COVID-19 Viral Genome Analysis Pipeline
Enabled by data from
XSpike
eXplore the Spike protein sequence in the SARS CoV-2 virus
Last update: Jan 20, 2022
Delta and Omicron, Jan 2022 Variants
Global
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Evaluating 593155 sequences of length 2749
Sampled from 2021-11-21 to 2022-01-14.
Specified Date Range: (datetime.date(2021, 11, 21), datetime.date(2022, 1, 20))
Highest entropy sites for: Global
Site Entropy
95 0.6874
145 0.6316
222 0.3771
19 0.3749
70 0.3684
484 0.3670
156 0.3546
371 0.3535
158 0.3532
950 0.3531
157 0.3530
477 0.3459
679 0.3454
681 0.3449
211 0.3432
796 0.3429
655 0.3421
212 0.3420
67 0.3407
452 0.3403
69 0.3393
954 0.3387
969 0.3383
764 0.3368
501 0.3355
339 0.3350
547 0.3348
446 0.3347
373 0.3324
143 0.3319
144 0.3316
375 0.3311
493 0.3304
505 0.3292
498 0.3290
440 0.3264
856 0.3259
981 0.3248
417 0.3201
496 0.3160
214 0.0157
142 0.2670
346 0.1567
1264 0.1471
5 0.0838
36 0.0818
112 0.0741
850 0.0683
Most highly correlated site-pairs for: Global
cramerV mutInfo
156 158 0.7099 0.3521
156 157 0.5772 0.3517
158 157 0.7072 0.3509
211 212 0.7715 0.3399
954 969 0.9993 0.3371
679 954 0.5761 0.3350
679 969 0.9978 0.3349
679 681 0.4934 0.3328
681 954 0.5739 0.3314
681 969 0.9940 0.3313
954 764 0.9949 0.3308
796 954 0.5742 0.3307
796 969 0.9946 0.3307
969 764 0.9949 0.3306
679 764 0.9947 0.3304
493 498 0.9978 0.3258 505 498 0.9972 0.3248 501 498 0.9941 0.3222 796 764 0.9932 0.3285 681 764 0.9909 0.3274 655 969 0.9897 0.3272 655 764 0.9862 0.3231 484 498 0.9855 0.3140 477 498 0.9854 0.3136 969 339 0.9844 0.3181 764 339 0.9822 0.3147 452 969 0.9819 0.3170 452 764 0.9813 0.3158 339 498 0.9794 0.3085 371 498 0.9793 0.3067
Most common patterns for local area, where Local = Global
1
11111111222233333444444444555666778899992
13667914444555111234777144578999004578695555686
596790522345678124296135706274368157591460604914
LTVAHVTSGVYYEFRNLRAGRSSSKNGLSEQGQNYTHNPNDINDQNLV Global UK Eu-UK NAmer Asia Africa SAmer Ocean Local Exact Pct [Context]
593155 192375 164111 206074 14956 1546 5903 8190 593155 <----------- Totals
.R......D...G--............R..........R....N.... 190039 31233 54427 101028 2180 153 938 80 190039 113614 59% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.D...G--............R..........R....N.... 185000 99321 42956 34456 2303 83 544 5337 185000 96360 52% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.D..HG--...V........R..........R....N.... 31124 27681 3320 85 31 2 1 4 31124 21809 70% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+Y145H,A222V
...V--I.D---...-I..D.LPFNKS.NARSRYHKYKHKY.K.HKF. 28359 556 6889 16222 1251 871 519 2051 28359 24255 85% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
.R..........G--............R..........R....N.... 17718 42 10849 3687 1507 0 1628 5 17718 10599 59% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
...V--I.D---...-I..DKLPFNKS.NARSRYHKYKHKY.K.HKF. 16853 81 1753 13425 1112 66 174 242 16853 16142 95% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron+R346K
.R....I.D..HG--...V........R..........R....N...L 13169 12897 221 29 17 4 0 1 13169 7613 57% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+Y145H,A222V
.R....I.....G--............R..........R....N.... 11618 120 8026 1741 751 5 865 110 11618 5695 49% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.RF...I.D..HG--...V........R..........R....N.... 8874 8555 221 91 6 0 0 1 8874 7118 80% [T19R,V36F,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+Y145H,A222V
.R......D...G--...V........R..........R....N.... 8862 1001 2500 4007 1303 1 43 7 8862 4026 45% [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+T95_,A222V
.R.....LD...G--............R..........R....N.... 7344 65 106 7168 2 0 3 0 7344 5278 71% [T19R,S112L,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta+S112L
.R....I.D...G--............R..........R..L.N.... 5239 425 4573 187 37 1 12 4 5239 3004 57% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] Delta
FR....I.D...G--............R..........R....N.... 3877 1760 1435 619 17 0 6 40 3877 2206 56% [L5F,T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.I......D..........D.FPFNK..NAR.RYH.YKHKY...HK.. 3495 19 3292 3 134 40 1 6 3495 2832 81% [T19I,L24S,P25-,P26-,A27-,G142D,V213G,G339D,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,S477N,T478K,E484A,Q493R,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] Omicron_BA.2
...V--I.D---...I-..D.LPFNKS.NARSRYHKYKHKY.K.HKF. 3148 14 1346 1447 7 172 152 10 3148 2525 80% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211I,L212-,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
FR......D...G--............R..........R....N.... 2907 464 1126 1277 17 4 19 0 2907 1630 56% [L5F,T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R...I..D...G--............R..........R....N.... 1968 10 6 1950 1 0 1 0 1968 850 43% [T19R,V70I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
.R......D...G--............R..........R....N...L 1922 297 278 398 933 1 7 8 1922 1059 55% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+V1264L
.R..........G--...V........R..........R....N.... 1868 1 495 59 1276 0 37 0 1868 1338 71% [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+T95_,A222V
.R......D...G--...V........R..........R....N...L 1826 22 189 1575 36 2 1 1 1826 738 40% [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+V1264L
...........................R..........R....N.... 1381 0 183 1198 0 0 0 0 1381 894 64% [L452R,T478K,D614G,P681R,D950N]
...V--I.D---.......D.LPFNKS.NARSRYHKYKHKY.K.HKF. 1352 0 1343 8 0 0 0 1 1352 911 67% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
.R..........G--............R..........R......... 1326 0 984 81 80 1 180 0 1326 722 54% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R]
.R....I.....G--............R..........R..L.N.... 1218 0 1191 5 21 0 0 1 1218 630 51% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] Delta
.R....I.D...G--............R.Q........R....N.... 1086 320 607 99 56 1 1 2 1086 358 32% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,D950N]
.R.........................R..........R....N.... 900 0 151 734 9 0 6 0 900 533 59% [T19R,L452R,T478K,D614G,P681R,D950N]
.R....I.D...G--............R..........R....N...L 843 346 178 289 27 0 1 2 843 395 46% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+V1264L
.R....I.....G--............R..........R......... 784 1 664 62 13 0 44 0 784 369 47% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R]
...V--I.D---...-I..D.LPF.KS.NARSRYHKYKHKY.K.HKF. 758 0 434 297 7 6 14 0 758 649 85% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
...V--I.D---.......................KYKHKY.K.HKF. 742 0 0 742 0 0 0 0 742 718 96% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
FR....I.D..HG--...V........R..........R....N.... 707 457 249 1 0 0 0 0 707 334 47% [L5F,T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+Y145H,A222V
...V--I.D---...I-..DKLPFNKS.NARSRYHKYKHKY.K.HKF. 620 0 196 377 4 5 34 4 620 593 95% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211I,L212-,G339D,R346K,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron+R346K
.R....I.D...G--...........VR..........R....N.... 595 192 103 143 44 0 4 109 595 412 69% [T19R,T95I,G142D,E156G,F157-,R158-,G446V,L452R,T478K,D614G,P681R,D950N] Delta
.R.V....D...G--............R..........R....N.... 562 286 94 177 3 0 2 0 562 268 47% [T19R,A67V,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
...V--I.D---...-I..DKLPF.KS.NARSRYHKYKHKY.K.HKF. 503 0 227 241 10 17 8 0 503 481 95% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron+R346K
.R......D...G--............R.Q........R....N.... 503 52 187 247 12 0 5 0 503 201 39% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,D950N]
.R......D...G--............R.A........R....N.... 475 15 426 25 8 0 0 1 475 256 53% [T19R,G142D,E156G,F157-,R158-,G181V,L452R,T478K,E484A,D614G,P681R,D950N]
.R....I.D...G--...S........R..........R....N.... 475 100 297 47 9 0 1 21 475 306 64% [T19R,T95I,G142D,E156G,F157-,R158-,A222S,L452R,T478K,D614G,P681R,D950N]
.R....I.D...G--...V........R..........R....N.... 436 111 159 108 15 0 42 1 436 112 25% [T19R,T95I,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N]
.R..Y.I.D...G--............R..........R....N.... 436 62 357 11 4 1 0 1 436 248 56% [T19R,H69Y,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R....I....HG--...V........R..........R....N.... 432 35 393 1 2 0 1 0 432 276 63% [T19R,T95I,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+Y145H,A222V
.R......D...G--............RI.........R....N.... 427 125 229 71 1 0 1 0 427 158 37% [T19R,G142D,E156G,F157-,R158-,L452R,S477I,T478K,D614G,P681R,D950N] Delta
.R......D...G--...........VR..........R....N.... 424 57 153 209 3 0 2 0 424 269 63% [T19R,G142D,E156G,F157-,R158-,G446V,L452R,T478K,D614G,P681R,D950N] Delta
.R.S....D...G--............R..........R....N.... 419 179 181 56 2 0 0 1 419 324 77% [T19R,A67S,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
...V--I.D---...-I..D.LPF...RNARSRYHKYKHKY.K.HKF. 408 20 30 357 1 0 0 0 408 369 90% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,L452R,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron+417_,440_,446_,L452R
.R....I.D...G--............R........Y.R....N.... 404 330 43 29 1 0 0 1 404 232 57% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,H655Y,P681R,D950N] Delta+FurinRelated
FR..........G--............R..........R....N.... 394 1 292 47 11 0 43 0 394 229 58% [L5F,T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R......D.-.G--............R..........R....N.... 391 128 69 186 3 0 5 0 391 234 59% [T19R,G142D,Y144-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R......D...G--............R..........R......... 375 6 159 185 7 0 18 0 375 211 56% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R]
.R...FI.D...G--............R..........R....N.... 372 298 56 8 3 0 1 6 372 263 70% [T19R,V70F,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
.R...II.D..HG--...V........R..........R....N.... 359 8 351 0 0 0 0 0 359 321 89% [T19R,V70I,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N]
.R....I.D.-.G--............R..........R....N.... 348 147 156 42 3 0 0 0 348 193 55% [T19R,T95I,G142D,Y144-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
...V--I.D---...I-..D.LPF.KS.NARSRYHKYKHKY.K.HKF. 344 0 99 245 0 0 0 0 344 297 86% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211I,L212-,G339D,S371L,S373P,S375F,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
.R...F..D...G--............R..........R....N.... 339 6 31 302 0 0 0 0 339 306 90% [T19R,V70F,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
...V..I.D---.......D.LPFNKS.NARSRYHKYKHKY.K.HKF. 304 0 304 0 0 0 0 0 304 239 78% [A67V,T95I,G142D,V143-,Y144-,Y145-,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
.R....I.D...G--..L.........R..........R....N.... 300 220 26 49 4 0 0 1 300 200 66% [T19R,T95I,G142D,E156G,F157-,R158-,R214L,L452R,T478K,D614G,P681R,D950N] Delta
.R......D...G--..L.........R..........R....N.... 297 25 139 124 9 0 0 0 297 224 75% [T19R,G142D,E156G,F157-,R158-,R214L,L452R,T478K,D614G,P681R,D950N] Delta
FR....I.....G--............R..........R....N.... 297 1 234 35 17 0 10 0 297 142 47% [L5F,T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R......D...G--............R........Y.R....N.... 286 27 58 194 5 0 2 0 286 204 71% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,H655Y,P681R,D950N] Delta+FurinRelated
.R....I.D...G--............R.Q........R..L.N.... 285 1 283 1 0 0 0 0 285 221 77% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,I850L,D950N]
.R..Y...D...G--............R..........R....N.... 279 30 116 131 1 0 1 0 279 226 81% [T19R,H69Y,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.D...G--............RI.........R....N.... 270 122 37 85 25 0 0 1 270 147 54% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,S477I,T478K,D614G,P681R,D950N] Delta
.R......D...G--............R.......I..R....N.... 258 64 52 140 0 0 2 0 258 140 54% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,T547I,D614G,P681R,D950N] Delta
.R....I.D...G--............RN.........R....N.... 247 102 123 22 0 0 0 0 247 195 78% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,S477N,T478K,D614G,P681R,D950N] Delta
...V--I.D---...-I..D.LPF....NARSRYHKYKHKY.K.HKF. 245 2 60 183 0 0 0 0 245 221 90% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
.R......D...G--.....K......R..........R....N.... 244 16 182 24 22 0 0 0 244 76 31% [T19R,T29A,G142D,E156G,F157-,R158-,T250I,R346K,L452R,T478K,D614G,P681R,P812L,D950N]
.R.V..I.D...G--............R..........R....N.... 243 124 86 33 0 0 0 0 243 136 55% [T19R,A67V,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
...V--I.D---...-I..D.LPFN.S.NARSRYHKYKHKY.K.HKF. 242 0 161 42 20 0 19 0 242 191 78% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
.R..........G--...V........R..........R......... 235 0 60 4 171 0 0 0 235 175 74% [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R]
.R....I.D...G--.........N..R..........R....N.... 216 81 11 122 2 0 0 0 216 85 39% [T19R,T95I,G142D,E156G,F157-,R158-,W258L,K417N,L452R,T478K,D614G,P681R,D950N]
.R.....L....G--............R..........R....N.... 208 0 6 200 1 0 1 0 208 137 65% [T19R,S112L,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta+S112L
.R..........G--...V........R..........R....N...L 200 0 42 149 2 1 5 1 200 95 47% [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+V1264L
.R...FI.D..HG--...V........R..........R....N.... 197 197 0 0 0 0 0 0 197 173 87% [T19R,V70F,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N]
...V--I.D---...-I..DKLPF....NARSRYHKYKHKY.K.HKF. 194 0 22 172 0 0 0 0 194 188 96% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron+R346K
.R....I.D...G--............R.K........R....N.... 190 47 120 11 12 0 0 0 190 86 45% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,E484K,D614G,S673T,P681R,D950N]
.R....I.D..................R..........R....N.... 185 0 119 42 24 0 0 0 185 95 51% [T19R,T95I,G142D,L452R,T478K,D614G,P681R,D950N]
.R..--I.D...G--............R..........R....N.... 185 52 111 8 0 0 0 14 185 132 71% [T19R,H69-,V70-,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
.R....I.....G--............R.Q........R....N.... 174 2 138 9 20 3 2 0 174 106 60% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,D950N]
.R.S..I.D...G--............R..........R....N.... 168 121 13 27 7 0 0 0 168 108 64% [T19R,A67S,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
FR....I.D..HG--...V........R..........R....N...L 166 162 4 0 0 0 0 0 166 97 58% [L5F,T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+Y145H,A222V
.R......D...G--............R..........H....N.... 165 1 9 155 0 0 0 0 165 147 89% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681H,D950N] Delta+FurinRelated
.R......D...G--..H.........R..........R....N.... 164 0 4 160 0 0 0 0 164 126 76% [T19R,G142D,E156G,F157-,R158-,R214H,L452R,T478K,D614G,P681R,D950N] Delta
...V--I.D---...............RNARSRYHKYKHKY.K.HKF. 163 0 163 0 0 0 0 0 163 153 93% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,L452R,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
............G--............R..........R....N.... 163 0 9 153 0 0 1 0 163 105 64% [E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
.R.V....D...G--...V........R..........R....N.... 162 65 60 2 7 0 28 0 162 111 68% [T19R,A67V,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+T95_,A222V
...V--I.D---...-I..D.LPF.KS........KYKHKY.K.HKF. 157 0 0 157 0 0 0 0 157 149 94% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,N440K,G446S,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
.R......D...G--............R.....Y....R....N.... 157 0 24 21 112 0 0 0 157 104 66% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,N501Y,D614G,P681R,D950N] Delta
.R..--..D...G--............R..........R....N.... 156 10 16 105 24 0 1 0 156 69 44% [T19R,H69-,V70-,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
.R......D...G--............RN.........R....N.... 152 1 80 70 1 0 0 0 152 138 90% [T19R,G142D,E156G,F157-,R158-,L452R,S477N,T478K,D614G,P681R,D950N] Delta
.R..........G--............R..........R....N...L 152 0 97 5 8 0 38 4 152 89 58% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+V1264L
.R....I.D..HG--...V........R.........IR....N...L 152 152 0 0 0 0 0 0 152 94 61% [S13T,T19R,T95I,S98F,G142D,Y145H,E156G,F157-,R158-,A222V,T323I,L452R,T478K,D614G,N679I,P681R,D950N,V1264L] Delta+FurinRelated
.R......D..................R..........R....N.... 139 0 60 71 8 0 0 0 139 77 55% [T19R,G142D,L452R,T478K,D614G,P681R,D950N]
.R....I.....G--...V........R..........R....N.... 138 0 54 4 11 0 69 0 138 46 33% [T19R,T95I,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,I834T,D950N]
.R....I.D...G--............R.A........R....N.... 137 3 40 90 3 1 0 0 137 67 48% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,E484A,D614G,P681R,D950N]
......................................R....N.... 136 0 123 13 0 0 0 0 136 87 63% [T478K,D614G,P681R,D950N]
.R..........G--............R.Q........R....N.... 136 0 119 7 0 0 10 0 136 97 71% [T19R,E156G,F157-,R158-,L452R,T478K,E484Q,Q613H,D614G,P681R,D950N]
.RF...I.D...G--............R..........R....N.... 133 79 12 40 1 0 0 1 133 77 57% [T19R,V36F,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
...V--I.D---...-I..D.LPFNKS.NA.....KYKHKY.K.HKF. 129 1 3 125 0 0 0 0 129 116 89% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
.R......D...G--...V........R.......I..R....N.... 118 1 2 100 14 0 1 0 118 66 55% [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,T547I,D614G,P681R,D950N] Delta+T95_,A222V
...V--I.D---...-I..D.LPFNKS........KYKHKY.K.HKF. 115 0 1 113 1 0 0 0 115 104 90% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
...V--I.D---...-I..DKLPFNKS.NA.....KYKHKY.K.HKF. 114 0 1 113 0 0 0 0 114 109 95% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
.R....I.D...G--............R..........R......... 112 2 62 42 1 0 5 0 112 43 38% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R]
FR.....LD...G--............R..........R....N.... 111 0 1 108 0 0 2 0 111 95 85% [L5F,T19R,S112L,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta+S112L
.R......D..HG--............R..........R....N.... 107 5 34 68 0 0 0 0 107 37 34% [T19R,G142D,Y145H,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.DF..G--............R..........R....N.... 107 63 26 15 3 0 0 0 107 51 47% [T19R,L54F,T95I,G142D,V143F,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.D...G--............R..........R.Y..N.... 107 78 13 16 0 0 0 0 107 56 52% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D796Y,D950N] Delta
.R......D...G--...S........R..........R....N.... 106 41 17 48 0 0 0 0 106 47 44% [T19R,G142D,E156G,F157-,R158-,A222S,L452R,T478K,D614G,P681R,D950N]
.R......D...G--............R.........TR....N.... 104 2 5 96 0 0 1 0 104 69 66% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,N679T,S680-,P681R,D950N,T1117I] Delta+FurinRelated
...V--I.D---...-I..DKLPF.KS........KYKHKY.K.HKF. 102 0 0 101 1 0 0 0 102 97 95% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,N440K,G446S,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
...V--I.D---.......D...............KYKHKY.K.HKF. 101 0 1 100 0 0 0 0 101 91 90% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,G339D,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
...V--I.D---...I-..DKLPF.KS.NARSRYHKYKHKY.K.HKF. 101 0 54 46 0 0 1 0 101 87 86% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211I,L212-,G339D,R346K,S371L,S373P,S375F,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron+R346K
........D...G--............R..........R....N.... 100 1 23 64 10 2 0 0 100 48 48% [G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
FR......D...G--...V........R..........R....N.... 97 8 40 40 9 0 0 0 97 30 30% [L5F,T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+T95_,A222V
......I.D...G--............R..........R....N.... 95 6 27 22 35 0 0 5 95 52 54% [T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
........---.........S............Y....H......... 94 7 82 4 0 1 0 0 94 78 82% [P9L,E96Q,C136-,N137-,D138-,P139-,F140-,L141-,G142-,V143-,Y144-,R190S,I210T,R346S,N394S,Y449N,F490R,N501Y,D614G,P681H,T859N,D936H] B.1.640.1
.R....I.D...G--I-..........R..........R....N.... 91 86 2 3 0 0 0 0 91 22 24% [T19R,T95I,G142D,E156G,F157-,R158-,N211I,L212-,L452R,T478K,D614G,P681R,D950N,V1094I] Delta
F..V--I.D---...-I..D.LPFNKS.NARSRYHKYKHKY.K.HKF. 90 0 25 50 6 3 4 2 90 80 88% [L5F,A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
.R....I.D...G--.....I......R..........R....N.... 90 4 4 79 0 0 0 3 90 64 71% [T19R,T95I,G142D,E156G,F157-,R158-,R346I,L452R,T478K,D614G,P681R,D950N,K1073N] Delta
.R....................................R....N.... 89 0 65 24 0 0 0 0 89 49 55% [T19R,T478K,D614G,P681R,D950N]
...V--I.D---...-I..DKLPFN.S.NARSRYHKYKHKY.K.HKF. 89 0 48 27 11 0 3 0 89 83 93% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,K417N,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron+R346K
FR....I.D...G--............R..........R..L.N.... 89 5 81 1 2 0 0 0 89 54 60% [L5F,T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] Delta
...V--I.D---...-I..DKLPFNKS........KYKHKY.K.HKF. 86 0 0 86 0 0 0 0 86 80 93% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,K417N,N440K,G446S,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
.R......D...G--.......................R....N.... 86 0 27 54 5 0 0 0 86 30 34% [T19R,G142D,E156G,F157-,R158-,T478K,D614G,P681R,D950N]
...V--I.D---...-I..D.LPF...RNARSRYHKYKH.Y.K.HKF. 85 43 17 24 0 1 0 0 85 72 84% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,L452R,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,D796Y,N856K,Q954H,N969K,L981F]
.R....I.D...G--............R..........R.G..N.... 84 0 80 4 0 0 0 0 84 69 82% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D796G,D950N,D1259Y] Delta
.R......D...G--............R.....S....R....N.... 84 0 80 3 1 0 0 0 84 77 91% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,N501S,D614G,P681R,D950N] Delta
...V--I.D---...-I.......NKS.NARSRYHKYKHKY.K.HKF. 83 0 0 83 0 0 0 0 83 74 89% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
.R...I......G--............R..........R....N.... 83 0 0 80 2 0 1 0 83 29 34% [T19R,V70I,E156G,F157-,R158-,Q414R,L452R,T478K,D614G,P681R,D950N]
.R....I.D--DG--............R..........R....N.... 81 77 1 2 1 0 0 0 81 67 82% [T19R,T95I,G142D,V143-,Y144-,Y145D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R..........G--............RI.........R....N.... 80 0 70 1 0 0 9 0 80 38 47% [T19R,E156G,F157-,R158-,A262S,L452R,S477I,T478K,D614G,P681R,D950N,G1167V] Delta
.R....I.D...G--............R.......I..R....N.... 80 37 14 28 1 0 0 0 80 32 40% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,T547I,D614G,P681R,D950N] Delta
.R....I.D...G--............R..........R.H..N.... 80 12 59 6 2 0 0 1 80 39 48% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D796H,D950N,D1259Y] Delta
.R....I.....G--............R..........R..L...... 80 0 80 0 0 0 0 0 80 50 62% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L]
.R....I.D...G--..H.........R..........R....N.... 79 37 5 37 0 0 0 0 79 64 81% [T19R,T95I,G142D,E156G,F157-,R158-,R214H,L452R,T478K,D614G,P681R,D950N] Delta
...V--I.D---.......DKLPFNKS.NARSRYHKYKHKY.K.HKF. 78 0 77 1 0 0 0 0 78 65 83% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,G339D,R346K,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron+R346K
.R....I.....G--............R..........R....N...L 78 0 56 9 10 0 3 0 78 35 44% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+V1264L
.R......D...G--............R..........R....N...M 78 6 36 35 0 0 1 0 78 61 78% [T19R,G142D,E156G,F157-,R158-,W258L,L452R,T478K,D614G,P681R,D950N,V1264M]
...V--I.D---...-I..D.LPFNKS.NARSRYHKYKH.Y.K.HKF. 77 1 65 9 1 0 1 0 77 69 89% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,D796Y,N856K,Q954H,N969K,L981F]
...V..I.D---...I-..D.LPFNKS.NARSRYHKYKHKY.K.HKF. 76 0 76 0 0 0 0 0 76 62 81% [A67V,T95I,G142D,V143-,Y144-,Y145-,N211I,L212-,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
F..V--I.D---...-I..DKLPFNKS.NARSRYHKYKHKY.K.HKF. 76 0 7 64 5 0 0 0 76 71 93% [L5F,A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron+R346K
...V--I.D---...-I..D.LPF...........KYKHKY.K.HKF. 74 0 0 74 0 0 0 0 74 69 93% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
.R......D...G--............R.K........R....N.... 74 18 33 23 0 0 0 0 74 36 48% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,E484K,D614G,P681R,D950N]
.R..........G--............R.A........R....N.... 73 0 71 1 1 0 0 0 73 34 46% [T19R,E156G,F157-,R158-,G181V,L452R,T478K,E484A,D614G,P681R,D950N]
.R....I.D..HG--...V.G......R..........R....N.... 72 17 55 0 0 0 0 0 72 48 66% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,R346G,L452R,T478K,D614G,P681R,D950N,D1260N] Delta+Y145H,A222V
.R....I....HG--...V........R..........R....N...L 71 16 47 2 3 0 2 1 71 24 33% [T19R,T95I,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+Y145H,A222V
.R..Y.I.....G--............R..........R....N.... 70 0 68 1 1 0 0 0 70 52 74% [T19R,H69Y,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.D...G--............R..........R....N...A 70 46 21 1 0 0 2 0 70 38 54% [T19R,T95I,G142D,E156G,F157-,R158-,G181V,L452R,T478K,D614G,P681R,D950N,V1264A]
.R.S.FI.D...G--............R..........R....N.... 69 69 0 0 0 0 0 0 69 68 98% [T19R,A67S,V70F,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
...V--I.D---...-I..DKLPFNKS.NARSRYHKYKHK..K.HKF. 68 0 68 0 0 0 0 0 68 68 100% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,N856K,Q954H,N969K,L981F]
.R....I....................R..........R....N.... 66 0 20 20 26 0 0 0 66 25 37% [T19R,T95I,L452R,T478K,D614G,P681R,D950N]
.R....I.D...G--............R..........H....N.... 65 45 5 13 1 0 0 1 65 39 60% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681H,D950N] Delta+FurinRelated
.R....I.....G--...........VR..........R....N.... 64 0 21 10 19 1 13 0 64 23 35% [T19R,T95I,E156G,F157-,R158-,G446V,L452R,T478K,D614G,P681R,D950N] Delta
.RF...I....HG--...V........R..........R....N.... 63 12 51 0 0 0 0 0 63 52 82% [T19R,V36F,T95I,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+Y145H,A222V
...V--I........-I..D.LPFNKS.NARSRYHKYKHKY.K.HKF. 61 0 7 9 0 45 0 0 61 42 68% [A67V,H69-,V70-,T95I,L141F,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
...V--I.D---.......DK..............KYKHKY.K.HKF. 60 0 0 60 0 0 0 0 60 58 96% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,G339D,R346K,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
...V--I.D---...-I..D.LPFNKS.N......KYKHKY.K.HKF. 60 0 0 60 0 0 0 0 60 43 71% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
.R..........G--............R.......I..R....N.... 59 0 40 6 0 0 13 0 59 20 33% [T19R,E156G,F157-,R158-,L452R,T478K,T547I,D614G,P681R,D950N] Delta
.R......DF..G--............R..........R....N.... 59 1 31 27 0 0 0 0 59 41 69% [T19R,G142D,V143F,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R......D...G--............R..........R.Y..N.... 58 6 12 38 0 0 2 0 58 39 67% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D796Y,D950N] Delta
.I....I.D..HG--...V........R..........R....N.... 58 58 0 0 0 0 0 0 58 58 100% [T19I,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N]
.R....I.D...G--...........SR..........R....N.... 57 23 13 21 0 0 0 0 57 16 28% [T19R,T95I,G142D,E156G,F157-,R158-,G446S,L452R,T478K,D614G,P681R,D950N] Delta
.R..........G--...V.......VR..........R....N.... 56 0 2 0 54 0 0 0 56 52 92% [T19R,E156G,F157-,R158-,A222V,G446V,L452R,T478K,D614G,P681R,D950N] Delta+T95_,A222V
.R......D...G--..S.........R..........R....N.... 56 49 0 7 0 0 0 0 56 48 85% [T19R,G142D,E156G,F157-,R158-,R214S,L452R,T478K,Q613H,D614G,P681R,V772I,D950N]
.R....N.D...G--............R..........R....N.... 55 0 46 9 0 0 0 0 55 40 72% [T19R,T95N,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,G1167V] Delta
.R.S........G--............R..........R....N.... 54 0 50 2 1 0 1 0 54 40 74% [T19R,A67S,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R..........G--...........VR..........R....N.... 53 0 17 11 8 0 17 0 53 36 67% [T19R,E156G,F157-,R158-,G446V,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.....G--...S........R..........R....N.... 53 0 51 1 1 0 0 0 53 40 75% [T19R,T95I,E156G,F157-,R158-,A222S,L452R,T478K,D614G,P681R,D950N]
.R..Y.I.D..HG--...V........R..........R....N.... 53 52 1 0 0 0 0 0 53 45 84% [T19R,H69Y,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+Y145H,A222V
...V--I.D---...-I..D.LPFNKS.NARSRYHKYKHKY.K.HK.. 52 0 2 50 0 0 0 0 52 48 92% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K]
.I......D...G--............R..........R....N.... 52 2 11 38 1 0 0 0 52 18 34% [T19I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
.R.V........G--...V........R..........R....N.... 52 0 42 0 10 0 0 0 52 23 44% [T19R,A67V,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,Q1208H,M1237I] Delta+T95_,A222V
...V--I.D---...-I..DKLPF...RNARSRYHKYKHKY.K.HKF. 50 1 13 34 2 0 0 0 50 48 96% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,L452R,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron+R346K
...........................R..........R..L.N.... 49 0 49 0 0 0 0 0 49 38 77% [L452R,T478K,D614G,P681R,I850L,D950N]
.R......D...--.............R..........R....N.... 49 1 0 47 1 0 0 0 49 35 71% [T19R,G142D,E156-,F157-,L452R,T478K,D614G,P681R,D950N]
....--I.D---...-I..D.LPFNKS.NARSRYHKYKHKY.K.HKF. 48 0 1 2 45 0 0 0 48 40 83% [H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
.R....I.D...G--............R.....Y....R....N.... 48 26 19 2 0 0 0 1 48 36 75% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,N501Y,D614G,P681R,D950N] Delta
.R......D...G--...........SR..........R....N.... 47 6 14 26 1 0 0 0 47 33 70% [T19R,G142D,E156G,F157-,R158-,G446S,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.D..HG--............R..........R....N.... 47 23 19 3 2 0 0 0 47 27 57% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R......D...G--...V........R.Q........R....N.... 47 0 43 0 3 1 0 0 47 28 59% [T19R,R21T,G142D,E156G,F157-,R158-,A222V,L452R,T478K,E484Q,Q613H,D614G,P681R,D950N] Delta+T95_,A222V
.R....I.D...G--..........Y.R..........R....N.... 47 47 0 0 0 0 0 0 47 47 100% [T19R,T95I,G142D,E156G,F157-,R158-,N440Y,L452R,T478K,D614G,P681R,D950N] Delta
.R....IAD...G--............R..........R....N.... 46 44 0 2 0 0 0 0 46 33 71% [T19R,T95I,S112A,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
.R....I.D...G--............R.....S....R....N.... 46 42 1 2 0 0 0 1 46 22 47% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,N501S,D614G,P681R,D950N] Delta
.R.........................R..........R......... 45 0 40 2 3 0 0 0 45 31 68% [T19R,L452R,T478K,D614G,P681R]
.R......D...G--...V.......VR..........R....N.... 45 1 10 17 16 0 1 0 45 32 71% [T19R,G142D,E156G,F157-,R158-,A222V,G446V,L452R,T478K,D614G,P681R,D950N] Delta+T95_,A222V
.R....I.D...G--.......L....R..........R....N.... 45 32 4 9 0 0 0 0 45 18 40% [V16F,T19R,T95I,G142D,E156G,F157-,R158-,S373L,L452R,T478K,D614G,P681R,D950N] Delta
.R...F......G--............R..........R....N.... 45 0 43 2 0 0 0 0 45 34 75% [T19R,V70F,E156G,F157-,R158-,L452R,T478K,K558N,D614G,P681R,D950N]
.R....I.D...G--I...........R..........R....N.... 45 42 0 3 0 0 0 0 45 40 88% [T19R,T95I,G142D,E156G,F157-,R158-,N211I,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.....G--............R..........R..L.N...L 44 0 44 0 0 0 0 0 44 39 88% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N,V1264L] Delta+V1264L
.R......DI..G--............R..........R....N.... 44 4 1 39 0 0 0 0 44 23 52% [T19R,G142D,V143I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1228L] Delta
.R....I...-.G--............R..........R....N.... 44 0 33 1 7 0 3 0 44 11 25% [T19R,T95I,Y144-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R.....LD.-.G--............R..........R....N.... 44 0 0 44 0 0 0 0 44 36 81% [T19R,S112L,G142D,Y144-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta+S112L
.R......D...G--..HV........RI.........R....N.... 44 0 0 44 0 0 0 0 44 38 86% [T19R,G142D,E156G,F157-,R158-,R214H,A222V,V289I,L452R,S477I,T478K,D614G,P681R,D950N]
...V--I.D---...............R.......KYKHKY.K.HKF. 43 0 33 10 0 0 0 0 43 35 81% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,L452R,T478K,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
.I....I.D...G--............R..........R....N.... 43 15 7 2 2 0 0 17 43 36 83% [T19I,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
.R....I.DI..G--............R..........R....N.... 43 36 0 7 0 0 0 0 43 27 62% [T19R,T95I,G142D,V143I,E156G,F157-,R158-,L452R,T478K,D614G,Q677H,P681R,D950N,A1016V] Delta+FurinRelated
.R.....LD...G--............R.A........R....N.... 43 0 0 43 0 0 0 0 43 37 86% [T19R,S112L,G142D,E156G,F157-,R158-,L452R,T478K,E484A,D614G,P681R,D950N]
...V--I.D---...-I..DK....KS.NARSRYHKYKHKY.K.HKF. 42 0 3 38 1 0 0 0 42 40 95% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
...V--I.D---...-I..D.....KS.NARSRYHKYKHKY.K.HKF. 42 0 14 24 3 1 0 0 42 37 88% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
.R....I.....G--............RI.........R....N.... 42 0 12 4 26 0 0 0 42 36 85% [T19R,T95I,E156G,F157-,R158-,L452R,S477I,T478K,D614G,P681R,D950N] Delta
.R..........G--............RN.........R....N.... 42 0 32 9 1 0 0 0 42 38 90% [T19R,E156G,F157-,R158-,L452R,S477N,T478K,D614G,P681R,D950N] Delta
.K....I.D...G--............R..........R....N.... 42 38 4 0 0 0 0 0 42 40 95% [T19K,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
....--....-..S............RR..........R....H.... 41 6 2 33 0 0 0 0 41 41 100% [H69-,V70-,D80G,E96Q,Y144-,F157S,L244-,H245Y,R246-,S247-,Y248-,A264V,G446R,L452R,T478R,D614G,P681R,T859N,D936H,D950H,N978S]
.R......D...G--.......L....R..........R....N.... 41 5 6 29 1 0 0 0 41 21 51% [T19R,G142D,E156G,F157-,R158-,S373L,L452R,T478K,D614G,P681R,D950N] Delta
.R......D...G--...........RR..........R....N.... 41 1 38 0 2 0 0 0 41 13 31% [T19R,G142D,E156G,F157-,R158-,G446R,L452R,T478K,D614G,P681R,D950N,A1226V] Delta
.R..........G--.....K......R..........R....N.... 41 0 35 0 6 0 0 0 41 14 34% [T19R,T29A,E156G,F157-,R158-,T250I,R346K,L452R,T478K,D614G,P681R,D950N]
FR...I..D...G--............R..........R....N.... 41 0 1 40 0 0 0 0 41 12 29% [L5F,T19R,V70I,G142D,E156G,F157-,R158-,Q414R,L452R,T478K,D614G,P681R,D950N]
...V--I.D---...-I..DKLPF...........KYKHKY.K.HKF. 40 0 0 40 0 0 0 0 40 39 97% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
.R....V.D...G--............R..........R....N.... 40 14 0 14 0 0 0 12 40 32 80% [T19R,T95V,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.D...G--S...........R..........R....N.... 40 0 1 39 0 0 0 0 40 35 87% [T19R,T95I,G142D,E156G,F157-,R158-,N211S,L452R,T478K,D614G,P681R,D950N] Delta
.R....V.D..HG--...V........R..........R....N.... 40 40 0 0 0 0 0 0 40 37 92% [T19R,T95V,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,A1078S]
.R..R.I.D..HG--...V........R..........R....N.... 40 40 0 0 0 0 0 0 40 38 95% [T19R,H69R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,T572I,D614G,P681R,D950N] Delta+Y145H,A222V
.RF...I.D..HG--...V........R..........H....N.... 40 40 0 0 0 0 0 0 40 33 82% [T19R,V36F,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681H,D950N,A1078T] Delta+FurinRelated
.R.V--I.D---G--............R..........R....N.... 39 7 12 10 5 0 5 0 39 21 53% [T19R,A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
FRF...I.D..HG--...V........R..........R....N.... 39 38 1 0 0 0 0 0 39 29 74% [L5F,T19R,V36F,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+Y145H,A222V
...V--I.D---...-I..D.LPFN...NARSRYHKYKHKY.K.HKF. 38 0 7 29 0 0 2 0 38 34 89% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
.R......D...G--.....I......R..........R....N.... 38 7 3 27 0 1 0 0 38 31 81% [T19R,G142D,E156G,F157-,R158-,R346I,L452R,T478K,D614G,P681R,D950N] Delta
.R..........G--.......................R....N.... 38 0 28 9 1 0 0 0 38 16 42% [T19R,E156G,F157-,R158-,T478K,D614G,P681R,D950N]
.R....I.D..HG--...V.......SR..........R....N.... 38 38 0 0 0 0 0 0 38 37 97% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,G446S,L452R,T478K,D614G,P681R,D950N] Delta+Y145H,A222V
...V--I.D---...I-..D.LPFN.S.NARSRYHKYKHKY.K.HKF. 37 0 18 15 0 0 4 0 37 33 89% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211I,L212-,G339D,S371L,S373P,S375F,K417N,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
FR....I.....G--............R..........R..L.N.... 37 0 37 0 0 0 0 0 37 27 72% [L5F,T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] Delta
.R....I.D..HG--...V.......VR..........R....N.... 37 33 4 0 0 0 0 0 37 15 40% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,G446V,L452R,T478K,D614G,P681R,D950N] Delta+Y145H,A222V
......I.D..................R..........R....N.... 36 0 35 1 0 0 0 0 36 24 66% [T95I,G142D,L452R,T478K,D614G,P681R,D950N]
.R.V........G--............R..........R....N.... 36 0 30 5 1 0 0 0 36 27 75% [T19R,A67V,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.D...G--............R.........SR....N.... 36 3 26 6 0 0 0 1 36 25 69% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,N679S,P681R,D950N] Delta+FurinRelated
...V--I.D---...-I..DKLPFNKS.N......KYKHKY.K.HKF. 35 0 1 34 0 0 0 0 35 26 74% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
.R..........G--....S.......R..........R....N.... 35 0 34 0 0 0 1 0 35 34 97% [T19R,E156G,F157-,R158-,G339S,L452R,T478K,D614G,P681R,D950N] Delta
.R....IPD...G--............R..........R....N.... 35 8 2 25 0 0 0 0 35 31 88% [T19R,T95I,S112P,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
.R......D...G--...V.......SR..........R....N.... 35 0 0 0 35 0 0 0 35 35 100% [T19R,G142D,E156G,F157-,R158-,A222V,G446S,L452R,T478K,D614G,P681R,D950N,M1237I] Delta+T95_,A222V
.R......D.-.G--...V........R..........R....N.... 35 0 3 28 4 0 0 0 35 16 45% [T19R,G142D,Y144-,E156G,F157-,R158-,A222V,L452R,T478K,Q613H,D614G,P681R,D950N] Delta+T95_,A222V
.R......D...G--....S.......R..........R....N.... 34 9 11 14 0 0 0 0 34 22 64% [T19R,G142D,E156G,F157-,R158-,G339S,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.D...G--...........VR.....T....R....N.... 34 4 0 0 30 0 0 0 34 27 79% [T19R,T95I,G142D,E156G,F157-,R158-,G446V,L452R,T478K,N501T,D614G,P681R,D950N] Delta
.R....I.D.-.G--............R.Q........R....N.... 34 3 0 9 22 0 0 0 34 10 29% [T19R,T95I,G142D,Y144-,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,D950N]
...V--I.D---.......D.....KS.NARSRYHKYKHKY.K.HKF. 33 0 16 17 0 0 0 0 33 30 90% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,G339D,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
...V--I.D---...-I..D.LPF.KS...RSRYHKYKHKY.K.HKF. 33 0 0 33 0 0 0 0 33 30 90% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,N440K,G446S,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
.R....I.D...G--.......................R....N.... 33 3 8 17 5 0 0 0 33 15 45% [T19R,T95I,G142D,E156G,F157-,R158-,T478K,D614G,P681R,D950N]
.R..........G--..L.........R..........R....N.... 33 0 32 1 0 0 0 0 33 29 87% [T19R,E156G,F157-,R158-,R214L,L452R,T478K,D614G,P681R,D950N] Delta
FR....I.D..HG--...V........R........Y.R....N...L 33 31 2 0 0 0 0 0 33 31 93% [L5F,L18F,T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,H655Y,P681R,D950N,V1264L] Delta+FurinRelated
...V--I.D---...I-..................KYKHKY.K.HKF. 32 0 0 32 0 0 0 0 32 30 93% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211I,L212-,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
...V--I.D---...-I..D.LPFNKS.NARSRYHKYKHK..K.HKF. 32 0 31 1 0 0 0 0 32 23 71% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,N856K,Q954H,N969K,L981F]
.R......D...G--............R...............N.... 32 0 9 23 0 0 0 0 32 13 40% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,D950N]
.R..........G--............R..........R..L.N.... 32 1 31 0 0 0 0 0 32 16 50% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] Delta
......................................R......... 31 0 20 0 11 0 0 0 31 17 54% [T478K,D614G,P681R]
.R......D...G--.....S......R..........R....N.... 31 0 3 27 0 0 1 0 31 19 61% [T19R,G142D,E156G,F157-,R158-,R346S,L452R,T478K,D614G,P681R,D950N] Delta
FR..........G--............R..........R......... 31 0 24 1 1 0 5 0 31 23 74% [L5F,T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R]
.R....I.D...G--............R..........R..L.N...L 31 6 24 0 1 0 0 0 31 19 61% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N,V1264L] Delta+V1264L
.R....I.....G--............R..........R.G..N.... 31 0 31 0 0 0 0 0 31 27 87% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D796G,D950N,D1259Y] Delta
.RI.....D...G--............R..........R....N.... 31 27 1 3 0 0 0 0 31 22 70% [T19R,V36I,G142D,E156G,F157-,R158-,D253G,L452R,T478K,D614G,P681R,D950N,A1078S] Delta
.R.........................R..........R..L.N.... 30 0 30 0 0 0 0 0 30 19 63% [T19R,L452R,T478K,D614G,P681R,I850L,D950N]
...V--I.D---...-I..DKLPFNKS.NARSRYHKYKH.Y.K.HKF. 30 0 28 2 0 0 0 0 30 22 73% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,D796Y,N856K,Q954H,N969K,L981F]
.R......N...G--............R..........R....N.... 30 1 0 29 0 0 0 0 30 15 50% [T19R,G142N,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.D...G--............R.Q.....I..R....N.... 30 0 30 0 0 0 0 0 30 19 63% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,E484Q,T547I,D614G,P681R,A845S,D950N]
.R....I.D..HG--...V........R.Q........R....N.... 30 29 1 0 0 0 0 0 30 29 96% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,E484Q,D614G,P681R,D950N] Delta+Y145H,A222V
...V--I.D---...-I..DKLPFNKS.NARSRYHKYKHKY.K.HK.. 29 0 0 29 0 0 0 0 29 27 93% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K]
.R....I.D..................R..........R..L.N.... 29 0 28 0 1 0 0 0 29 16 55% [T19R,T95I,G142D,L452R,T478K,D614G,P681R,I850L,D950N]
.R....I.D...G--............R.........YR....N.... 29 4 24 0 1 0 0 0 29 20 68% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,N679Y,P681R,D950N] Delta+FurinRelated
.R......D...G--...V........R.......I..R....N...L 29 0 0 29 0 0 0 0 29 27 93% [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,T547I,D614G,P681R,D950N,V1264L] Delta+V1264L
.R..--..D...G--............R..........R....N...L 29 0 0 0 29 0 0 0 29 20 68% [T19R,H69-,V70-,G142D,E156G,F157-,R158-,D215N,L452R,T478K,D614G,P681R,D950N,V1264L]
........D..................R..........R....N.... 28 0 26 1 1 0 0 0 28 13 46% [G142D,L452R,T478K,D614G,P681R,D950N]
.I......D..........D.FPFN...NAR.RYH.YKHKY...HK.. 28 0 19 0 9 0 0 0 28 28 100% [T19I,L24S,P25-,P26-,A27-,G142D,V213G,G339D,S371F,S373P,S375F,T376A,D405N,R408S,K417N,S477N,T478K,E484A,Q493R,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K]
...V--I.D---...-I..DKLPF.KS...RSRYHKYKHKY.K.HKF. 28 0 0 28 0 0 0 0 28 26 92% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,N440K,G446S,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
.R....I.D...G--............R..........R.N..N.... 28 3 0 25 0 0 0 0 28 28 100% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D796N,D950N] Delta
.R..........G--............R........Y.R....N.... 28 0 13 8 3 0 4 0 28 16 57% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,H655Y,P681R,D950N] Delta+FurinRelated
.R......D...G--............Q..........R....N.... 28 0 7 21 0 0 0 0 28 16 57% [T19R,G142D,E156G,F157-,R158-,L452Q,T478K,D614G,P681R,D950N]
.R.....LD...G--............R..........R....N...L 28 0 0 28 0 0 0 0 28 28 100% [T19R,S112L,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+V1264L
.R....I.D...G--.S..........R..........R....N.... 28 2 9 12 0 5 0 0 28 14 50% [T19R,T95I,G142D,E156G,F157-,R158-,L212S,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.D...G--...V........R..........R..L.N.... 28 0 28 0 0 0 0 0 28 20 71% [T19R,T95I,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,I850L,D950N]
.R....I.DF.HG--...V........R..........R....N.... 28 28 0 0 0 0 0 0 28 28 100% [T19R,T95I,G142D,V143F,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+Y145H,A222V
...V--I.D---.......D.LPFNKS.NARSRYHKYKH...K.HKF. 27 0 27 0 0 0 0 0 27 26 96% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N856K,Q954H,N969K,L981F]
IR......D...G--............R..........R....N.... 27 0 0 27 0 0 0 0 27 26 96% [L5I,T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R......D...G--.........N..R..........R....N.... 27 2 7 18 0 0 0 0 27 16 59% [T19R,G142D,E156G,F157-,R158-,K417N,L452R,T478K,D614G,P681R,D950N]
.R....I.D...G--............R........R.R....N.... 27 24 2 1 0 0 0 0 27 20 74% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,E554G,D614G,H655R,P681R,D950N,D1163Y]
.R....I.....G--............R.Q........R......... 27 0 24 1 0 0 2 0 27 21 77% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R]
.R......D...G--I-..........R..........R....N.... 27 4 12 10 1 0 0 0 27 24 88% [T19R,G142D,E156G,F157-,R158-,N211I,L212-,L452R,T478K,D614G,P681R,D950N] Delta
......I...............................R....N.... 26 0 26 0 0 0 0 0 26 12 46% [T95I,T478K,D614G,P681R,D950N]
...V--I.D---...-I..D.LPFNKS.NARSRYH.YKHKY.K.HKF. 26 0 14 12 0 0 0 0 26 24 92% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
.R......D...G--.......P....R..........R....N.... 26 0 8 18 0 0 0 0 26 15 57% [T19R,G142D,E156G,F157-,R158-,S373P,L452R,T478K,D614G,P681R,D950N] Delta
.R...F.LD...G--............R..........R....N.... 26 1 0 25 0 0 0 0 26 17 65% [T19R,V70F,S112L,G142D,E156G,F157-,R158-,Q414K,L452R,T478K,D614G,P681R,D950N] Delta+S112L
.R........-.G--............R..........R....N.... 26 0 12 2 2 0 10 0 26 12 46% [T19R,Y144-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R.V--I.....G--............R..........R....N.... 26 0 17 0 6 0 3 0 26 8 30% [T19R,A67V,H69-,V70-,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
......................................R..L.N.... 25 0 24 0 1 0 0 0 25 15 60% [T478K,D614G,P681R,I850L,D950N]
.R....I.---.G--............R..........R....N.... 25 1 3 20 0 0 0 1 25 19 76% [L8F,T19R,T95I,L141-,G142-,V143-,Y144-,E156G,F157-,R158-,L452R,T478K,T549S,D614G,P681R,A846S,D950N] Delta
...V--I.D---G--............R.......KYKHKY.K.HKF. 25 1 18 4 0 0 2 0 25 16 64% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,E156G,F157-,R158-,L452R,T478K,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
....--I.D---...-I..DKLPFNKS.NARSRYHKYKHKY.K.HKF. 25 0 0 0 25 0 0 0 25 24 96% [H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
...V--I.D---...-I..D.LPFNKS.NARSRYHKYKHKY.K.HKFM 25 1 15 2 4 0 0 3 25 25 100% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F,V1264M] Omicron_BA.1
.R....I.D...G--............R..........R...KN.... 25 0 6 0 0 0 0 19 25 19 76% [S12F,T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,N856K,D950N] Delta
.R..Y.......G--............R..........R....N.... 25 1 22 1 0 0 1 0 25 10 40% [T19R,H69Y,E156G,F157-,R158-,L452R,T478K,D614G,P681R,G842S,D950N] Delta
.R....I.D...G--.....S......R..........R....N.... 25 5 19 1 0 0 0 0 25 22 88% [T19R,T95I,G142D,E156G,F157-,R158-,R346S,L452R,T478K,D614G,P681R,D950N] Delta
.R......D...G--...V........R..........R......... 25 0 10 4 11 0 0 0 25 15 60% [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R]
.R..........G--............R..........R.Y..N.... 25 0 0 1 0 0 24 0 25 20 80% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D796Y,D950N] Delta
.R...II.D...G--............R..........R....N.... 25 20 0 4 0 0 0 1 25 10 40% [V16F,T19R,V70I,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
.R......D...G--...V...P....R..........R....N.... 25 0 25 0 0 0 0 0 25 25 100% [T19R,G142D,E156G,F157-,R158-,A222V,S373P,L452R,T478K,D614G,P681R,D950N] Delta+T95_,A222V
................................................ 24 0 17 4 2 1 0 0 24 12 50% []
...V--I.D---...-I..D.LPF.KS.N......KYKHKY.K.HKF. 24 0 0 24 0 0 0 0 24 19 79% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,N440K,G446S,S477N,T478K,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
.R......Y...G--............R..........R....N.... 24 8 6 10 0 0 0 0 24 21 87% [T19R,G142Y,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R......D...G--............RG.........R....N.... 24 1 5 18 0 0 0 0 24 12 50% [T19R,G142D,E156G,F157-,R158-,L452R,S477G,T478K,D614G,P681R,D950N] Delta
.R....I.D...G--............R.........TR....N.... 24 11 4 6 0 0 0 3 24 14 58% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,N679T,S680-,P681R,D950N] Delta+FurinRelated
FRF...I.D...G--............R..........R....N.... 24 17 7 0 0 0 0 0 24 19 79% [L5F,T19R,V36F,T95I,D138Y,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1128I] Delta
...V--I.D---...-I..DKLPF...RNARSRYHKYKH.Y.K.HKF. 23 10 9 4 0 0 0 0 23 19 82% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,L452R,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,D796Y,N856K,Q954H,N969K,L981F]
.R......D...G--............R..........R..L.N.... 23 0 23 0 0 0 0 0 23 9 39% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] Delta
FR......D...G--...V........R..........R....N...L 23 2 0 20 1 0 0 0 23 9 39% [L5F,T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+V1264L
.R......D---G--............R..........R....N.... 22 0 13 4 2 1 2 0 22 18 81% [T19R,G142D,V143-,Y144-,Y145-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
...V--I.D---...-I..DKLPFN...NARSRYHKYKHKY.K.HKF. 22 0 2 18 2 0 0 0 22 21 95% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,K417N,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron+R346K
...V--I.---....-I..DKLPFNKS.NARSRYHKYKHKY.K.HKF. 22 0 1 17 4 0 0 0 22 22 100% [A67V,H69-,V70-,T95I,G142-,V143-,Y144-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron+R346K
.R......D...G--............RR.........R....N.... 22 1 11 9 1 0 0 0 22 11 50% [T19R,G142D,E156G,F157-,R158-,L452R,S477R,T478K,D614G,P681R,D950N] Delta
.R....ILD...G--............R..........R....N.... 22 3 6 13 0 0 0 0 22 15 68% [T19R,T95I,S112L,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta+S112L
.R....I.D...V--............R..........R....N.... 22 12 5 5 0 0 0 0 22 9 40% [T19R,T95I,G142D,E156V,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
FR.S....D...G--............R..........R....N.... 22 5 1 16 0 0 0 0 22 21 95% [L5F,T19R,A67S,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
FR....I.....G--............R..........R......... 22 0 21 1 0 0 0 0 22 9 40% [L5F,T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R]
.R....I.D..HG--...V........R........Y.R....N.... 22 21 1 0 0 0 0 0 22 18 81% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,H655Y,P681R,D950N] Delta+FurinRelated
.R..--......G--............R..........R....N.... 22 0 11 10 0 0 1 0 22 7 31% [T19R,H69-,V70-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
.I.................D.FPFNK..NAR.RYH.YKHKY...HK.. 21 0 21 0 0 0 0 0 21 16 76% [T19I,L24S,P25-,P26-,A27-,V213G,G339D,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,S477N,T478K,E484A,Q493R,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K]
...V--I.D---...-I..D.LPFNKS.NARSRYHK.KHKY.K.HKF. 21 0 18 3 0 0 0 0 21 12 57% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
...V--I.D---...-I..D.LPF..S.NARSRYHKYKHKY.K.HKF. 21 0 2 19 0 0 0 0 21 17 80% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
...V--I.D---...-I..D.LPFNKS...RSRYHKYKHKY.K.HKF. 21 0 2 19 0 0 0 0 21 19 90% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
...V--I.---....-I..D.LPFNKS.NARSRYHKYKHKY.K.HKF. 21 0 0 21 0 0 0 0 21 21 100% [A67V,H69-,V70-,T95I,G142-,V143-,Y144-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
.R....I.D....--............R..........R....N.... 21 0 1 20 0 0 0 0 21 16 76% [T19R,T95I,G142D,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
.R......D...G--........A...R..........R....N.... 21 0 21 0 0 0 0 0 21 19 90% [T19R,G142D,E156G,F157-,R158-,S375A,L452R,T478K,D614G,P681R,D950N] Delta
.RF.....D...G--............R..........R....N.... 21 0 3 18 0 0 0 0 21 10 47% [T19R,V36F,G142D,E156G,F157-,R158-,T299I,L452R,T478K,D614G,P681R,D950N]
.R..........G--............R.....Y....R....N.... 21 0 1 1 19 0 0 0 21 13 61% [T19R,E156G,F157-,R158-,L452R,T478K,N501Y,D614G,P681R,D950N] Delta
.R....I.D...G--E...........R..........R....N.... 21 3 18 0 0 0 0 0 21 18 85% [T19R,T95I,G142D,E156G,F157-,R158-,N211E,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.D..HG--...V........RN.........R....N.... 21 21 0 0 0 0 0 0 21 21 100% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,S477N,T478K,D614G,P681R,D950N] Delta+Y145H,A222V
...V--I.D---...-I..D.LPFNK..NARSRYHKYKHKY.K.HKF. 20 0 4 15 1 0 0 0 20 18 90% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
.R....I.....G--............RN.........R....N.... 20 0 19 1 0 0 0 0 20 8 40% [T19R,T95I,E156G,F157-,R158-,L452R,S477N,T478K,D614G,P681R,D950N] Delta
.R.........HG--............R..........R....N.... 20 0 14 0 6 0 0 0 20 7 35% [T19R,Y145H,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R.....LD...G--............R..........R......... 20 0 0 20 0 0 0 0 20 17 85% [T19R,S112L,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R]
.R....I.D..HG--............R..........R....N...L 20 8 0 0 12 0 0 0 20 11 55% [T19R,S71P,T95I,G142D,Y145H,E156G,F157-,R158-,L452R,T478K,D614G,P681R,T859N,D950N,V1264L]
.R.....LD...G--............RN.........R....N.... 20 0 1 19 0 0 0 0 20 20 100% [T19R,S112L,G142D,E156G,F157-,R158-,L452R,S477N,T478K,D614G,P681R,D950N] Delta+S112L
.R.V..I.D..HG--...V........R..........R....N.... 20 14 6 0 0 0 0 0 20 15 75% [T19R,A67V,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+Y145H,A222V
.I....I.D..HG--...V........R..........R....N...L 20 20 0 0 0 0 0 0 20 20 100% [L18F,T19I,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L]
...V--I.D---.......................KYKH...K.HKF. 19 0 0 19 0 0 0 0 19 18 94% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,T547K,D614G,H655Y,N679K,P681H,N856K,Q954H,N969K,L981F]
...V--I.D---..............S.NARSRYHKYKHKY.K.HKF. 19 0 15 3 1 0 0 0 19 18 94% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
.R....I.D...G--............RR.........R....N.... 19 15 2 2 0 0 0 0 19 11 57% [T19R,T95I,G142D,E156G,F157-,R158-,D228H,L452R,S477R,T478K,D614G,P681R,D950N,V1228L] Delta
.R.....LD...G--............RI.........R....N.... 19 0 0 19 0 0 0 0 19 18 94% [T19R,S112L,G142D,E156G,F157-,R158-,L452R,S477I,T478K,D614G,P681R,R683Q,D950N] Delta+S112L
.R..........G--...V........R.......I..R....N.... 19 0 1 0 18 0 0 0 19 9 47% [T19R,E156G,F157-,R158-,D215G,A222V,L452R,T478K,T547I,D614G,P681R,D950N] Delta+T95_,A222V
.R......DA..G--............R..........R....N.... 19 0 0 18 1 0 0 0 19 18 94% [T19R,G142D,V143A,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
...........................................N.... 18 0 15 3 0 0 0 0 18 12 66% [T478K,D614G,D950N]
........D---...-I.......NKS.NARSRYHK.KHKY...HKF. 18 0 0 18 0 0 0 0 18 15 83% [G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,N679K,P681H,N764K,D796Y,Q954H,N969K,L981F]
...V--I.D---...-I..DK.......NARSRYHKYKHKY.K.HKF. 18 0 0 18 0 0 0 0 18 17 94% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
FR....I.D...G--...V........R..........R....N.... 18 15 2 1 0 0 0 0 18 15 83% [L5F,T19R,T95I,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N]
.R......D..HG--...V........R..........R....N.... 18 7 11 0 0 0 0 0 18 10 55% [T19R,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+T95_,A222V
.R....I.D...G--............RT.........R....N.... 18 2 0 15 1 0 0 0 18 11 61% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,S477T,T478K,D614G,P681R,D950N,K1073N] Delta
.R....I.D...G--............Q..........R....N.... 18 4 13 1 0 0 0 0 18 10 55% [T19R,T95I,D138H,G142D,E156G,F157-,R158-,E180V,L452Q,T478K,D614G,P681R,D950N,I1114T]
.R......D...G--...V........R..........R...SN.... 18 0 18 0 0 0 0 0 18 17 94% [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,N856S,D950N] Delta+T95_,A222V
.R......D...G--.....G......R..........R....N.... 18 0 1 17 0 0 0 0 18 10 55% [T19R,G142D,E156G,F157-,R158-,R346G,L452R,T478K,D614G,P681R,D950N] Delta
.R.S....D...G--...V........R..........R....N.... 18 0 18 0 0 0 0 0 18 10 55% [V11I,T19R,A67S,G142D,E156G,F157-,R158-,A222V,S255F,L452R,T478K,D614G,P681R,D950N] Delta+T95_,A222V
FR....I.D...G--...........VR..........R....N.... 18 10 8 0 0 0 0 0 18 9 50% [L5F,T19R,T95I,G142D,E156G,F157-,R158-,A262S,G446V,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.....G--...........VR.....T....R....N.... 18 0 5 1 12 0 0 0 18 8 44% [T19R,T95I,E156G,F157-,R158-,G446V,L452R,T478K,N501T,D614G,P681R,D950N] Delta
.R......D...G--..Y.........R..........R....N.... 18 0 0 18 0 0 0 0 18 17 94% [T19R,G142D,E156G,F157-,R158-,R214Y,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.D...G----..........R..........R....N.... 18 11 7 0 0 0 0 0 18 8 44% [T19R,T95I,G142D,E156G,F157-,R158-,N211-,L212-,L452R,T478K,D614G,P681R,D950N,H1101Q] Delta
........................T....K...Y..YK.......... 17 0 0 0 0 0 17 0 17 11 64% [L18F,T20N,P26S,D138Y,R190S,R246G,T284I,K417T,E484K,N501Y,D614G,H655Y,N679K,T1027I,V1176F] Gamma+FurinRelated
.R....I.----G--............R..........R....N.... 17 16 1 0 0 0 0 0 17 14 82% [T19R,H66R,T95I,P139-,F140-,L141-,G142-,V143-,Y144-,Y145-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,K1073T] Delta
...V--I.D---...I-..DKLPF...RNARSRYHKYKHKY.K.HKF. 17 0 0 17 0 0 0 0 17 14 82% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211I,L212-,G339D,R346K,S371L,S373P,S375F,L452R,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron+R346K
...V..I.D---.......DKLPFNKS.NARSRYHKYKHKY.K.HKF. 17 0 17 0 0 0 0 0 17 17 100% [A67V,T95I,G142D,V143-,Y144-,Y145-,G339D,R346K,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
...V--I.D---...-I..DK..............KYKHKY.K.HKF. 17 0 0 17 0 0 0 0 17 17 100% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
...V--I.D---...-I.......NKS.NARSRYHKYKH...K.HKF. 17 0 0 17 0 0 0 0 17 16 94% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N856K,Q954H,N969K,L981F]
.R....I.D...G--...........RR..........R....N.... 17 1 2 1 10 0 0 3 17 12 70% [T19R,T95I,G142D,E156G,F157-,R158-,G446R,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.D...G--............W..........R....N.... 17 12 2 3 0 0 0 0 17 14 82% [T19R,T95I,G142D,E156G,F157-,R158-,L452W,T478K,D614G,P681R,D950N]
.R....I.D...G--............RG.........R....N.... 17 2 5 9 1 0 0 0 17 5 29% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,S477G,T478K,D614G,P681R,D950N] Delta
.R......DF..G--...V........R..........R....N.... 17 0 2 15 0 0 0 0 17 10 58% [T19R,G142D,V143F,E156G,F157-,R158-,D215N,A222V,L452R,T478K,D614G,P681R,D950N,C1247S] Delta+T95_,A222V
.R....I.D...G--............R..........L....N.... 17 13 0 3 1 0 0 0 17 6 35% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681L,D950N]
....--.......................................... 16 0 16 0 0 0 0 0 16 11 68% [H69-,V70-,L189F,N439K,D614G,V772I]
...V--I.D---.......................KYKHK..K.HKF. 16 0 0 16 0 0 0 0 16 15 93% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,T547K,D614G,H655Y,N679K,P681H,N764K,N856K,Q954H,N969K,L981F]
...V--I.D---...-I..D.LPFNKS.N.RSRYHKYKHKY.K.HKF. 16 0 8 8 0 0 0 0 16 13 81% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
...V--I.D---...-I..DKLPF.KS.N......KYKHKY.K.HKF. 16 0 0 16 0 0 0 0 16 9 56% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,N440K,G446S,S477N,T478K,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
.R....A.D...G--............R..........R....N.... 16 0 3 13 0 0 0 0 16 11 68% [T19R,T95A,G142D,E156G,F157-,R158-,Q173R,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.D...G--.....K......R..........R....N.... 16 12 2 2 0 0 0 0 16 7 43% [T19R,T95I,G142D,E156G,F157-,R158-,R346K,L452R,T478K,D614G,P681R,D950N] Delta
.R....I....HG--...V........R..........R......... 16 0 16 0 0 0 0 0 16 13 81% [T19R,T95I,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R]
.R....I.....G--............R.........YR....N.... 16 0 16 0 0 0 0 0 16 12 75% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,N679Y,P681R,D950N,F1103L] Delta+FurinRelated
.R..--I.....G--............R..........R....N.... 16 0 11 3 1 0 1 0 16 8 50% [T19R,H69-,V70-,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
FR..........G--...V........R..........R......... 16 0 2 0 14 0 0 0 16 13 81% [L5F,T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R]
.R....................................R..L.N.... 15 0 15 0 0 0 0 0 15 9 60% [T19R,T478K,D614G,P681R,I850L,D950N]
...V--I.D---...I...D.LPFNKS.NARSRYHKYKHKY.K.HKF. 15 0 0 15 0 0 0 0 15 11 73% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
...V--I.D---...-IL.D.LPFNKS.NARSRYHKYKHKY.K.HKF. 15 0 8 7 0 0 0 0 15 15 100% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,R214L,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
...V--..D---...-I..D.LPFNKS.NARS...KYKHKY.K.HKF. 15 0 0 0 0 0 15 0 15 14 93% [A67V,H69-,V70-,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
...V--I.D---...-I..D.LPFNKS.NA.....KYKHKY.K.HK.. 15 0 0 15 0 0 0 0 15 15 100% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K]
...V--I.D---...-I..D.LPF......RSRYHKYKHKY.K.HKF. 15 0 0 15 0 0 0 0 15 13 86% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
.R......D...G--............R..........R...SN.... 15 1 3 11 0 0 0 0 15 11 73% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,N856S,D950N] Delta
.R....I.D...G--............R.Q........R....N...L 15 0 0 13 2 0 0 0 15 13 86% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,T747I,D950N,V1264L] Delta+V1264L
.R...A..D...G--............R..........R....N.... 15 1 11 3 0 0 0 0 15 10 66% [T19R,V70A,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
.R....I.D...G--............R..........R....S.... 15 12 3 0 0 0 0 0 15 11 73% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950S]
.R......D...G--............R.V........R....N.... 15 0 13 2 0 0 0 0 15 7 46% [T19R,G142D,E156G,F157-,R158-,P251L,S349P,L452R,T478K,E484V,D614G,P681R,D950N]
.R....I.D...G--...........VR.Q...T....R....N.... 15 1 0 0 14 0 0 0 15 13 86% [T19R,T95I,G142D,E156G,F157-,R158-,G446V,L452R,T478K,E484Q,N501T,D614G,P681R,D950N]
.R....I.D..HG--...V........R.......I..R....N.... 15 13 2 0 0 0 0 0 15 13 86% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,T547I,D614G,P681R,D950N] Delta+Y145H,A222V
.R....I.D..HG--...V...P....R..........R....N.... 15 14 1 0 0 0 0 0 15 14 93% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,R246G,S373P,L452R,T478K,D614G,P681R,D950N] Delta+Y145H,A222V
.R....I...-.G--............R.Q........R....N.... 15 1 0 0 14 0 0 0 15 4 26% [T19R,T95I,Y144-,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,D950N]
...........................R..........R....N...L 14 0 4 10 0 0 0 0 14 7 50% [L452R,T478K,D614G,P681R,D950N,V1264L]
....--....-......................Y....H......... 14 0 9 3 2 0 0 0 14 9 64% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] Alpha
...V--I.D---...-I..DKLPF..S.NARSRYHKYKHKY.K.HKF. 14 0 0 14 0 0 0 0 14 13 92% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron+R346K
...V--I.D---...-I..D....NKS.NARSRYHKYKHKY.K.HKF. 14 0 6 5 1 0 2 0 14 10 71% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
...V--I.D---...-I..DKLPF......RSRYHKYKHKY.K.HKF. 14 0 0 14 0 0 0 0 14 13 92% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
.R....I.D.....G............R..........R....N.... 14 0 14 0 0 0 0 0 14 11 78% [T19R,T95I,G142D,R158G,L452R,T478K,D614G,P681R,D950N]
.R....I.D...--.............R..........R....N.... 14 0 1 13 0 0 0 0 14 6 42% [T19R,T95I,G142D,E156-,F157-,L452R,T478K,D614G,P681R,D950N]
.R....I.D...G--.......P....R..........R....N.... 14 3 7 4 0 0 0 0 14 10 71% [T19R,T95I,G142D,E156G,F157-,R158-,S373P,L452R,T478K,D614G,P681R,D950N] Delta
IR....I.D...G--............R..........R....N.... 14 13 0 1 0 0 0 0 14 13 92% [L5I,T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R......D...G--............R.........SR....N.... 14 2 9 3 0 0 0 0 14 11 78% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,N679S,P681R,D950N] Delta+FurinRelated
.R....I.D...G--..........K.R..........R....N.... 14 2 1 0 0 0 11 0 14 12 85% [T19R,T95I,G142D,E156G,F157-,R158-,N440K,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.D...G--...P........R..........R....N.... 14 6 6 2 0 0 0 0 14 8 57% [T19R,T95I,G142D,E156G,F157-,R158-,A222P,L452R,T478K,D614G,P681R,D950N]
.R....I.D...G--........F...R..........R....N.... 14 3 5 2 0 0 0 4 14 5 35% [T19R,T95I,G142D,E156G,F157-,R158-,S375F,L452R,T478K,D614G,P681R,D950N] Delta
.R...I.LD...G--............R..........R....N.... 14 0 0 14 0 0 0 0 14 12 85% [T19R,V70I,S112L,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta+S112L
.G......D...G--............R..........R....N.... 14 5 7 2 0 0 0 0 14 11 78% [T19G,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
.R.....LD...G--............R.......I..R....N.... 14 0 0 14 0 0 0 0 14 7 50% [T19R,S112L,G142D,E156G,F157-,R158-,L452R,T478K,T547I,D614G,P681R,D950N] Delta+S112L
.R....I....HG--............R..........R....N.... 14 0 13 0 1 0 0 0 14 13 92% [T19R,T95I,Y145H,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R..N...D...G--............R..........R....N.... 14 0 1 11 2 0 0 0 14 10 71% [T19R,H69N,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.D..HG--...VD.......R..........R....N.... 14 14 0 0 0 0 0 0 14 10 71% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,G339D,L452R,T478K,D614G,P681R,D950N] Delta+Y145H,A222V
.R....I.D...G--............R..........R..V.N.... 14 14 0 0 0 0 0 0 14 7 50% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850V,D950N] Delta
.R....I.D...G--...V........R........Y.R....N.... 14 0 0 14 0 0 0 0 14 10 71% [T19R,T95I,G142D,E156G,F157-,R158-,A222V,V289I,L452R,T478K,D614G,H655Y,P681R,D950N] Delta+FurinRelated
FR....I.D...G--............R.Q........R....N.... 14 2 1 9 2 0 0 0 14 10 71% [L5F,T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,D950N]
.R....I.D..HG--...V........R.......I..R....N...L 14 14 0 0 0 0 0 0 14 14 100% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,T547I,D614G,P681R,D950N,V1264L] Delta+Y145H,A222V
.R....I.D..HG--...V........R.......K..R....N...L 14 14 0 0 0 0 0 0 14 10 71% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,V327I,L452R,T478K,T547K,D614G,P681R,D950N,V1264L] Delta+Y145H,A222V
.R.........................R.................... 13 0 13 0 0 0 0 0 13 12 92% [T19R,L452R,T478K,D614G]
...V--I.D---...I-..D.....KS.NARSRYHKYKHKY.K.HKF. 13 0 3 9 0 0 1 0 13 12 92% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211I,L212-,G339D,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
F..V--I.D---...I-..D.LPFNKS.NARSRYHKYKHKY.K.HKF. 13 0 6 4 0 2 1 0 13 7 53% [L5F,A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211I,L212-,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
...V--I.D---...I-..D.FPFNKS.NAR.RYH.YKHKY...HK.. 13 0 3 0 0 10 0 0 13 13 100% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211I,L212-,G339D,S371F,S373P,S375F,D405N,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K]
...V--I.D---...-I..D.LPFNKS.NARSRYHKYKHKY...HKF. 13 0 2 11 0 0 0 0 13 11 84% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K,L981F]
...V--I.D---...-I..D.L..NKS.NARSRYHKYKHKY.K.HKF. 13 0 0 2 11 0 0 0 13 13 100% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
...V--I.D---...-I..DK...NKS.NARSRYHKYKHKY.K.HKF. 13 0 1 11 1 0 0 0 13 13 100% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
...V--I.D---...-I..D......S.NARSRYHKYKHKY.K.HKF. 13 0 5 7 1 0 0 0 13 10 76% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
...........................RN.........R....N.... 13 0 0 13 0 0 0 0 13 12 92% [L452R,S477N,T478K,D614G,P681R,D950N]
.R..........--.............R..........R....N.... 13 0 8 5 0 0 0 0 13 6 46% [T19R,E156-,F157-,L452R,T478K,D614G,P681R,D950N]
.R......D...G--............R.......K..R....N.... 13 1 6 6 0 0 0 0 13 7 53% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,T547K,D614G,P681R,D950N] Delta
.R....I.....G--............R.A........R....N.... 13 0 6 4 2 1 0 0 13 7 53% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,E484A,D614G,P681R,D950N]
.R....I.D...G--............R...............N.... 13 0 6 6 0 0 0 1 13 4 30% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,D950N]
.R...FI.....G--............R..........R....N.... 13 0 12 0 0 0 1 0 13 10 76% [T19R,V70F,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
.R....L.D...G--............R..........R....N.... 13 11 2 0 0 0 0 0 13 12 92% [T19R,T95L,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.....G--............R.........SR....N.... 13 0 12 1 0 0 0 0 13 12 92% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,N679S,P681R,D950N] Delta+FurinRelated
FR......D...G--............R..........R....N...L 13 0 6 3 4 0 0 0 13 5 38% [L5F,T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+V1264L
.R....I.D..HG--...V........R..H.......R....N.... 13 13 0 0 0 0 0 0 13 11 84% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,Q493H,D614G,P681R,D950N,M1229I] Delta+Y145H,A222V
-R......D...G--............R..........R....N.... 13 0 10 0 0 0 3 0 13 8 61% [L5-,T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R....I...............................R....N.... 12 0 6 6 0 0 0 0 12 4 33% [T19R,T95I,D614G,P681R,D950N]
...V--I.D---...I-..D...............KYKHKY.K.HKF. 12 0 0 12 0 0 0 0 12 12 100% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211I,L212-,G339D,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
...V--I.D---................NARSRYHKYKHKY.K.HKF. 12 0 8 4 0 0 0 0 12 11 91% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
...V--I.D---...-I..DKLPFNKS.NARSRYHKYKHKY...HKF. 12 0 0 12 0 0 0 0 12 11 91% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K,L981F]
...V--I.D---...-I..D..PFNKS.NARSRYHKYKHKY.K.HKF. 12 0 0 12 0 0 0 0 12 8 66% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
...V--I.D---...-I..................KYKHKY.K.HKF. 12 0 0 12 0 0 0 0 12 11 91% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
...V--I.D---...-I..D.LPF....NARSRYHKYKH.Y.K.HKF. 12 0 3 9 0 0 0 0 12 11 91% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,D796Y,N856K,Q954H,N969K,L981F]
.R......D...G--....D.......R..........R....N.... 12 0 5 7 0 0 0 0 12 5 41% [T19R,G142D,E156G,F157-,R158-,G339D,L452R,T478K,D614G,P681R,D950N] Delta
.R......D...G--............R.D........R....N.... 12 0 3 9 0 0 0 0 12 9 75% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,E484D,D614G,P681R,D950N]
.R...L..D...G--............R..........R....N.... 12 0 1 10 1 0 0 0 12 9 75% [T19R,V70L,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
.R......D...G--.........T..R..........R....N.... 12 2 9 1 0 0 0 0 12 11 91% [T19R,G142D,E156G,F157-,R158-,K417T,L452R,T478K,D614G,P681R,D950N]
.R..........G--............R..........R........L 12 0 9 0 0 0 3 0 12 5 41% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,V1264L]
.R....I.D...G--.....G......R..........R....N.... 12 2 3 7 0 0 0 0 12 6 50% [T19R,T95I,G142D,E156G,F157-,R158-,R346G,L452R,T478K,T572I,D614G,P681R,D950N] Delta
.R..........G--............R.K........R....N.... 12 0 11 1 0 0 0 0 12 7 58% [T19R,E156G,F157-,R158-,L452R,T478K,E484K,D614G,S640F,P681R,D950N]
FR..Y...D...G--............R..........R....N.... 12 1 0 11 0 0 0 0 12 9 75% [L5F,T19R,H69Y,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,A701V,D950N] Delta
.R....I.D...G--............R..........R....T.... 12 0 0 0 0 0 0 12 12 12 100% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950T]
.R....I.D.-.G--............R..........R..L.N.... 12 1 7 0 0 0 4 0 12 7 58% [T19R,T95I,G142D,Y144-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] Delta
.R.....LD...G--...V........R..........R....N.... 12 0 0 12 0 0 0 0 12 6 50% [T19R,S112L,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,E654V,P681R,D950N] Delta+T95_,A222V
.R..R...D...G--............R..........R....N.... 12 0 1 11 0 0 0 0 12 4 33% [T19R,H69R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,L841I,D950N] Delta
.R....I.D...G--............RNQ........R....N.... 12 9 3 0 0 0 0 0 12 12 100% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,S477N,T478K,E484Q,D614G,P681R,D950N]
.R....I.D..HG--...V.......DR..........R....N.... 12 12 0 0 0 0 0 0 12 11 91% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,Q414K,G446D,L452R,T478K,D614G,P681R,D950N] Delta+Y145H,A222V
.R..........G--............R.....S....R....N.... 12 0 12 0 0 0 0 0 12 12 100% [T19R,E156G,F157-,R158-,L452R,T478K,N501S,D614G,P681R,D950N] Delta
.R....I.D..HG--...V........R..........H....N...L 12 12 0 0 0 0 0 0 12 10 83% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,T299I,L452R,T478K,D614G,P681H,D950N,V1264L] Delta+FurinRelated
.R....I.D..HG--...I........R..........R....N.... 12 12 0 0 0 0 0 0 12 12 100% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222I,L452R,T478K,D614G,P681R,D950N]
...........................R...............N.... 11 0 1 10 0 0 0 0 11 4 36% [L452R,T478K,D614G,D950N]
.R....I.D---G--............R..........R....N.... 11 0 9 0 2 0 0 0 11 8 72% [T19R,T95I,G142D,V143-,Y144-,Y145-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
...V--I.D---...I-..DK..............KYKHKY.K.HKF. 11 0 0 11 0 0 0 0 11 9 81% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211I,L212-,G339D,R346K,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
...V--I.D---...I-..DKLPFN.S.NARSRYHKYKHKY.K.HKF. 11 0 8 3 0 0 0 0 11 10 90% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211I,L212-,G339D,R346K,S371L,S373P,S375F,K417N,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron+R346K
...V--I.D---.............KS.NARSRYHKYKHKY.K.HKF. 11 1 2 7 0 0 1 0 11 10 90% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
...V--I.D---...-I..DK.PFNKS.NARSRYHKYKHK..K.HKF. 11 0 11 0 0 0 0 0 11 10 90% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,N856K,Q954H,N969K,L981F]
...V--I.D---...-I..D.LPF.K..NARSRYHKYKHKY.K.HKF. 11 0 1 9 0 0 1 0 11 9 81% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,N440K,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
...V--I.D---...-I..DKLPFNKS.NA.....KYKHKY.K.HK.. 11 0 0 11 0 0 0 0 11 11 100% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K]
...V--I....D...-I..D.LPFNKS.NARSRYHKYKHKY.K.HKF. 11 0 11 0 0 0 0 0 11 9 81% [A67V,H69-,V70-,T95I,Y145D,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
......I.D..................R..........R..L.N.... 11 0 11 0 0 0 0 0 11 5 45% [T95I,G142D,L452R,T478K,D614G,P681R,I850L,D950N]
.R....I.....--.............R..........R....N.... 11 0 6 5 0 0 0 0 11 6 54% [T19R,T95I,E156-,F157-,L452R,T478K,D614G,P681R,D950N]
.R....I.....G--...V........R..........R......... 11 0 6 1 4 0 0 0 11 6 54% [T19R,T95I,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R]
FR......D...G--............W..........R....N.... 11 0 1 10 0 0 0 0 11 11 100% [L5F,T19R,G142D,E156G,F157-,R158-,L452W,T478K,D614G,P681R,D950N]
.R....I.....G--............R.Q........R..L.N.... 11 0 11 0 0 0 0 0 11 5 45% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,I850L,D950N]
.R....I.D...G--............R.....T....R....N.... 11 1 7 0 2 0 1 0 11 7 63% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,N501T,D614G,P681R,D950N] Delta
.......LD...G--............R..........R....N.... 11 0 0 11 0 0 0 0 11 6 54% [S112L,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,E1202Q]
.R....I.D...G--............R.........KR....N.... 11 0 1 10 0 0 0 0 11 10 90% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,N679K,P681R,P809S,G946R,D950N] Delta+FurinRelated
.R.V...LD...G--............R..........R....N.... 11 0 0 11 0 0 0 0 11 10 90% [T19R,A67V,S112L,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta+S112L
.R....I.D...G--....D.......R..........R....N.... 11 0 9 2 0 0 0 0 11 4 36% [T19R,T95I,G142D,E156G,F157-,R158-,G339D,L452R,T478K,D614G,P681R,D950N,D1259Y] Delta
FR......D...G--..L.........R..........R....N.... 11 5 0 6 0 0 0 0 11 6 54% [L5F,T19R,G142D,E156G,F157-,R158-,R214L,L452R,T478K,D614G,P681R,D950N] Delta
.R...F......G--...........RR..........R....N.... 11 0 0 0 0 0 11 0 11 10 90% [T19R,V70F,E156G,F157-,R158-,G446R,L452R,T478K,D614G,P681R,D950N]
.R....I.D..HG--...V.......VR..........R....N...L 11 11 0 0 0 0 0 0 11 5 45% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,G446V,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+Y145H,A222V
FR......D.-.G--............R..........R....N.... 11 2 7 2 0 0 0 0 11 8 72% [L5F,T19R,G142D,Y144-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.RF...I.D..HG--...V........RG.........R....N.... 11 11 0 0 0 0 0 0 11 11 100% [T19R,V36F,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,S477G,T478K,D614G,P681R,D950N] Delta+Y145H,A222V
........D.............................R....N.... 10 0 10 0 0 0 0 0 10 4 40% [G142D,T478K,D614G,P681R,D950N]
...V--I.D---......................HKYKHKY.K.HKF. 10 0 0 10 0 0 0 0 10 10 100% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
...V--I.D---...-I..DKLPFNK..NARSRYHKYKHKY.K.HKF. 10 0 1 9 0 0 0 0 10 10 100% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,K417N,N440K,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron+R346K
...V--I.D---...-I..D.LPFNKS.NARSRY.KYKHKY.K.HKF. 10 1 6 1 1 1 0 0 10 8 80% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
...V--I.D---...-I..D.LPFNKS.NARSRYHKYKH...K.HKF. 10 0 2 8 0 0 0 0 10 7 70% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N856K,Q954H,N969K,L981F]
...V--I.D---...-I..DKLPFNKS.NAR....KYKHKY.K.HKF. 10 0 0 10 0 0 0 0 10 10 100% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
...V--I.D---...-I..DKLPF.K..NARSRYHKYKHKY.K.HKF. 10 0 0 10 0 0 0 0 10 10 100% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,N440K,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron+R346K
...V--I.D---...-I..DKLPFNKS...RSRYHKYKHKY.K.HKF. 10 0 0 9 1 0 0 0 10 10 100% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,K417N,N440K,G446S,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F]
.R.........................RN.........R....N.... 10 0 0 10 0 0 0 0 10 10 100% [T19R,L452R,S477N,T478K,D614G,P681R,D950N]
.R....I.....G--.....I......R..........R....N.... 10 0 3 6 1 0 0 0 10 4 40% [T19R,T95I,E156G,F157-,R158-,R346I,L452R,T478K,D614G,P681R,D950N,K1073N] Delta
.R....I.D...G--............R.....I....R....N.... 10 2 4 3 1 0 0 0 10 6 60% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,N501I,D614G,P681R,D950N] Delta
.R....I.D.H.G--............R..........R....N.... 10 6 1 3 0 0 0 0 10 3 30% [T19R,T95I,G142D,Y144H,E156G,F157-,R158-,L452R,T478K,D614G,S640F,P681R,D950N] Delta
.R..........G--............R.......I..R......... 10 0 10 0 0 0 0 0 10 4 40% [T19R,E156G,F157-,R158-,L452R,T478K,T547I,D614G,V622F,P681R]
.R.S..I.....G--............R..........R....N.... 10 0 1 4 5 0 0 0 10 2 20% [Q14H,T19R,A67S,T95I,E156G,F157-,R158-,F306L,L452R,T478K,D614G,P681R,D950N] Delta
.R..........G--............Q..........R....N.... 10 0 10 0 0 0 0 0 10 7 70% [T19R,E156G,F157-,R158-,L452Q,T478K,D614G,P681R,D950N,H1083Y]
.R....I.....G--............R.......I..R....N.... 10 0 4 3 3 0 0 0 10 6 60% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,T547I,D614G,P681R,D950N] Delta
.R......D...G--............R.G........R....N.... 10 0 8 2 0 0 0 0 10 8 80% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,E484G,D614G,P681R,D950N]
.R......D...G--............R..........R.H..N.... 10 1 2 6 1 0 0 0 10 8 80% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D796H,D950N] Delta
FR....I....HG--...V........R..........R....N.... 10 0 10 0 0 0 0 0 10 8 80% [L5F,T19R,T95I,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,Q779E,D950N,P1162S] Delta+Y145H,A222V
.R....I.D...G--...........VR..........R..L.N.... 10 2 8 0 0 0 0 0 10 4 40% [T19R,T95I,G142D,E156G,F157-,R158-,G446V,L452R,T478K,D614G,P681R,I850L,D950N] Delta
.R......D...G--..LV........R..........R....N.... 10 0 9 1 0 0 0 0 10 5 50% [T19R,G142D,E156G,F157-,R158-,R214L,A222V,L452R,T478K,D614G,P681R,D950N,P1162S] Delta+T95_,A222V
FR...FI.D...G--............R..........R....N.... 10 10 0 0 0 0 0 0 10 8 80% [L5F,T19R,V70F,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N]
.R.....LD...G--....S.......R..........R....N.... 10 0 0 10 0 0 0 0 10 9 90% [T19R,S112L,G142D,E156G,F157-,R158-,G339S,L452R,T478K,D614G,P681R,D950N] Delta+S112L
.R....I.....G--..........K.R..........R....N.... 10 0 0 0 0 0 10 0 10 8 80% [T19R,T95I,E156G,F157-,R158-,N440K,L452R,T478K,D614G,P681R,D950N] Delta
.R......D...G--...V...L...VR..........R....N.... 10 0 0 10 0 0 0 0 10 10 100% [T19R,G142D,E156G,F157-,R158-,A222V,S373L,G446V,L452R,T478K,D614G,P681R,D950N] Delta+T95_,A222V
.R....I.D.-.G--............R.K........R....N.... 10 1 5 2 2 0 0 0 10 9 90% [T19R,T95I,G142D,Y144-,E156G,F157-,R158-,L452R,T478K,E484K,D614G,S673T,P681R,D950N]
.RF...I.D..HG--...V........R..........R....N...F 10 10 0 0 0 0 0 0 10 10 100% [T19R,V36F,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264F] Delta+Y145H,A222V
.R.S..I.D..HG--...V........R..........R....N.... 10 3 7 0 0 0 0 0 10 10 100% [T19R,A67S,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+Y145H,A222V
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last modified: Mon Jan 10 22:17 2022
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Questions or comments? Contact us at seq-info@lanl.gov.
