2=Delta
...........---................K................... 20 0 19 0 1 0 0 0 20 9 45% [P9L,C136-,N137-,D138-,P139-,F140-,L141-,G142-,V143-,Y144-,D215G,H245P,E484K,D614G,N679K,E780K]
......Y.G....-...S.........R...........N..H....... 20 0 0 20 0 0 0 0 20 14 70% [P25T,H69Y,D80G,Y144-,F157S,L452R,D614G,T791I,T859N,D950H] B.1.526.1
..R......I..D...--G........R.K......R.....N.....N. 19 18 0 1 0 0 0 0 19 12 63% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N,K1191N] B.1.617.2=Delta
..R.........D...--G.V......R.K.....HR.....N....... 19 2 12 2 2 0 0 1 19 7 36% [T19R,R21T,G142D,E156-,F157-,R158G,A222V,L452R,T478K,D614G,Q677H,P681R,D950N] B.1.617.2=Delta+A222V
F.R.........D...--G........R.K......R.....N......L 19 0 0 1 18 0 0 0 19 17 89% [L5F,T19R,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N,V1264L] B.1.617.2=Delta
..R...--...................R.K......R.....N....... 19 0 16 3 0 0 0 0 19 9 47% [T19R,H69-,V70-,L452R,T478K,D614G,P681R,D950N]
.........I...-................K.T...H............. 19 0 17 1 0 1 0 0 19 17 89% [T95I,Y144-,E484K,N501T,D614G,P681H,D796H] B.1.1.318
..R............................................... 18 0 18 0 0 0 0 0 18 17 94% [T19R,D614G]
..R......I.......CG........R.K......R.....N....... 18 0 0 18 0 0 0 0 18 16 88% [T19R,T95I,F157C,R158G,L452R,T478K,D614G,P681R,D950N]
..R.........D...--G........R.K......R.....N.....N. 18 3 5 10 0 0 0 0 18 9 50% [T19R,S112L,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N,K1191N] B.1.617.2=Delta
..R......I..D...--G........R.K......R....FN....... 18 15 0 1 2 0 0 0 18 11 61% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,S939F,D950N] B.1.617.2=Delta
..R......I..D-..--G........R.K......R.....N....... 18 15 3 0 0 0 0 0 18 10 55% [T19R,T95I,G142D,Y144-,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R....G.I..D...--G........R.K......R.....N....... 18 18 0 0 0 0 0 0 18 18 100% [T19R,V70G,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N]
........YI...-................K.....H............. 18 0 0 0 0 18 0 0 18 18 100% [D80Y,T95I,Y144-,W258L,E484K,D614G,P681H,D796H] B.1.1.318
.R....--.I........S...........K................... 18 0 0 18 0 0 0 0 18 7 38% [L18R,H69-,V70-,T95I,R158S,E484K,D614G,A688V,N764K,E1258D]
..R.........D...--G........R.K...S..R.....N....... 17 2 14 0 1 0 0 0 17 13 76% [T19R,G142D,E156-,F157-,R158G,L452R,T478K,A570S,D614G,P681R,D950N] B.1.617.2=Delta
..R.........D...--G........R.K......R...Y.N....... 17 3 2 10 2 0 0 0 17 9 52% [T19R,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D936Y,D950N] B.1.617.2=Delta
F........I...-.........G......K......V............ 17 0 3 5 0 0 9 0 17 14 82% [L5F,T95I,Y144-,D253G,E484K,D614G,A701V] B.1.526=Iota
.F.NS......Y.......S.....T....K.Y.Y.........I..F.L 17 0 1 11 0 0 5 0 17 10 58% [L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F,V1264L] P.1=Gamma
......--.....-..........K.......YD..H.I....A.H.... 17 0 17 0 0 0 0 0 17 14 82% [H69-,V70-,Y144-,R346K,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
..R.....Y...D...--G........R.K......R.....N....... 16 5 3 8 0 0 0 0 16 10 62% [T19R,D80Y,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R......I..D...--G.V......R.K......R.....N....... 16 10 3 2 1 0 0 0 16 9 56% [T19R,T95I,G142D,E156-,F157-,R158G,A222V,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta+A222V
..R.........D...--G........RGK......R.....N....... 16 0 0 16 0 0 0 0 16 10 62% [T19R,S112L,G142D,E156-,F157-,R158G,L452R,S477G,T478K,D614G,P681R,D950N] B.1.617.2=Delta
.................S..........N.K...Y.H...H......... 16 0 0 16 0 0 0 0 16 14 87% [T29I,F32L,M153T,F157S,G252V,S477N,E484K,D614G,H655Y,P681H,D936H,D1260H]
.........I...SN.........K.....K.Y...H............. 16 0 1 13 0 0 2 0 16 9 56% [T95I,Y144S,Y145N,R346K,E484K,N501Y,D614G,P681H]
..............................K.........NF..I..... 16 0 15 0 1 0 0 0 16 15 93% [I210T,E484K,D614G,D936N,S939F,T1027I]
F.....--.I...-..................YD..H.I....A.H.... 16 13 3 0 0 0 0 0 16 9 56% [L5F,H69-,V70-,T95I,Y144-,N501Y,A570D,V595I,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
......--...Y.-..................YD..HVI....A.H.... 16 0 16 0 0 0 0 0 16 8 50% [H69-,V70-,D138Y,Y144-,N501Y,A570D,D614G,P681H,A701V,T716I,S982A,D1118H] B.1.1.7=Alpha
..R.........D...--G........R.K......R.I...N....... 15 6 3 3 3 0 0 0 15 13 86% [T19R,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,T716I,D950N] B.1.617.2=Delta
.F.NS......Y.......S.....T....K.Y.Y.........I..FN. 15 0 13 1 0 0 1 0 15 12 80% [L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F,K1191N] P.1=Gamma
...........Y........................R............. 15 0 1 0 1 13 0 0 15 7 46% [D138Y,N450K,D614G,P681R]
......--...H....................YD..H.I....A.H.... 15 0 15 0 0 0 0 0 15 11 73% [H69-,V70-,D138H,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H]
F.....--.....-..................YD..H.I....A.H..N. 15 0 1 14 0 0 0 0 15 9 60% [L5F,H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H,K1191N] B.1.1.7=Alpha
......--.....-......S...........YD..H.I....A.H.... 15 0 10 5 0 0 0 0 15 15 100% [H69-,V70-,Y144-,A222S,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
.....V--.....-...........R....K.YD..HVI....A.H..N. 15 0 0 15 0 0 0 0 15 14 93% [A67V,H69-,V70-,Y144-,K417R,E484K,N501Y,A570D,D614G,P681H,A701V,T716I,S982A,D1118H,K1191N] Alpha+E484K
..R.......................................N....... 14 0 14 0 0 0 0 0 14 11 78% [T19R,D614G,D950N]
...........................R.K.................... 14 0 14 0 0 0 0 0 14 14 100% [L452R,T478K,D614G]
....................V........K......H............. 14 0 0 14 0 0 0 0 14 10 71% [A222V,T478K,D614G,P681H,T732A] B.1.1.519
..R......I...-..--G........R.K......R.....N....... 14 0 14 0 0 0 0 0 14 13 92% [T19R,T95I,Y144-,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R......IF.D...--G........R.K......R.....N....... 14 14 0 0 0 0 0 0 14 7 50% [T19R,T95I,S98F,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
........GI..D-................K.....H............. 14 14 0 0 0 0 0 0 14 9 64% [D80G,T95I,G142D,Y144-,N439K,E484K,D614G,P681H,I1130V,D1139H]
............--.R...........R...................... 14 0 0 14 0 0 0 0 14 3 21% [L141Y,G142-,V143-,Y144-,W152R,D215Y,T240I,A263S,L452R,D614G] A.2.5.2
........G....-...S.........R........Y..N..H....... 14 0 0 14 0 0 0 0 14 14 100% [D80G,Y144-,F157S,L452R,D614G,P681Y,T859N,D950H] B.1.526.1
......................................I........... 14 0 12 1 0 1 0 0 14 11 78% [Q414K,N450K,D614G,T716I] B.1.214.2
......--.....-..................YD..H.I....A...... 14 0 6 5 3 0 0 0 14 10 71% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A]
F.....--.....-..................YDY.H.I....A.H.... 14 0 13 1 0 0 0 0 14 13 92% [L5F,H69-,V70-,Y144-,N501Y,A570D,D614G,H655Y,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
......--.....-.L................YD..H.I....A.H.... 14 6 4 3 1 0 0 0 14 6 42% [H69-,V70-,Y144-,W152L,N501Y,A570D,D614G,P681H,T716I,P809S,S982A,D1118H]
......--.....-..................Y...H.I....A.H.... 14 0 7 6 1 0 0 0 14 8 57% [H69-,V70-,Y144-,N501Y,D614G,P681H,T716I,S982A,D1118H]
.F....--.....-..................YD..H.I....A.H..N. 14 0 0 14 0 0 0 0 14 14 100% [L18F,H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H,K1191N] B.1.1.7=Alpha
......--.....-.R.......G........YD..H.I....A.H.... 14 0 14 0 0 0 0 0 14 13 92% [H69-,V70-,Y144-,W152R,D253G,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] Alpha+W152R
......--.I...-................K.YD..H.I....A.H.... 14 1 13 0 0 0 0 0 14 14 100% [H69-,V70-,T95I,Y144-,E484K,N501Y,A570D,D614G,P681H,T716I,L938F,S982A,D1118H] Alpha+E484K
......--..F.....................YD..H.I....A.H.... 14 0 14 0 0 0 0 0 14 10 71% [H69-,V70-,S98F,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H]
......--.......................................... 13 0 13 0 0 0 0 0 13 8 61% [I68K,H69-,V70-,S71-,G72-,T73-,N74-,G75-,T76-,K77-,D614G]
..RI.....I..D...--G........R.K......R.....N....... 13 12 1 0 0 0 0 0 13 11 84% [T19R,T20I,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........D...--G.V......R.K......R.....N.I..... 13 11 0 0 2 0 0 0 13 13 100% [T19R,G142D,E156-,F157-,R158G,A222V,L452R,T478K,D614G,P681R,D950N,T1027I] B.1.617.2=Delta+A222V
..R.............--G.V.L....R.K......R.....N....... 13 0 12 0 1 0 0 0 13 7 53% [T19R,E156-,F157-,R158G,A222V,P251L,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta+A222V
..R.....YI..D...--G........R.K......R.....N....... 13 7 0 6 0 0 0 0 13 8 61% [T19R,D80Y,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
.F.NS......Y--.....S.....T....K.Y.Y.........I..F.. 13 0 2 4 0 0 7 0 13 3 23% [L18F,T20N,P26S,D138Y,L141-,G142-,V143-,Y144-,R190S,K417T,E484K,N501Y,D614G,H655Y,A845S,T1027I,V1176F] P.1=Gamma
...........................Q...S.......N.......... 13 0 5 5 0 0 3 0 13 6 46% [G75V,T76I,L452Q,F490S,D614G,T859N]
F....................---...Q...S.......N.......... 13 0 0 0 0 0 13 0 13 8 61% [L5F,G75V,T76I,R246N,S247-,Y248-,L249-,T250-,P251-,G252-,D253-,L452Q,F490S,D614G,T859N] C.37=Lambda
..R........................R.K..Y...R.....N....... 12 0 11 0 1 0 0 0 12 9 75% [T19R,L452R,T478K,N501Y,D614G,P681R,D950N]
..R........Y....--G........R.K......R.....N....... 12 0 1 7 1 0 3 0 12 10 83% [T19R,D138Y,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R......I..D...--G........R.K..Y...R.....N....... 12 10 0 2 0 0 0 0 12 8 66% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,N501Y,D614G,P681R,D950N] B.1.617.2=Delta
.F...V..A................N....K.Y....V............ 12 0 6 2 4 0 0 0 12 11 91% [L18F,A67V,D80A,D215G,L242-,A243-,L244-,K417N,E484K,N501Y,D614G,A701V] B.1.351=Beta
......--.......R........S..R.......H..........L... 12 0 0 12 0 0 0 0 12 11 91% [S12F,H69-,V70-,W152R,R346S,L452R,D614G,Q677H,A899S,P1162L] C.36
.R.......I........S.......KM........H.......I..... 12 0 1 10 0 0 1 0 12 2 16% [L18R,T95I,R158S,N440K,L452M,D614G,P681H,A688V,S735A,T1027I]
......--G.FH.-..................YD..H.I....A.H.... 12 0 12 0 0 0 0 0 12 11 91% [H69-,V70-,D80G,S98F,D138H,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
....L.--.....-..................YD..H.I....A.H.... 12 0 11 0 0 0 1 0 12 11 91% [P26L,H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
..........................................N....... 11 0 11 0 0 0 0 0 11 11 100% [D614G,D950N]
..........F....................................... 11 0 11 0 0 0 0 0 11 7 63% [S98F,D614G]
.F..................V............................. 11 2 9 0 0 0 0 0 11 4 36% [L18F,A222V,D614G] GV-clade
...............................................F.. 11 0 1 1 0 0 9 0 11 1 9% [E471X,V1176F]
..R.................................R.....N....... 11 0 11 0 0 0 0 0 11 9 81% [T19R,D614G,P681R,D950N]
..R........................R.K......R............. 11 0 3 3 1 4 0 0 11 5 45% [T19R,L452R,T478K,D614G,P681R]
..R......I..D...--G........R.K......R...E.N....... 11 11 0 0 0 0 0 0 11 8 72% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D936E,D950N] B.1.617.2=Delta
F.R......I......--G........R.K......R.....N....... 11 2 4 3 2 0 0 0 11 5 45% [L5F,T19R,T95I,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R...--.....-..--G........R.K......R.....N....... 11 2 5 3 0 1 0 0 11 9 81% [T19R,H69-,V70-,Y144-,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N]
..R.........D...--G.S......R.K......R.....N....... 11 2 2 7 0 0 0 0 11 7 63% [T19R,G142D,E156-,F157-,R158G,A222S,L452R,T478K,D614G,E661D,P681R,D950N]
..R.........D...--G........R.K.....HR.....N....... 11 0 2 6 3 0 0 0 11 9 81% [T19R,G142D,E156-,F157-,R158G,L452R,T478K,D614G,Q677H,P681R,D950N] B.1.617.2=Delta
..R.........D...--G........R.K......R.....N...L... 11 11 0 0 0 0 0 0 11 7 63% [T19R,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N,P1162L] B.1.617.2=Delta
F.R.........D...--G........R.KQ.....R.....N....... 11 0 0 11 0 0 0 0 11 7 63% [L5F,T19R,K77T,G142D,E156-,F157-,R158G,L452R,T478K,E484Q,D614G,P681R,D950N] B.1.617.2=Delta
.F......A................N....K.Y..R.V............ 11 0 2 0 0 9 0 0 11 6 54% [L18F,D80A,D215G,L242-,A243-,L244-,K417N,E484K,N501Y,D614G,Q677R,A701V,L752X] B.1.351=Beta
.........I...T..........K.....K.Y...H............. 11 0 0 11 0 0 0 0 11 6 54% [T95I,Y144T,R346K,E484K,N501Y,D614G,P681H,E1258D]
.........I.....L..............K................... 11 0 8 0 3 0 0 0 11 8 72% [T95I,W152L,E484K,D614G,G769V,A1020S] R.1
.F.NS..F...Y.......S.....T....K.Y.Y.........I..F.. 11 10 0 0 0 0 1 0 11 10 90% [L18F,T20N,P26S,V70F,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] P.1=Gamma
.F.NS......Y.......S.....T..I.K.Y.Y.........I..F.. 11 0 1 10 0 0 0 0 11 11 100% [L18F,T20N,P26S,D138Y,R190S,K417T,S477I,E484K,N501Y,D614G,H655Y,T1027I,V1176F] P.1=Gamma
.F........................K...K.........NF..I..... 11 0 0 0 11 0 0 0 11 11 100% [L18F,I210T,N440K,E484K,D614G,D936N,S939F,T1027I]
......--........................YD..H.I......H.... 11 0 11 0 0 0 0 0 11 9 81% [H69-,V70-,N501Y,A570D,D614G,P681H,T716I,D1118H]
F.....--..FH.-..................YD..H.I....A.H.... 11 0 1 10 0 0 0 0 11 7 63% [V3G,L5F,H69-,V70-,S98F,D138H,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
........Y......................................... 10 0 10 0 0 0 0 0 10 7 70% [D80Y,D614G]
..............................K................... 10 0 7 3 0 0 0 0 10 6 60% [E484K,D614G]
..R.............--G........R.KQ.....R.....N....... 10 0 1 8 1 0 0 0 10 5 50% [T19R,K77T,E156-,F157-,R158G,L452R,T478K,E484Q,D614G,P681R,D950N] B.1.617.2=Delta
..R......I......--G........R.K..Y...R.....N....... 10 0 10 0 0 0 0 0 10 3 30% [T19R,T95I,E156-,F157-,R158G,L452R,T478K,N501Y,D614G,P681R,D950N] B.1.617.2=Delta
..R.............--G........R.K......R............L 10 0 2 0 8 0 0 0 10 9 90% [T19R,E156-,F157-,R158G,L452R,T478K,D614G,P681R,V1264L]
..R.............--G.VS.....R.K......R............. 10 0 0 0 0 10 0 0 10 4 40% [T19R,E156-,F157-,R158G,A222V,T250S,L452R,T478K,D614G,P681R]
..R......I..D...--G........R.K......L.....N....... 10 9 1 0 0 0 0 0 10 7 70% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681L,D950N]
..R...--.I..D...--G........R.K......R.....N....... 10 6 4 0 0 0 0 0 10 7 70% [T19R,H69-,V70-,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N]
..R......I..D...--G........R.K.L....R.....N....... 10 10 0 0 0 0 0 0 10 5 50% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,F490L,D614G,P681R,A879S,D950N] B.1.617.2=Delta
F....V--.....-................K....H.............. 10 0 10 0 0 0 0 0 10 6 60% [L5F,Q52R,A67V,H69-,V70-,A123V,Y144-,E484K,D614G,Q677H,F888L] B.1.525=Eta
FF......A................N....K.Y....V............ 10 0 9 0 0 1 0 0 10 4 40% [L5F,L18F,D80A,D215G,L242-,A243-,L244-,K417N,E484K,N501Y,D614G,A701V] B.1.351=Beta
.........I..............K.....K.Y...H.....N....... 10 0 5 4 0 0 1 0 10 9 90% [T95I,R346K,E484K,N501Y,D614G,P681H,D950N]
............--.............RN..................... 10 0 1 0 0 0 9 0 10 6 60% [L141Y,G142-,V143-,Y144-,D215Y,L452R,S477N,D614G] A.2.5.2
......--....--..................YD..H.I....A.H.... 10 0 9 1 0 0 0 0 10 8 80% [H69-,V70-,L141-,G142-,V143-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
......--.....-..................YD..H.I....A.H..NL 10 0 0 10 0 0 0 0 10 6 60% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H,K1191N,V1264L] B.1.1.7=Alpha
......--.....-....S.............YD..H.I....A.H.... 10 0 0 0 10 0 0 0 10 10 100% [H69-,V70-,Y144-,R158S,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
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last modified: Wed Jul 14 06:34 2021
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