COVID-19 Viral Genome Analysis Pipeline
Enabled by data from
XSpike
eXplore the Spike protein sequence in the SARS CoV-2 virus
Last update: Sep 12, 2021
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Evaluating 401327 sequences of length 2071
Sampled from 2021-07-02 to 2021-08-31.
Specified Date Range: (datetime.date(2021, 7, 2), datetime.date(2021, 8, 31))
Highest entropy sites for: Global
Site Entropy
95 0.6796
142 0.5796
222 0.3206
681 0.3180
950 0.2972
158 0.2849
156 0.2823
157 0.2810
452 0.2744
478 0.2686
19 0.2649
501 0.2213
70 0.1920
144 0.1778
570 0.1534
69 0.1505
716 0.1462
1118 0.1433
982 0.1420
484 0.1266
138 0.1182
1264 0.1056
417 0.1026
18 0.0957
1027 0.0913
20 0.0856
26 0.0851
655 0.0837
112 0.0835
1176 0.0813
190 0.0794
289 0.0774
251 0.0699
145 0.0618
5 0.0543
77 0.0536
1104 0.0487
719 0.0439
250 0.0422
67 0.0396
21 0.0392
850 0.0374
1074 0.0351
181 0.0339
253 0.0332
1162 0.0322
29 0.0308
677 0.0291
346 0.0281
27 0.0281
Most highly correlated site-pairs for: Global
cramerV mutInfo
156 157 0.4996 0.2755
158 156 0.5789 0.2744
158 157 0.6707 0.2707
157 478 0.5566 0.2442
156 478 0.5563 0.2441
681 478 0.5601 0.2425
158 478 0.5526 0.2413
681 157 0.4800 0.2408
681 156 0.4797 0.2407
452 478 0.5576 0.2397
681 158 0.5536 0.2387
681 452 0.4870 0.2336
478 19 0.5513 0.2317
157 452 0.4731 0.2309
157 19 0.4722 0.2303
570 982 0.7037 0.1390
570 1118 0.7002 0.1369
1118 982 0.6998 0.1370
716 982 0.6913 0.1348
417 1176 0.6882 0.0747
1176 190 0.6879 0.0746
716 1118 0.6871 0.1327
69 982 0.6871 0.1334
70 982 0.6871 0.1334
20 1176 0.6869 0.0742
70 1118 0.6865 0.1332
69 1118 0.6865 0.1332
655 190 0.6753 0.0729
138 1176 0.6748 0.0717
417 655 0.6735 0.0724
Most common patterns for local area, where Local = Global
1111111
1111111111222223444455666778990011112
1122222667791344455589255584157807578115582701676
58901679790752824567810201396728410571690027448264
LLTTRPATAHVKTSDGYYEFRGRATPDVRKLTENAHQPTTIDSTNVDPVV Global UK Eu-UK NAmer Asia Africa SAmer Ocean Local Exact Pct [Context]
401327 128132 135888 116083 13359 355 5485 2025 401327 <----------- Totals
..R.........I..D..G--.........RK.....R...N........ 126894 92846 18880 10083 3458 9 489 1129 126894 99951 78% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--.........RK.....R...N........ 104997 18031 46833 39271 457 102 257 46 104997 89193 84% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R...............G--.........RK.....R...N........ 32589 485 13479 17500 539 51 535 0 32589 26313 80% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--..V......RK.....R...N........ 16109 2449 8400 4037 985 12 204 22 16109 12849 79% [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R.........I.....G--.........RK.....R...N........ 13459 931 7059 4440 319 8 42 660 13459 10639 79% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
.........--.....-................YD..HI...A...H... 10789 251 5477 2975 2001 5 45 35 10789 5859 54% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
.F.N.S........Y.......S......T..KY.Y.......I....F. 4995 6 1035 1867 10 0 2077 0 4995 2839 56% [L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] P.1=Gamma
..R..........L.D..G--.........RK.....R...N........ 4278 3 20 4245 4 0 4 2 4278 3404 79% [T19R,S112L,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R...............G--..V......RK.....R...N........ 4210 132 1831 1591 653 1 1 1 4210 3231 76% [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R............D..G--..V...I..RK.....R...N........ 3581 3 2 3569 4 0 3 0 3581 3220 89% [T19R,G142D,E156G,F157-,R158-,A222V,V289I,L452R,T478K,D614G,P681R,D950N] Delta+A222V
.................................................. 3153 1 3084 58 1 2 5 2 3153 2928 92% [D614G] G-clade
..R............D..G--.........RK.....R...N.......L 2888 14 217 89 2557 0 0 11 2888 2602 90% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1264L] B.1.617.2=Delta
..R...............G--.........RK.....R............ 2812 4 1007 1497 47 3 254 0 2812 2132 75% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R]
..R............D..G--....L....RK.....R...N........ 2339 687 1522 87 24 0 19 0 2339 1546 66% [T19R,G142D,E156G,F157-,R158-,P251L,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R........T...D..G--.........RK.....R...N........ 2188 11 306 1863 5 2 1 0 2188 1662 75% [T19R,K77T,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I..D.HG--..V......RK.....R...N........ 2152 2125 26 0 0 0 0 1 2152 1876 87% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R.........I.HD..G--.........RK.....R...N........ 1971 1777 78 116 0 0 0 0 1971 1323 67% [T19R,T95I,D138H,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R..........L....G--.........RK.....R...N........ 1931 0 14 1916 1 0 0 0 1931 1603 83% [T19R,S112L,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--..V......RK.....R...N.......L 1829 126 99 1587 15 2 0 0 1829 1197 65% [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+A222V
..R.........I..D..G--.........RK.....R.I.N........ 1825 35 1731 34 2 0 20 3 1825 1639 89% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,T719I,D950N] B.1.617.2=Delta
..R...............G--..V...I..RK.....R...N........ 1656 0 2 1651 2 0 1 0 1656 1478 89% [T19R,E156G,F157-,R158-,A222V,V289I,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R.........I..D..G--.........RK.....R...N...L.... 1615 154 192 1249 18 0 2 0 1615 895 55% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1104L] B.1.617.2=Delta
..R...............G--....L....RK.....R...N........ 1518 29 1467 13 7 1 1 0 1518 1288 84% [T19R,E156G,F157-,R158-,P251L,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--..V......RK.....R...N..S....L 1304 14 24 1251 3 0 12 0 1304 1127 86% [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,N1074S,V1264L] Delta+A222V
..R.T..........D..G--..V......RK.....R...N........ 1274 32 1230 2 2 0 8 0 1274 1104 86% [T19R,R21T,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R.........I..D..G--.........RK.....R..LN........ 1205 10 1160 27 8 0 0 0 1205 899 74% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] B.1.617.2=Delta
..R.........I.....G--.........RK.....R...N...L.... 1088 27 139 905 5 0 12 0 1088 568 52% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1104L] B.1.617.2=Delta
............I...SN..........K...KY...H...N........ 1059 2 64 877 1 0 115 0 1059 613 57% [T95I,+143T,Y144S,Y145N,R346K,E484K,N501Y,D614G,P681H,D950N] B.1.621
..R........T......G--.........RK.....R...N........ 1026 2 118 903 3 0 0 0 1026 812 79% [T19R,K77T,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I..D..G--.........RK.....R...N.....S.. 1006 969 20 14 3 0 0 0 1006 906 90% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,P1162S] B.1.617.2=Delta
..R.........I.....G--.........RK.....R.I.N........ 964 15 938 11 0 0 0 0 964 889 92% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,T719I,D950N] B.1.617.2=Delta
..R....A.......D..G--...I.....RK.....R...N........ 938 33 874 23 5 0 0 3 938 442 47% [T19R,T29A,G142D,E156G,F157-,R158-,T250I,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R...............G--..V......RK.....R...N.......L 937 0 28 858 48 0 3 0 937 673 71% [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+A222V
F.R.........I..D..G--.........RK.....R...N........ 887 587 114 95 91 0 0 0 887 656 73% [L5F,T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I.....G--.........RK.....R............ 843 43 343 423 18 1 9 6 843 646 76% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R]
.................................Y................ 795 0 795 0 0 0 0 0 795 756 95% [N501Y,D614G] G-clade
..R.......F.I..D..G--.........RK.....R...N........ 780 725 52 1 2 0 0 0 780 618 79% [T19R,V70F,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
..R.........I..D..G--.........RK....HR...N........ 749 155 497 78 13 1 5 0 749 503 67% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,Q677H,P681R,D950N] B.1.617.2=Delta
F.R............D..G--.........RK.....R...N........ 747 96 261 378 10 0 2 0 747 611 81% [L5F,T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R...............G--..V......RK.....R...N..S....L 732 5 20 701 3 0 3 0 732 617 84% [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,N1074S,V1264L] Delta+A222V
..R.......I....D..G--.........RK.....R...N........ 569 1 3 565 0 0 0 0 569 355 62% [T19R,V70I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
..R...S........D..G--.........RK.....R...N........ 540 66 445 18 1 0 10 0 540 478 88% [T19R,A27S,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R...............G--..V......RK.....R............ 537 0 143 191 203 0 0 0 537 419 78% [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R]
..R.............................K........N........ 502 0 502 0 0 0 0 0 502 498 99% [T19R,E484K,D614G,D950N]
................................K..........I...... 496 0 40 1 455 0 0 0 496 442 89% [I210T,N440K,E484K,D614G,D936N,S939F,T1027I] B.1.619
.F.N.S........Y.......S......T..KY.Y.H.....I....F. 480 0 91 73 1 0 315 0 480 370 77% [L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,P681H,T1027I,V1176F] P.1=Gamma
..R............D..G--V........RK.....R...N........ 478 33 334 110 1 0 0 0 478 376 78% [T19R,G142D,E156G,F157-,R158-,G181V,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
.FR.........I..D..G--.........RK.....R...N........ 463 431 20 12 0 0 0 0 463 301 65% [L18F,T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.....V......D..G--..V......RK.....R...N........ 455 4 367 28 2 0 54 0 455 436 95% [T19R,A67V,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R.........I.....G--.........RK....HR...N........ 447 7 408 21 2 0 9 0 447 322 72% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,Q677H,P681R,D950N] B.1.617.2=Delta
..R.......I.......G--.........RK.....R...N........ 446 0 3 442 1 0 0 0 446 341 76% [T19R,V70I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
..R............D..G--..V..A...RK.....R...N........ 444 3 435 3 3 0 0 0 444 337 75% [T19R,G142D,E156G,F157-,R158-,A222V,D253A,L452R,T478K,D614G,P681R,D950N,D979E] Delta+A222V
..R.....V......D..G--.........RK.....R...N........ 421 391 7 23 0 0 0 0 421 373 88% [T19R,T22I,A67V,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.......F....D..G--..V.....NRK.....R...N........ 409 0 1 407 0 0 1 0 409 367 89% [T19R,V70F,G142D,E156G,F157-,R158-,A222V,K417N,L452R,T478K,D614G,P681R,D950N] Delta-AY.2
..R....A..........G--...I.....RK.....R...N........ 406 15 370 14 7 0 0 0 406 162 39% [T19R,T29A,E156G,F157-,R158-,T250I,T299I,L452R,T478K,Q613H,D614G,P681R,D950N] B.1.617.2=Delta
........................---...Q................... 396 0 41 80 3 1 271 0 396 254 64% [G75V,T76I,R246N,S247-,Y248-,L249-,T250-,P251-,G252-,D253-,L452Q,F490S,D614G,T859N] C.37=Lambda
..R.....V...I..D..G--.........RK.....R...N........ 396 386 3 6 1 0 0 0 396 358 90% [T19R,A67V,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R...S.....I..D..G--.........RK.....R...N........ 384 24 17 343 0 0 0 0 384 336 87% [T19R,A27S,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I.....G--.........RK.....R..LN........ 376 0 346 7 23 0 0 0 376 204 54% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] B.1.617.2=Delta
..R...............G--V........RK.....R...N........ 358 9 317 21 8 0 3 0 358 246 68% [T19R,E156G,F157-,R158-,G181V,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
F.R...............G--.........RK.....R...N........ 348 3 139 190 13 0 3 0 348 258 74% [L5F,T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--.........RK.....R............ 340 0 259 60 14 2 5 0 340 284 83% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R]
..R...........................RK.....R...N........ 337 1 124 44 167 0 1 0 337 241 71% [T19R,L452R,T478K,D614G,P681R,D950N]
..R............D..G--.........RK.....R..LN........ 326 0 326 0 0 0 0 0 326 303 92% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] B.1.617.2=Delta
.R..........I.......S................H.....I...... 323 0 0 323 0 0 0 0 323 190 58% [L18R,T95I,R158S,N440K,D614G,P681H,A688V,S735A,T1027I]
F........--.....-................YD..HI...A...H... 313 7 160 130 15 0 0 1 313 130 41% [L5F,H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
..R...............G--.........RK..S..R...N........ 310 1 307 1 1 0 0 0 310 275 88% [T19R,E156G,F157-,R158-,L452R,T478K,A570S,D614G,P681R,D950N] B.1.617.2=Delta
..R.....S......D..G--.........RK.....R...N........ 307 17 280 9 0 0 1 0 307 276 89% [T19R,A67S,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.I.......I..D..G--.........RK.....R...N........ 306 298 0 5 3 0 0 0 306 267 87% [T19R,R21I,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.T.............G--..V......RK.....R...N........ 296 9 286 0 1 0 0 0 296 260 87% [T19R,R21T,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R.........I..D..G--E........RK.....R...N........ 280 274 5 0 1 0 0 0 280 261 93% [T19R,T95I,G142D,E156G,F157-,R158-,G181E,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R...............G--..........K.....R...N........ 267 0 245 18 4 0 0 0 267 256 95% [T19R,E156G,F157-,R158-,T478K,D614G,P681R,D950N]
..R............D..G--.........RK.....RI..N........ 242 71 9 22 1 0 139 0 242 190 78% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,T716I,D950N] B.1.617.2=Delta
..R..............................Y................ 241 0 241 0 0 0 0 0 241 241 100% [T19R,N501Y,D614G]
..R.........I.....G--.........RK.....R.......L.... 236 0 4 226 0 0 6 0 236 44 18% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,V1104L]
..R..............................Y.......N........ 222 0 222 0 0 0 0 0 222 222 100% [T19R,N501Y,D614G,D950N]
..............................R......R............ 218 0 218 0 0 0 0 0 218 218 100% [L452R,D614G,P681R]
..R............D..--..........RK.....R...N........ 217 0 217 0 0 0 0 0 217 212 97% [T19R,G142D,S155R,E156-,F157-,L452R,T478K,D614G,P681R,D950N]
..R...............G--.........RK.....R...N.......L 214 1 118 18 75 0 0 2 214 173 80% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1264L] B.1.617.2=Delta
..R.........I..D..G--.....G...RK.....R...N........ 204 196 4 1 3 0 0 0 204 177 86% [T19R,T95I,G142D,E156G,F157-,R158-,D253G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--.........RK...Y.R...N........ 202 10 162 30 0 0 0 0 202 124 61% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,H655Y,P681R,P792S,D950N] B.1.617.2=Delta
..R.........I..D..G--.........RK.....R...N.......L 202 188 8 2 4 0 0 0 202 173 85% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1264L] B.1.617.2=Delta
..R...............G--.........RK..S..R............ 196 0 195 0 1 0 0 0 196 182 92% [T19R,E156G,F157-,R158-,L452R,T478K,A570S,D614G,P681R]
............I...-...............K....H............ 194 2 126 24 1 41 0 0 194 143 73% [T95I,Y144-,E484K,D614G,P681H,D796H] B.1.1.318
..R.........I..D..G--V........RK.....R...N........ 194 161 19 1 12 0 0 1 194 166 85% [T19R,T95I,G142D,E156G,F157-,R158-,G181V,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
.........--...H.-................YD..HI...A...H... 194 7 129 53 4 1 0 0 194 78 40% [H69-,V70-,D138H,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
..R.........I..D..G--........NRK.....R...N........ 190 42 15 127 4 0 0 2 190 130 68% [T19R,T95I,G142D,E156G,F157-,R158-,W258L,K417N,L452R,T478K,D614G,P681R,D950N] Delta-AY.1
............I...SN..........KN..KY...H...N........ 188 17 7 159 1 0 4 0 188 170 90% [T95I,+143T,Y144S,Y145N,R346K,K417N,E484K,N501Y,D614G,P681H,D950N] B.1.621
..R...S...........G--.........RK.....R...N........ 187 13 163 8 2 0 1 0 187 154 82% [T19R,A27S,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
F.R.........I.....G--.........RK.....R...N........ 187 3 93 82 9 0 0 0 187 131 70% [L5F,T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R..S......I..D..G--.........RK.....R...N........ 184 147 32 4 1 0 0 0 184 106 57% [T19R,P26S,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I..D..G--...N.....RK.....R...N........ 184 183 1 0 0 0 0 0 184 166 90% [T19R,T95I,G142D,E156G,F157-,R158-,T250N,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..............................R................... 182 0 177 4 0 0 1 0 182 173 95% [L452R,D614G]
.........--.....-...............KYD..HI...A...H... 182 1 113 7 59 0 2 0 182 124 68% [H69-,V70-,Y144-,E484K,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] Alpha+E484K
..R............D..G-..........RK.....R...N........ 172 0 172 0 0 0 0 0 172 171 99% [T19R,G142D,E156G,F157-,L452R,T478K,D614G,P681R,D950N]
..R.......F.......G--..V.....NRK.....R...N........ 166 0 0 166 0 0 0 0 166 142 85% [T19R,V70F,E156G,F157-,R158-,A222V,K417N,L452R,T478K,D614G,P681R,D950N] Delta-AY.2
..R...............G--..V...I..RK.....R............ 151 0 0 151 0 0 0 0 151 133 88% [T19R,E156G,F157-,R158-,A222V,V289I,L452R,T478K,D614G,P681R]
..R...............G--..V..A...RK.....R...N........ 150 1 146 2 1 0 0 0 150 125 83% [T19R,E156G,F157-,R158-,A222V,D253A,L452R,T478K,D614G,P681R,D950N,D979E] Delta+A222V
........V--.....-................YD..HI...A...H... 150 1 148 0 1 0 0 0 150 132 88% [A67V,H69-,V70-,S98F,Y144-,N501Y,A570D,D614G,P681H,T716I,D936Y,S982A,D1118H] B.1.1.7=Alpha
..R...............G--.........RK.....R..LN........ 146 0 146 0 0 0 0 0 146 125 85% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] B.1.617.2=Delta
..R..........L....G--.........RK.....R............ 141 0 2 138 1 0 0 0 141 113 80% [T19R,S112L,E156G,F157-,R158-,L452R,T478K,D614G,P681R]
..R...S.....I.....G--.........RK.....R...N........ 140 0 4 136 0 0 0 0 140 126 90% [T19R,A27S,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
.................................Y.......N........ 139 0 139 0 0 0 0 0 139 137 98% [N501Y,D614G,D950N]
...............Y-.............R................... 138 0 2 133 0 0 3 0 138 59 42% [L141-,G142Y,V143-,Y144-,+214AAG,D215Y,L452R,D614G]
..R.........I..D..G--.........RK.....RI..N........ 134 132 0 2 0 0 0 0 134 109 81% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,T716I,D950N] B.1.617.2=Delta
..............................RK.................. 133 0 132 0 1 0 0 0 133 131 98% [L452R,T478K,D614G]
..R............D..G--.........RK.....R...N.....L.. 131 22 36 72 0 0 1 0 131 114 87% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,P1162L] B.1.617.2=Delta
..R.........I..D..G--.........RK...Y.R...N........ 129 89 0 37 3 0 0 0 129 109 84% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,H655Y,P681R,D950N] B.1.617.2=Delta
F...........I.............G.....K................. 125 0 1 85 0 0 39 0 125 73 58% [L5F,T95I,D253G,E484K,D614G,A701V] B.1.526=Iota
................-..S..........R..........H........ 118 0 0 118 0 0 0 0 118 68 57% [D80G,Y144-,F157S,L452R,D614G,T859N,D950H] B.1.526.1
..R............D..G--.........RK....HR...N........ 114 3 61 47 3 0 0 0 114 72 63% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,Q677H,P681R,D950N] B.1.617.2=Delta
..R...........................RK.....R............ 113 0 26 3 82 2 0 0 113 42 37% [T19R,L452R,T478K,D614G,P681R]
.F...........................N..KY................ 112 0 58 6 9 39 0 0 112 70 62% [L18F,D80A,D215G,L242-,A243-,L244-,K417N,E484K,N501Y,D614G,A701V] B.1.351=Beta
..R........T......G--.........RK.....R............ 109 0 5 104 0 0 0 0 109 83 76% [T19R,K77T,E156G,F157-,R158-,L452R,T478K,D614G,P681R]
..R...............G--.........RK.Y...R...N........ 105 0 105 0 0 0 0 0 105 103 98% [T19R,E156G,F157-,R158-,L452R,T478K,N501Y,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--..........K.....R...N........ 105 0 92 13 0 0 0 0 105 80 76% [T19R,G142D,E156G,F157-,R158-,T478K,D614G,P681R,D950N]
F.R............D..G--..V......RK.....R...N........ 105 21 20 49 15 0 0 0 105 61 58% [L5F,T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R.I..........D..G--.........RK.....R...N........ 105 5 68 30 1 1 0 0 105 94 89% [T19R,R21I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R........T...D..G--.........RKQ....R...N........ 104 0 1 103 0 0 0 0 104 91 87% [T19R,K77T,G142D,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I..D..G--.........RK.....R............ 104 2 89 7 6 0 0 0 104 81 77% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R]
................................KY................ 102 0 102 0 0 0 0 0 102 91 89% [E484K,N501Y,D614G]
..R....I....I..D..G--.........RK.....R...N........ 102 91 10 1 0 0 0 0 102 89 87% [T19R,T29I,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R..............................Y...R...N........ 101 0 101 0 0 0 0 0 101 101 100% [T19R,N501Y,D614G,P681R,D950N]
..R...............G--....L....RK.....R............ 96 0 92 3 0 0 1 0 96 83 86% [T19R,E156G,F157-,R158-,P251L,L452R,T478K,D614G,P681R]
..R.........I..D..G--......L..RK.....R...N........ 95 94 0 0 1 0 0 0 95 89 93% [T19R,T95I,G142D,E156G,F157-,R158-,V289L,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R............D-.G--.........RK.....R...N........ 93 40 22 30 0 1 0 0 93 63 67% [T19R,G142D,Y144-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R......--.......G--.........RK.....R...N........ 92 5 50 37 0 0 0 0 92 65 70% [T19R,H69-,V70-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
..R............D..G--..V......RK.....R...N.....S.. 89 20 43 25 1 0 0 0 89 67 75% [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,P1162S] Delta+A222V
..R............D..G--..V......RK.....R............ 88 3 25 7 53 0 0 0 88 70 79% [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R]
..R.........I..D..G--.........RK.....R...N.I...... 88 71 10 7 0 0 0 0 88 35 39% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,T1027I] B.1.617.2=Delta
..R.I.............G--.........RK.....R...N........ 88 0 80 6 2 0 0 0 88 74 84% [T19R,R21I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
...............D..G--.........RK.....R...N........ 83 5 36 42 0 0 0 0 83 72 86% [G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
..R.........I..D..G--..V......RK.....R...N........ 83 19 52 4 8 0 0 0 83 37 44% [T19R,T95I,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R............................................... 82 0 80 2 0 0 0 0 82 71 86% [T19R,D614G]
..R.....S...I..D..G--.........RK.....R...N........ 81 59 18 2 2 0 0 0 81 75 92% [T19R,A67S,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
.........--.....-................YD.HHI...A...H... 79 1 62 11 5 0 0 0 79 48 60% [H69-,V70-,Y144-,N501Y,A570D,D614G,Q677H,P681H,V687L,T716I,S982A,D1118H] B.1.1.7=Alpha
..R............D..G--..V.L....RK.....R...N........ 77 0 63 0 14 0 0 0 77 69 89% [T19R,G142D,E156G,F157-,R158-,A222V,P251L,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R.........I..D.HG--..V......RK.....R...N.......L 77 77 0 0 0 0 0 0 77 73 94% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+A222V
..R......................................N........ 75 0 75 0 0 0 0 0 75 74 98% [T19R,D614G,D950N]
..R............D..............RK.....R...N........ 74 0 43 9 22 0 0 0 74 64 86% [T19R,G142D,L452R,T478K,D614G,P681R,D950N]
..R.........I..D-.G--.........RK.....R...N........ 74 18 53 3 0 0 0 0 74 67 90% [T19R,T95I,G142D,Y144-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I..D..G--.........RK.....R...N.....L.. 73 63 3 7 0 0 0 0 73 47 64% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,P1162L] B.1.617.2=Delta
.....S...--.....-...............K....H.....I..H... 73 0 3 0 69 1 0 0 73 48 65% [P26S,H69-,V70-,V126A,Y144-,L242-,A243-,L244-,H245Y,S477N,E484K,D614G,P681H,T1027I,D1118H] B.1.620
F...........I.............G....................... 70 0 0 69 0 0 1 0 70 27 38% [L5F,T95I,D253G,S477N,D614G,A701V] B.1.526=Iota
..R.........I.YD..G--.........RK.....R...N........ 70 20 48 2 0 0 0 0 70 62 88% [T19R,T95I,D138Y,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I..D..G--.........RK.....R...N......F. 69 64 2 2 1 0 0 0 69 67 97% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1176F] B.1.617.2=Delta
................................K................. 68 0 63 1 4 0 0 0 68 52 76% [E484K,D614G]
F.R.........I.HD..G--.........RK.....R...N........ 68 68 0 0 0 0 0 0 68 38 55% [L5F,T19R,T95I,D138H,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I.....G--.........RK.....R.I.......... 68 0 67 1 0 0 0 0 68 62 91% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,T719I]
..RI...........D..G--.........RK.....R...N........ 67 3 31 26 7 0 0 0 67 48 71% [T19R,T20I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I..D.HG--.........RK.....R...N........ 67 65 0 2 0 0 0 0 67 66 98% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--.........RK..S..R...N........ 66 32 31 1 2 0 0 0 66 32 48% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,A570S,D614G,P681R,D950N] B.1.617.2=Delta
.............................N..KY................ 66 0 37 0 0 29 0 0 66 24 36% [D80A,D215G,L242-,A243-,L244-,K417N,E484K,N501Y,D614G,A701V] B.1.351=Beta
................-..S..........R......H...H........ 65 0 0 65 0 0 0 0 65 56 86% [D80G,Y144-,F157S,L452R,D614G,P681H,T859N,D950H] B.1.526.1
..R............D..G--.........RK.....R...N...L.... 64 5 33 13 12 1 0 0 64 46 71% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1104L] B.1.617.2=Delta
..R........T......G--.........RKQ....R...N........ 63 0 0 63 0 0 0 0 63 49 77% [T19R,K77T,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,D950N] B.1.617.2=Delta
..............................RK.....R............ 62 0 61 1 0 0 0 0 62 61 98% [L452R,T478K,D614G,P681R]
.F.N.S........Y.......S......T..KY.Y.R.....I....F. 62 1 5 0 0 0 56 0 62 40 64% [L18F,T20N,P26S,D138Y,R190S,K417T,T470N,E484K,N501Y,D614G,H655Y,P681R,T1027I,V1176F,C1235F] P.1=Gamma
..R...............G--.........RK.....R...N...L.... 61 1 36 19 4 1 0 0 61 47 77% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1104L] B.1.617.2=Delta
.FR............D..G--.........RK.....R...N........ 61 8 16 36 0 0 1 0 61 38 62% [L18F,T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
.........--.................S.R.....H............. 59 0 33 25 1 0 0 0 59 31 52% [S12F,H69-,V70-,W152R,R346S,L452R,D614G,Q677H,A899S] C.36
..R.........I.....G--.........RK.....R...N.....A.. 59 0 0 0 0 0 0 59 59 53 89% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,P1162A] B.1.617.2=Delta
..R............D..G--..VS.....RK.....R...N........ 58 4 40 8 2 2 0 2 58 52 89% [T19R,G142D,E156G,F157-,R158-,A222V,T250S,L452R,T478K,D614G,P681R,D950N] Delta+A222V
.........--...H.-....V...........YD..HI...A...H... 58 2 56 0 0 0 0 0 58 54 93% [H69-,V70-,S98F,D138H,Y144-,G181V,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
..RI........I..D..G--.........RK.....R...N........ 57 23 28 4 2 0 0 0 57 51 89% [T19R,T20I,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
.F.N.S................S......T..KY.Y.......I....F. 57 0 16 17 0 0 24 0 57 31 54% [L18F,T20N,P26S,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] P.1=Gamma
.....................................R............ 56 0 30 0 25 0 1 0 56 30 53% [D614G,P681R] Near-Furin
....I...................---...Q................... 54 1 53 0 0 0 0 0 54 52 96% [R21I,G75V,T76I,R246N,S247-,Y248-,L249-,T250-,P251-,G252-,D253-,L452Q,F490S,T572I,D614G,Q675H,T859N] C.37=Lambda
..R............D..G--..S......RK.....R...N........ 54 1 4 49 0 0 0 0 54 40 74% [T19R,G142D,E156G,F157-,R158-,A222S,L452R,T478K,D614G,E661D,P681R,D950N]
..R...............G--..V......RK.....R...........L 54 0 0 49 5 0 0 0 54 38 70% [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,V1264L]
..R...............G--................R...N........ 53 0 17 35 1 0 0 0 53 42 79% [T19R,E156G,F157-,R158-,D614G,P681R,D950N]
F.R............D..G--..V...I..RK.....R...N........ 53 0 0 53 0 0 0 0 53 50 94% [L5F,T19R,G142D,E156G,F157-,R158-,A222V,V289I,L452R,T478K,D614G,P681R,D950N] Delta+A222V
............I...SN..........K...KY...H............ 52 0 1 46 0 0 5 0 52 29 55% [T95I,+143T,Y144S,Y145N,R346K,E484K,N501Y,D614G,P681H]
..R......--.....-.G--.........RK.....R...N........ 51 0 14 37 0 0 0 0 51 48 94% [T19R,H69-,V70-,Y144-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
..R......Y..I..D..G--.........RK.....R...N........ 50 31 18 1 0 0 0 0 50 38 76% [T19R,H69Y,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
.........--.I...-................YD..HI...A...H... 49 0 35 10 4 0 0 0 49 40 81% [H69-,V70-,T95I,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
...............................K.....H............ 48 0 2 45 1 0 0 0 48 33 68% [T478K,D614G,P681H,T732A] B.1.1.519
..R............D..G--R........RK.....R...N........ 48 1 2 44 1 0 0 0 48 41 85% [T19R,G142D,E156G,F157-,R158-,G181R,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I..D..G--.........RK.....R..VN........ 48 48 0 0 0 0 0 0 48 45 93% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850V,D950N] B.1.617.2=Delta
..R.......G.I..D..G--.........RK.....R...N........ 48 47 1 0 0 0 0 0 48 40 83% [T19R,V70G,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
.........--.....-................YD..HI...A....... 48 0 45 3 0 0 0 0 48 42 87% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,A701V,T716I,S982A]
............I..D..G--.........R......R............ 47 0 47 0 0 0 0 0 47 43 91% [T95I,G142D,E156G,F157-,R158-,L452R,D614G,P681R]
.........--.....-................YD...I...A...H... 47 0 46 1 0 0 0 0 47 46 97% [H69-,V70-,Y144-,N501Y,A570D,D614G,T716I,S982A,D1118H]
........D--.....-................YD..HI...A...H... 47 0 0 47 0 0 0 0 47 46 97% [A67D,H69-,V70-,Y144-,F490S,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] Alpha+F490S
..R.........I.................RK.....R............ 46 0 7 2 37 0 0 0 46 16 34% [T19R,T95I,L452R,T478K,D614G,P681R]
..................G--.........RK.....R...N........ 45 0 24 19 0 1 1 0 45 36 80% [E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
..R...............G--.........RK.....R...N.....L.. 45 0 14 30 1 0 0 0 45 33 73% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,P1162L] B.1.617.2=Delta
..R.........I.....G--........NRK.....R...N........ 45 2 6 37 0 0 0 0 45 36 80% [T19R,T95I,E156G,F157-,R158-,W258L,K417N,L452R,T478K,D614G,P681R,D950N] Delta-AY.1
.F...S........Y.......S......T..KY.Y.......I....F. 45 0 1 30 0 0 14 0 45 34 75% [L18F,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F]
.........--.....-................YD..HI...A...HS.. 44 1 34 7 2 0 0 0 44 25 56% [H69-,V70-,I100T,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H,P1162S] B.1.1.7=Alpha
.........................................N........ 43 0 43 0 0 0 0 0 43 41 95% [D614G,D950N]
..R............D..G--.........RK.....R...N......F. 43 2 38 3 0 0 0 0 43 17 39% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,Q836E,D950N,V1176F] B.1.617.2=Delta
..R.........I...-.G--.........RK.....R...N........ 43 0 43 0 0 0 0 0 43 37 86% [T19R,T95I,Y144-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I.................RK.....R...N........ 43 0 31 9 3 0 0 0 43 38 88% [T19R,T95I,L452R,T478K,D614G,P681R,D950N]
..R.........I.....G--..V......RK.....R...N........ 42 2 15 8 17 0 0 0 42 28 66% [T19R,T95I,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R...............G--..V......RK.....R......S..... 42 0 0 42 0 0 0 0 42 35 83% [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,N1074S]
..RA...........D..G--..V...I..RK.....R...N........ 42 0 0 42 0 0 0 0 42 41 97% [T19R,T20A,G142D,E156G,F157-,R158-,A222V,V289I,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R....A....I.HD..G--.........RK.....R...N........ 42 42 0 0 0 0 0 0 42 41 97% [T19R,T29A,T95I,D138H,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I..D..G--..........K.....R...N........ 41 3 37 1 0 0 0 0 41 39 95% [T19R,T95I,G142D,E156G,F157-,R158-,T478K,D614G,P681R,D950N]
..R...............G--.........RK....HR...N........ 41 5 16 19 1 0 0 0 41 27 65% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,Q677H,P681R,D950N] B.1.617.2=Delta
..R....I.......D..G--.........RK.....R...N........ 41 0 11 29 0 0 1 0 41 28 68% [T19R,T29I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
FF.N.S........Y.......S......T..KY.Y.......I....F. 41 0 0 10 0 0 31 0 41 29 70% [L5F,L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] P.1=Gamma
........V--.....-............R..KYD..HI...A...H... 41 0 0 41 0 0 0 0 41 21 51% [A67V,H69-,V70-,Y144-,K417R,E484K,N501Y,A570D,D614G,P681H,A701V,T716I,S982A,D1118H,K1191N] Alpha+E484K
...............D..G--.........R......R............ 40 0 40 0 0 0 0 0 40 26 65% [G142D,E156G,F157-,R158-,L452R,D614G,P681R]
.R..........I.......S.........M......H.....I...... 40 0 0 40 0 0 0 0 40 12 30% [L18R,T95I,R158S,L176F,N440K,L452M,D614G,P681H,A688V,S735A,T1027I]
..R.......F....D..G--.........RK.....R...N........ 40 1 20 19 0 0 0 0 40 32 80% [T19R,V70F,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
F.R............D..G--..V......RK.....R...N..S....L 40 0 0 40 0 0 0 0 40 29 72% [L5F,T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,N1074S,V1264L] Delta+A222V
..R.........I.....G--.........RK....HR............ 40 0 26 3 1 0 10 0 40 29 72% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,Q677H,P681R]
..R.....S.........G--.........RK.....R...N........ 40 4 26 10 0 0 0 0 40 31 77% [T19R,A67S,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.....S...I..D..G--.........RK.....R...N.....S.. 40 40 0 0 0 0 0 0 40 39 97% [T19R,A67S,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,P1162S] B.1.617.2=Delta
..R...............G--..V.L....RK.....R...N........ 39 0 37 1 1 0 0 0 39 36 92% [T19R,E156G,F157-,R158-,A222V,P251L,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R...V...........G--.........RK.....R...N........ 38 0 32 6 0 0 0 0 38 33 86% [T19R,A27V,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R...V...........G--.........RK.....R............ 38 0 37 1 0 0 0 0 38 23 60% [T19R,A27V,E156G,F157-,R158-,L452R,T478K,D614G,P681R]
F.R.........I..D.HG--..V......RK.....R...N........ 38 38 0 0 0 0 0 0 38 37 97% [L5F,T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R......--.....-.............RK.....R...N........ 38 0 25 13 0 0 0 0 38 26 68% [T19R,H69-,V70-,Y144-,L452R,T478K,D614G,P681R,D950N]
.........--.....-....A...........YD..HI...A...H... 38 0 0 38 0 0 0 0 38 33 86% [H69-,V70-,Y144-,G181A,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
..R.........I..D..G--.........RK.....H...N........ 35 6 28 0 1 0 0 0 35 31 88% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681H,D950N]
..R.........I.AD..G--.........RK.....R...N........ 35 35 0 0 0 0 0 0 35 27 77% [T19R,T95I,D138A,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
.......I...........S............K..Y.H............ 35 0 5 30 0 0 0 0 35 30 85% [T29I,F32L,M153T,F157S,G252V,S477N,E484K,D614G,H655Y,P681H,D936H,D1260H]
..R............D..G--.........RK.....R...N.....S.. 34 3 5 24 2 0 0 0 34 25 73% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,P1162S] B.1.617.2=Delta
..R............D..G--..V...L..RK.....R...N........ 34 2 22 0 10 0 0 0 34 29 85% [T19R,G142D,E156G,F157-,R158-,A222V,V289L,L452R,T478K,D614G,P681R,D950N] Delta+A222V
F.R............D..G--..V......RK.....R...N.......L 34 0 2 32 0 0 0 0 34 23 67% [L5F,T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+A222V
F.R............D..G--..V......RK.....R...N......FL 34 0 0 34 0 0 0 0 34 31 91% [L5F,T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,P809S,D950N,V1176F,V1264L] Delta+A222V
..R........TI.....G--.........RK.....R...N........ 34 0 34 0 0 0 0 0 34 25 73% [Q14H,T19R,K77T,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.......I.......G--.........RK.....R............ 34 0 0 34 0 0 0 0 34 26 76% [T19R,V70I,E156G,F157-,R158-,L452R,T478K,D614G,P681R]
..R.........I.....G--.........RK.Y...R..LN........ 34 0 34 0 0 0 0 0 34 33 97% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,N501Y,D614G,P681R,I850L,D950N] B.1.617.2=Delta
..R...............G--..S......RK.....R...N........ 33 0 5 28 0 0 0 0 33 20 60% [T19R,E156G,F157-,R158-,A222S,L452R,T478K,D614G,E661D,P681R,D950N]
..R.T.......I..D..G--.........RK.....R...N........ 33 27 2 1 3 0 0 0 33 16 48% [T19R,R21T,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
F.R...............G--..V......RK.....R...N........ 33 0 3 20 10 0 0 0 33 15 45% [L5F,T19R,E156G,F157-,R158-,A222V,V367L,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R.........I..D..G--.........RK.....R...N.....A.. 33 0 0 0 0 0 0 33 33 33 100% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,P1162A] B.1.617.2=Delta
.........--.....-................YD..HV...A...H... 33 1 27 4 1 0 0 0 33 23 69% [H69-,V70-,Y144-,N501Y,A570D,D614G,T632I,P681H,T716V,G932V,S982A,D1118H]
..R.........I..D..G--...I.....RK.....R...N........ 32 28 0 4 0 0 0 0 32 22 68% [T19R,T95I,G142D,E156G,F157-,R158-,T250I,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R...........Y...G--.........RK.....R...N........ 32 0 5 17 0 0 10 0 32 28 87% [T19R,D138Y,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..............................RK.....R...N........ 31 0 7 24 0 0 0 0 31 20 64% [L452R,T478K,D614G,P681R,D950N]
..R..................................R...N........ 31 0 29 2 0 0 0 0 31 25 80% [T19R,D614G,P681R,D950N]
........V--.....-...............K...H............. 31 0 27 3 1 0 0 0 31 22 70% [Q52R,A67V,H69-,V70-,Y144-,E484K,D614G,Q677H,F888L] B.1.525=Eta
..R..............................Y...R............ 31 0 31 0 0 0 0 0 31 31 100% [T19R,N501Y,D614G,P681R]
F...........I...SN..........K...KY...H...N........ 30 0 0 24 0 0 6 0 30 10 33% [L5F,T95I,+143T,Y144S,Y145N,R346K,E484K,N501Y,D614G,P681H,D950N] B.1.621
..R...V.....I..D..G--.........RK.....R...N........ 30 19 9 2 0 0 0 0 30 26 86% [T19R,A27V,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
...............D..G--.........RK.Y...R...N........ 30 0 30 0 0 0 0 0 30 30 100% [G142D,E156G,F157-,R158-,L452R,T478K,N501Y,D614G,P681R,D950N]
..R............D..G--..........K.....R..LN........ 30 0 30 0 0 0 0 0 30 27 90% [T19R,G142D,E156G,F157-,R158-,T478K,D614G,P681R,I850L,D950N]
..R.........I..D..G--.........RK.Y...H...N........ 30 0 30 0 0 0 0 0 30 30 100% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,N501Y,D614G,P681H,D950N]
..RI...........D..G--..V......RK.....R...N........ 29 0 28 1 0 0 0 0 29 28 96% [T19R,T20I,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,S1252F] Delta+A222V
..R.........I..D..G--.........RK.Y...R..LN........ 29 0 29 0 0 0 0 0 29 29 100% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,N501Y,D614G,P681R,I850L,D950N] B.1.617.2=Delta
..R.............-.G--.........RK.....R...N........ 29 0 14 14 1 0 0 0 29 17 58% [T19R,Y144-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R..L......I..D..G--.........RK.....R...N........ 29 23 5 0 1 0 0 0 29 27 93% [T19R,P26L,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
.....................................R...N........ 29 0 26 3 0 0 0 0 29 19 65% [V130A,D614G,P681R,D950N]
............I...............K...KY...H...N........ 28 0 2 26 0 0 0 0 28 16 57% [T95I,R346K,E484K,N501Y,D614G,P681H,D950N]
..R....I..........G--.........RK.....R...N........ 28 0 5 22 0 0 1 0 28 25 89% [T19R,T29I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
F.R...S........D..G--.........RK.....R...N........ 28 0 28 0 0 0 0 0 28 16 57% [L5F,T19R,A27S,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--...I.....RK.........N........ 28 0 28 0 0 0 0 0 28 28 100% [T19R,G142D,E156G,F157-,R158-,T250I,L452R,T478K,D614G,D950N]
..R..................................R............ 28 0 28 0 0 0 0 0 28 24 85% [T19R,D614G,P681R]
..RI..............G--.........RK.....R...N........ 27 0 2 25 0 0 0 0 27 19 70% [T19R,T20I,E156G,F157-,R158-,P174S,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I.....G--..........K.....R...N........ 27 0 22 3 2 0 0 0 27 25 92% [T19R,T95I,E156G,F157-,R158-,T478K,D614G,P681R,D950N]
..R...............G--.........RK.....R...........L 27 0 18 4 5 0 0 0 27 23 85% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,V1264L]
.................................Y...R...N........ 27 0 27 0 0 0 0 0 27 27 100% [N501Y,D614G,P681R,D950N]
...............................K.................. 27 0 27 0 0 0 0 0 27 27 100% [T478K,D614G]
..R...............G--.........RK...Y.R...N........ 26 0 3 23 0 0 0 0 26 18 69% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,H655Y,P681R,D950N] B.1.617.2=Delta
..R....................V......RK.....R...N........ 26 0 7 3 16 0 0 0 26 18 69% [T19R,A222V,L452R,T478K,D614G,P681R,D950N]
..R...........................RK.Y...R...N........ 26 0 26 0 0 0 0 0 26 20 76% [T19R,L452R,T478K,N501Y,D614G,P681R,D950N]
F.R...............G--....L....RK.....R...N........ 25 0 25 0 0 0 0 0 25 22 88% [L5F,T19R,E156G,F157-,R158-,P251L,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
.............................N.................... 25 0 25 0 0 0 0 0 25 25 100% [K417N,D614G]
..G.........I..D..G--.........RK.....R...N........ 24 23 1 0 0 0 0 0 24 17 70% [T19G,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
..R.....V.........G--..V......RK.....R...N........ 24 2 20 2 0 0 0 0 24 14 58% [T19R,A67V,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R............D..G--V........RK.....R...N.......L 24 2 22 0 0 0 0 0 24 22 91% [T19R,G142D,E156G,F157-,R158-,G181V,L452R,T478K,D614G,P681R,D950N,V1264L] B.1.617.2=Delta
..R.........I..D..G--..S......RK.....R...N........ 24 13 6 5 0 0 0 0 24 15 62% [T19R,T95I,G142D,E156G,F157-,R158-,A222S,L452R,T478K,D614G,P681R,D950N]
F.R...............G--.........RK.....R............ 24 0 6 17 0 0 1 0 24 19 79% [L5F,T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R]
..R...............G--..V......RK.....R......S....L 24 0 0 24 0 0 0 0 24 22 91% [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,N1074S,V1264L]
..R.........I..D..G--.........RKQ....R...N........ 24 23 1 0 0 0 0 0 24 21 87% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--.........RK.....R.I.N........ 24 0 16 8 0 0 0 0 24 23 95% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,T719I,D950N] B.1.617.2=Delta
.........--.....-....V...........YD..HI...A...H... 24 0 2 11 11 0 0 0 24 17 70% [H69-,V70-,Y144-,G181V,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
.........--.....-................YD..HI...A...H.F. 24 4 15 5 0 0 0 0 24 20 83% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H,V1176F] B.1.1.7=Alpha
..R......Y.....D..G--.........RK.....R...N........ 23 10 2 11 0 0 0 0 23 16 69% [T19R,H69Y,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--V.V......RK.....R...N........ 23 3 6 14 0 0 0 0 23 16 69% [T19R,G142D,E156G,F157-,R158-,G181V,A222V,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R..S......I.....G--.........RK.....R...N........ 23 1 20 2 0 0 0 0 23 15 65% [T19R,P26S,L54F,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I.....G--.........RK.....R...N.....S.. 23 9 13 1 0 0 0 0 23 21 91% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,P1162S] B.1.617.2=Delta
..R.........I.....G--.........RK.....R...N.....L.. 22 1 3 18 0 0 0 0 22 19 86% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,P1162L] B.1.617.2=Delta
..R...............G--R........RK.....R...N........ 22 0 0 22 0 0 0 0 22 20 90% [T19R,E156G,F157-,R158-,G181R,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
............I..D..G--.........RK.....R...N........ 22 9 3 10 0 0 0 0 22 17 77% [T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
..R....A..........G--...I.....RK.....R............ 22 0 20 2 0 0 0 0 22 13 59% [T19R,T29A,E156G,F157-,R158-,T250I,L452R,T478K,D614G,P681R]
..R...............G--..VS.....RK.....R...N........ 22 1 13 0 1 7 0 0 22 19 86% [T19R,E156G,F157-,R158-,A222V,T250S,L452R,T478K,D614G,P681R,D950N] Delta+A222V
F.R............D..G--....L....RK.....R...N........ 22 4 18 0 0 0 0 0 22 18 81% [L5F,T19R,G142D,E156G,F157-,R158-,P251L,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--.........RK.........N........ 22 0 11 11 0 0 0 0 22 18 81% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,D950N]
..R.........I......--.........RK.....R...N........ 22 0 0 21 0 0 0 1 22 22 100% [T19R,T95I,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
..R........T..................RK.....R...N........ 22 0 21 1 0 0 0 0 22 22 100% [T19R,K77T,L452R,T478K,D614G,P681R,D950N]
..R...V.......................RK.....R...N........ 22 0 22 0 0 0 0 0 22 18 81% [T19R,A27V,L452R,T478K,D614G,P681R,D950N]
.F.N.S........Y.......S......T..KY.YH......I....F. 22 0 0 11 0 0 11 0 22 8 36% [L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,Q677H,T1027I,V1176F] P.1=Gamma
.........--.....-......V.........YD..HI...A...H... 22 0 4 15 3 0 0 0 22 11 50% [H69-,V70-,Y144-,M177I,D178H,A222V,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
...I.....--.....-................YD..HI...A...H... 22 0 11 4 7 0 0 0 22 20 90% [T20I,H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] Alpha+T20I
..R.......F.......G--..V.....NRK.....R............ 21 0 0 21 0 0 0 0 21 17 80% [T19R,V70F,E156G,F157-,R158-,A222V,K417N,L452R,T478K,D614G,P681R]
..R.....S......D..G--..V......RK.....R...N........ 21 0 21 0 0 0 0 0 21 21 100% [T19R,A67S,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R.......L.I..D..G--.........RK.....R...N........ 21 2 19 0 0 0 0 0 21 15 71% [T19R,V70L,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
..R...............G--..V......RK.....R...N..S..... 21 0 1 20 0 0 0 0 21 19 90% [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,N1074S] Delta+A222V
..R.........I..D..G--.........RK.Y...R...N........ 21 19 1 1 0 0 0 0 21 19 90% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,N501Y,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I..D..............RK.....R...N........ 21 0 14 2 5 0 0 0 21 17 80% [T19R,T95I,G142D,L452R,T478K,D614G,P681R,D950N]
..........................G.....KY................ 21 0 21 0 0 0 0 0 21 21 100% [D253G,E484K,N501Y,D614G]
..R.....V......D..G--..V......RK.....R...N.......L 20 0 0 20 0 0 0 0 20 18 90% [T19R,A67V,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+A222V
.FR.........I.....G--.........RK.....R...N........ 20 4 9 4 2 1 0 0 20 16 80% [L18F,T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I.....G--V........RK.....R...N...L.... 20 0 4 16 0 0 0 0 20 16 80% [T19R,T95I,E156G,F157-,R158-,G181V,L452R,T478K,D614G,P681R,D950N,V1104L] B.1.617.2=Delta
..R.....V...I.....G--.........RK.....R...N........ 20 4 7 8 1 0 0 0 20 16 80% [T19R,A67V,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R...V........D..G--.........RK.....R...N........ 20 0 6 14 0 0 0 0 20 20 100% [T19R,A27V,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I..D..G--.........RKQ....R...N...L.... 20 16 3 1 0 0 0 0 20 19 95% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,D950N,V1104L] B.1.617.2=Delta
..R.........I..D..G--.......S.RK.....R...N........ 20 20 0 0 0 0 0 0 20 20 100% [T19R,T95I,G142D,E156G,F157-,R158-,R346S,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
.........--.....-...........T....YD..HI...A...H... 20 0 0 18 2 0 0 0 20 19 95% [H69-,V70-,Y144-,R346T,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
.................................YD..HI...A...H... 20 0 1 18 0 0 1 0 20 11 55% [N501Y,A570D,D614G,P681H,T716I,S982A,D1118H]
.........--.....-................YD..HI...A..LH... 20 0 20 0 0 0 0 0 20 15 75% [H69-,V70-,Y144-,W152R,N501Y,A570D,D614G,P681H,T716I,S982A,V1104L,D1118H] Alpha+W152R
.................................Y....I........... 20 0 20 0 0 0 0 0 20 20 100% [N501Y,D614G,T716I]
F.R........T...D..G--.........RKQ....R...N........ 19 0 0 19 0 0 0 0 19 18 94% [L5F,T19R,K77T,G142D,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,D950N] B.1.617.2=Delta
..R..L.........D..G--.........RK.....R...N........ 19 1 4 14 0 0 0 0 19 17 89% [T19R,P26L,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..I.........I..D..G--.........RK.....R...N........ 19 11 7 1 0 0 0 0 19 16 84% [T19I,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
F.R.........I..D..G--.........RK.....R...N...L.... 19 0 0 15 4 0 0 0 19 13 68% [L5F,T19R,T95I,K97E,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1104L] B.1.617.2=Delta
..R....S....I..D..G--.........RK.....R...N........ 19 1 0 0 18 0 0 0 19 19 100% [T19R,T29S,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.......F.I.....G--.........RK.....R...N........ 19 5 14 0 0 0 0 0 19 16 84% [T19R,V70F,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
..R...V...I....D..G--.........RK.....R...N........ 19 0 0 19 0 0 0 0 19 17 89% [T19R,A27V,V70I,G142D,E156G,F157-,R158-,M177I,L452R,T478K,D614G,P681R,D950N]
..R.........I..D..--..........RK.....R...N........ 19 0 19 0 0 0 0 0 19 19 100% [T19R,T95I,G142D,S155R,E156-,F157-,L452R,T478K,D614G,P681R,D950N]
..R.........I...SN.............K.........N........ 19 0 19 0 0 0 0 0 19 19 100% [T19R,T95I,+143T,Y144S,Y145N,M153I,E154-,T478K,D614G,D950N]
.................................Y...R............ 19 0 19 0 0 0 0 0 19 19 100% [N501Y,D614G,P681R]
............I..................................... 19 0 19 0 0 0 0 0 19 19 100% [T95I,D614G]
FF..........I.............G....................... 18 0 0 18 0 0 0 0 18 15 83% [L5F,L18F,T95I,D253G,S477N,D614G,Q957R] B.1.526.2
..R............D..G--.........RKQ....R...N........ 18 6 3 7 2 0 0 0 18 12 66% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,D950N] B.1.617.2=Delta
..R...............G--..........K.Y...R...N........ 18 0 18 0 0 0 0 0 18 18 100% [T19R,E156G,F157-,R158-,T478K,N501Y,D614G,P681R,D950N]
..R.......F.......G--.........RK.....R...N........ 18 1 9 8 0 0 0 0 18 16 88% [T19R,V70F,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
F.R.........I.....G--.........RK.....R............ 18 1 8 6 0 0 3 0 18 12 66% [L5F,T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R]
..R.....V.........G--.........RK.....R...N........ 18 0 3 15 0 0 0 0 18 12 66% [T19R,A67V,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.....V...I..D..G--.........RK.....R.I.N........ 18 18 0 0 0 0 0 0 18 17 94% [T19R,A67V,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,T719I,D950N] B.1.617.2=Delta
.F.N.S........Y......VS......T..KY.Y.......I....F. 18 0 0 11 0 0 7 0 18 12 66% [L18F,T20N,P26S,D138Y,G181V,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] P.1=Gamma
.F.......--.....-................YD..HI...A...H... 18 0 5 12 0 0 1 0 18 14 77% [L18F,H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
.........--.....-................Y....I...A....... 18 0 18 0 0 0 0 0 18 18 100% [H69-,V70-,Y144-,N501Y,D614G,T716I,S982A]
.........--.....-................Y....I........... 18 0 18 0 0 0 0 0 18 18 100% [H69-,V70-,Y144-,N501Y,D614G,T716I]
............I...........................L......... 18 0 18 0 0 0 0 0 18 18 100% [T95I,D614G,I850L]
..R.........I..................................... 18 0 18 0 0 0 0 0 18 18 100% [T19R,T95I,D614G]
.FR............D..G--..V......RK.....R...N........ 17 0 5 12 0 0 0 0 17 13 76% [L18F,T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R......--.I..D..G--.........RK.....R...N........ 17 14 3 0 0 0 0 0 17 11 64% [T19R,H69-,V70-,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
F.R...............G--..V...I..RK.....R...N........ 17 0 0 17 0 0 0 0 17 17 100% [L5F,T19R,E156G,F157-,R158-,A222V,V289I,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R.........I..D..G--V........RK.....R...N...L.... 17 3 6 8 0 0 0 0 17 14 82% [T19R,T95I,G142D,E156G,F157-,R158-,G181V,L452R,T478K,D614G,P681R,D950N,V1104L] B.1.617.2=Delta
F.R...S...........G--.........RK.....R...N........ 17 0 17 0 0 0 0 0 17 11 64% [L5F,T19R,A27S,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R......--....D..G--.........RK.....R...N........ 17 5 2 9 0 0 1 0 17 13 76% [T19R,H69-,V70-,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
..R...........................RKKY...R...N........ 17 0 17 0 0 0 0 0 17 15 88% [T19R,L452R,T478K,E484K,N501Y,D614G,P681R,D950N]
..R...........................RK.........N........ 17 0 16 1 0 0 0 0 17 17 100% [T19R,L452R,T478K,D614G,D950N]
.F.N.S........Y.......S.........KY.Y.......I....F. 17 0 4 8 0 0 5 0 17 10 58% [L18F,T20N,P26S,D138Y,R190S,E484K,N501Y,D614G,H655Y,T1027I,V1176F] P.1=Gamma
..R...........YD..G--.........RK.....R...N........ 16 2 5 9 0 0 0 0 16 15 93% [T19R,D138Y,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--........NRK.....R...N........ 16 2 2 12 0 0 0 0 16 14 87% [T19R,G142D,E156G,F157-,R158-,K417N,L452R,T478K,D614G,P681R,D950N]
..R.........I..D..G--.......I.RK.....R...N........ 16 0 3 13 0 0 0 0 16 13 81% [T19R,T95I,G142D,E156G,F157-,R158-,R346I,L452R,T478K,D614G,P681R,D950N,K1073N] B.1.617.2=Delta
..R.........I.....G--................R...N........ 16 0 13 3 0 0 0 0 16 9 56% [T19R,T95I,E156G,F157-,R158-,D614G,P681R,D950N]
..R..S.........D..G--.........RK.....R...N........ 16 4 7 5 0 0 0 0 16 14 87% [T19R,P26S,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--..V......RK.....R...N......F. 16 1 11 1 3 0 0 0 16 14 87% [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1176F] Delta+A222V
..I............D..G--.........RK.....R...N........ 16 6 7 3 0 0 0 0 16 12 75% [T19I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
..R........T...D..G--V........RK.....R...N........ 16 0 0 16 0 0 0 0 16 14 87% [T19R,K77T,G142D,E156G,F157-,R158-,G181V,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R...............G--.........RK.....R.I.N........ 16 0 14 1 1 0 0 0 16 15 93% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,T719I,D950N] B.1.617.2=Delta
..R............D..G--................R...N........ 16 0 3 13 0 0 0 0 16 13 81% [T19R,G142D,E156G,F157-,R158-,D614G,P681R,D950N]
..R...............G--.........RKK....R...N........ 16 0 11 5 0 0 0 0 16 15 93% [T19R,E156G,F157-,R158-,L452R,T478K,E484K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I....HG--..V......RK.....R...N........ 16 6 10 0 0 0 0 0 16 15 93% [T19R,T95I,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R............D.......V......RK.....R...N........ 16 0 10 0 6 0 0 0 16 12 75% [T19R,G142D,A222V,L452R,T478K,D614G,P681R,D950N]
..I......--.....-................YD..HI...A...H... 16 0 11 3 2 0 0 0 16 9 56% [T19I,H69-,V70-,Y144-,K147E,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
F........--.....-................YD..HI...A...Y... 16 0 2 14 0 0 0 0 16 10 62% [L5F,H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118Y]
........S--.....-................YD..HI...A...H... 16 2 5 9 0 0 0 0 16 9 56% [A67S,H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
..R.............................KY................ 16 0 16 0 0 0 0 0 16 16 100% [T19R,E484K,N501Y,D614G]
.............................N...Y................ 15 0 15 0 0 0 0 0 15 14 93% [K417N,N501Y,D614G]
...S....................---...Q................... 15 0 0 15 0 0 0 0 15 12 80% [T20S,G75V,T76I,R246N,S247-,Y248-,L249-,T250-,P251-,G252-,D253-,L452Q,F490S,D614G,T859N] C.37=Lambda
..R............D..G--.........WK.....R...N........ 15 1 6 8 0 0 0 0 15 15 100% [T19R,G142D,E156G,F157-,R158-,L452W,T478K,D614G,P681R,D950N]
.FR...............G--.........RK.....R...N........ 15 1 3 9 1 0 1 0 15 12 80% [L18F,T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R..L............G--.........RK.....R...N........ 15 0 5 9 0 0 1 0 15 12 80% [T19R,P26L,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
F.R...............G--..V......RK.....R...N..S....L 15 0 0 15 0 0 0 0 15 14 93% [L5F,T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,N1074S,V1264L] Delta+A222V
F.R..........L.D..G--.........RK.....R...N........ 15 0 0 15 0 0 0 0 15 9 60% [L5F,T19R,S112L,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I..D...--.........RK.....R...N........ 15 0 2 13 0 0 0 0 15 14 93% [T19R,T95I,G142D,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
..R............................K.....R...N........ 15 0 15 0 0 0 0 0 15 13 86% [T19R,T478K,D614G,P681R,D950N]
.F.NIS........Y.......S......T..KY.Y.......I....F. 15 0 0 14 0 0 1 0 15 15 100% [L18F,T20N,R21I,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] P.1=Gamma
.........--.....-....E...........YD..HI...A...H... 15 0 15 0 0 0 0 0 15 15 100% [H69-,V70-,Y144-,M153K,G181E,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H,Q1201R] B.1.1.7=Alpha
..R.........I..D..G--R........RK.....R...N........ 14 10 0 4 0 0 0 0 14 6 42% [T19R,T95I,G142D,E156G,F157-,R158-,G181R,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R...............G--.........RK.....R...N.....S.. 14 0 3 11 0 0 0 0 14 12 85% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,P1162S] B.1.617.2=Delta
..R............D..G--..V......RK....HR...N........ 14 1 9 3 1 0 0 0 14 12 85% [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,Q677H,P681R,D950N] Delta+A222V
..R.....V.........G--..V......RK.....R...N.......L 14 0 0 14 0 0 0 0 14 12 85% [T19R,A67V,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+A222V
..R...............G--..V......RK.....R...N.....S.. 14 0 6 8 0 0 0 0 14 13 92% [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,P1162S] Delta+A222V
............I.....G--.........RK.....R...N........ 14 0 14 0 0 0 0 0 14 5 35% [T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
..RA..............G--..V...I..RK.....R...N........ 14 0 0 14 0 0 0 0 14 13 92% [T19R,T20A,E156G,F157-,R158-,A222V,V289I,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R...............G--V........RK.....R............ 14 0 12 1 0 0 1 0 14 13 92% [T19R,E156G,F157-,R158-,G181V,L452R,T478K,D614G,P681R]
..R...............G--.........RK.....R...N......F. 14 0 11 3 0 0 0 0 14 6 42% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,Q836E,D950N,V1176F] B.1.617.2=Delta
..R.........I.....G--.........RK.Y...R...N........ 14 0 14 0 0 0 0 0 14 9 64% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,N501Y,D614G,P681R,D950N] B.1.617.2=Delta
-.R............D..G--.........RK.....R...N........ 14 0 12 2 0 0 0 0 14 10 71% [L5-,T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.......F.I..D..G--.........RK.....R..LN........ 14 0 14 0 0 0 0 0 14 14 100% [T19R,V70F,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N]
..R....................V......RK.....R............ 14 0 0 0 14 0 0 0 14 8 57% [T19R,A222V,L452R,T478K,D614G,P681R]
........VS......................K................. 14 0 14 0 0 0 0 0 14 14 100% [A67V,H69S,E484K,D614G,F888L]
.............................T..KY................ 14 0 14 0 0 0 0 0 14 14 100% [K417T,E484K,N501Y,D614G]
.........--......................YD..HI...A...H... 14 0 10 1 3 0 0 0 14 7 50% [H69-,V70-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
................................KY.......N........ 14 0 14 0 0 0 0 0 14 9 64% [E484K,N501Y,D614G,D950N]
.R..........I.......S...........Q....H.....I...... 13 0 2 11 0 0 0 0 13 5 38% [L18R,T95I,R158S,N440K,E484Q,D614G,P681H,A688V,S735A,T1027I]
..R...S.....I.....G--.........RK.....R............ 13 0 1 12 0 0 0 0 13 10 76% [T19R,A27S,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R]
F.R...............G--..V......RK.....R...N.......L 13 0 0 12 1 0 0 0 13 10 76% [L5F,T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+A222V
..R.........I.....G--.........RK.....R..L......... 13 0 9 1 3 0 0 0 13 5 38% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L]
..R.........I..D-DG--.........RK.....R...N........ 13 12 1 0 0 0 0 0 13 8 61% [T19R,T95I,A123T,G142D,V143-,Y144-,Y145D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--....................N........ 13 0 13 0 0 0 0 0 13 12 92% [T19R,G142D,E156G,F157-,R158-,D614G,D950N]
F.R........T......G--.........RKQ....R...N........ 13 0 0 13 0 0 0 0 13 12 92% [L5F,T19R,K77T,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,D950N] B.1.617.2=Delta
..R........T...D..G--.........RK.....R...N.....S.. 13 0 0 13 0 0 0 0 13 13 100% [T19R,K77T,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,P1162S] B.1.617.2=Delta
F.R.........I.....G--.........RK.....R..LN........ 13 0 13 0 0 0 0 0 13 11 84% [L5F,T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] B.1.617.2=Delta
...................S..........R......R............ 13 0 13 0 0 0 0 0 13 13 100% [F157S,L452R,D614G,P681R]
................-......V......RRQ..Y.....N........ 13 0 1 12 0 0 0 0 13 9 69% [P9L,C136F,Y144-,A222V,A243-,L244-,L452R,T478R,E484Q,D614G,H655Y,D950N]
.F.N.S........Y..............T..KY.Y.......I....F. 13 0 1 2 0 0 10 0 13 8 61% [L18F,T20N,P26S,D138Y,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F]
.F.N.S........---.....S......T..KY.Y.......I....F. 13 0 0 1 0 0 12 0 13 9 69% [L18F,T20N,P26S,D138-,P139Y,F140-,L141-,G142-,V143-,Y144-,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] P.1=Gamma
...I............................K..........I...... 13 0 0 0 13 0 0 0 13 12 92% [T20I,I210T,N440K,E484K,D614G,D936N,S939F,T1027I] B.1.619
................................................F. 13 0 13 0 0 0 0 0 13 13 100% [D614G,V1176F]
................................K........N........ 12 0 12 0 0 0 0 0 12 8 66% [N440K,E484K,D614G,D936N,S939F,D950N]
..............................RK.Y................ 12 0 12 0 0 0 0 0 12 12 100% [L452R,T478K,N501Y,D614G]
.RI.........I.......S................H.....I...... 12 0 2 10 0 0 0 0 12 8 66% [L18R,T19I,T95I,R158S,N440K,D614G,P681H,A688V,S735A,S939F,T1027I]
..............H.........---...Q................... 12 0 0 12 0 0 0 0 12 6 50% [G75V,T76I,D138H,R246N,S247-,Y248-,L249-,T250-,P251-,G252-,D253-,L452Q,F490S,D614G,T859N,A1020S] C.37=Lambda
F.......................---...Q................... 12 0 0 1 0 0 11 0 12 9 75% [L5F,G75V,T76I,R246N,S247-,Y248-,L249-,T250-,P251-,G252-,D253-,L452Q,F490S,D614G,T859N] C.37=Lambda
............I...SN..........KN..KY...H............ 12 0 0 12 0 0 0 0 12 5 41% [T95I,+143T,Y144S,Y145N,R346K,K417N,E484K,N501Y,D614G,P681H]
..............................RKKY...R............ 12 0 12 0 0 0 0 0 12 10 83% [L452R,T478K,E484K,N501Y,D614G,P681R]
..R............D..G--.........R......R...N........ 12 0 10 2 0 0 0 0 12 10 83% [T19R,G142D,E156G,F157-,R158-,L452R,D614G,P681R,D950N]
..R............D..G--......I..RK.....R...N........ 12 1 1 10 0 0 0 0 12 11 91% [T19R,G142D,E156G,F157-,R158-,V289I,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--....L....RK.....R............ 12 0 12 0 0 0 0 0 12 11 91% [T19R,G142D,E156G,F157-,R158-,P251L,L452R,T478K,D614G,P681R]
..R...............G--.........RKQ....R...N........ 12 0 4 5 3 0 0 0 12 8 66% [T19R,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--.........RK.....R...N.......F 12 0 0 1 11 0 0 0 12 10 83% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1264F] B.1.617.2=Delta
.F.N.S...--...Y.......S......T..KY.Y.......I....F. 12 0 0 0 0 0 12 0 12 8 66% [L18F,T20N,P26S,H69-,V70-,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,Q675H,T1027I,V1176F] P.1=Gamma
.........--.....-................Y...HI...A...H... 12 0 8 3 1 0 0 0 12 8 66% [H69-,V70-,Y144-,N501Y,D614G,P681H,T716I,S982A,D1118H]
..R...........................RK.................. 12 0 11 1 0 0 0 0 12 12 100% [T19R,L452R,T478K,D614G]
..R.........I.................RK.................. 12 0 12 0 0 0 0 0 12 12 100% [T19R,T95I,L452R,T478K,D614G]
..R.............................K....R...N........ 12 0 12 0 0 0 0 0 12 12 100% [T19R,E484K,D614G,P681R,D950N]
..................G--..........K.....R...N........ 11 0 9 2 0 0 0 0 11 11 100% [E156G,F157-,R158-,T478K,D614G,P681R,D950N]
..R...............G--.........RK.........N........ 11 0 10 1 0 0 0 0 11 6 54% [T19R,E156G,F157-,R158-,N440K,L452R,T478K,D614G,D950N]
..R...............G--..........K.....R..LN........ 11 0 11 0 0 0 0 0 11 10 90% [T19R,E156G,F157-,R158-,T478K,D614G,P681R,I850L,D950N]
..R........TI..D..G--.........RK.....R...N........ 11 0 0 11 0 0 0 0 11 10 90% [T19R,K77T,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--.........RK.....L...N........ 11 5 3 3 0 0 0 0 11 6 54% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681L,D950N]
..R............D..G--..V......RKQ....R...N........ 11 0 11 0 0 0 0 0 11 11 100% [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,E484Q,D614G,P681R,D950N] Delta+A222V
..R......Y.....D..G--..V......RK.....R...N........ 11 2 9 0 0 0 0 0 11 10 90% [T19R,H69Y,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+A222V
F.R...............G--..V......RK.....R............ 11 0 0 2 9 0 0 0 11 6 54% [L5F,T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R]
..R.........I.....G--..S......RK.....R...N........ 11 1 9 1 0 0 0 0 11 10 90% [T19R,T95I,E156G,F157-,R158-,A222S,L452R,T478K,D614G,P681R,D950N]
..R...............G--..V...L..RK.....R...N........ 11 0 5 0 6 0 0 0 11 5 45% [T19R,E156G,F157-,R158-,A222V,V289L,L452R,T478K,D614G,P681R,D950N] Delta+A222V
F.R............D..G--.........RK.....R...N.......L 11 0 0 2 9 0 0 0 11 11 100% [L5F,T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1264L] B.1.617.2=Delta
.F......V--.....................KT................ 11 0 3 8 0 0 0 0 11 9 81% [L18F,A67V,I68-,H69-,V70-,G257S,E484K,F490S,N501T,D614G,T859N]
.........--.....-................YDY.HI...A...H... 11 0 5 5 1 0 0 0 11 5 45% [H69-,V70-,Y144-,N501Y,A570D,D614G,H655Y,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
.................................Y.Y.............. 11 0 11 0 0 0 0 0 11 11 100% [Y449H,N501Y,F565L,H655Y]
..............Y................................... 10 0 9 1 0 0 0 0 10 9 90% [D138Y,S477N,A522S,D614G,Q675R,A845S]
..R............D..G--.........RK.....R...N....Y... 10 1 2 5 2 0 0 0 10 8 80% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,D1118Y] B.1.617.2=Delta
..R............D..G--...I.....RK.....R...N........ 10 1 6 1 0 2 0 0 10 4 40% [T19R,G142D,E156G,F157-,R158-,T250I,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R...............G--.........RK.....R...N....Y... 10 0 6 1 3 0 0 0 10 7 70% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,D1118Y] B.1.617.2=Delta
..R......Y........G--.........RK.....R...N........ 10 0 7 2 0 0 1 0 10 6 60% [T19R,H69Y,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R...........YD..G--..V......RK.....R...N........ 10 8 2 0 0 0 0 0 10 9 90% [T19R,D138Y,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R.........I..D..G--.........RK..S..R...N........ 10 5 3 2 0 0 0 0 10 3 30% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,A570S,D614G,P681R,D950N] B.1.617.2=Delta
F.R.........I.....G--.........RK.....R...N...L.... 10 0 1 9 0 0 0 0 10 7 70% [L5F,T19R,T95I,K97E,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1104L] B.1.617.2=Delta
..R.........I..D..G--..V......RK.....R...N...L.... 10 1 1 8 0 0 0 0 10 9 90% [T19R,T95I,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1104L] Delta+A222V
..R.........I..D..G--.........RK.....R...N....Y... 10 4 1 4 1 0 0 0 10 8 80% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,D1118Y] B.1.617.2=Delta
..R........T......G--V........RK.....R...N........ 10 0 0 10 0 0 0 0 10 5 50% [T19R,K77T,E156G,F157-,R158-,G181V,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R........R...D..G--.........RK.....R...N.......L 10 0 0 0 10 0 0 0 10 10 100% [T19R,K77R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1264L] B.1.617.2=Delta
..R.I..........D..G--....L....RK.....R...N........ 10 2 8 0 0 0 0 0 10 10 100% [T19R,R21I,G142D,E156G,F157-,R158-,P251L,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--.........RK.....R...N.I...... 10 0 1 9 0 0 0 0 10 7 70% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,T1027I] B.1.617.2=Delta
..R.........I.....G--.........RK.....RI..N........ 10 1 9 0 0 0 0 0 10 10 100% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,T716I,D950N] B.1.617.2=Delta
..R.........I..D..G--.........RK.....L...N........ 10 4 5 0 1 0 0 0 10 9 90% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681L,D950N]
..R............D..G--.....A...RK.....R...N........ 10 0 8 2 0 0 0 0 10 10 100% [T19R,G142D,E156G,F157-,R158-,D253A,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R...........................RK..S..R...N........ 10 0 10 0 0 0 0 0 10 10 100% [T19R,L452R,T478K,A570S,D614G,P681R,D950N]
..R...........................RK.Y.......N........ 10 0 10 0 0 0 0 0 10 10 100% [T19R,L452R,T478K,N501Y,D614G,D950N]
....................................H............. 10 0 9 1 0 0 0 0 10 7 70% [D614G,Q677H] Near-Furin
.F.N.S........Y.-.....S......T..KY.Y.......I....F. 10 0 0 2 0 0 8 0 10 5 50% [L18F,T20N,P26S,D138Y,Y144-,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] P.1=Gamma
.F.N.S........Y--.....S......T..KY.Y.......I....F. 10 0 0 5 0 0 5 0 10 7 70% [L18F,T20N,P26S,D138Y,L141-,G142-,V143-,Y144-,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] P.1=Gamma
.............................T..KY.........I...... 10 0 10 0 0 0 0 0 10 10 100% [K417T,E484K,N501Y,D614G,T1027I]
.........--.....-................YD..HI...A...H..L 10 0 4 2 4 0 0 0 10 5 50% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H,V1264L] B.1.1.7=Alpha
.........--.....-.........G......YD..HI...A...H... 10 0 5 3 2 0 0 0 10 7 70% [H69-,V70-,Y144-,D253G,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
.....H...--.....-................YD..HI...A...H... 10 0 0 10 0 0 0 0 10 7 70% [P26H,H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,A684V,T716I,L938F,S982A,D1118H] B.1.1.7=Alpha
..................V--...........K..........I...... 10 0 10 0 0 0 0 0 10 7 70% [E156V,F157-,R158-,V159-,F306L,E484K,S494P,D614G,E780A,D839V,T1027I]
......S......................N..KY................ 10 2 0 4 4 0 0 0 10 4 40% [A27S,D80A,D215G,L242-,A243-,L244-,K417N,E484K,N501Y,D614G,A701V] B.1.351=Beta
..R.........I..................K.....R...N........ 10 0 10 0 0 0 0 0 10 8 80% [T19R,T95I,T478K,D614G,P681R,D950N]
.F.N.S.......................T..KY..............F. 10 0 10 0 0 0 0 0 10 10 100% [L18F,T20N,P26S,K417T,E484K,N501Y,D614G,V1176F]
.........--.....-.............RK..D..HI...A...H... 10 0 10 0 0 0 0 0 10 4 40% [H69-,V70-,Y144-,L452R,T478K,A570D,D614G,P681H,T716I,S982A,D1118H]
..............................RK.Y...R...N........ 10 0 10 0 0 0 0 0 10 10 100% [L452R,T478K,N501Y,D614G,P681R,D950N]
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last modified: Fri Sep 10 02:06 2021
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Questions or comments? Contact us at seq-info@lanl.gov.
