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COVID-19 Viral Genome Analysis Pipeline
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XSPIKE

eXplore the SPIKE protein sequence in the SARS CoV-2 virus

Last update: Jul 31, 2021
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NOTE: We are NOT tracking insertions in Spike sequences in this output; insertions are still very rare, but are found on occasion.

In particular, we have found them associated with a few rare Pango lineages including:
B.1.621 T95I, insert144T, Y144S, Y145N, R346K, E484K, N501Y, D614G, P681H, D950N
A.2.5.2 del141-143, insert215AGG, D215Y, L452R, D614G
AT.1 P9L, del136-144, D215G, H245P, E484K, D614G, N679K, insert679GIAL, E780K
B.1.214.2 insert214TDR, Q414K, N450K, D614G, T716I

Where 'insert' indicates an insertion at the given position followed by the list amino acids added, and 'del' indicates a deletion.

Global
Variants color key
Evaluating 222078 sequences of length 1274
Sampled from 2021-05-27 to 2021-07-26.
Specified Date Range: (datetime.date(2021, 5, 27), datetime.date(2021, 7, 26))
Highest entropy sites for: Global
  Site Entropy
   681  0.8315
   142  0.7054
   157  0.6871
   950  0.6763
   452  0.6747
    95  0.6726
   158  0.6666
   156  0.6609
    19  0.6584
   478  0.6530
   501  0.6326
    70  0.6221
   144  0.6084
  1118  0.5920
    69  0.5918
   570  0.5893
   716  0.5886
   982  0.5875
   484  0.2492
   222  0.2492
   138  0.2299
   417  0.2044
  1027  0.1944
    18  0.1942
    20  0.1900
    26  0.1828
   655  0.1771
  1176  0.1758
   190  0.1747
     5  0.1032
   152  0.0911
   253  0.0723
  1264  0.0615
   251  0.0595
   701  0.0536
   936  0.0473
    80  0.0455
   440  0.0440
   477  0.0435
   859  0.0420
    98  0.0414
  1162  0.0408
  1191  0.0405
   145  0.0399
   677  0.0393
   490  0.0366
   939  0.0354
   346  0.0354
   250  0.0350
    67  0.0345


Most highly correlated site-pairs for: Global
               cramerV  mutInfo
   157    156   0.5008   0.6572
   157    158   0.4997   0.6544
   158    156   0.5076   0.6472
   158     19   0.4960   0.6335
   681     19   0.4966   0.6327
   157     19   0.4964   0.6319
   681    157   0.5029   0.6278
   681    158   0.4950   0.6265
    19    478   0.5715   0.6240
   156     19   0.4935   0.6220
   157    950   0.7919   0.6195
   158    478   0.5690   0.6188
   157    478   0.5688   0.6172
   681    156   0.4919   0.6156
   681    478   0.5700   0.6151


    20   1176   0.9842   0.1661
  1176    190   0.9830   0.1654
   417   1176   0.9770   0.1615
   655   1176   0.9753   0.1634
    26   1176   0.9668   0.1610
   138   1176   0.9618   0.1576
    18   1176   0.9392   0.1543
  1027     26   0.9251   0.1541
  1027     20   0.9201   0.1520
  1027    190   0.9184   0.1509
  1027   1176   0.9131   0.1491
   417   1027   0.9123   0.1479
  1027    655   0.9113   0.1485
   138   1027   0.8987   0.1438
  1027     18   0.8874   0.1436


Most common patterns for local area, where Local = Global
                                            111111
           111111111222234444444556667789999011112
 1122667899344455559255541457789075780153358216796
58906790058824526780201367027840105711696902782614
LLTTPAHVDTSDGYYWEFRRATPDRKNLSTEFNAHQPATTDSDSTDPVKV  Global     UK  Eu-UK  NAmer   Asia Africa  SAmer  Ocean  Local  Exact  Pct [Context]
                                                    200763  90116  62264  35233   7655   1032   4102    361 200763 <----------- Totals
..R......I..D...--G........R.K......R.....N.......   67813  62017   3922   1105    573     81      8    107  67813  48468  71% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
......--.....-..................YD..H.I....A.H....   43427   4676  26504   9825   2184     89    105     44  43427  28495  65% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
..R.........D...--G........R.K......R.....N.......   25953  12296   6194   6854    391    201      5     12  25953  17692  68% [T19R,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........D...--G.V......R.K......R.....N.......    9431   4845   3201    994    329     47      1     14   9431   6714  71% [T19R,G142D,E156-,F157-,R158G,A222V,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta+A222V
.F.NS......Y.......S.....T....K.Y.Y.........I..F..    7689      7   1223   3817     15      0   2626      1   7689   4883  63% [L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] P.1=Gamma
..R.............--G........R.K......R.....N.......    6320    164   3514   1467    919    184     71      1   6320   4408  69% [T19R,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R......I......--G........R.K......R.....N.......    3802    455   2387    625    201     22      3    109   3802   2525  66% [T19R,T95I,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
......--.....-.R................YD..H.I....A.H....    2248      2   2220     22      1      0      0      3   2248   1867  83% [H69-,V70-,Y144-,W152R,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] Alpha+W152R
F.....--.....-..................YD..H.I....A.H....    1682     48    923    676     33      1      1      0   1682   1095  65% [L5F,H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
......--.....-..................YD..H.I....A.H..N.    1151      5     36   1102      5      0      1      2   1151    861  74% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H,K1191N] B.1.1.7=Alpha
..R.............--G.V......R.K......R.....N.......    1051     88    506    259    182     15      0      1   1051    711  67% [T19R,E156-,F157-,R158G,A222V,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta+A222V
..R.........D...--G........R.K......R.....N......L     868      7     36     33    786      0      0      6    868    696  80% [T19R,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N,V1264L] B.1.617.2=Delta
..........................K...K.........NF..I.....     855      0     57      2    795      1      0      0    855    760  88% [I210T,N440K,E484K,D614G,D936N,S939F,T1027I] 
..R.........D...--G...L....R.K......R.....N.......     848    663    179      1      5      0      0      0    848    501  59% [T19R,G142D,E156-,F157-,R158G,P251L,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R......I.HD...--G........R.K......R.....N.......     760    751      2      5      2      0      0      0    760    570  75% [T19R,T95I,D138H,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
......--..F..-..................YD..H.I....A.H....     698     25    519    144      6      1      3      0    698    465  66% [H69-,V70-,S98F,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
F........I.............G......K......V............     675      0     24    536      0      0    115      0    675    499  73% [L5F,T95I,D253G,E484K,D614G,A701V] B.1.526=Iota
.............................K......H.............     601      0      2    598      1      0      0      0    601    403  67% [T478K,D614G,P681H,T732A] B.1.1.519
.....................---...Q...S.......N..........     544      3     87     97      1      0    356      0    544    321  59% [G75V,T76I,R246N,S247-,Y248-,L249-,T250-,P251-,G252-,D253-,L452Q,F490S,D614G,T859N] C.37=Lambda
......--...H.-..................YD..H.I....A.H....     538      6    525      5      2      0      0      0    538    333  61% [H69-,V70-,D138H,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
..R......I..D...--G........R.K......R.....N...S...     504    502      0      0      2      0      0      0    504    375  74% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N,P1162S] B.1.617.2=Delta
..................................................     474     13    290    137     26      0      2      6    474    253  53% [D614G] G-clade
.........I...SN.........K.....K.Y...H.....N.......     464      5    192    184      3      0     80      0    464    360  77% [T95I,Y144S,Y145N,R346K,E484K,N501Y,D614G,P681H,D950N] 
......--..FH.-..................YD..H.I....A.H....     464      9    108    340      5      0      2      0    464    333  71% [H69-,V70-,S98F,D138H,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
.F.NS......Y.......S.....T....K.Y.Y.H.......I..F..     452      1    226     12      0      0    213      0    452    394  87% [L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,P681H,T1027I,V1176F] P.1=Gamma
..R.........D...--G.V......R.K......R.....N......L     448      8     27    399     13      0      1      0    448    153  34% [T19R,G142D,E156-,F157-,R158G,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] B.1.617.2=Delta+A222V
........G....-...S.........R...........N..H.......     438      0      1    437      0      0      0      0    438    276  63% [D80G,Y144-,F157S,L452R,D614G,T859N,D950H] B.1.526.1
..R....F.I..D...--G........R.K......R.....N.......     394    392      2      0      0      0      0      0    394    280  71% [T19R,V70F,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] 
......--.....-................K.YD..H.I....A.H....     391      9    359     14      6      1      2      0    391    223  57% [H69-,V70-,Y144-,E484K,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] Alpha+E484K
F........I.............G....N.....................     388      0      2    385      1      0      0      0    388    258  66% [L5F,T95I,D253G,S477N,D614G,Q957R] B.1.526.2
..R......I..D.H.--G.V......R.K......R.....N.......     379    378      1      0      0      0      0      0    379    299  78% [T19R,T95I,G142D,Y145H,E156-,F157-,R158G,A222V,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta+A222V
......--.....-..................YD..HVI....A.H....     371      2    323     45      1      0      0      0    371    243  65% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,A701V,T716I,S982A,D1118H] B.1.1.7=Alpha
..R....F....D...--G.V....N.R.K......R.....N.......     351      0      0    351      0      0      0      0    351    200  56% [T19R,V70F,G142D,E156-,F157-,R158G,A222V,K417N,L452R,T478K,D614G,P681R,D950N] B.1.617.2=AY.2
F.R......I..D...--G........R.K......R.....N.......     330    299     21      7      3      0      0      0    330    233  70% [L5F,T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
...I..--.....-..................YD..H.I....A.H....     326     38    257     30      0      1      0      0    326    264  80% [T20I,H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] Alpha+T20I
.........I...-................K.....H.............     307     22    223     48      5      7      0      2    307    210  68% [T95I,Y144-,E484K,D614G,P681H,D796H] B.1.1.318
......--.......R........S..R.......H..............     268     11    223     28      2      0      0      4    268    155  57% [S12F,H69-,V70-,W152R,R346S,L452R,D614G,Q677H,A899S] C.36
......--.....-..................YD.HH.I....A.H....     254     66    168     20      0      0      0      0    254     72  28% [H69-,V70-,Y144-,N501Y,A570D,D614G,Q677H,P681H,V687L,T716I,S982A,D1118H] B.1.1.7=Alpha
......--.....-............S.....YD..H.I....A.H....     253      0    253      0      0      0      0      0    253    220  86% [H69-,V70-,Y144-,N440S,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
..R.............--G.V......R.K......R.....N......L     249      0     14    206     29      0      0      0    249    102  40% [T19R,E156-,F157-,R158G,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] B.1.617.2=Delta+A222V
.....V--.....-................K....H..............     245      1    112    123      2      5      0      2    245    105  42% [Q52R,A67V,H69-,V70-,Y144-,E484K,D614G,Q677H,F888L] B.1.525=Eta
..R......I......--G........R.K......R.............     244     10    166     50      4      5      1      8    244    128  52% [T19R,T95I,E156-,F157-,R158G,L452R,T478K,D614G,P681R] 
.F......A................N....K.Y....V............     241      2    128     17     26     68      0      0    241     86  35% [L18F,D80A,D215G,L242-,A243-,L244-,K417N,E484K,N501Y,D614G,A701V] B.1.351=Beta
............................N.....................     239      0    161     78      0      0      0      0    239    113  47% [S477N,D614G] 
......--.....-..................YD..H......A.HS..L     232      0    232      0      0      0      0      0    232    189  81% [H69-,V70-,Y144-,Y449S,N501Y,A570D,D614G,P681H,S982A,D1118H,P1162S,V1264L] 
..R.............--G........R.K......R.............     219      0    155     39      3     22      0      0    219    143  65% [T19R,E156-,F157-,R158G,L452R,T478K,D614G,P681R] 
......--........................YD..H.I....A.H....     202      0    192      8      2      0      0      0    202    144  71% [H69-,V70-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] 
....S.--.....-..............N.K.....H.......IH....     198      0     24     11    154      9      0      0    198    148  74% [P26S,H69-,V70-,V126A,Y144-,L242-,A243-,L244-,H245Y,S477N,E484K,D614G,P681H,T1027I,D1118H] B.1.620
..R.............--G...L....R.K......R.....N.......     196     13    178      3      2      0      0      0    196    176  89% [T19R,E156-,F157-,R158G,P251L,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
F.R.........D...--G........R.K......R.....N.......     187     67     55     60      3      2      0      0    187    116  62% [L5F,T19R,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..............................K.....H.I...........     177      0    177      0      0      0      0      0    177    175  98% [R102G,E484K,S494P,D614G,P681H,T716I] B.1.575
F.....--.....-.................SYD..H.I....A.H....     172      0    170      2      0      0      0      0    172    126  73% [L5F,H69-,V70-,Y144-,F490S,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] Alpha+F490S
.F.NS......Y.......S..........K.Y.Y.........I..F..     168      0      2    166      0      0      0      0    168    122  72% [L18F,T20N,P26S,D138Y,R190S,E484K,N501Y,D614G,H655Y,T1027I,V1176F] P.1=Gamma
......--.I...-..................YD..H.I....A.H....     168      0    138     28      2      0      0      0    168    116  69% [H69-,V70-,T95I,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
F........I.............G....N........V............     164      0      0    163      0      0      1      0    164    125  76% [L5F,T95I,D253G,S477N,D614G,A701V] B.1.526=Iota
......--.....-.............M....YD..H.I....A.H....     164      0    163      1      0      0      0      0    164    144  87% [H69-,V70-,Y144-,L452M,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
.F....--.....-..................YD..H.I....A.H....     161      1    104     55      0      0      1      0    161     92  57% [L18F,H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
..R..V...I..D...--G........R.K......R.....N.......     152    151      1      0      0      0      0      0    152    128  84% [T19R,A67V,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R..............CG........R.K......R.....N.......     151      0      0    151      0      0      0      0    151    124  82% [T19R,F157C,R158G,L452R,T478K,D614G,P681R,D950N] 
..R........................R.K......R.....N.......     140      1     48     24     65      2      0      0    140    100  71% [T19R,L452R,T478K,D614G,P681R,D950N] 
..R......I..D...--G....G...R.K......R.....N.......     140    140      0      0      0      0      0      0    140     87  62% [T19R,T95I,G142D,E156-,F157-,R158G,D253G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
......--.....-..................YD..H.I.Y..A.H....     136      0    127      9      0      0      0      0    136    127  93% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,D936Y,S982A,D1118H] B.1.1.7=Alpha
......--.....-..................YD..H.I..F.A.H....     135      0    112     20      3      0      0      0    135     64  47% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S939F,S982A,D1118H] B.1.1.7=Alpha
..R.............--G........R.K......R.....N......L     132      0     14      7    111      0      0      0    132    108  81% [T19R,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N,V1264L] B.1.617.2=Delta
........A................N....K.Y....V............     132      1     65     11     20     32      0      3    132     49  37% [D80A,D215G,L242-,A243-,L244-,K417N,E484K,N501Y,D614G,A701V] B.1.351=Beta
......--....V-..................YD..H.I....A.H....     127     42     77      7      0      0      1      0    127     91  71% [H69-,V70-,G142V,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
......--.....-.................SYD..H.I....A.H....     125     19     70     35      1      0      0      0    125     85  68% [H69-,V70-,Y144-,F490S,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] Alpha+F490S
.FR......I..D...--G........R.K......R.....N.......     122    118      3      0      1      0      0      0    122     92  75% [L18F,T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
......--...Y.-..................YD..H.I....A.H....     119      2    113      3      0      1      0      0    119     72  60% [H69-,V70-,D138Y,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
......--.....-......V...........YD..H.I....A.H....     118      1     70     47      0      0      0      0    118     64  54% [H69-,V70-,Y144-,A222V,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
........G....-...S.........R........H..N..H.......     115      0      0    115      0      0      0      0    115     91  79% [D80G,Y144-,F157S,L452R,D614G,P681H,T859N,D950H] B.1.526.1
......--.....-..................YD..H.I....A.HS...     115      1     99     13      2      0      0      0    115     57  49% [H69-,V70-,I100T,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H,P1162S] B.1.1.7=Alpha
......--.....-..................YD..H.I....A.H...L     110      3     98      7      1      1      0      0    110     58  52% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H,V1264L] B.1.1.7=Alpha
..R.........D...--G........R.K......R.............     108      0     69     35      4      0      0      0    108     66  61% [T19R,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R] 
...............C...........R......................     103      0      1     99      0      0      3      0    103     49  47% [S13I,W152C,L452R,D614G] B.1.429/7=Epsilon
.F.NS..............S.....T....K.Y.Y.........I..F..     102      0     20     61      0      0     21      0    102     35  34% [L18F,T20N,P26S,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] 
..R........YD...--G.V......R.K......R.....N.......      96     95      1      0      0      0      0      0     96     80  83% [T19R,D138Y,G142D,E156-,F157-,R158G,A222V,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta+A222V
............--.............R......................      95      0      2     93      0      0      0      0     95     41  43% [L141Y,G142-,V143-,Y144-,D215Y,L452R,D614G] A.2.5.2
....................................R.............      93      0      3      1     89      0      0      0     93     51  54% [N439K,D614G,P681R] 
FF.......I.............G....N.....................      82      0      0     82      0      0      0      0     82     62  75% [L5F,L18F,T95I,D253G,S477N,D614G,Q957R] B.1.526.2
..R......I..D...--G......N.R.K......R.....N.......      81      4     39     26     12      0      0      0     81     59  72% [T19R,T95I,G142D,E156-,F157-,R158G,W258L,K417N,L452R,T478K,D614G,P681R,D950N] B.1.617.2=AY.1
FF.NS......Y.......S.....T....K.Y.Y.........I..F..      81      0     12     38      0      0     31      0     81     61  75% [L5F,L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] P.1=Gamma
.........I..D..............R..Q.....R.............      78      4     63      0      9      2      0      0     78     52  66% [T95I,G142D,E154K,L452R,E484Q,D614G,P681R,Q1071H] B.1.617.1=Kappa
..R.........D...--G.V..A...R.K......R.....N.......      77      0     74      0      3      0      0      0     77     65  84% [T19R,G142D,E156-,F157-,R158G,A222V,D253A,L452R,T478K,D614G,P681R,D950N,D979E] B.1.617.2=Delta+A222V
.....S--.....-..................YD..H.I....A.H....      77     11     50     14      0      1      1      0     77     34  44% [A67S,H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
......--.....-..................YD..R.I....A.H....      75      0     67      7      0      1      0      0     75     53  70% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681R,T716I,S982A,D1118H] 
..R......I..D...--G..N.....R.K......R.....N.......      73     73      0      0      0      0      0      0     73     57  78% [T19R,T95I,G142D,E156-,F157-,R158G,T250N,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
......--.....-..............I...YD..H.I....A.H....      72      0     69      3      0      0      0      0     72     62  86% [H69-,V70-,Y144-,Y449H,S477I,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
..R......I..D...--G........R.K.....HR.....N.......      71     33     30      4      4      0      0      0     71     54  76% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,Q677H,P681R,D950N] B.1.617.2=Delta
.....V--.....-..................YD..H.I....A.H....      69      8     55      5      1      0      0      0     69     43  62% [A67V,H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
......--.....-..................YD..H.I....A.H.F..      68      6     27     34      1      0      0      0     68     52  76% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H,V1176F] B.1.1.7=Alpha
......--.....-.................LYD..H.I....A.H....      67     45     15      5      2      0      0      0     67     55  82% [H69-,V70-,Y144-,F490L,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] 
......--.....-..................YD....I....A.H....      67      0     61      6      0      0      0      0     67     49  73% [H69-,V70-,Y144-,N501Y,A570D,D614G,T716I,S982A,D1118H] 
.....V--..F..-..................YD..H.I.Y..A.H....      66      0     65      0      1      0      0      0     66     65  98% [A67V,H69-,V70-,S98F,Y144-,N501Y,A570D,D614G,P681H,T716I,D936Y,S982A,D1118H] B.1.1.7=Alpha
F.R.............--G........R.K......R.....N.......      65      0     29     30      4      2      0      0     65     41  63% [L5F,T19R,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.S....I..D...--G........R.K......R.....N.......      65     65      0      0      0      0      0      0     65     46  70% [T19R,P26S,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
.R.......I........S.......K.........H.......I.....      63      0      6     57      0      0      0      0     63     49  77% [L18R,T95I,R158S,N440K,D614G,P681H,A688V,S735A,T1027I] 
......--.....-H.................YD..H.I....A.H....      63      0     63      0      0      0      0      0     63     47  74% [H69-,V70-,Y144-,Y145H,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
..R.........D...--G.V......R.K......R.....N.....N.      61     10      1     50      0      0      0      0     61     57  93% [T19R,G142D,E156-,F157-,R158G,A222V,L452R,T478K,D614G,P681R,D950N,K1191N] B.1.617.2=Delta+A222V
.R.......I........S.................H.......I.....      61      0      0     61      0      0      0      0     61     31  50% [L18R,T95I,R158S,D614G,P681H,A688V,S735A,T1027I] 
..R.............--G.V......R.K......R.............      60      0     20     12     27      1      0      0     60     35  58% [T19R,E156-,F157-,R158G,A222V,L452R,T478K,D614G,P681R] 
.F.NS.--...Y.......S.....T....K.Y.Y.........I..F..      60      0      0      0      0      0     60      0     60     56  93% [L18F,T20N,P26S,H69-,V70-,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] P.1=Gamma
..R.........D...--G.V.L....R.K......R.....N.......      59      1     56      0      2      0      0      0     59     32  54% [T19R,G142D,E156-,F157-,R158G,A222V,P251L,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta+A222V
......--.....-..................YDY.H.I....A.H....      58      3     48      2      5      0      0      0     58     30  51% [H69-,V70-,Y144-,T284I,N501Y,A570D,D614G,H655Y,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
..R.........D...--G.V......R.K......R.....N...S...      56     54      0      2      0      0      0      0     56     45  80% [T19R,G142D,E156-,F157-,R158G,A222V,L452R,T478K,D614G,P681R,D950N,P1162S] B.1.617.2=Delta+A222V
..R......I..D...--G........R.K......R...H.N.......      55     40      1     14      0      0      0      0     55     42  76% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D936H,D950N] B.1.617.2=Delta
..R.........D...--G.VS.....R.K......R.....N.......      54      3     16      4      1     25      0      5     54     26  48% [T19R,G142D,E156-,F157-,R158G,A222V,T250S,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta+A222V
..R.........D...--G..I.....R.K......R.....N.......      54      2     41      6      3      0      0      2     54     37  68% [T19R,T29A,G142D,E156-,F157-,R158G,T250I,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
................................YD..H.I....A.H....      54      0     32     21      0      0      1      0     54     38  70% [N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] 
..I...--.....-..................YD..H.I....A.H....      54      0     45      7      2      0      0      0     54     33  61% [T19I,H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
......--.....-.............R....YD..H.I....A.H....      54     53      0      1      0      0      0      0     54     38  70% [T22I,H69-,V70-,Y144-,L452R,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
..R.........D..L--G........R.K......R.....N.......      53      1     46      6      0      0      0      0     53     48  90% [T19R,G142D,W152L,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N,L1141W] B.1.617.2=Delta
F.....--.....-..................YD..H.I....A.Y....      53      0     39     14      0      0      0      0     53     43  81% [L5F,H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118Y] 
......--.....-L.................YD..H.I....A.H....      51     39     12      0      0      0      0      0     51     43  84% [H69-,V70-,Y144-,Y145L,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
....S.--.....-..................YD..H.I....A.H....      51      2     39      9      1      0      0      0     51     23  45% [P26S,H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
......--.....-................Q.YD..H.I....A.H....      50      0     41      8      1      0      0      0     50     33  66% [H69-,V70-,Y144-,E484Q,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] 
..R...--........--G........R.K......R.....N.......      50      9     24     15      1      1      0      0     50     37  74% [T19R,H69-,V70-,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] 
..R..S...I..D...--G........R.K......R.....N.......      50     46      4      0      0      0      0      0     50     41  82% [T19R,A67S,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
................................Y.................      49      0     47      1      1      0      0      0     49     43  87% [N501Y,D614G] 
.FR......I..D...--G........R.K......R....FN.......      49     49      0      0      0      0      0      0     49     35  71% [L18F,T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,S939F,D950N] B.1.617.2=Delta
......--Y....-..................YD..H.I....A.H....      48      0     24     23      1      0      0      0     48     32  66% [H69-,V70-,D80Y,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
....................V.............................      47      0     47      0      0      0      0      0     47     22  46% [A222V,D614G] GV-clade
..R......I......--G........R.K.....HR.....N.......      47      0     45      2      0      0      0      0     47     36  76% [T19R,T95I,E156-,F157-,R158G,L452R,T478K,D614G,Q677H,P681R,D950N] B.1.617.2=Delta
...S.................---...Q...S.......N..........      47      0      0     47      0      0      0      0     47     29  61% [T20S,G75V,T76I,R246N,S247-,Y248-,L249-,T250-,P251-,G252-,D253-,L452Q,F490S,D614G,T859N] C.37=Lambda
................---...........K.............I.....      47      2     44      1      0      0      0      0     47     34  72% [E156-,F157-,R158-,F306L,E484K,S494P,D614G,E780A,D839V,T1027I] B.1.1.523
......--.....-...L..............YD..H.I....A.H....      47      0      0     47      0      0      0      0     47     31  65% [H69-,V70-,Y144-,F157L,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
.....D--.....-.................SYD..H.I....A.H....      47      0      0     47      0      0      0      0     47     43  91% [A67D,H69-,V70-,Y144-,F490S,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] Alpha+F490S
.F.NS......Y.......S.....T....K.Y.Y.....Y...I..F..      46      0      6     40      0      0      0      0     46     36  78% [L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,D936Y,T1027I,V1176F] P.1=Gamma
..R......I..D...--G........R.K......R.....N....F..      45     43      0      0      2      0      0      0     45     39  86% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N,V1176F] B.1.617.2=Delta
......--.....-..................YD.RH.I....A.H....      45      0     43      0      2      0      0      0     45     27  60% [H69-,V70-,Y144-,N501Y,A520S,A570D,D614G,Q677R,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
..R......I..D...--G........R.K......R.I...N.......      44     44      0      0      0      0      0      0     44     36  81% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,T716I,D950N] B.1.617.2=Delta
..R.............--G..I.....R.K......R.....N.......      42      2     33      3      3      1      0      0     42     26  61% [T19R,T29A,E156-,F157-,R158G,T250I,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........D..............R.K......R.....N.......      41      0      6      2     33      0      0      0     41     30  73% [T19R,G142D,L452R,T478K,D614G,P681R,D950N] 
..R......I.................R.K......R.....N.......      41      0     10     21     10      0      0      0     41     13  31% [T19R,T95I,L452R,T478K,D614G,P681R,D950N] 
F.R.........D...--G.V......R.K......R.....N.......      41     24      4      9      4      0      0      0     41     36  87% [L5F,T19R,G142D,E156-,F157-,R158G,A222V,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta+A222V
......--.....-..................YD..HSI....A.H....      41     16     17      8      0      0      0      0     41     32  78% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,A701S,T716I,S982A,D1118H] B.1.1.7=Alpha
..R.............--G.VS.....R.K......R.....N.......      40      0      4      0      0     35      0      1     40     28  70% [T19R,E156-,F157-,R158G,A222V,T250S,L452R,T478K,D614G,P681R,L752X,D950N] B.1.617.2=Delta+A222V
..R......I..D...--G........R.K......R.....N...L...      40     35      0      5      0      0      0      0     40     20  50% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N,P1162L] B.1.617.2=Delta
.F.NS......Y.-.....S.....T....K.Y.Y.........I..F..      39      0      4     14      0      0     21      0     39     20  51% [L18F,T20N,P26S,D138Y,Y144-,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] P.1=Gamma
...I......................K...K.........NF..I.....      39      0      0      0     39      0      0      0     39     38  97% [T20I,I210T,N440K,E484K,D614G,D936N,S939F,T1027I] 
..R.............--G..........K......R.....N.......      38      0     36      2      0      0      0      0     38     38 100% [T19R,E156-,F157-,R158G,T478K,D614G,P681R,D950N] 
..R......I..D...--G........R.K....Y.R.....N.......      38     23      1     13      1      0      0      0     38     27  71% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,H655Y,P681R,D950N] B.1.617.2=Delta
.....V--.....-...........R....K.YD..H.I....A.H..N.      38      0      0     38      0      0      0      0     38     34  89% [A67V,H69-,V70-,Y144-,K417R,E484K,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H,K1191N] Alpha+E484K
..R...............G........R.K......R.....N.......      37      0      0     37      0      0      0      0     37     31  83% [T19R,R158G,L452R,T478K,D614G,P681R,D950N] 
..R.........D...--G..........K......R.....N.......      37      0      3     34      0      0      0      0     37     26  70% [T19R,G142D,E156-,F157-,R158G,T478K,D614G,P681R,D950N] 
...............L..............K...................      36      0      0      1     35      0      0      0     36     29  80% [W152L,E484K,D614G,G769V] R.1
..R.........D...--G........R.KQ.....R.....N.......      35      4      0     28      2      1      0      0     35     22  62% [T19R,K77T,G142D,E156-,F157-,R158G,L452R,T478K,E484Q,D614G,P681R,D950N] B.1.617.2=Delta
..R......I..D...--G........R.K......R...N.N.......      35     35      0      0      0      0      0      0     35     31  88% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D936N,D950N] B.1.617.2=Delta
..R......I......--G......N.R.K......R.....N.......      35      1     30      3      1      0      0      0     35     17  48% [T19R,T95I,E156-,F157-,R158G,W258L,K417N,L452R,T478K,D614G,P681R,D950N] B.1.617.2=AY.1
......--...H.-.................SYD..H.I....A.H....      35      0      2      0     23     10      0      0     35     32  91% [H69-,V70-,D138H,Y144-,F490S,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] Alpha+F490S
..R..............CG........R.K......R.............      34      0      0     34      0      0      0      0     34     28  82% [T19R,F157C,R158G,L452R,T478K,D614G,P681R] 
..R.......F.D...--G........R.K......R.....N.......      34     29      2      2      1      0      0      0     34     24  70% [T19R,S98F,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R....F........--G.V....N.R.K......R.....N.......      34      0      0     34      0      0      0      0     34     27  79% [T19R,V70F,E156-,F157-,R158G,A222V,K417N,L452R,T478K,D614G,P681R,D950N] B.1.617.2=AY.2
..R......I..D...--G........R.K......R.....N......L      34     33      1      0      0      0      0      0     34     21  61% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N,V1264L] B.1.617.2=Delta
......--.......R........S..RN......H..............      34      0     24     10      0      0      0      0     34     16  47% [S12F,H69-,V70-,W152R,R346S,L452R,S477N,D614G,Q677H,A845S,A899S] C.36
......--.....-.........G........YD..H.I....A.H....      34      1     25      8      0      0      0      0     34     23  67% [H69-,V70-,Y144-,D253G,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
..R.........D...--G.V......R.K......R.............      33      0     27      1      5      0      0      0     33     13  39% [T19R,G142D,E156-,F157-,R158G,A222V,L452R,T478K,D614G,P681R] 
..R......I..D...--G........R.K......R..I..N.......      32     30      0      2      0      0      0      0     32     28  87% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,T859I,D950N] B.1.617.2=Delta
.........I...SN.........KN....K.Y...H.....N.......      32     13      1     16      1      0      1      0     32     25  78% [T95I,Y144S,Y145N,R346K,K417N,E484K,N501Y,D614G,P681H,D950N] 
.F..S......Y.......S.....T....K.Y.Y.........I..F..      32      0      0     12      0      0     20      0     32     20  62% [L18F,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] 
............D..............R..Q.....R.............      31      2      0      1      3      1      0     24     31     20  64% [G142D,E154K,L452R,E484Q,D614G,P681R,Q1071H,H1101Y] B.1.617.1=Kappa
..R...--.....-.............R.K......R.....N.......      31      1     18     12      0      0      0      0     31     18  58% [T19R,H69-,V70-,Y144-,L452R,T478K,D614G,P681R,D950N] 
..R......I..D..............R.K......R.....N.......      31      0      1     17     13      0      0      0     31     10  32% [T19R,T95I,G142D,L452R,T478K,D614G,P681R,D950N] 
......--.....-..................YD..H.I....A.HL...      31      2     20      9      0      0      0      0     31     27  87% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H,P1162L] B.1.1.7=Alpha
.R.......I........S...........Q.....H.......I.....      30      0      0     30      0      0      0      0     30     22  73% [L18R,T95I,R158S,E484Q,D614G,P681H,A688V,S735A,T1027I] 
....H.--.....-..................YD..H.I....A.H....      30      1      1     28      0      0      0      0     30     13  43% [P26H,H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,L938F,S982A,D1118H] B.1.1.7=Alpha
..R......I..D...--G........RIK......R.....N.......      29     21      0      8      0      0      0      0     29     24  82% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,S477I,T478K,D614G,P681R,D950N] B.1.617.2=Delta
......--.....-..................YD..H.I....A.Y....      29      0     20      9      0      0      0      0     29     17  58% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118Y] 
.F.NS......Y.......S.....T....K.Y.Y.R.......I..F..      28      0      0      2      0      0     26      0     28     23  82% [L18F,T20N,P26S,D138Y,R190S,K417T,T470N,E484K,N501Y,D614G,H655Y,P681R,T1027I,V1176F,C1235F] P.1=Gamma
...........................R.......H..............      27      0     26      0      1      0      0      0     27     13  48% [S12F,L452R,A520S,D614G,Q677H,S689I] 
......--.....-..................YD..H.I.H..A.H....      27     10     14      2      1      0      0      0     27     17  62% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,D936H,S982A,D1118H] B.1.1.7=Alpha
......--.....-..................YD..H.I....A.HQ...      27      0     27      0      0      0      0      0     27     27 100% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H,P1162Q,Q1208H] B.1.1.7=Alpha
..R.............--G.V..A...R.K......R.....N.......      26      1     24      0      1      0      0      0     26     23  88% [T19R,E156-,F157-,R158G,A222V,D253A,L452R,T478K,D614G,P681R,D950N,D979E] B.1.617.2=Delta+A222V
..R..V......D...--G.V......R.K......R.....N.......      26      1     25      0      0      0      0      0     26     26 100% [T19R,A67V,G142D,E156-,F157-,R158G,A222V,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta+A222V
..R......I..D...--G........R.K......R.............      25      0     19      3      1      0      0      2     25     17  68% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R] 
..R..S......D...--G........R.K......R.....N.......      25      1     21      2      0      1      0      0     25     21  84% [T19R,A67S,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R......I..D...--G........R.K......R...Y.N.......      25     22      3      0      0      0      0      0     25     19  76% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D936Y,D950N] B.1.617.2=Delta
F........I...SN.........K.....K.Y...H.....N.......      25      0      1      1      0      0     23      0     25     25 100% [L5F,T95I,Y144S,Y145N,R346K,E484K,N501Y,D614G,P681H,D950N] 
.F.NS......Y.............T....K.Y.Y.........I..F..      25      0      5     15      0      0      5      0     25     17  68% [L18F,T20N,P26S,D138Y,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] 
......--.....F..................YD..H.I....A.H....      25      0     17      7      1      0      0      0     25     11  44% [H69-,V70-,V143-,Y144F,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] 
......-F.....-..................YD..H.I....A.H....      25      7     10      7      1      0      0      0     25     20  80% [H69-,V70F,S71-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] 
..R....I....D...--G........R.K......R.....N.......      24      0      0     24      0      0      0      0     24     11  45% [T19R,V70I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] 
.F...--.......................KST......N..........      24      0      8     16      0      0      0      0     24     24 100% [L18F,A67-,I68-,H69-,G257S,E484K,F490S,N501T,D614G,T859N] 
F.....--...H.-..................YD..H.I....A.H....      24      0     24      0      0      0      0      0     24     19  79% [L5F,H69-,V70-,D138H,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
......--.....-..............R...YD..H.I....A.H....      24      0     22      2      0      0      0      0     24     17  70% [H69-,V70-,Y144-,S477R,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
......--.....-..V...............YD..H.I....A.H....      24      0     24      0      0      0      0      0     24     21  87% [H69-,V70-,Y144-,E156V,N501Y,A570D,D614G,S680F,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
......--.....-..................YD..H.I......H....      23      3     15      4      1      0      0      0     23     15  65% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,D1118H] 
..R.............--G........R.K..Y...R.....N.......      23      0     23      0      0      0      0      0     23     21  91% [T19R,E156-,F157-,R158G,L452R,T478K,N501Y,D614G,P681R,D950N] B.1.617.2=Delta
..R......I..D...--G........R.K......R.....N.I.....      23     23      0      0      0      0      0      0     23     13  56% [T19R,T95I,G142D,E156-,F157-,R158G,L216F,L452R,T478K,D614G,P681R,D950N,T1027I,G1124V] B.1.617.2=Delta
.F.NS......Y.......S.....T....K.Y.YH........I..F..      23      0      4     10      0      0      9      0     23     15  65% [L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,Q677H,T1027I,V1176F] P.1=Gamma
......--.....-........T.........YD..H.I....A.H....      23      0     23      0      0      0      0      0     23     23 100% [H69-,V70-,Y144-,P251T,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
..G......I..D...--G........R.K......R.....N.......      22     21      1      0      0      0      0      0     22     15  68% [T19G,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] 
......--.....-..................YD..H.V....A.H....      22      1     19      2      0      0      0      0     22     10  45% [H69-,V70-,Y144-,N501Y,A570D,D614G,T632I,P681H,T716V,G932V,S982A,D1118H] 
......--.....-...................D..H.I....A.H....      21      0     14      5      1      0      1      0     21      9  42% [H69-,V70-,Y144-,A570D,D614G,P681H,T716I,S982A,D1118H] 
..R.........D...--G.V......R.K......RS....N.......      21      0      1      0     20      0      0      0     21     13  61% [T19R,G142D,E156-,F157-,R158G,A222V,L452R,T478K,D614G,P681R,A701S,D950N,A1078S] B.1.617.2=Delta+A222V
..R...Y..I..D...--G........R.K......R.....N.......      21     20      1      0      0      0      0      0     21     19  90% [T19R,H69Y,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
F.R......I.HD...--G........R.K......R.....N.......      21     21      0      0      0      0      0      0     21     19  90% [L5F,T19R,T95I,D138H,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
.F.NSS.....Y.......S.....T....K.Y.Y.........I..F..      21      0      2     12      0      0      7      0     21     20  95% [L18F,T20N,P26S,A67S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] P.1=Gamma
...............C...........R........H.............      21      0      0     21      0      0      0      0     21     13  61% [S13I,W152C,W258L,L452R,D614G,P681H] B.1.429/7=Epsilon
......--.....-...............I..YD..H.I....A.H....      21      0     19      2      0      0      0      0     21      8  38% [H69-,V70-,Y144-,T478I,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
.............-..................YD..H.I....A.H....      20      0     17      1      1      1      0      0     20     16  80% [Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] 
............D..............R.K......H.............      20      0     20      0      0      0      0      0     20      9  45% [G142D,K182R,L452R,T478K,D614G,P681H,D796Y,C1235F] 
..R.........D...--G........R.K....Y.R.....N.......      20      4     15      1      0      0      0      0     20     12  60% [T19R,G142D,E156-,F157-,R158G,L452R,T478K,D614G,H655Y,P681R,P792S,D950N] B.1.617.2=Delta
...........---................K...................      20      0     19      0      1      0      0      0     20      9  45% [P9L,C136-,N137-,D138-,P139-,F140-,L141-,G142-,V143-,Y144-,D215G,H245P,E484K,D614G,N679K,E780K] 
......Y.G....-...S.........R...........N..H.......      20      0      0     20      0      0      0      0     20     14  70% [P25T,H69Y,D80G,Y144-,F157S,L452R,D614G,T791I,T859N,D950H] B.1.526.1
..R......I..D...--G........R.K......R.....N.....N.      19     18      0      1      0      0      0      0     19     12  63% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N,K1191N] B.1.617.2=Delta
..R.........D...--G.V......R.K.....HR.....N.......      19      2     12      2      2      0      0      1     19      7  36% [T19R,R21T,G142D,E156-,F157-,R158G,A222V,L452R,T478K,D614G,Q677H,P681R,D950N] B.1.617.2=Delta+A222V
F.R.........D...--G........R.K......R.....N......L      19      0      0      1     18      0      0      0     19     17  89% [L5F,T19R,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N,V1264L] B.1.617.2=Delta
..R...--...................R.K......R.....N.......      19      0     16      3      0      0      0      0     19      9  47% [T19R,H69-,V70-,L452R,T478K,D614G,P681R,D950N] 
.........I...-................K.T...H.............      19      0     17      1      0      1      0      0     19     17  89% [T95I,Y144-,E484K,N501T,D614G,P681H,D796H] B.1.1.318
..R...............................................      18      0     18      0      0      0      0      0     18     17  94% [T19R,D614G] 
..R......I.......CG........R.K......R.....N.......      18      0      0     18      0      0      0      0     18     16  88% [T19R,T95I,F157C,R158G,L452R,T478K,D614G,P681R,D950N] 
..R.........D...--G........R.K......R.....N.....N.      18      3      5     10      0      0      0      0     18      9  50% [T19R,S112L,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N,K1191N] B.1.617.2=Delta
..R......I..D...--G........R.K......R....FN.......      18     15      0      1      2      0      0      0     18     11  61% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,S939F,D950N] B.1.617.2=Delta
..R......I..D-..--G........R.K......R.....N.......      18     15      3      0      0      0      0      0     18     10  55% [T19R,T95I,G142D,Y144-,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R....G.I..D...--G........R.K......R.....N.......      18     18      0      0      0      0      0      0     18     18 100% [T19R,V70G,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] 
........YI...-................K.....H.............      18      0      0      0      0     18      0      0     18     18 100% [D80Y,T95I,Y144-,W258L,E484K,D614G,P681H,D796H] B.1.1.318
.R....--.I........S...........K...................      18      0      0     18      0      0      0      0     18      7  38% [L18R,H69-,V70-,T95I,R158S,E484K,D614G,A688V,N764K,E1258D] 
..R.........D...--G........R.K...S..R.....N.......      17      2     14      0      1      0      0      0     17     13  76% [T19R,G142D,E156-,F157-,R158G,L452R,T478K,A570S,D614G,P681R,D950N] B.1.617.2=Delta
..R.........D...--G........R.K......R...Y.N.......      17      3      2     10      2      0      0      0     17      9  52% [T19R,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D936Y,D950N] B.1.617.2=Delta
F........I...-.........G......K......V............      17      0      3      5      0      0      9      0     17     14  82% [L5F,T95I,Y144-,D253G,E484K,D614G,A701V] B.1.526=Iota
.F.NS......Y.......S.....T....K.Y.Y.........I..F.L      17      0      1     11      0      0      5      0     17     10  58% [L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F,V1264L] P.1=Gamma
......--.....-..........K.......YD..H.I....A.H....      17      0     17      0      0      0      0      0     17     14  82% [H69-,V70-,Y144-,R346K,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
..R.....Y...D...--G........R.K......R.....N.......      16      5      3      8      0      0      0      0     16     10  62% [T19R,D80Y,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R......I..D...--G.V......R.K......R.....N.......      16     10      3      2      1      0      0      0     16      9  56% [T19R,T95I,G142D,E156-,F157-,R158G,A222V,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta+A222V
..R.........D...--G........RGK......R.....N.......      16      0      0     16      0      0      0      0     16     10  62% [T19R,S112L,G142D,E156-,F157-,R158G,L452R,S477G,T478K,D614G,P681R,D950N] B.1.617.2=Delta
.................S..........N.K...Y.H...H.........      16      0      0     16      0      0      0      0     16     14  87% [T29I,F32L,M153T,F157S,G252V,S477N,E484K,D614G,H655Y,P681H,D936H,D1260H] 
.........I...SN.........K.....K.Y...H.............      16      0      1     13      0      0      2      0     16      9  56% [T95I,Y144S,Y145N,R346K,E484K,N501Y,D614G,P681H] 
..............................K.........NF..I.....      16      0     15      0      1      0      0      0     16     15  93% [I210T,E484K,D614G,D936N,S939F,T1027I] 
F.....--.I...-..................YD..H.I....A.H....      16     13      3      0      0      0      0      0     16      9  56% [L5F,H69-,V70-,T95I,Y144-,N501Y,A570D,V595I,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
......--...Y.-..................YD..HVI....A.H....      16      0     16      0      0      0      0      0     16      8  50% [H69-,V70-,D138Y,Y144-,N501Y,A570D,D614G,P681H,A701V,T716I,S982A,D1118H] B.1.1.7=Alpha
..R.........D...--G........R.K......R.I...N.......      15      6      3      3      3      0      0      0     15     13  86% [T19R,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,T716I,D950N] B.1.617.2=Delta
.F.NS......Y.......S.....T....K.Y.Y.........I..FN.      15      0     13      1      0      0      1      0     15     12  80% [L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F,K1191N] P.1=Gamma
...........Y........................R.............      15      0      1      0      1     13      0      0     15      7  46% [D138Y,N450K,D614G,P681R] 
......--...H....................YD..H.I....A.H....      15      0     15      0      0      0      0      0     15     11  73% [H69-,V70-,D138H,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] 
F.....--.....-..................YD..H.I....A.H..N.      15      0      1     14      0      0      0      0     15      9  60% [L5F,H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H,K1191N] B.1.1.7=Alpha
......--.....-......S...........YD..H.I....A.H....      15      0     10      5      0      0      0      0     15     15 100% [H69-,V70-,Y144-,A222S,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
.....V--.....-...........R....K.YD..HVI....A.H..N.      15      0      0     15      0      0      0      0     15     14  93% [A67V,H69-,V70-,Y144-,K417R,E484K,N501Y,A570D,D614G,P681H,A701V,T716I,S982A,D1118H,K1191N] Alpha+E484K
..R.......................................N.......      14      0     14      0      0      0      0      0     14     11  78% [T19R,D614G,D950N] 
...........................R.K....................      14      0     14      0      0      0      0      0     14     14 100% [L452R,T478K,D614G] 
....................V........K......H.............      14      0      0     14      0      0      0      0     14     10  71% [A222V,T478K,D614G,P681H,T732A] B.1.1.519
..R......I...-..--G........R.K......R.....N.......      14      0     14      0      0      0      0      0     14     13  92% [T19R,T95I,Y144-,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R......IF.D...--G........R.K......R.....N.......      14     14      0      0      0      0      0      0     14      7  50% [T19R,T95I,S98F,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
........GI..D-................K.....H.............      14     14      0      0      0      0      0      0     14      9  64% [D80G,T95I,G142D,Y144-,N439K,E484K,D614G,P681H,I1130V,D1139H] 
............--.R...........R......................      14      0      0     14      0      0      0      0     14      3  21% [L141Y,G142-,V143-,Y144-,W152R,D215Y,T240I,A263S,L452R,D614G] A.2.5.2
........G....-...S.........R........Y..N..H.......      14      0      0     14      0      0      0      0     14     14 100% [D80G,Y144-,F157S,L452R,D614G,P681Y,T859N,D950H] B.1.526.1
......................................I...........      14      0     12      1      0      1      0      0     14     11  78% [Q414K,N450K,D614G,T716I] B.1.214.2
......--.....-..................YD..H.I....A......      14      0      6      5      3      0      0      0     14     10  71% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A] 
F.....--.....-..................YDY.H.I....A.H....      14      0     13      1      0      0      0      0     14     13  92% [L5F,H69-,V70-,Y144-,N501Y,A570D,D614G,H655Y,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
......--.....-.L................YD..H.I....A.H....      14      6      4      3      1      0      0      0     14      6  42% [H69-,V70-,Y144-,W152L,N501Y,A570D,D614G,P681H,T716I,P809S,S982A,D1118H] 
......--.....-..................Y...H.I....A.H....      14      0      7      6      1      0      0      0     14      8  57% [H69-,V70-,Y144-,N501Y,D614G,P681H,T716I,S982A,D1118H] 
.F....--.....-..................YD..H.I....A.H..N.      14      0      0     14      0      0      0      0     14     14 100% [L18F,H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H,K1191N] B.1.1.7=Alpha
......--.....-.R.......G........YD..H.I....A.H....      14      0     14      0      0      0      0      0     14     13  92% [H69-,V70-,Y144-,W152R,D253G,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] Alpha+W152R
......--.I...-................K.YD..H.I....A.H....      14      1     13      0      0      0      0      0     14     14 100% [H69-,V70-,T95I,Y144-,E484K,N501Y,A570D,D614G,P681H,T716I,L938F,S982A,D1118H] Alpha+E484K
......--..F.....................YD..H.I....A.H....      14      0     14      0      0      0      0      0     14     10  71% [H69-,V70-,S98F,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] 
......--..........................................      13      0     13      0      0      0      0      0     13      8  61% [I68K,H69-,V70-,S71-,G72-,T73-,N74-,G75-,T76-,K77-,D614G] 
..RI.....I..D...--G........R.K......R.....N.......      13     12      1      0      0      0      0      0     13     11  84% [T19R,T20I,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........D...--G.V......R.K......R.....N.I.....      13     11      0      0      2      0      0      0     13     13 100% [T19R,G142D,E156-,F157-,R158G,A222V,L452R,T478K,D614G,P681R,D950N,T1027I] B.1.617.2=Delta+A222V
..R.............--G.V.L....R.K......R.....N.......      13      0     12      0      1      0      0      0     13      7  53% [T19R,E156-,F157-,R158G,A222V,P251L,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta+A222V
..R.....YI..D...--G........R.K......R.....N.......      13      7      0      6      0      0      0      0     13      8  61% [T19R,D80Y,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
.F.NS......Y--.....S.....T....K.Y.Y.........I..F..      13      0      2      4      0      0      7      0     13      3  23% [L18F,T20N,P26S,D138Y,L141-,G142-,V143-,Y144-,R190S,K417T,E484K,N501Y,D614G,H655Y,A845S,T1027I,V1176F] P.1=Gamma
...........................Q...S.......N..........      13      0      5      5      0      0      3      0     13      6  46% [G75V,T76I,L452Q,F490S,D614G,T859N] 
F....................---...Q...S.......N..........      13      0      0      0      0      0     13      0     13      8  61% [L5F,G75V,T76I,R246N,S247-,Y248-,L249-,T250-,P251-,G252-,D253-,L452Q,F490S,D614G,T859N] C.37=Lambda
..R........................R.K..Y...R.....N.......      12      0     11      0      1      0      0      0     12      9  75% [T19R,L452R,T478K,N501Y,D614G,P681R,D950N] 
..R........Y....--G........R.K......R.....N.......      12      0      1      7      1      0      3      0     12     10  83% [T19R,D138Y,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R......I..D...--G........R.K..Y...R.....N.......      12     10      0      2      0      0      0      0     12      8  66% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,N501Y,D614G,P681R,D950N] B.1.617.2=Delta
.F...V..A................N....K.Y....V............      12      0      6      2      4      0      0      0     12     11  91% [L18F,A67V,D80A,D215G,L242-,A243-,L244-,K417N,E484K,N501Y,D614G,A701V] B.1.351=Beta
......--.......R........S..R.......H..........L...      12      0      0     12      0      0      0      0     12     11  91% [S12F,H69-,V70-,W152R,R346S,L452R,D614G,Q677H,A899S,P1162L] C.36
.R.......I........S.......KM........H.......I.....      12      0      1     10      0      0      1      0     12      2  16% [L18R,T95I,R158S,N440K,L452M,D614G,P681H,A688V,S735A,T1027I] 
......--G.FH.-..................YD..H.I....A.H....      12      0     12      0      0      0      0      0     12     11  91% [H69-,V70-,D80G,S98F,D138H,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
....L.--.....-..................YD..H.I....A.H....      12      0     11      0      0      0      1      0     12     11  91% [P26L,H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
..........................................N.......      11      0     11      0      0      0      0      0     11     11 100% [D614G,D950N] 
..........F.......................................      11      0     11      0      0      0      0      0     11      7  63% [S98F,D614G] 
.F..................V.............................      11      2      9      0      0      0      0      0     11      4  36% [L18F,A222V,D614G] GV-clade
...............................................F..      11      0      1      1      0      0      9      0     11      1   9% [E471X,V1176F] 
..R.................................R.....N.......      11      0     11      0      0      0      0      0     11      9  81% [T19R,D614G,P681R,D950N] 
..R........................R.K......R.............      11      0      3      3      1      4      0      0     11      5  45% [T19R,L452R,T478K,D614G,P681R] 
..R......I..D...--G........R.K......R...E.N.......      11     11      0      0      0      0      0      0     11      8  72% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D936E,D950N] B.1.617.2=Delta
F.R......I......--G........R.K......R.....N.......      11      2      4      3      2      0      0      0     11      5  45% [L5F,T19R,T95I,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R...--.....-..--G........R.K......R.....N.......      11      2      5      3      0      1      0      0     11      9  81% [T19R,H69-,V70-,Y144-,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] 
..R.........D...--G.S......R.K......R.....N.......      11      2      2      7      0      0      0      0     11      7  63% [T19R,G142D,E156-,F157-,R158G,A222S,L452R,T478K,D614G,E661D,P681R,D950N] 
..R.........D...--G........R.K.....HR.....N.......      11      0      2      6      3      0      0      0     11      9  81% [T19R,G142D,E156-,F157-,R158G,L452R,T478K,D614G,Q677H,P681R,D950N] B.1.617.2=Delta
..R.........D...--G........R.K......R.....N...L...      11     11      0      0      0      0      0      0     11      7  63% [T19R,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N,P1162L] B.1.617.2=Delta
F.R.........D...--G........R.KQ.....R.....N.......      11      0      0     11      0      0      0      0     11      7  63% [L5F,T19R,K77T,G142D,E156-,F157-,R158G,L452R,T478K,E484Q,D614G,P681R,D950N] B.1.617.2=Delta
.F......A................N....K.Y..R.V............      11      0      2      0      0      9      0      0     11      6  54% [L18F,D80A,D215G,L242-,A243-,L244-,K417N,E484K,N501Y,D614G,Q677R,A701V,L752X] B.1.351=Beta
.........I...T..........K.....K.Y...H.............      11      0      0     11      0      0      0      0     11      6  54% [T95I,Y144T,R346K,E484K,N501Y,D614G,P681H,E1258D] 
.........I.....L..............K...................      11      0      8      0      3      0      0      0     11      8  72% [T95I,W152L,E484K,D614G,G769V,A1020S] R.1
.F.NS..F...Y.......S.....T....K.Y.Y.........I..F..      11     10      0      0      0      0      1      0     11     10  90% [L18F,T20N,P26S,V70F,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] P.1=Gamma
.F.NS......Y.......S.....T..I.K.Y.Y.........I..F..      11      0      1     10      0      0      0      0     11     11 100% [L18F,T20N,P26S,D138Y,R190S,K417T,S477I,E484K,N501Y,D614G,H655Y,T1027I,V1176F] P.1=Gamma
.F........................K...K.........NF..I.....      11      0      0      0     11      0      0      0     11     11 100% [L18F,I210T,N440K,E484K,D614G,D936N,S939F,T1027I] 
......--........................YD..H.I......H....      11      0     11      0      0      0      0      0     11      9  81% [H69-,V70-,N501Y,A570D,D614G,P681H,T716I,D1118H] 
F.....--..FH.-..................YD..H.I....A.H....      11      0      1     10      0      0      0      0     11      7  63% [V3G,L5F,H69-,V70-,S98F,D138H,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
........Y.........................................      10      0     10      0      0      0      0      0     10      7  70% [D80Y,D614G] 
..............................K...................      10      0      7      3      0      0      0      0     10      6  60% [E484K,D614G] 
..R.............--G........R.KQ.....R.....N.......      10      0      1      8      1      0      0      0     10      5  50% [T19R,K77T,E156-,F157-,R158G,L452R,T478K,E484Q,D614G,P681R,D950N] B.1.617.2=Delta
..R......I......--G........R.K..Y...R.....N.......      10      0     10      0      0      0      0      0     10      3  30% [T19R,T95I,E156-,F157-,R158G,L452R,T478K,N501Y,D614G,P681R,D950N] B.1.617.2=Delta
..R.............--G........R.K......R............L      10      0      2      0      8      0      0      0     10      9  90% [T19R,E156-,F157-,R158G,L452R,T478K,D614G,P681R,V1264L] 
..R.............--G.VS.....R.K......R.............      10      0      0      0      0     10      0      0     10      4  40% [T19R,E156-,F157-,R158G,A222V,T250S,L452R,T478K,D614G,P681R] 
..R......I..D...--G........R.K......L.....N.......      10      9      1      0      0      0      0      0     10      7  70% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681L,D950N] 
..R...--.I..D...--G........R.K......R.....N.......      10      6      4      0      0      0      0      0     10      7  70% [T19R,H69-,V70-,T95I,G142D,E156-,F157-,R158G,L452R,T478K,D614G,P681R,D950N] 
..R......I..D...--G........R.K.L....R.....N.......      10     10      0      0      0      0      0      0     10      5  50% [T19R,T95I,G142D,E156-,F157-,R158G,L452R,T478K,F490L,D614G,P681R,A879S,D950N] B.1.617.2=Delta
F....V--.....-................K....H..............      10      0     10      0      0      0      0      0     10      6  60% [L5F,Q52R,A67V,H69-,V70-,A123V,Y144-,E484K,D614G,Q677H,F888L] B.1.525=Eta
FF......A................N....K.Y....V............      10      0      9      0      0      1      0      0     10      4  40% [L5F,L18F,D80A,D215G,L242-,A243-,L244-,K417N,E484K,N501Y,D614G,A701V] B.1.351=Beta
.........I..............K.....K.Y...H.....N.......      10      0      5      4      0      0      1      0     10      9  90% [T95I,R346K,E484K,N501Y,D614G,P681H,D950N] 
............--.............RN.....................      10      0      1      0      0      0      9      0     10      6  60% [L141Y,G142-,V143-,Y144-,D215Y,L452R,S477N,D614G] A.2.5.2
......--....--..................YD..H.I....A.H....      10      0      9      1      0      0      0      0     10      8  80% [H69-,V70-,L141-,G142-,V143-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
......--.....-..................YD..H.I....A.H..NL      10      0      0     10      0      0      0      0     10      6  60% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H,K1191N,V1264L] B.1.1.7=Alpha
......--.....-....S.............YD..H.I....A.H....      10      0      0      0     10      0      0      0     10     10 100% [H69-,V70-,Y144-,R158S,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha

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last modified: Wed Jul 14 06:34 2021



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