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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: Dec 6, 2023

Dates of current data

Delta and Omicron Variants
Global
Wuhan reference
Early 2021 Variants color key
Delta Variants color key
Delta Omicron Variants color key

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Evaluating 93732 sequences of length 1698
Sampled from 2023-10-07 to 2023-12-01.
Specified Date Range: ['2023-10-07', '2023-12-06']
Highest entropy sites for: Global
  Site Entropy
   455  0.7956
   157  0.7741
   452  0.7349
    52  0.7055
   478  0.5916
   456  0.5567
   146  0.5353
   252  0.4437
   445  0.4004
   490  0.3848
   180  0.3697
   213  0.3619
   554  0.3595
    83  0.3534
   183  0.3519
   368  0.3414
   346  0.3272
   521  0.3193
   158  0.3136
   245  0.3104
   212  0.3066
   681  0.3031
   481  0.2995
   484  0.2976
   356  0.2964
   450  0.2883
   264  0.2871
   621  0.2802
   704  0.2779
   939  0.2779
    69  0.2768
   211  0.2765
  1143  0.2761
   127  0.2756
   570  0.2754
   332  0.2753
   216  0.2743
   403  0.2740
    70  0.2701
    50  0.2671
    21  0.2626
   483  0.2397
   475  0.2298
   701  0.2246
    16  0.0063
   253  0.2193
   185  0.2154


Most highly correlated site-pairs for: Global
               cramerV  mutInfo
   157    452   0.8072   0.6016
   445    213   0.4844   0.3223
   213    368   0.6948   0.3175
   490    368   0.6949   0.3174
   445    368   0.6950   0.3171
   445    490   0.4936   0.3169
   183    368   0.6923   0.3159
   213    183   0.4398   0.3155
   490    183   0.4912   0.3142
   490    213   0.5031   0.3141
   445    183   0.4396   0.3137
   452    445   0.5339   0.3074
   157    445   0.6537   0.3057
   146    445   0.4332   0.3056
   146    213   0.4331   0.3047


   127    570   0.9974   0.2724
  1143    570   0.9972   0.2710
  1143    127   0.9969   0.2709
   445    570   0.9968   0.2689
   445    127   0.9961   0.2686
   452    570   0.9944   0.2654
   452    127   0.9939   0.2653
   570    332   0.9935   0.2689
   445    332   0.9935   0.2666
   127     50   0.9934   0.2606
   245    332   0.9933   0.2837
   127    332   0.9932   0.2688
   264    332   0.9927   0.2785
  1143    332   0.9925   0.2666
   445     50   0.9923   0.2578


Most common patterns for local area, where Local = Global
                                              1
       1111111222222223333444444444444555667791
12556782455888111145563456045555778889257280034
61029037678035123652342668350256581340140111493
VRSQHVVVHFREQNNLVLHGDAIRKLRVNLLFATNVEFPEAPPASSP  Global     UK  Eu-UK  NAmer   Asia Africa  SAmer  Ocean   Local  Exact  Pct [Context]
                                                  93732   7905  31139  37549  10348    209   1331   5251   67783 <----------- Totals
...H..A.Q...E...E..V...T.I.P..FL.K..AS....H....    9700    387   1686   2739   3829      0     28   1031    9700   4419  45% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..A.QL..E...E..V...T.I.P.R.L.K..AS....H....    9252    243   1109   7473    110      0     40    277    9252   5880  63% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,F157L,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L452R,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..A.Q...E...E..V...T.I.P...L.K..AS....H....    8161    800   2352   3612    828      2     80    487    8161   4291  52% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V...T.I.P..FLVK..AS....H....    3253    323   1254   1329     64      0    179    104    3253   1585  48% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,A475V,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V...T.I.P...L.R..AS....HV...    2508    178    541   1662     48      1     28     50    2508   1430  57% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,A701V,N764K,D796Y,Q954H,N969K] 
...H..A.Q...E...E..V...T.I.P..FL.K..AS....H.L..    2053    263   1134    567     40      0      6     43    2053   1023  49% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,S704L,N764K,D796Y,Q954H,N969K] 
......A.Q..VE...E..V...T.I.P...L.R..AS....H....    1970    193    355   1323     39      0     11     49    1970   1154  58% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,E180V,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q..VE...E..V...T.I.P.....R..AS....H....    1937    276    512    916    194      0      4     35    1937    318  16% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,E180V,Q183E,V213E,G252V,K304N,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
.TL.--.F.SG...-IGFN..DV.T.KHDWS..KK-K..KVSR..FL    1911     24   1287    469     52      0     28     51    1911   1330  69% [+16MPLF,T19I,R21T,L24-,P25-,P26-,A27S,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445H,G446S,N450D,L452W,L455S,N460K,S477N,T478K,N481K,V483-,E484K,F486P,Q498R,N501Y,Y505H,E554K,A570V,D614G,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L] 
......A.Q...E...E..V...T.I.P..FL.K..AS....H.L..    1593    119    405    739    157      0    142     31    1593    691  43% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,T573I,D614G,H655Y,N679K,P681H,S704L,N764K,D796Y,Q954H,N969K] 
.TL.--.F.SG...-IGFN..DV.T.KHDW...KK-K..KVSR..FL    1418     69    841    300    120      0      1     87    1418    766  54% [+16MPLF,T19I,R21T,L24-,P25-,P26-,A27S,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445H,G446S,N450D,L452W,N460K,S477N,T478K,N481K,V483-,E484K,F486P,Q498R,N501Y,Y505H,E554K,A570V,D614G,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L] 
......A.Q..VE...E..V...T.I.P.....R..AST...H....    1231    239    409    498     14      0      1     70    1231    606  49% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,E180V,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,P521T,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
.........L...D..G......T.....RFL.K..A.....H....    1093     94    428    427     71      0      2     71    1093    566  51% [T19I,L24-,P25-,P26-,A27S,G142D,K147E,W152R,F157L,N185D,I210V,V213G,G257S,G339H,R346T,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,K444T,G446S,L452R,L455F,F456L,N460K,S477N,T478K,E484A,F486S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,L858I,Q954H,N969K] 
......A.Q...E...E..V...T.I.P...L.K..AS....H....    1062     33    197    614     59      0    144     15    1062    544  51% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q..VE...E..V...T.I.P..FL.R..AS....H....    1051    143    161    665     38      0      5     39    1051    725  68% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,E180V,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..A.QL..E...E..V...T.I.P...L.K..AS....H....    1045    129    162    666     27      0      4     57    1045    661  63% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,F157L,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V...T.I.P.....R..AS....H....     848     72    371    337     54      0      0     14     848     99  11% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,Q613H,D614G,H655Y,N679K,P681H,A688V,N764K,D796Y,Q954H,N969K] 
......A.Q..VE...E..V...T.I.P.....R..ASS...H....     802    281    258    242      7      0      2     12     802    341  42% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,K147N,E180V,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,P521S,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...ED..E...G..T.I.P.....R..ASS...H....     733    101    436    157     13      2      1     23     733    400  54% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,N185D,V213E,D253G,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,P521S,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E...G..T.I.P.....R..ASS...H....     516     75    191    200     38      0      2     10     516    152  29% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,D253G,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,P521S,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V...T.I.P.....K..AS....H....     508     34    127    147    172      0      3     25     508     58  11% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,Y200C,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,T572I,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..A.KL..E...E..V...T.I.P.R.L.K..AS....H....     502      6     38    444      6      0      1      7     502    321  63% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146K,F157L,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L452R,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..A.K...E...E..V...T.I.P...L.K..AS....H....     473     68    120    229     45      0      1     10     473    181  38% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146K,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V...T.I.P..FL.K..AS....H....     468     53    147    190     12      0     29     37     468    157  33% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,V511I,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V...T.I.P...L.KK.AP....RV...     462     95    143    219      4      0      0      1     462    317  68% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478K,N481K,E484A,F486P,F490P,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681R,A701V,N764K,D796Y,Q954H,N969K] 
......A.Q...EI..E...G..T.I.P.....R..ASS...H....     447     83    143    182     30      1      1      7     447    191  42% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,N185I,F186-,V213E,D253G,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,P521S,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..A.QL..E...E..V...T.I.P..FL.K..AS....H....     430     12     93    124    145      0      1     55     430    245  56% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,F157L,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E...G..T.I.P.....K..ASS...H....     413     33     85    238     35      0      2     20     413    144  34% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,K182N,Q183E,V213E,D253G,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,P521S,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..A.Q...E...E..VG..T.I.P...L.K..AS....H....     403    110    135    133      7      0      4     14     403    211  52% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,D253G,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..A.K...E...E..V...T.I.P..FL.K..AS....H....     388     28     48    111    150      0      0     51     388    173  44% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146K,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
.........--....S.......S.....R...K..A.....H....     313      9     32      9     18      0      0    245     313    111  35% [T19I,P25S,G142D,Y144-,E156G,F157-,R158-,P209L,L212S,D215H,A222V,A243-,L244-,S256L,R346S,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,G446S,L452R,S477N,T478K,E484A,F486P,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N703I,N764K,D796Y,Q954H,N969K] 
......A.Q..VE...E..V...T.I.P.....R..AS.K..H....     253      3    211     35      3      1      0      0     253    158  62% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,E180V,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,E554K,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q..VE...E..V...T.I.P...L.R..AS.K..HV...     211     34     87     54     21      0      0     15     211    127  60% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,E180V,K182Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,E554K,D614G,H655Y,N679K,P681H,A701V,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V...T.I.P..FLVI..AS.K..H....     190    109     31     26      3      0      0     21     190     85  44% [T19I,L24-,P25-,P26-,A27S,F79S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,A475V,S477N,T478I,E484A,F486P,F490S,Q498R,N501Y,Y505H,E554K,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V...T.I.P...L.R..AS.K..HV...     176     15     84     59      5      0      0     13     176    104  59% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,E554K,D614G,H655Y,N679K,P681H,A701V,N764K,D796Y,Q954H,N969K] 
...H..A.Q...E...E..V...T.I.PD.FL.K..AS....H.L..     174      2      2    163      5      0      0      2     174    117  67% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N450D,L455F,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,S704L,N764K,D796Y,Q954H,N969K] 
...H..A.Q...E...E..V...T.I.P...L.R..AS....H....     155      6     86     53      5      0      1      4     155    104  67% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V...T.IKP.....K..AS....HV...     150     14    100     30      1      0      0      5     150     93  62% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,A344T,R346T,L368I,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478K,E484A,F486P,F490S,S494P,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,A701V,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V...T.I.P..FLVK..AS.K..H.L..     142      2     15     75      1      0     48      1     142     78  54% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,A475V,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,E554K,D614G,H655Y,N679K,P681H,S704L,N764K,D796Y,Q954H,N969K] 
...H..A.QL..E...E..V...T.I.P.R.L.K..AS....H.L..     142      0      4    136      2      0      0      0     142     68  47% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,F157L,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L452R,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,S704L,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V...T.IKP.....K..AS....H....     139     11      8     87     13      0      0     20     139     47  33% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,L513F,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V...T.I.P...L.K..KS....H....     138      1     53     57     27      0      0      0     138     60  43% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,L242I,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478K,E484K,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.K...E...E..V...T.I.P...L.R..AS....HV...     136     10     24     97      1      0      4      0     136     59  43% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146K,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,A701V,N764K,D796Y,Q954H,N969K] 
...H..A.Q...E...E..V...T.I.P..FL.R..AS....H....     126      6     56     28     28      0      0      8     126     51  40% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,K182Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V...T.IKP.....R..AS....H....     123     15     26     62      4      7      0      9     123     30  24% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,L335S,G339H,R346T,L368I,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.K..VE...E..V...T.I.P...L.R..AS....H....     122     23     21     74      0      0      0      4     122     47  38% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146K,E180V,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E.YV...TTI.P.....R..AS.K..H.L..     119     22     32     65      0      0      0      0     119     44  36% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,D215H,H245Y,G252V,G339H,R346T,K356T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,E554K,D614G,H655Y,N679K,P681H,S704L,N764K,D796Y,Q954H,N969K] 
...H..A.Q...E...E..V...T.I.P..FLVK..AS....H....     114     13     56     10     26      0      0      9     114     72  63% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,A475V,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
.........--....S.............M...K..A.....H....     113      0      0      0      7      0      0    106     113     84  74% [T19I,P25S,G142D,Y144-,E156G,F157-,R158-,P209L,L212S,D215H,A222V,A243-,L244-,S256L,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,G446S,L452M,S477N,T478K,E484A,F486P,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N703I,N764K,D796Y,Q954H,N969K] 
...H..A..L..E...E..V...T.I.P.R.L.K..AS....H....     106      0      3     99      4      0      0      0     106     87  82% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,F157L,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L452R,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V...T.I.P.....K..AS.K..H....      97      3     15     37     41      0      0      1      97     52  53% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,E554K,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V...TTI.P.....K..AS....H....      97      2     18     32     13      0      0     32      97     22  22% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,R190S,V213E,G252V,G339H,R346T,K356T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,T572I,D614G,H655Y,N679K,P681H,N764K,D796Y,A899S,Q954H,N969K,A1070T] 
...H..A.K...E...E..V...T.I.P..FL.K..AS....H.L..      96      4     48     41      2      0      0      1      96     29  30% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146K,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,S704L,N764K,D796Y,Q954H,N969K] 
...H..A.Q...E...E..V...T.I.P..WL.K..AS....H....      90     25     54      7      4      0      0      0      90     38  42% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455W,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
.TL.--.F.SG...-IGFN..DV.T.KHDW..VKK-K..KVSR..FL      90      2     86      2      0      0      0      0      90     77  85% [+16MPLF,T19I,R21T,L24-,P25-,P26-,A27S,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445H,G446S,N450D,L452W,N460K,A475V,S477N,T478K,N481K,V483-,E484K,F486P,Q498R,N501Y,Y505H,E554K,A570V,D614G,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L] 
...H..A.Q...E...E..V...TTI.P...L.K..AS....H....      87      0      2      5     76      0      0      4      87     18  20% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,K356T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V...T.I.P..FLVK..AS....H.L..      85      9     27     29      1      0     19      0      85     31  36% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,A475V,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,S704L,N764K,D796Y,Q954H,N969K] 
...R..A.Q...E...E...G..T.I.PD....R..ASS...H....      83      1     15     24     19      0      0     24      83     34  40% [T19I,L24-,P25-,P26-,A27S,Q52R,V83A,G142D,Y144-,H146Q,K182N,Q183E,V213E,D253G,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N450D,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,P521S,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K,V1122A] 
......A.K...E...E..V...T.I.P..FLVK..AS....H....      83      5     31     37      0      0      9      1      83     32  38% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146K,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,A475V,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
.........L...D..G......T.....RFL.K..A.....H.L..      83      7     65      9      0      0      0      2      83     64  77% [T19I,L24-,P25-,P26-,A27S,G142D,K147E,W152R,F157L,N185D,I210V,V213G,G257S,G339H,R346T,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,K444T,G446S,L452R,L455F,F456L,N460K,S477N,T478K,E484A,F486S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,S704L,N764K,D796Y,L858I,Q954H,N969K] 
......A.Q..VE...E..V...T.I.P...L.R..AS.K..H....      76      7     44     17      1      0      0      7      76     42  55% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,E180V,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,E554K,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..A.-...E...E..V...T.I.P..FL.K..AS....H....      75      1     10     11     38      0      0     15      75     14  18% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,V143D,Y144Q,Y145-,H146-,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..A.Q...E...E..V...T.I.P.R.L.K..AS....H....      74      1     26     20     22      0      0      5      74     42  56% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L452R,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V...T.I.P...L.R..AP.K..HV...      74      0      3     65      2      0      0      4      74     65  87% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478R,E484A,F486P,F490P,Q498R,N501Y,Y505H,E554K,D614G,H655Y,N679K,P681H,A701V,N764K,D796Y,Q954H,N969K] 
...H..A.Q...E...E..V...T.I.P...L.K..AP....H....      72      0      2     54     15      0      0      1      72     54  75% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478K,E484A,F486P,F490P,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..T.Q...E...E..V...T.I.P..FL.K..AS....H....      61      0      0      2      0      0      0     59      61     41  67% [T19X,L24-,P25-,P26-,A27S,Q52H,V83T,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.K...E...E...G..T.I.P.....K..ASS...H....      59      3     21     32      3      0      0      0      59     13  22% [T19I,L24-,P25-,P26-,A27S,V83A,F140-,G142D,Y144-,H146K,K182N,Q183E,V213E,D253G,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,P521S,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V...T.I.P...L.R..AS....H....      58      1     21     34      1      0      0      1      58     20  34% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.K..VE...E..V...T.I.P.....R..AS....H....      58     17      7     25      6      0      0      3      58      6  10% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144X,H146K,E180V,Q183E,V213E,G252V,K304N,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V...T.I.P...L.K..AS....H.L..      58      1      1     56      0      0      0      0      58     31  53% [T19I,L24-,P25-,P26-,A27S,G75A,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,S704L,N764K,D796Y,Q954H,N969K] 
......A.K...E...E..V...T.I.P..FL.K..AS....H.L..      57      6     23     19      2      0      7      0      57     20  35% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146K,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,T573I,D614G,H655Y,N679K,P681H,S704L,N764K,D796Y,Q954H,N969K] 
......A.K...E...E..V...T.I.P...L.K..AS....H....      57      2      8     31      4      0      8      4      57     29  50% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146K,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..A.Q...E...E..V...T.I.P.QFL.K..AS....H....      55      0      0      1      4      0      0     50      55     27  49% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L452Q,L455F,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V...T.I.P...L.K..AS....HV...      55      3     30     16      6      0      0      0      55     21  38% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,A701V,N764K,D796Y,Q954H,N969K] 
......A.QL...D..G......T.....RFL.K..A.....H....      53     15     27      8      1      0      0      2      53     33  62% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,F157L,N185D,I210V,V213G,G257S,G339H,R346T,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,K444T,G446S,L452R,L455F,F456L,N460K,S477N,T478K,E484A,F486S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,L858I,Q954H,N969K] 
......A.Q...E...E..V...T.I.P...L.KK.AS....RV...      53      1     22     26      2      0      0      2      53     40  75% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478K,N481K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681R,A701V,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E...G..T.I.PD....R..ASS...H....      51      2      9     24      6      0      0     10      51     17  33% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,K182N,Q183E,V213E,D253G,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N450D,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,P521S,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E...G..T.I.P........ASS...H....      50      7     15      8      8      3      0      9      50      6  12% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,G184V,V213E,D253G,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,E484A,F486P,F490S,Q498R,N501Y,Y505H,P521S,D614G,E654K,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K,T1117K] 
......A.Q...ED..E..V...T.I.P..FLVK..AS....H.L..      50      1      2     32      0      0     15      0      50     39  78% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,N185D,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,A475V,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,S704L,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V...T.I.P.....R..AST...H....      48      6      3     39      0      0      0      0      48     17  35% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,P521T,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.K..VE...E..V...T.I.P..FL.R..AS....H....      47      7      4     32      2      0      0      2      47     28  59% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146K,E180V,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...HY.A.Q...E...E..V...T.I.P...L.K..AS....H....      47      1      1     32     13      0      0      0      47     31  65% [T19I,L24-,P25-,P26-,A27S,Q52H,H69Y,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V...TTI.P..FL.K..AS....H....      46     22      8     15      0      0      0      1      46     30  65% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,K356T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,V511I,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V...T.I.P.....R..AS.K..H....      44      3     26     12      1      0      0      2      44     20  45% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,E554K,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..A.QL..E.I.E..V...T.I.P...L.K..AS....H....      43      0      1     42      0      0      0      0      43     42  97% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,F157L,Q183E,N211I,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E...G..T.I.P...L.K..ASS...H....      42      8     13     21      0      0      0      0      42      9  21% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,D253G,R273S,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,P521S,D614G,H655Y,N679K,P681H,A688V,N764K,D796Y,Q954H,N969K] 
......A.K...E...E..V...T.I.P.....R..AS....H....      42      7     16     10      5      0      0      4      42      4   9% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,H146K,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,Q613H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q..VE...E..V...T.I.P.Q...R..AS....H....      42      7     25      7      0      0      0      3      42     19  45% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,E180V,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L452Q,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..A.KL..E...E..V...T.I.P...L.K..AS....H....      41      6      7     22      3      0      0      3      41     17  41% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146K,F157L,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..A.-...E...E..V...T.I.P...L.K..AS....H....      41      8      8     20      4      0      0      1      41      7  17% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y145P,H146-,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..A.Q...ED..E..V...T.I.P..FL.K..AS....H....      41      1      5     15      7      0      0     13      41     23  56% [Q14K,T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,Q183E,N185D,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..A.QL..E...E..VE..T.I.P.R.L.K..AS....H....      41      0      0     41      0      0      0      0      41     32  78% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,F157L,Q183E,V213E,G252V,D253E,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L452R,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
.........L......G......T.....R...K..A.....H....      41      1      2     24     11      0      0      3      41     20  48% [T19I,L24-,P25-,P26-,A27S,G142D,K147E,W152R,F157L,I210V,V213G,D215G,G257S,G339H,R346T,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,K444T,G446S,L452R,N460K,S477N,T478K,E484A,F486S,Q498R,N501Y,Y505H,Q613H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...ED..E..V...T.I.P...L.K..AS....H....      40      0      1     13      0      0     26      0      40     21  52% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,N185D,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..A.KL..E...E..V...T.I.P..FL.K..AS....H....      39      0      2      3     32      0      0      2      39     22  56% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146K,F157L,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
.........--....S.......S...A.R...K..A.....H....      37      0      0      0      0      0      0     37      37     33  89% [T19I,P25S,G142D,Y144-,E156G,F157-,R158-,P209L,L212S,D215H,A222V,A243-,L244-,S256L,R346S,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445A,G446S,L452R,S477N,T478K,E484A,F486P,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N703I,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E...G..T.I.PD....K..ASS...H....      36      2     24     10      0      0      0      0      36      8  22% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,K182N,Q183E,V213E,D253G,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N450D,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,P521S,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V...TTI.P.....R..AS....H....      36      0      1      2     33      0      0      0      36     27  75% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,K356T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V...T.I.P...L.K..AS.K..H....      36      0     11     15      1      0      8      1      36     15  41% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,E554K,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..A.K...E...E..V...T.I.P...L.R..AS....H....      36      0      3     33      0      0      0      0      36     34  94% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146K,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...D...G..T.I.P.....R..ASS...H....      35      0      1     33      0      0      0      1      35     19  54% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213D,D253G,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,P521S,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...HY.A.K...E...E..V...T.I.P..FL.K..AS....H....      34      0      0     34      0      0      0      0      34     16  47% [T19I,L24-,P25-,P26-,A27S,Q52H,H69Y,V83A,G142D,Y144-,H146K,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,E654V,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...EI..E...G..T.I.P.....R..ASSK..H....      33      8     13      8      2      0      0      2      33     17  51% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,N185I,F186-,V213E,D253G,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,P521S,E554K,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q..VE...E..V...T.I.P..FLVR..AS....H....      31      0      0     28      3      0      0      0      31     28  90% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,E180V,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,A475V,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
.........L.D.D..G......T.....RFL.K..A.....H....      30      0      0     30      0      0      0      0      30     30 100% [T19I,L24-,P25-,P26-,A27S,G142D,K147E,W152R,F157L,E180D,N185D,I210V,V213G,G257S,G339H,R346T,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,K444T,G446S,L452R,L455F,F456L,N460K,S477N,T478K,E484A,F486S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,L858I,Q954H,N969K] 
......A.Q...E...E..V...T.I.P..FL.I..AS.K..H....      30      3     12      8      7      0      0      0      30     18  60% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478I,E484A,F486P,F490S,Q498R,N501Y,Y505H,E554K,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.K...ED..E...G..T.I.P.....R..ASS...H....      28      4     19      5      0      0      0      0      28     11  39% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146K,Q183E,N185D,V213E,D253G,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,P521S,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.K..VE...E..V...T.I.P.....R..AST...H....      28      7      5     14      2      0      0      0      28     10  35% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146K,E180V,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,P521T,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V...T.I.P...L.R..AS...SHV...      28      0      0     28      0      0      0      0      28     23  82% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,P621S,H655Y,N679K,P681H,A701V,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V...T.I.P..FL.K..AS.Q..H....      27      0      2     23      0      0      2      0      27     24  88% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,E554Q,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K,P1162S] 
......A.K...E...E..V...T.I.P.....K..AS....H....      26      1      4      5     12      0      1      3      26      4  15% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146K,Q183E,Y200C,I210T,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..A.Q...E...E..V...T.I.P..FL.K..AS.K..H....      26      0     25      1      0      0      0      0      26      9  34% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,E554K,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V...T.I.P.....K..ASS...H....      25      0      5     15      3      0      0      2      25     10  40% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,I410V,K417N,N440K,V445P,G446S,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,P521S,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V...T.I.P..FLVR..AS....H....      25      2      0     23      0      0      0      0      25     23  92% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,A475V,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..S.Q...E...E..V...T.I.P..FL.K..AS....H.L..      25      2     22      1      0      0      0      0      25     12  48% [T19I,L24-,P25-,P26-,A27S,Q52H,V83S,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,S704L,N764K,D796Y,Q954H,N969K] 
.G.......--.....G...G..T.....R...K..A....SH....      25      0     11      2     11      0      0      1      25     13  52% [L18F,T19R,R21G,T95I,G142D,Y144-,W152L,E156G,F157-,R158-,F186L,V213G,D253G,G339D,R346T,S371F,S373P,S375F,T376A,D405N,R408S,K417N,D420N,N440K,G446D,L452R,S477N,T478K,E484A,F486P,Q498R,N501Y,Y505H,D614G,P621S,H655Y,N679K,P681H,A706V,N764K,D796Y,Q954H,N969K,T1117I,D1153Y] 
......A.Q...E...E..V...T.I.P..FL.R..AS....H.L..      24      0      3     17      0      0      4      0      24     11  45% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,T573I,D614G,H655Y,N679K,P681H,S704L,N764K,D796Y,Q954H,N969K] 
...H..A.K...E...E..V...TTI.P...L.K..AS....H....      24      1      0     19      4      0      0      0      24     15  62% [Q14R,T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146K,Q183E,V213E,G252V,G339H,R346T,K356T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,A845S,I909V,Q954H,N969K,D1084Y] 
........Q...E...E..V...T.I.P..FLVK..AS....H....      24      0     10      0      0      0     14      0      24      6  25% [T19I,L24-,P25-,P26-,A27S,P85X,F86X,N87X,D88X,G89X,V90X,Y91X,F92X,A93X,G142D,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,A475V,S477N,T478K,E484A,F486P,F490S,Q498X,P499X,T500X,N501X,G502X,V503X,G504X,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..A.Q..VE...E..V...T.I.P.....R..ASS...H....      23     17      4      2      0      0      0      0      23      8  34% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,K147N,E180V,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,P521S,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...EI..E..V...T.I.P..FLVI..AS.K..H....      22     20      0      0      2      0      0      0      22     19  86% [T19I,L24-,P25-,P26-,A27S,F79S,V83A,G142D,Y144-,H146Q,Q183E,N185I,F186-,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,A475V,S477N,T478I,E484A,F486P,F490S,Q498R,N501Y,Y505H,E554K,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..A.Q..VE...E..V...T.I.P.....R..AS....H....      22      2      8      8      2      0      0      2      22      9  40% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,E180V,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..A.QL..E...E..V...T.I.P.W.L.K..AS....H....      22      0      1     21      0      0      0      0      22     20  90% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,F157L,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L452W,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E...G..T.I.P.....Q..ASS...H....      22      0      0     21      0      0      0      1      22     16  72% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,F186L,V213E,D253G,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478Q,E484A,F486P,F490S,Q498R,N501Y,Y505H,P521S,D614G,H655Y,N679K,P681H,N764K,T768S,D796Y,Q954H,N969K,V1129I] 
...H..A.Q...E...E..V...T.I.P...L.KK.AS....H....      22      0     11      8      2      0      0      1      22     10  45% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478K,N481K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H--A.Q...E...E..V...T.I.P...L.K..AS....H....      22      0      3     18      1      0      0      0      22     16  72% [T19I,L24-,P25-,P26-,A27S,Q52H,H69-,V70-,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V.....I.P..FLVK..AS....H....      21      0      0      0      0      0     21      0      21      7  33% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,A475V,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..A.Q...G...E..V...T.I.P..FL.K..AS....H....      20      0      0      1     11      0      0      8      20     12  60% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,Q183G,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..A.Q...E...E..V...T.I.P.....R..AS....H....      20      0      6     14      0      0      0      0      20     10  50% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,A348S,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K,D1168H] 
...H....QL..E...E..V...T.I.P.R.L.K..AS....H....      20      0      6     14      0      0      0      0      20     10  50% [T19I,L24-,P25-,P26-,A27S,Q52H,G142D,Y144-,H146Q,F157L,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L452R,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..A.Q...E...E..V...T.I.P..FL.KK.AS....H....      20      1      6      3     10      0      0      0      20      9  45% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478K,N481K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N703S,N764K,D796Y,Q954H,N969K] 
...H..A.Q...E...E..V...T.I.P...L.K..AS....H.L..      19      3      6      7      1      0      0      2      19      7  36% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,S704L,N764K,D796Y,Q954H,N969K] 
......A.-...E...E..V...T.I.P..FLVK..AS....H....      19      1     10      6      0      0      2      0      19      3  15% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,V143D,Y144Q,Y145-,H146-,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,A475V,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..A.QL..E...E..V...T.I.P...L.K..AS.K..H....      19     19      0      0      0      0      0      0      19      7  36% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,F157L,K182I,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,E554K,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..A.QL..E...E..V...T.I.P..FL.R..AS....H....      19      1     15      2      0      0      0      1      19     14  73% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,F157L,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
.TL.--.F.SG...-IGFN..DV.T..HDWS..KK-K..KVSR..FL      19      0     19      0      0      0      0      0      19     15  78% [+16MPLF,T19I,R21T,L24-,P25-,P26-,A27S,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,K356T,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445H,G446S,N450D,L452W,L455S,N460K,S477N,T478K,N481K,V483-,E484K,F486P,Q498R,N501Y,Y505H,E554K,A570V,D614G,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L] 
......A.Q...E...E...G..T.I.P.....N..ASS...H....      18      3      6      5      3      0      0      1      18      9  50% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,D253G,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478N,E484A,F486P,F490S,Q498R,N501Y,Y505H,P521S,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..A.Q...E...E..V...T.I.P...L.K..AS...SH....      18      0      9      7      2      0      0      0      18     11  61% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,P621S,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..VG..T.I.P...L.R..AS....HV...      18      0      3     11      0      0      0      4      18      5  27% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,D253G,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478R,E484A,F486P,F490S,S494P,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,A701V,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V...T.I.P..FLVK..AS.G..H....      18      0      1      0      1      0      0     16      18      8  44% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,A475V,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,E554G,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.K...E...E..V...T.I.P..FL.K..AS....H....      18      1      5      7      1      0      0      4      18      2  11% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146K,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,V511I,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K,P1162S] 
...H..A.QL..E...E..V...T.I.P..FL.K..AS....R....      18      0     18      0      0      0      0      0      18     16  88% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,F157L,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681R,N764K,D796Y,Q954H,N969K] 
.TL.--.F.SG.....GFN..DV.T.KHDWS..KK-K..KVSR..FL      17      0     17      0      0      0      0      0      17     11  64% [T19I,R21T,L24-,P25-,P26-,A27S,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,V213G,L216F,H245N,A264D,I332V,G339H,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445H,G446S,N450D,L452W,L455S,N460K,S477N,T478K,N481K,V483-,E484K,F486P,Q498R,N501Y,Y505H,E554K,A570V,D614G,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L] 
......A.Q...E...E..V...T.I.P.....K..AS....H.L..      17      0      3     14      0      0      0      0      17      4  23% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,H146Q,Q183E,Y200C,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,Y451H,N460K,S477N,T478K,E484A,F486P,F490S,S494P,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,S704L,N764K,D796Y,Q954H,N969K,D1139H] 
.TL.--.F.SG...-IGFN..DVTT.KHDWS..KK-K..KVSR..FL      17      0     17      0      0      0      0      0      17      9  52% [+16MPLF,T19I,R21T,L24-,P25-,P26-,A27S,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445H,G446S,N450D,L452W,L455S,N460K,S477N,T478K,N481K,V483-,E484K,F486P,Q498R,N501Y,Y505H,E554K,A570V,D614G,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L] 
...H....Q...E...E..V...T.I.P..FL.K..AS....H....      16      0     11      2      3      0      0      0      16      7  43% [T19I,L24-,P25-,P26-,A27S,Q52H,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..A.Q...ED..E..V...T.I.P...L.K..AS....H....      16      0      3      9      4      0      0      0      16      9  56% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,Q183E,N185D,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...D...E..V...T.I.P..FLVK..AS....H....      16      1      0      0      0      0      0     15      16      7  43% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,K182I,Q183D,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,A475V,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
.........--....S.......S.....M...K..A.....H....      16      0      1      0      0      0      0     15      16      5  31% [T19I,P25S,G142D,Y144-,E156G,F157-,R158-,P209L,L212S,D215H,A222V,A243-,L244-,S256L,A260D,R346S,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,G446S,L452M,S477N,T478K,E484A,F486P,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N703I,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V...T.I.P.M.L.R..AS....HV...      16     11      0      5      0      0      0      0      16     12  75% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L452M,F456L,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,A701V,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V...T.I.P.....KY.AS....H....      16      0     16      0      0      0      0      0      16     16 100% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,Y200C,V213E,D215H,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478K,N481Y,E484A,F486P,F490S,Q498R,N501Y,Y505H,T572I,D614G,H655Y,N679K,P681H,N764K,D796Y,I844T,Q954H,N969K] 
....Y.A.Q...E...E..V...T.I.P...L.R..AS....HV...      16      0      1      9      0      0      0      6      16     10  62% [T19I,L24-,P25-,P26-,A27S,H69Y,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,A701V,N764K,D796Y,Q954H,N969K] 
...H....Q...E...E..V...T.I.P...L.K..AS....H....      16      0     12      4      0      0      0      0      16      9  56% [T19I,L24-,P25-,P26-,A27S,Q52H,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.K..VE...E..V...T.I.P.....R..AS.K..H....      15      2     10      3      0      0      0      0      15      9  60% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146K,E180V,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,E554K,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..A.QL..E...E..V...T.I.P.R.L.K..AS....H..F.      15      0      0     15      0      0      0      0      15     14  93% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,F157L,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L452R,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,S939F,Q954H,N969K] 
...H..A.-L..E...E..V...T.I.P.R.L.K..AS....H....      15      0      3     10      1      0      0      1      15      4  26% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,V143D,Y144Q,Y145-,H146-,F157L,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L452R,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.-...E...E..V...T.I.P...L.R..AS....HV...      15      2      6      7      0      0      0      0      15      3  20% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,V143X,Y144Q,Y145-,H146-,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,A701V,N764K,D796Y,Q954H,N969K] 
......A.Q...EI..E..V...T.I.P..FLVK..AS....H....      15      0      3     12      0      0      0      0      15     10  66% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,N185I,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,A475V,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
F..H..A.QL..E...E..V...T.I.P.R.L.K..AS....H....      15      0      4     11      0      0      0      0      15      9  60% [V16F,T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,F157L,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L452R,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..A.QL..E.I.E..V...T.I.P.R.L.K..AS....H....      15      1      2      0      0      0      0     12      15     10  66% [T19X,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,F157L,Q183E,N211I,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L452R,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K,T1117I] 
......A.Q...E...E..V...T.I.P.....R..AST...HV...      14      3     10      0      1      0      0      0      14     10  71% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,P521T,D614G,H655Y,N679K,P681H,A701V,N764K,D796Y,Q954H,N969K] 
......A.-...E...E..V...T.I.P...L.K..AS....H....      14      0      1      9      2      0      2      0      14      2  14% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y145R,H146-,Q183E,V213E,P251S,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478K,E484A,F486P,F490S,S494P,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K,I1114T] 
......T.Q...E...E..V...TTI.P...L.KK.AP....RV...      14      0      0     14      0      0      0      0      14     14 100% [T19I,L24-,P25-,P26-,A27S,V83T,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,K356T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478K,N481K,E484A,F486P,F490P,Q498R,N501Y,Y505H,T572I,D614G,H655Y,N679K,P681R,A701V,N764K,D796Y,Q954H,N969K] 
.TL.--.F......-IGFN..DV.T.KHDWS..KK-K..KVSR..FL      14      0     14      0      0      0      0      0      14     11  78% [+16MPLF,T19I,R21T,L24-,P25-,P26-,A27S,S50L,H69-,V70-,V127F,G142D,Y144-,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445H,G446S,N450D,L452W,L455S,N460K,S477N,T478K,N481K,V483-,E484K,F486P,Q498R,N501Y,Y505H,E554K,A570V,D614G,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L] 
......A.Q...EI..E...G..T.I.P...L.R..ASS...H....      14      1      5      7      0      0      0      1      14     10  71% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,N185I,F186-,V213E,D253G,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,P521S,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.QL..E...E..V...T.I.P.....K..ASS...H....      14     10      4      0      0      0      0      0      14      9  64% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,F157L,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,I410V,K417N,N440K,V445P,G446S,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,P521S,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,Q957H,N969K,V1264L] 
......A.Q...E...E..V...T.I.P..FLVK..AS....H..F.      14      2     11      1      0      0      0      0      14     13  92% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,A475V,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,S939F,Q954H,N969K] 
...H..A.Q.G.E...E..V...T.I.P...L.K..AS....H....      14      0      0      2      4      0      0      8      14     10  71% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,R158G,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H....Q...E...E..V...T.I.P..FL.K..AS....H.L..      14      0     14      0      0      0      0      0      14      5  35% [T19I,L24-,P25-,P26-,A27S,Q52H,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,S704L,N764K,D796Y,Q954H,N969K] 
......A.Q..D--..E..V...T.I.P...L.K..AS.K..H....      14      0      6      6      0      0      2      0      14     11  78% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,E180D,G181-,K182-,Q183-,G184-,N185-,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,E554K,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
.T..--.F.SG...-IGFN..DV.T.KHDWS..KK-K..KVSR..FL      13      0     13      0      0      0      0      0      13      6  46% [+16MPLF,T19I,R21T,L24-,P25-,P26-,A27S,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445H,G446S,N450D,L452W,L455S,N460K,S477N,T478K,N481K,V483-,E484K,F486P,Q498R,N501Y,Y505H,E554K,A570V,D614G,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L] 
......A.Q...E...E..V...T.I.P.....R..ASS...H....      13      0     11      2      0      0      0      0      13     10  76% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,P521S,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.K...E...E...G..T.I.P.....R..ASS...H....      13      0      4      9      0      0      0      0      13      2  15% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146K,Q183E,V213E,D253G,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,P521S,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E...G..T.I.PD..L.K..ASS...H....      13      0      8      3      2      0      0      0      13      5  38% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,D253G,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N450D,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,P521S,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K,T1231A] 
......A.Q...ED..E..V...T.I.P..FL.K..AS....H.L..      13      0      6      5      0      0      2      0      13      7  53% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,N185D,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,S704L,N764K,D796Y,Q954H,N969K] 
....--..........G......T.....R...K..A.....H....      13      1      9      1      1      0      0      1      13      1   7% [M1X,F2X,V3X,F4X,L5X,V6X,L7X,L8X,P9X,L10X,V11X,S12X,S13X,T19I,L24-,P25-,P26-,A27S,H69-,V70-,G75V,G142D,Y144-,N164S,V213G,G339D,R346T,S371F,S373P,S375F,T376A,T385I,D405N,R408S,K417N,N440K,K444T,L452R,N460K,S477N,T478K,E484A,F486V,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,A899S,Q954H,N969K,K1245R] Omicron_BA.4andBA.5
......A.K...E...E..V...T.IKP.....K..AS....HV...      12      1      3      8      0      0      0      0      12      5  41% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146K,Q183E,V213E,G252V,G339H,A344T,R346T,L368I,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478K,E484A,F486P,F490S,S494P,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,A701V,N764K,D796Y,Q954H,N969K] 
.........L...D..E......T.....RFL.K..A.....H....      12      2      3      6      1      0      0      0      12      5  41% [T19I,L24-,P25-,P26-,A27S,G142D,K147E,W152R,F157L,N185D,I210V,V213E,G257S,G339H,R346T,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,K444T,G446S,L452R,L455F,F456L,N460K,S477N,T478K,E484A,F486S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,L858I,Q954H,N969K] 
...H..A.QL..E...E..V...T.I...R.L.K..AS....H....      12      0      1     11      0      0      0      0      12      7  58% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,F157L,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,G446S,L452R,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
.-L.--.F.SG...-IGFN..DV.T.KHDWS..KK-K..KVSR..FL      12      0     12      0      0      0      0      0      12      5  41% [N17M,+17P,+18FNFI,R21-,L24-,P25-,P26-,A27S,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445H,G446S,N450D,L452W,L455S,N460K,S477N,T478K,N481K,V483-,E484K,F486P,Q498R,N501Y,Y505H,E554K,A570V,D614G,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L] 
...H..A.Q...E...E..V...T.I.P..FL.K..AS....H..F.      12      0      1      0     10      0      0      1      12      9  75% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,S939F,Q954H,N969K] 
......A.Q..VE...E..V...T.I.P.....R..AS.Q..H....      12      2      9      0      1      0      0      0      12      9  75% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,E180V,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,E554Q,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V...T.I.P.....R..ASQ...H....      12      7      0      5      0      0      0      0      12      3  25% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,Y200C,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,P521Q,T572I,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
.........L...D..G......T..K..RFL.K..A.....H....      12      0      0     12      0      0      0      0      12      4  33% [T19I,L24-,P25-,P26-,A27S,G142D,K147E,W152R,F157L,N185D,I210V,V213G,G257S,G339H,R346T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,K444T,G446S,L452R,L455F,F456L,N460K,S477N,T478K,E484A,F486S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,L858I,Q954H,N969K,L981I] 
...HY.A.Q...E...E..V...T.I.P..FL.K..AS....H.L..      12      2      0     10      0      0      0      0      12      9  75% [T19I,L24-,P25-,P26-,A27S,Q52H,H69Y,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,S704L,N764K,D796Y,Q954H,N969K] 
......A.Q...EI..E..V...T.I.P.R.L.R..AS.K..HV...      12      0      0      0      0      0      0     12      12     11  91% [T19X,L24-,P25-,P26-,A27S,I68T,V83A,G142D,Y144-,H146Q,Q183E,N185I,F186-,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L452R,F456L,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,E554K,D614G,H655Y,N679K,P681H,A701V,N764K,D796Y,Q954H,N969K,A1020S] 
...H..A.KL..E...E..V...T.I.P.R.L.K..AS.D..H....      11      0      0     11      0      0      0      0      11     11 100% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146K,F157L,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L452R,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,E554D,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.QL..E...E..V...TTI.P.....K..AS....H....      11      0      0     10      1      0      0      0      11     10  90% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,F157L,Q183E,V213E,G252V,G339H,R346T,K356T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,T572I,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
.........L..KD..G......T.....RFL.K..A.....H....      11      0      4      6      1      0      0      0      11      7  63% [T19I,L24-,P25-,P26-,A27S,G142D,K147E,W152R,F157L,Q183K,N185D,I210V,V213G,G257S,G339H,R346T,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,K444T,G446S,L452R,L455F,F456L,N460K,S477N,T478K,E484A,F486S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,L858I,Q954H,N969K] 
.TL.--.F......-IGFN..DV.T.KHDW...KK-K..KVSR..FL      11      0     11      0      0      0      0      0      11      5  45% [+16MPLF,T19I,R21T,L24-,P25-,P26-,A27S,S50L,H69-,V70-,V127F,G142D,Y144-,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445H,G446S,N450D,L452W,N460K,S477N,T478K,N481K,V483-,E484K,F486P,Q498R,N501Y,Y505H,E554K,A570V,D614G,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L,M1229I] 
......A.K...EI..E...G..T.I.P.....R..ASS...H....      11      0      3      7      1      0      0      0      11      5  45% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146K,Q183E,N185I,F186-,V213E,D253G,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,P521S,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..A.Q...E...E..V...T.I.P..FLVK..AS....H.L..      11      0      9      1      1      0      0      0      11      5  45% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,A475V,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,S704L,N764K,D796Y,Q954H,N969K] 
......A.QL..E...E..V...T.I.P...L.R..AS....HV...      11      0      1      8      2      0      0      0      11      5  45% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,F157L,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,A701V,N764K,D796Y,Q954H,N969K] 
...H..A.Q...E...E..V...T.I.P...L.K..AS....H..F.      11      6      5      0      0      0      0      0      11      7  63% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,S939F,Q954H,N969K] 
...H..A.Q...E...E..V...TTI.P..FL.K..AS....H....      11      0      2      3      6      0      0      0      11      3  27% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,K356T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N703I,N764K,D796Y,Q954H,N969K] 
......A.QL..E...E..V...T.I.P..WL.K..AS....H....      11     10      1      0      0      0      0      0      11      8  72% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,F157L,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455W,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..A.Q...E...E..V...T.I.P..FL.KS.AS....H....      10      0      1      3      6      0      0      0      10      3  30% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478K,N481S,G482-,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K,D1153Y] 
...H..A.....E...E..V...T.I.P..FL.K..AS....H....      10      1      1      0      8      0      0      0      10      6  60% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..A.Q...E...E..VG..T.I.P...L.K..AS....H.L..      10      5      5      0      0      0      0      0      10      6  60% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,D253G,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,S704L,N764K,D796Y,Q954H,N969K] 
...H..A.QL..E...E..V...T.I.P.RFL.K..AS....H....      10      0      1      9      0      0      0      0      10      8  80% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,F157L,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L452R,L455F,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...H..A.QL..E...E..V...T.I.P.R.L.K..AS....R....      10      0      0     10      0      0      0      0      10      5  50% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,F157L,Q183E,T208M,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L452R,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681R,N764K,D796Y,Q954H,N969K] 
......A.Q...EI..E.YV...TTI.P.....R..AS.K..H.L..      10      1      5      4      0      0      0      0      10      4  40% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,N185I,F186-,V213E,D215H,H245Y,G252V,G339H,R346T,K356T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,E554K,D614G,H655Y,N679K,P681H,S704L,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V...T.I.P..FL.K..ASS...H.L..      10      0      1      0      0      0      9      0      10      7  70% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,P521S,D614G,H655Y,N679K,P681H,S704L,N764K,D796Y,Q954H,N969K] 
...H..A.Q...D...E..V...T.I.P..FL.K..AS....H....      10      4      0      5      1      0      0      0      10      3  30% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,Q183D,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K,P1140X] 
......A.Q...E...E..V...T.I.P.....K..AS....HV...      10      0      7      3      0      0      0      0      10      5  50% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144X,Y145X,H146Q,Q183E,V213E,G252V,G339H,A344T,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478K,E484A,F486P,F490S,S494P,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,A701V,N764K,D796Y,Q954H,N969K] 
......A.K...E...E..VG..T.I.P...L.R..AS....HV...      10      0      0     10      0      0      0      0      10      6  60% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146K,Q183E,V213E,G252V,D253G,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478R,E484A,F486P,F490S,S494P,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,A701V,N764K,D796Y,Q954H,N969K] 
...H..A.Q.......E..V...T.I.P...L.K..AS....H....      10      0      0     10      0      0      0      0      10      2  20% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,T547I,D614G,H655Y,N679K,P681H,N764K,K795X,D796X,F797X,G798X,G799X,F800X,N801X,F802X,S803X,Q804X,I805X,L806X,P807X,D808X,P809X,S810X,K811X,P812X,S813X,K814X,R815X,S816X,F817X,I818X,E819X,D820X,L821X,L822X,F823X,N824X,K825X,V826X,T827X,L828X,A829X,D830X,A831X,G832X,F833X,I834X,K835X,Q836X,Y837X,G838X,D839X,C840X,L841X,G842X,D843X,I844X,A845X,A846X,R847X,D848X,L849X,I850X,C851X,A852X,Q853X,K854X,F855X,N856X,G857X,L858X,T859X,V860X,L861X,P862X,P863X,L864X,L865X,T866X,D867X,E868X,M869X,I870X,A871X,Q872X,Y873X,T874X,S875X,A876X,Q954H,N969K] 
...H..A.Q...E...E..V...TTI.P...L.K..AS....R....      10      0      7      3      0      0      0      0      10      8  80% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,K356T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681R,N764K,D796Y,Q954H,N969K] 
...H..A.QS..E...E..V...T.I.P..FL.K..AS....H....      10      0      1      0      9      0      0      0      10      7  70% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,F157S,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V...T.I.P..FL.KK.AS....H.L..      10      0      6      3      0      0      1      0      10      5  50% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478K,N481K,E484A,F486P,F490S,Q498R,N501Y,Y505H,T573I,D614G,H655Y,N679K,P681H,S704L,N764K,D796Y,Q954H,N969K] 
......A.Q..VE...E..V...T.I.P.....R..ASS...H.L..      10      1      0      9      0      0      0      0      10      7  70% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,K147N,E180V,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,P521S,D614G,H655Y,N679K,P681H,S704L,N764K,D796Y,Q954H,N969K] 
...H..A.Q..QE...E..V...T.I.P..FL.R..AS....H....      10      0     10      0      0      0      0      0      10      5  50% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,E180Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417X,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V...T.I.P.R...K..AS....H....      10      0      0      8      2      0      0      0      10      7  70% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L452R,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,Q613H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
.TL.--.F.SG...-IGFN..DV.T.KHDW...KR-K..KVSR..FL      10      0     10      0      0      0      0      0      10     10 100% [+16MPLF,T19I,R21T,L24-,P25-,P26-,A27S,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445H,G446S,N450D,L452W,N460K,S477N,T478K,N481R,V483-,E484K,F486P,Q498R,N501Y,Y505H,E554K,A570V,D614G,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L,V1228L] 
...H..A.Q...E...E..V...T.I.P..FL.R..AS....H.L..      10      0      3      7      0      0      0      0      10      4  40% [T19I,L24-,P25-,P26-,A27S,Q52H,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478R,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,S704L,N764K,D796Y,Q954H,N969K] 
......A.Q...E...E..V.....I.P..FL.K..AS....H.L..      10      0      0      0      0      0     10      0      10      5  50% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,L455F,F456L,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,T573I,D614G,H655Y,N679K,P681H,S704L,N764K,D796Y,Q954H,N969K] 

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