COVID-19 Viral Genome Analysis Pipeline
Enabled by data from
Most common spike forms based on Pango lineage designations
Last update: Dec 3, 2021
Sequences: Short list of Last 60 days
As new lineages emerge, there are often many sequences with many ambiguous base calls. Our pipeline filters out such sequences, and as a consequence we undercount the number of sequences in GISAID that have been specified as members of related Pango lineages. Our strategy, however, enables us to use strictly high quality sequences to identify and track the common Spike forms in emerging lineages.
COMMON FORMS OF SPIKE WITH A GIVEN PANGO LINEAGE DESIGNATION
For each lineage, we show the most common forms of Spike, as well as their counts within (and percentages of) the lineage. [Note that if a lineage contains several divergent forms of Spike, the consensus form might not be found among these common forms.] Also shown is the Hamming distance (HD) between each form and the most common form in that lineage. Deletions relative to the ancestral reference strain are indicated with a dash (e.g. the two amino acid deletion in Delta variant are indicated as: 'E156-,F157-'), and insertions are denoted by a plus sign (e.g. B.1.621 usually has an extra T at position 143, it is written '+143T').
We show the 5 most common forms. This output is based on sequences sampled in the last 60 days from our last update, from 2021-10-04 to 2021-11-28.
Pango Lineage Form Form Lineage Count Count Pct HD [Spike form as mutation string] AY.4 170422 93321 54.8% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.4 170422 3567 2.1% 1 [T19R,T95I,D138H,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.4 170422 3065 1.8% 1 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.4 170422 2944 1.7% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,L1141F] AY.4 170422 2479 1.5% 1 [L5F,T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.43 44202 23523 53.2% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.43 44202 4373 9.9% 1 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.43 44202 760 1.7% 1 [V6F,T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.43 44202 418 0.9% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,S813I,D950N] AY.43 44202 406 0.9% 1 [T19R,A67S,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.103 41179 18840 45.8% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.103 41179 6835 16.6% 1 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.103 41179 692 1.7% 1 [T19R,D80Y,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.103 41179 317 0.8% 2 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R] AY.103 41179 246 0.6% 1 [L5F,T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.25 35047 14230 40.6% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.25 35047 5578 15.9% 1 [T19R,S112L,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.25 35047 2557 7.3% 1 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.25 35047 1938 5.5% 2 [T19R,S112L,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.25 35047 326 0.9% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,A846S,D950N] AY.4.2 33980 18936 55.7% 0 [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] (consensus) AY.4.2 33980 4175 12.3% 1 [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] AY.4.2 33980 825 2.4% 2 [S13T,T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] AY.4.2 33980 485 1.4% 1 [T19R,V36F,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] AY.4.2 33980 478 1.4% 2 [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,T299I,L452R,T478K,D614G,P681R,D950N,V1264L] B.1.617.2 30416 10640 35.0% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) B.1.617.2 30416 4618 15.2% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2 30416 2426 8.0% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] B.1.617.2 30416 426 1.4% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D574N,D614G,P681R,D950N] B.1.617.2 30416 377 1.2% 2 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,G1167V] AY.122 29471 10687 36.3% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.122 29471 2974 10.1% 1 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.122 29471 1324 4.5% 2 [T19R,G142D,E156G,F157-,R158-,W258R,L452R,T478K,D614G,P681R,D950N,A1078S] AY.122 29471 955 3.2% 1 [T19R,G142D,E156G,F157-,R158-,T240I,L452R,T478K,D614G,P681R,D950N] AY.122 29471 873 3.0% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,Q613H,D614G,P681R,D950N] AY.44 29228 14183 48.5% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.44 29228 4549 15.6% 1 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.44 29228 314 1.1% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,H1101Y] AY.44 29228 250 0.9% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.44 29228 180 0.6% 2 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R] AY.3 19650 8003 40.7% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.3 19650 3000 15.3% 1 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.3 19650 662 3.4% 1 [T19R,V70I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.3 19650 389 2.0% 2 [T19R,V70I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.3 19650 274 1.4% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,T1117I] AY.98 9677 5192 53.7% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.98 9677 490 5.1% 2 [T19R,G142D,E156G,F157-,R158-,P251L,L452R,T478K,D614G,P681R,D950N,D1127G] AY.98 9677 417 4.3% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,G1219V] AY.98 9677 354 3.7% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1176F] AY.98 9677 318 3.3% 1 [T19R,E96V,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.39 8957 3073 34.3% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.39 8957 1228 13.7% 1 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.39 8957 719 8.0% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] AY.39 8957 233 2.6% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,K1073N] AY.39 8957 147 1.6% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.5 8206 5187 63.2% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.5 8206 359 4.4% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,Q613H,D614G,P681R,D950N] AY.5 8206 237 2.9% 1 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.5 8206 163 2.0% 1 [T19R,G142D,E156G,F157-,R158-,T376I,L452R,T478K,D614G,P681R,D950N] AY.5 8206 128 1.6% 1 [T19R,G142D,E156G,F157-,R158-,T323I,L452R,T478K,D614G,P681R,D950N] AY.119 6680 1610 24.1% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.119 6680 941 14.1% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,P809S,D950N] AY.119 6680 846 12.7% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,Q675H,P681R,D950N] AY.119 6680 443 6.6% 1 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.119 6680 360 5.4% 2 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,P809S,D950N] AY.120 6132 2835 46.2% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.120 6132 984 16.0% 1 [T19R,T51I,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.120 6132 170 2.8% 1 [T19R,T95I,G142D,E156G,F157-,R158-,V407I,L452R,T478K,D614G,P681R,D950N] AY.120 6132 155 2.5% 2 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R] AY.120 6132 141 2.3% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,Q613H,D614G,P681R,D950N] AY.4.2.1 5357 4209 78.6% 0 [T19R,V36F,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] (consensus) AY.4.2.1 5357 94 1.8% 1 [T19R,V36F,G75R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] AY.4.2.1 5357 93 1.7% 1 [T19R,V36F,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,A899S,D950N] AY.4.2.1 5357 92 1.7% 2 [T19R,V36F,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.4.2.1 5357 77 1.4% 1 [T19R,V36F,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,A672V,P681R,D950N] AY.100 5034 1884 37.4% 0 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.100 5034 1124 22.3% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.100 5034 134 2.7% 1 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R] AY.100 5034 56 1.1% 2 [L5F,T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.100 5034 51 1.0% 1 [T19R,P82T,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.46.6 3947 1649 41.8% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.46.6 3947 907 23.0% 1 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.46.6 3947 233 5.9% 1 [T19R,H69Y,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.46.6 3947 76 1.9% 1 [T19R,G142D,E156G,F157-,R158-,T323K,L452R,T478K,D614G,P681R,D950N] AY.46.6 3947 46 1.2% 2 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R] AY.122.1 3797 2526 66.5% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.122.1 3797 178 4.7% 1 [T19R,T95I,G142D,E156G,F157-,R158-,E180Q,L452R,T478K,D614G,P681R,D950N] AY.122.1 3797 112 2.9% 2 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,T791I,D950N] AY.122.1 3797 44 1.2% 2 [T19R,T95I,G142D,E156G,F157-,R158-,L242F,L452R,T478K,D614G,P681R,D950N,C1236S] AY.122.1 3797 44 1.2% 2 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,A623V,P681R,D950N,A1070V] AY.6 3731 1621 43.4% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.6 3731 424 11.4% 2 [T19R,T22I,A67V,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.6 3731 133 3.6% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,A1078S] AY.6 3731 90 2.4% 1 [T19R,G142D,E156G,F157-,R158-,S255F,L452R,T478K,D614G,P681R,D950N] AY.6 3731 85 2.3% 2 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,E1207D,V1264L] AY.26 3657 1054 28.8% 0 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] (consensus) AY.26 3657 581 15.9% 1 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,N1074S,V1264L] AY.26 3657 361 9.9% 1 [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] AY.26 3657 199 5.4% 2 [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,N1074S,V1264L] AY.26 3657 71 1.9% 1 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,T547I,D614G,P681R,D950N,V1264L] AY.98.1 3528 1807 51.2% 0 [T19R,G142D,E156G,F157-,R158-,P251L,L452R,T478K,D614G,P681R,D950N] (consensus) AY.98.1 3528 532 15.1% 1 [T19R,E156G,F157-,R158-,P251L,L452R,T478K,D614G,P681R,D950N] AY.98.1 3528 73 2.1% 1 [T19R,G142D,E156G,F157-,R158-,P251L,L452R,T478K,D614G,P681R,A942S,D950N] AY.98.1 3528 56 1.6% 2 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.98.1 3528 50 1.4% 1 [L18F,T19R,G142D,E156G,F157-,R158-,P251L,L452R,T478K,D614G,P681R,D950N] AY.20 3400 939 27.6% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1104L] (consensus) AY.20 3400 587 17.3% 1 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1104L] AY.20 3400 229 6.7% 1 [T19R,T95I,K97E,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1104L] AY.20 3400 159 4.7% 2 [T19R,T95I,K97E,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1104L] AY.20 3400 90 2.6% 2 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,V1104L] AY.47 3344 1749 52.3% 0 [T19R,G142D,E156G,F157-,R158-,A222V,V289I,L452R,T478K,D614G,P681R,D950N] (consensus) AY.47 3344 625 18.7% 1 [T19R,E156G,F157-,R158-,A222V,V289I,L452R,T478K,D614G,P681R,D950N] AY.47 3344 48 1.4% 1 [T19R,G142D,E156G,F157-,R158-,A222V,V289I,L452R,T478K,D614G,P681R,D950N,M1229I] AY.47 3344 33 1.0% 1 [T19R,G142D,E156G,F157-,R158-,A222V,V289I,L452R,T478K,F490L,D614G,P681R,D950N] AY.47 3344 32 1.0% 2 [T19R,E156G,F157-,R158-,A222V,V289I,L452R,T478K,D614G,P681R] AY.39.1 3162 1427 45.1% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.39.1 3162 520 16.4% 1 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.39.1 3162 123 3.9% 1 [S12F,T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.39.1 3162 98 3.1% 1 [T19R,T95I,G142D,E156G,F157-,R158-,G219D,L452R,T478K,D614G,P681R,D950N] AY.39.1 3162 97 3.1% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,E484A,D614G,P681R,D950N] AY.9.2 3110 1355 43.6% 0 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] (consensus) AY.9.2 3110 273 8.8% 1 [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] AY.9.2 3110 170 5.5% 1 [T19R,G142D,E156G,F157-,R158-,D215H,A222V,L452R,T478K,D614G,P681R,D950N] AY.9.2 3110 113 3.6% 4 [T19R,A67V,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,Q1208H,M1237I] AY.9.2 3110 101 3.2% 1 [T19R,A67V,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] AY.27 3087 1843 59.7% 0 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,Q613H,D614G,P681R,D950N] (consensus) AY.27 3087 564 18.3% 1 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] AY.27 3087 86 2.8% 1 [T19R,G142D,E156G,F157-,R158-,L179F,A222V,L452R,T478K,Q613H,D614G,P681R,D950N] AY.27 3087 32 1.0% 1 [L8F,T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,Q613H,D614G,P681R,D950N] AY.27 3087 30 1.0% 1 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,Q613H,D614G,Q675H,P681R,D950N] AY.33 3079 588 19.1% 0 [T19R,T29A,G142D,E156G,F157-,R158-,T250I,L452R,T478K,Q613H,D614G,P681R,D950N] (consensus) AY.33 3079 520 16.9% 1 [T19R,T29A,G142D,E156G,F157-,R158-,T250I,L452R,T478K,D614G,P681R,D950N] AY.33 3079 245 8.0% 1 [T19R,T29A,G142D,E156G,F157-,R158-,T250I,T299I,L452R,T478K,Q613H,D614G,P681R,D950N] AY.33 3079 127 4.1% 2 [T19R,T29A,E156G,F157-,R158-,T250I,L452R,T478K,D614G,P681R,D950N] AY.33 3079 92 3.0% 3 [T19R,T29A,E156G,F157-,R158-,T250I,G446V,L452R,T478K,D614G,P681R,D950N] AY.102 2952 1691 57.3% 0 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.102 2952 55 1.9% 1 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,E1202Q] AY.102 2952 35 1.2% 1 [T19R,H69Y,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.102 2952 30 1.0% 3 [T19R,T95I,L452R,T478K,D614G,P681R,D950N] AY.102 2952 30 1.0% 4 [T19R,D80Y,T95I,E156G,F157-,R158-,T323I,L452R,T478K,D614G,P681R,D950N,A1020S,T1027I] AY.46 2856 1010 35.4% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.46 2856 579 20.3% 3 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] AY.46 2856 109 3.8% 1 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.46 2856 78 2.7% 4 [T19R,T95I,E156G,F157-,R158-,E281Q,L452R,T478K,D614G,P681R,I850L,D950N] AY.46 2856 59 2.1% 1 [T19R,E132A,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.34 2753 771 28.0% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,Q677H,P681R,D950N] (consensus) AY.34 2753 423 15.4% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,Q677H,P681R,D950N,L1265F] AY.34 2753 167 6.1% 2 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.34 2753 153 5.6% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,Q677H,P681R,T859I,D950N] AY.34 2753 123 4.5% 1 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,Q677H,P681R,D950N] AY.117 2433 1243 51.1% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.117 2433 400 16.4% 1 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.117 2433 56 2.3% 1 [T19R,T95I,G142D,E156G,F157-,R158-,P251S,L452R,T478K,D614G,P681R,D950N] AY.117 2433 52 2.1% 2 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,T604I,D614G,P681R,D950N] AY.117 2433 48 2.0% 1 [T19R,T95I,G142D,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.111 2322 1505 64.8% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.111 2322 85 3.7% 3 [T19R,T95I,G142D,E156G,F157-,R158-,N211-,L212I,L452R,T478K,D614G,P681R,D950N,V1094I] AY.111 2322 59 2.5% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,K1191N] AY.111 2322 48 2.1% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,H1101Y] AY.111 2322 46 2.0% 3 [T19R,T95I,G142D,E156G,F157-,R158-,N211-,L212I,L452R,T478K,A522S,D614G,P681R,D950N] AY.42 2305 440 19.1% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.42 2305 202 8.8% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.42 2305 174 7.5% 1 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.42 2305 154 6.7% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,T719I,D950N] AY.42 2305 85 3.7% 2 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,T719I,D950N] AY.36 2293 1410 61.5% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1104L] (consensus) AY.36 2293 183 8.0% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,D950N,V1104L] AY.36 2293 118 5.1% 1 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1104L] AY.36 2293 36 1.6% 2 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,S640F,P681R,D950N,V1104L] AY.36 2293 33 1.4% 2 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,D950N,V1104L] AY.118 2202 1053 47.8% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.118 2202 411 18.7% 1 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.118 2202 83 3.8% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1264L] AY.118 2202 41 1.9% 2 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1264L] AY.118 2202 19 0.9% 2 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R] AY.9.1 1967 637 32.4% 0 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] (consensus) AY.9.1 1967 307 15.6% 1 [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] AY.9.1 1967 143 7.3% 1 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,Q675K,P681R,D950N] AY.9.1 1967 107 5.4% 2 [T19R,G142D,E156G,F157-,R158-,A222V,T250I,S255F,L452R,T478K,D614G,P681R,D950N] AY.9.1 1967 105 5.3% 3 [V11I,T19R,A67S,G142D,E156G,F157-,R158-,A222V,S255F,L452R,T478K,D614G,P681R,D950N] AY.121 1967 678 34.5% 0 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.121 1967 366 18.6% 2 [T19R,T29I,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.121 1967 55 2.8% 1 [T19R,T95I,E156G,F157-,R158-,E180Q,L452R,T478K,D614G,P681R,D950N] AY.121 1967 48 2.4% 1 [T19R,T29I,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.121 1967 41 2.1% 1 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R] AY.3.1 1871 931 49.8% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.3.1 1871 324 17.3% 1 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.3.1 1871 25 1.3% 2 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,M1233I] AY.3.1 1871 20 1.1% 2 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R] AY.3.1 1871 18 1.0% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,A846V,D950N] AY.4.5 1804 1035 57.4% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,D1259Y] (consensus) AY.4.5 1804 91 5.0% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,G769V,D950N,D1259Y] AY.4.5 1804 79 4.4% 1 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,D1259Y] AY.4.5 1804 68 3.8% 2 [L18F,T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,Q613H,D614G,P681R,D950N,D1259Y] AY.4.5 1804 49 2.7% 1 [T19R,S60C,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,D1259Y] AY.113 1773 860 48.5% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.113 1773 280 15.8% 1 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.113 1773 26 1.5% 2 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R] AY.113 1773 17 1.0% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D796Y,D950N] AY.113 1773 16 0.9% 1 [T19R,T95I,D138Y,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.99.2 1443 586 40.6% 0 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.99.2 1443 248 17.2% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.99.2 1443 120 8.3% 1 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R] AY.99.2 1443 12 0.8% 2 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R] AY.99.2 1443 11 0.8% 1 [L5F,T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.69 1440 787 54.7% 0 [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] (consensus) AY.69 1440 153 10.6% 1 [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R] AY.69 1440 89 6.2% 1 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] AY.69 1440 23 1.6% 1 [T19R,E156G,F157-,R158-,A222V,L452R,P463S,T478K,D614G,P681R,D950N] AY.69 1440 16 1.1% 3 [T19R,A222V,L452R,T478K,D614G,P681R,D950N] AY.23 1261 681 54.0% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1264L] (consensus) AY.23 1261 57 4.5% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,A845S,D950N,V1264L] AY.23 1261 56 4.4% 3 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D586N,Q607K,D614G,P681R,D950N,E1262V,V1264L] AY.23 1261 52 4.1% 1 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1264L] AY.23 1261 18 1.4% 2 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D586N,D614G,P681R,D950N,E1262V,V1264L] AY.75 1152 490 42.5% 0 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] (consensus) AY.75 1152 194 16.8% 1 [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] AY.75 1152 40 3.5% 2 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,T573I,D614G,T638I,P681R,D950N] AY.75 1152 18 1.6% 3 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] AY.75 1152 13 1.1% 1 [L18F,T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] AY.85 1039 315 30.3% 0 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.85 1039 272 26.2% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.85 1039 88 8.5% 1 [T19R,T95I,E156G,F157-,R158-,F306L,L452R,T478K,D614G,P681R,D950N] AY.85 1039 23 2.2% 4 [Q14H,T19R,K77T,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,E1207D] AY.85 1039 14 1.3% 3 [Q14H,T19R,K77T,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,E1207D] AY.114 940 349 37.1% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.114 940 119 12.7% 1 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.114 940 103 11.0% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.114 940 54 5.7% 2 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.114 940 22 2.3% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,S640F,P681R,D950N] AY.108 888 202 22.7% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] AY.108 888 180 20.3% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.108 888 57 6.4% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,I850L,D950N] AY.108 888 48 5.4% 2 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,D950N] AY.108 888 41 4.6% 2 [T19R,T95I,G142D,E156G,F157-,R158-,Y248H,L452R,T478K,D614G,P681R,D950N] AY.23.1 883 631 71.5% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,L1234I,V1264L] (consensus) AY.23.1 883 109 12.3% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1264L] AY.23.1 883 45 5.1% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1230L,L1234I,V1264L] AY.23.1 883 13 1.5% 3 [T19R,G142D,L452R,T478K,D614G,P681R,D950N,L1234I,V1264L] AY.23.1 883 7 0.8% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,A903S,D950N,L1234I,V1264L] AY.93 838 387 46.2% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.93 838 89 10.6% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.93 838 58 6.9% 1 [T19R,G142D,E156G,F157-,R158-,W258L,L452R,T478K,D614G,P681R,D950N] AY.93 838 49 5.8% 2 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,T859N,D950N] AY.93 838 29 3.5% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,T547I,D614G,P681R,D950N] AY.39.1.1 825 779 94.4% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.39.1.1 825 8 1.0% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,P809L,D950N] AY.39.1.1 825 6 0.7% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,R765H,D950N] AY.39.1.1 825 5 0.6% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I692F,D950N] AY.39.1.1 825 2 0.2% 1 [T19R,T95I,G142D,E156G,F157-,R158-,V382A,L452R,T478K,D614G,P681R,D950N] AY.46.4 721 364 50.5% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,E661D,P681R,D950N] (consensus) AY.46.4 721 140 19.4% 1 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,E661D,P681R,D950N] AY.46.4 721 45 6.2% 1 [T19R,G142D,E156G,F157-,R158-,A222S,L452R,T478K,D614G,E661D,P681R,D950N] AY.46.4 721 19 2.6% 2 [T19R,E156G,F157-,R158-,A222S,L452R,T478K,D614G,E661D,P681R,D950N] AY.46.4 721 8 1.1% 2 [T19R,P26L,E156G,F157-,R158-,L452R,T478K,D614G,E661D,P681R,D950N] AY.54 709 342 48.2% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.54 709 92 13.0% 1 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.54 709 34 4.8% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.54 709 16 2.3% 1 [T19R,G142D,E156G,F157-,R158-,S255F,L452R,T478K,D614G,P681R,D950N] AY.54 709 14 2.0% 3 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] AY.116 679 134 19.7% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.116 679 99 14.6% 2 [T19R,G142D,E156G,F157-,R158-,Q173H,L452R,T478K,D614G,P681R,D950N] AY.116 679 74 10.9% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,P1162L] AY.116 679 50 7.4% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.116 679 27 4.0% 1 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.109 623 351 56.3% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.109 623 84 13.5% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,H1058Y] AY.109 623 44 7.1% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,E484K,D614G,P681R,D950N] AY.109 623 13 2.1% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.109 623 8 1.3% 2 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.9 580 249 42.9% 0 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] (consensus) AY.9 580 60 10.3% 1 [T19R,G142D,E156G,F157-,R158-,L189F,A222V,L452R,T478K,D614G,P681R,D950N] AY.9 580 53 9.1% 1 [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] AY.9 580 42 7.2% 2 [T19R,G142D,E156G,F157-,R158-,D215H,A222V,L452R,T478K,D614G,P681R,D950N,I1169V] AY.9 580 10 1.7% 1 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,Q675H,P681R,D950N] AY.30 551 249 45.2% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.30 551 117 21.2% 1 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.30 551 19 3.4% 4 [T19R,L452R,T478K,D614G,P681R,D950N] AY.30 551 14 2.5% 1 [T19R,G142D,E156G,F157-,R158-,G181V,L452R,T478K,D614G,P681R,D950N] AY.30 551 12 2.2% 1 [T19R,G142D,E156G,F157-,R158-,A262S,L452R,T478K,D614G,P681R,D950N] AY.80 547 218 39.9% 0 [T19R,T20I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.80 547 204 37.3% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.80 547 44 8.0% 2 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,A1020S] AY.80 547 16 2.9% 2 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,A701S,D950N] AY.80 547 9 1.6% 3 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.14 540 312 57.8% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.14 540 65 12.0% 1 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.14 540 13 2.4% 2 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] AY.14 540 12 2.2% 2 [T19R,G142D,Y144-,E156G,F157-,R158-,A348S,L452R,T478K,D614G,P681R,D950N] AY.14 540 11 2.0% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,T547I,D614G,P681R,D950N] AY.66 521 426 81.8% 0 [T19R,G142D,E156G,F157-,R158-,A222V,A260T,L452R,T478K,D614G,P681R,D950N] (consensus) AY.66 521 15 2.9% 1 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] AY.66 521 9 1.7% 2 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,Q613H,D614G,P681R,D950N] AY.66 521 7 1.3% 3 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.66 521 5 1.0% 5 [T19R,T95I,S98F,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] AY.92 506 290 57.3% 0 [T19R,T95I,G142D,E156G,F157-,R158-,D178N,L452R,T478K,D614G,P681R,D950N] (consensus) AY.92 506 34 6.7% 1 [T19R,T95I,E156G,F157-,R158-,D178N,L452R,T478K,D614G,P681R,D950N] AY.92 506 30 5.9% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.92 506 15 3.0% 1 [T19R,T95I,G142D,E156G,F157-,R158-,D178N,L452R,T478K,D614G,P681R,D950N,P1162S] AY.92 506 12 2.4% 1 [T19R,T95I,G142D,E156G,F157-,R158-,D178N,L452R,T478K,S494L,D614G,P681R,D950N] AY.7.1 501 159 31.7% 0 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.7.1 501 147 29.3% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.7.1 501 61 12.2% 2 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,A688V,D950N] AY.7.1 501 32 6.4% 1 [T19R,E156G,F157-,R158-,L452R,T478K,E484A,D614G,P681R,D950N] AY.7.1 501 9 1.8% 2 [T19R,E156G,F157-,R158-,A263V,L452R,T478K,D614G,P681R,D950N,V1033A] AY.5.4 478 202 42.3% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.5.4 478 82 17.2% 1 [T19R,D80Y,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.5.4 478 58 12.1% 1 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.5.4 478 27 5.6% 2 [T19R,D80Y,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.5.4 478 8 1.7% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,T739I,D950N] AY.120.1 476 244 51.3% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.120.1 476 68 14.3% 1 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.120.1 476 9 1.9% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,P1162L] AY.120.1 476 9 1.9% 3 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,N679T,S680-,P681R,D950N] AY.120.1 476 7 1.5% 5 [T19R,L452R,T478K,D614G,P681R,D950N] AY.90 412 232 56.3% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.90 412 53 12.9% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.90 412 42 10.2% 1 [T19R,G142D,E156G,F157-,R158-,P174S,L452R,T478K,D614G,P681R,D950N] AY.90 412 16 3.9% 2 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.90 412 11 2.7% 2 [T19R,G142D,E156G,F157-,R158-,P174S,L452R,T478K,D574Y,D614G,P681R,D950N] AY.41 401 100 24.9% 0 [T19R,G142D,E156G,F157-,R158-,A262S,L452R,S477I,T478K,D614G,P681R,D950N,G1167V] (consensus) AY.41 401 90 22.4% 1 [T19R,E156G,F157-,R158-,A262S,L452R,S477I,T478K,D614G,P681R,D950N,G1167V] AY.41 401 30 7.5% 4 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.41 401 19 4.7% 3 [T19R,E156G,F157-,R158-,A262S,L452R,S477I,T478K,Q613H,D614G,P681R,D950N,G1167V,K1191N] AY.41 401 13 3.2% 1 [T19R,G142D,E156G,F157-,R158-,A262S,L452R,S477I,T478K,D614G,T678I,P681R,D950N,G1167V] AY.116.1 395 161 40.8% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.116.1 395 37 9.4% 1 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.116.1 395 25 6.3% 1 [T19R,T95I,G142D,E156G,F157-,R158-,F306L,L452R,T478K,D614G,P681R,D950N] AY.116.1 395 20 5.1% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,A1026S] AY.116.1 395 14 3.5% 1 [S12F,T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.107 385 186 48.3% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,H1101Y] (consensus) AY.107 385 64 16.6% 1 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,H1101Y] AY.107 385 19 4.9% 1 [T19R,T95I,G142D,V143F,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,H1101Y] AY.107 385 12 3.1% 5 [T19R,L452R,T478K,D614G,P681R,D950N,H1101Y] AY.107 385 10 2.6% 2 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,H1101Y] AY.45 377 130 34.5% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.45 377 35 9.3% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.45 377 31 8.2% 2 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.45 377 21 5.6% 2 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] AY.45 377 17 4.5% 3 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,T747I,D936N,D950N] AY.46.5 346 275 79.5% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.46.5 346 34 9.8% 1 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.46.5 346 10 2.9% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,A623S,P681R,D950N] AY.46.5 346 8 2.3% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,S939F,D950N] AY.46.5 346 2 0.6% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,I1132V] AY.7 341 259 76.0% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.7 341 26 7.6% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,T747I,D950N] AY.7 341 14 4.1% 1 [L5F,T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.7 341 6 1.8% 1 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.7 341 6 1.8% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,T1076I] AY.101 338 86 25.4% 0 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.101 338 73 21.6% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.101 338 39 11.5% 2 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R] AY.101 338 26 7.7% 1 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R] AY.101 338 8 2.4% 2 [T19R,T95I,G142D,E156G,F157-,R158-,V308L,L452R,T478K,D614G,P681R,D950N] AY.84 333 103 30.9% 0 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.84 333 77 23.1% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.84 333 21 6.3% 2 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.84 333 13 3.9% 1 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R] AY.84 333 13 3.9% 3 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,T747I,I850L,D950N] AY.4.4 329 171 52.0% 0 [L5F,T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,S929T,D950N] (consensus) AY.4.4 329 23 7.0% 1 [L5F,T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,S929T,D950N] AY.4.4 329 23 7.0% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,S929T,D950N] AY.4.4 329 13 4.0% 2 [L5F,T19R,T95I,I101T,E156G,F157-,R158-,L452R,T478K,D614G,P681R,S929T,D950N] AY.4.4 329 9 2.7% 3 [L5F,T19R,D80Y,T95I,E156G,F157-,R158-,L452R,S477I,T478K,D614G,P681R,S929T,D950N] AY.39.2 328 237 72.3% 0 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,K1073N] (consensus) AY.39.2 328 44 13.4% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,K1073N] AY.39.2 328 7 2.1% 1 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,V635A,P681R,D950N,K1073N] AY.39.2 328 5 1.5% 1 [L5F,T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,K1073N] AY.39.2 328 3 0.9% 3 [T19R,G75V,T76I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,K1073N] AY.106 313 67 21.4% 0 [T19R,T95I,E156G,F157-,R158-,S255F,L452R,T478K,D614G,P681R,D950N] (consensus) AY.106 313 39 12.5% 1 [T19R,T95I,G142D,E156G,F157-,R158-,S255F,L452R,T478K,D614G,P681R,D950N] AY.106 313 36 11.5% 3 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.106 313 21 6.7% 2 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.106 313 14 4.5% 1 [T19R,T95I,E156G,F157-,R158-,S255F,L452R,T478K,D614G,P681R,D950N,A1087S] AY.72 305 157 51.5% 0 [T19R,G142D,E156G,F157-,R158-,F201L,A222V,L452R,T478K,D614G,P681R,D950N] (consensus) AY.72 305 94 30.8% 1 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] AY.72 305 7 2.3% 2 [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] AY.72 305 5 1.6% 3 [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1122L] AY.72 305 4 1.3% 1 [T19R,G142D,E156G,F157-,R158-,F201L,A222V,T323A,L452R,T478K,D614G,P681R,D950N] AY.5.3 304 151 49.7% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.5.3 304 41 13.5% 1 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.5.3 304 19 6.2% 1 [T19R,G142D,E156G,F157-,R158-,A263V,L452R,T478K,D614G,P681R,D950N] AY.5.3 304 9 3.0% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,K1191N] AY.5.3 304 7 2.3% 1 [T19R,P25T,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.65 303 133 43.9% 0 [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] (consensus) AY.65 303 23 7.6% 1 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] AY.65 303 21 6.9% 4 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,A701S,D950N,K1191N] AY.65 303 18 5.9% 2 [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R] AY.65 303 12 4.0% 1 [T19R,E156G,F157-,R158-,A222V,L452R,T478K,E583D,D614G,P681R,D950N,V1264L] AY.62 294 149 50.7% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.62 294 25 8.5% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,E1207D] AY.62 294 18 6.1% 2 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] AY.62 294 16 5.4% 4 [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,N978S] AY.62 294 13 4.4% 1 [T19R,A27S,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.74 284 180 63.4% 0 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] (consensus) AY.74 284 12 4.2% 3 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,H655Y,P681R,D950N] AY.74 284 12 4.2% 1 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,E1188D] AY.74 284 9 3.2% 1 [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] AY.74 284 7 2.5% 1 [T19R,G142D,E156G,F157-,R158-,A222V,P337L,L452R,T478K,D614G,P681R,D950N] AY.110 280 135 48.2% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.110 280 29 10.4% 1 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.110 280 21 7.5% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.110 280 7 2.5% 2 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.110 280 4 1.4% 2 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,T1009I] AY.79 279 106 38.0% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.79 279 76 27.2% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.79 279 39 14.0% 2 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.79 279 6 2.2% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,H655Y,P681R,D950N] AY.79 279 5 1.8% 3 [T19R,E156G,F157-,R158-,R214L,L452R,T478K,D614G,P681R,D950N] AY.46.1 278 163 58.6% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.46.1 278 23 8.3% 1 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.46.1 278 13 4.7% 2 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,D1127Y] AY.46.1 278 8 2.9% 1 [T19R,P85L,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.46.1 278 7 2.5% 2 [Q14H,T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.46.2 263 61 23.2% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.46.2 263 41 15.6% 1 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.46.2 263 22 8.4% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,P809S,D950N] AY.46.2 263 14 5.3% 2 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,P809S,D950N] AY.46.2 263 12 4.6% 2 [T19R,S98P,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.4.3 261 59 22.6% 0 [T19R,P26S,L54F,T95I,G142D,E156G,F157-,R158-,A262S,L452R,T478K,D614G,P681R,D950N,A1078S] AY.4.3 261 54 20.7% 2 [T19R,P26S,L54F,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.4.3 261 34 13.0% 4 [T19R,P26S,L54F,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,H1101Y] AY.4.3 261 30 11.5% 3 [T19R,P26S,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.4.3 261 16 6.1% 3 [T19R,P26S,L54F,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.13 243 88 36.2% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.13 243 38 15.6% 1 [T19R,G142D,E156G,F157-,R158-,I210-,L452R,T478K,D614G,P681R,D950N] AY.13 243 28 11.5% 1 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.13 243 13 5.3% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.13 243 7 2.9% 2 [T19R,E156G,F157-,R158-,I210-,L452R,T478K,D614G,P681R,D950N] AY.105 231 58 25.1% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.105 231 52 22.5% 1 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.105 231 27 11.7% 2 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.105 231 17 7.4% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,K1191N] AY.105 231 6 2.6% 2 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R] AY.73 229 110 48.0% 0 [T19R,G142D,W152L,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] (consensus) AY.73 229 33 14.4% 1 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] AY.73 229 20 8.7% 2 [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] AY.73 229 19 8.3% 2 [T19R,G142D,E156G,F157-,R158-,I210V,A222V,L452R,T478K,D614G,P681R,D950N] AY.73 229 7 3.1% 2 [T19R,D88N,G142D,W152L,E156G,F157-,R158-,A222V,L452R,T478K,P681R,D950N] AY.34.1 223 126 56.5% 0 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,Q677H,P681R,D950N,L1265F] (consensus) AY.34.1 223 18 8.1% 2 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,Q677H,P681R] AY.34.1 223 15 6.7% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,Q677H,P681R,D950N,L1265F] AY.34.1 223 13 5.8% 1 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,Q677H,P681R,L1265F] AY.34.1 223 2 0.9% 1 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,Q677H,P681R,D950N] AY.37 222 35 15.8% 0 [T19R,G142D,E156G,F157-,R158-,A222V,V367L,L452R,T478K,D614G,P681R,D950N] AY.37 222 33 14.9% 1 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] (consensus) AY.37 222 27 12.2% 1 [T19R,E156G,F157-,R158-,A222V,V367L,L452R,T478K,D614G,P681R,D950N] AY.37 222 18 8.1% 3 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.37 222 11 5.0% 5 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] AY.59 208 60 28.8% 0 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] (consensus) AY.59 208 55 26.4% 1 [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] AY.59 208 20 9.6% 1 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] AY.59 208 5 2.4% 1 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,Q613H,D614G,P681R,D950N] AY.59 208 4 1.9% 1 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,T678P,P681R,D950N] AY.86 204 129 63.2% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.86 204 12 5.9% 1 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.86 204 11 5.4% 2 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,A845S,D950N] AY.86 204 8 3.9% 1 [T19R,T95I,G142D,E156G,F157-,R158-,G181V,L452R,T478K,D614G,P681R,D950N] AY.86 204 6 2.9% 2 [T19R,R21I,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.51 184 98 53.3% 0 [T19R,E156G,F157-,R158-,L452R,T478K,A520S,D614G,P681R,D950N] (consensus) AY.51 184 42 22.8% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,A520S,D614G,P681R,D950N] AY.51 184 7 3.8% 2 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.51 184 6 3.3% 1 [T19R,E156G,F157-,R158-,L452R,T478K,A520S,D614G,P681R] AY.51 184 3 1.6% 1 [T19R,E156G,F157-,R158-,L452R,T478K,A520S,E583D,D614G,P681R,D950N] AY.70 177 61 34.5% 0 [T19R,R21T,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] (consensus) AY.70 177 54 30.5% 1 [T19R,R21T,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] AY.70 177 10 5.6% 3 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,N1074S,V1264L] AY.70 177 8 4.5% 2 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.70 177 7 4.0% 3 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,T547I,D614G,P681R,D950N,P1069S] AY.46.3 172 66 38.4% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.46.3 172 50 29.1% 1 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.46.3 172 9 5.2% 2 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R] AY.46.3 172 6 3.5% 2 [T19R,W64C,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.46.3 172 4 2.3% 3 [T19R,T51I,E156G,F157-,R158-,L452R,T478K,D614G,P681R] AY.58 171 64 37.4% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.58 171 50 29.2% 2 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] AY.58 171 12 7.0% 1 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.58 171 6 3.5% 3 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,P479S,D614G,P681R,D950N] AY.58 171 4 2.3% 3 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,T547I,D614G,P681R,D950N] AY.1 167 90 53.9% 0 [T19R,T95I,G142D,E156G,F157-,R158-,W258L,K417N,L452R,T478K,D614G,P681R,D950N] (consensus) AY.1 167 20 12.0% 1 [T19R,T95I,E156G,F157-,R158-,W258L,K417N,L452R,T478K,D614G,P681R,D950N] AY.1 167 10 6.0% 1 [T19R,T95I,G142D,E156G,F157-,R158-,W258L,K417N,L452R,T478K,D614G,P681R,D950N,M1237I] AY.1 167 5 3.0% 1 [T19R,L54F,T95I,G142D,E156G,F157-,R158-,W258L,K417N,L452R,T478K,D614G,P681R,D950N] AY.1 167 5 3.0% 5 [T19R,W258L,K417N,L452R,T478K,D614G,P681R,D950N] AY.43.1 167 103 61.7% 0 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.43.1 167 31 18.6% 1 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R] AY.43.1 167 8 4.8% 1 [T19R,S98F,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.43.1 167 7 4.2% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.43.1 167 4 2.4% 2 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R] AY.91 164 38 23.2% 0 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.91 164 34 20.7% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.91 164 20 12.2% 2 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.91 164 12 7.3% 1 [T19R,E156G,F157-,R158-,G181V,L452R,T478K,D614G,P681R,D950N] AY.91 164 5 3.0% 3 [T19R,G142D,E156G,F157-,R158-,Y200H,L452R,T478K,D614G,P681R,D950N,D1259H] AY.120.2.1 155 114 73.5% 0 [T19R,H66Y,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.120.2.1 155 33 21.3% 1 [T19R,H66Y,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.120.2.1 155 1 0.6% 1 [T19R,H66Y,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,G1124V] AY.120.2.1 155 1 0.6% 2 [L5F,T19R,H66Y,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.120.2.1 155 1 0.6% 1 [T19R,H66Y,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,R847K,D950N] AY.43.2 153 101 66.0% 0 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.43.2 153 19 12.4% 1 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R] AY.43.2 153 10 6.5% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.43.2 153 3 2.0% 1 [L8-,T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.43.2 153 2 1.3% 1 [T19R,E156G,F157-,R158-,L452R,E471Q,T478K,D614G,P681R,D950N] AY.32 151 34 22.5% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,T572I,D614G,P681R,D950N] (consensus) AY.32 151 30 19.9% 2 [T19R,Y28F,G142D,E156G,F157-,R158-,L216F,L452R,T478K,T572I,D614G,P681R,D950N] AY.32 151 20 13.2% 1 [T19R,E156G,F157-,R158-,L452R,T478K,T572I,D614G,P681R,D950N] AY.32 151 13 8.6% 3 [T19R,Y28F,T95I,G142D,E156G,F157-,R158-,L216F,L452R,T478K,T572I,D614G,P681R,D950N] AY.32 151 6 4.0% 3 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.28 151 107 70.9% 0 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,A701S,D950N,A1078S] (consensus) AY.28 151 4 2.6% 1 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T470I,T478K,D614G,P681R,A701S,D950N,A1078S] AY.28 151 3 2.0% 1 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,A701S,D950N,A1078S,I1221L] AY.28 151 2 1.3% 2 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T470I,T478K,D614G,V622F,P681R,A701S,D950N,A1078S] AY.28 151 2 1.3% 1 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,N540K,D614G,P681R,A701S,D950N,A1078S] AY.64 141 72 51.1% 0 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,K1191N] (consensus) AY.64 141 27 19.1% 1 [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,K1191N] AY.64 141 6 4.3% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,K1191N] AY.64 141 5 3.5% 2 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,K1191N] AY.64 141 4 2.8% 2 [L5F,T19R,G142D,H146L,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,K1191N] AY.88 141 49 34.8% 0 [T19R,T124S,G142D,E156G,F157-,R158-,L452R,T478K,D614G,S680F,P681R,D950N] AY.88 141 13 9.2% 2 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.88 141 13 9.2% 1 [T19R,T20I,T124S,G142D,E156G,F157-,R158-,L452R,T478K,D614G,S680F,P681R,D950N] AY.88 141 12 8.5% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,S680F,P681R,D950N] (consensus) AY.88 141 8 5.7% 2 [T19R,G142D,E156G,F157-,R158-,Q414R,L452R,T478K,D614G,S680F,P681R,D950N] AY.61 137 32 23.4% 0 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] AY.61 137 25 18.2% 1 [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] (consensus) AY.61 137 18 13.1% 1 [T19R,P85S,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] AY.61 137 13 9.5% 2 [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] AY.61 137 8 5.8% 2 [T19R,P85S,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] AY.83 133 64 48.1% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.83 133 56 42.1% 1 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.83 133 5 3.8% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.83 133 3 2.3% 2 [T19R,E156G,F157-,R158-,G252V,L452R,T478K,D614G,P681R,D950N] AY.83 133 1 0.8% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,A845V,D950N] AY.7.2 131 51 38.9% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.7.2 131 35 26.7% 1 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.7.2 131 6 4.6% 1 [T19R,G142D,E156G,F157-,R158-,P174S,L452R,T478K,D614G,P681R,D950N] AY.7.2 131 5 3.8% 1 [L5F,T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.7.2 131 5 3.8% 2 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,G1219C,M1237I] AY.63 123 62 50.4% 0 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,K814R,D950N] (consensus) AY.63 123 42 34.1% 1 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] AY.63 123 4 3.3% 2 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,S704L,D950N] AY.63 123 4 3.3% 2 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,C1243F] AY.63 123 4 3.3% 2 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,A1078S] AY.35 123 39 31.7% 0 [T19R,K77T,G142D,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,D808E,D950N] AY.35 123 36 29.3% 1 [T19R,K77T,G142D,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,D950N] (consensus) AY.35 123 16 13.0% 3 [T19R,K77T,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.35 123 5 4.1% 1 [T19R,K77T,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,D808E,D950N] AY.35 123 4 3.3% 2 [T19R,K77T,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,D950N] AY.104 117 74 63.2% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,T572I,D614G,P681R,D950N] (consensus) AY.104 117 6 5.1% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.104 117 2 1.7% 1 [S12F,T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,T572I,D614G,P681R,D950N] AY.104 117 2 1.7% 2 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.104 117 2 1.7% 3 [T19R,H69Y,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.57 116 76 65.5% 0 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] (consensus) AY.57 116 12 10.3% 3 [T19R,L54F,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.57 116 9 7.8% 4 [T19R,L54F,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.57 116 6 5.2% 3 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.57 116 3 2.6% 2 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.1.7 115 50 43.5% 0 [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] (consensus) B.1.1.7 115 10 8.7% 1 [H69-,V70-,Y144-,E484K,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7 115 9 7.8% 2 [H69-,V70-,Y144-,V213L,E484K,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7 115 4 3.5% 3 [H69-,V70-,Y144-,E484K,N501Y,A570D,D614G,Q677H,P681H,A688S,T716I,S982A,D1118H] B.1.1.7 115 3 2.6% 2 [H69-,V70-,Y144-,S155G,V367F,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] AY.94 106 28 26.4% 0 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.94 106 21 19.8% 2 [T19R,G142D,E156G,F157-,R158-,D215Y,L452R,T478K,D614G,P681R,D950N] AY.94 106 16 15.1% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.94 106 11 10.4% 3 [T19R,G142D,E156G,F157-,R158-,D215Y,L452R,T478K,D614G,P681R,S689I,D950N] AY.94 106 7 6.6% 2 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] AY.67 94 21 22.3% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.67 94 13 13.8% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.67 94 8 8.5% 3 [T19R,G142D,E156G,F157-,R158-,A222V,A262S,L452R,T478K,D614G,P681R,D950N] AY.67 94 7 7.4% 4 [T19R,G142D,E156G,F157-,R158-,A222V,A262S,L452R,T478K,Q613H,D614G,P681R,D950N] AY.67 94 5 5.3% 5 [T19R,G142D,E156G,F157-,R158-,A222V,A262S,L452R,T478K,Q613H,D614G,P681R,D950N,L1265F] AY.99.1 92 31 33.7% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.99.1 92 30 32.6% 1 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.99.1 92 3 3.3% 2 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,Q1208H] AY.99.1 92 3 3.3% 2 [T19R,E156G,F157-,R158-,L452R,S459F,T478K,D614G,P681R,D950N] AY.99.1 92 3 3.3% 2 [T19R,Q23H,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,S704L,D950N] AY.78 86 28 32.6% 0 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.78 86 9 10.5% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.78 86 6 7.0% 1 [L5F,T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.78 86 5 5.8% 3 [T19R,D80N,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N,M1229I] AY.78 86 4 4.7% 2 [T19R,P25T,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1176F] AY.96 85 38 44.7% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.96 85 7 8.2% 2 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.96 85 7 8.2% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.96 85 6 7.1% 4 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,A846V,A1078S] AY.96 85 5 5.9% 3 [T19R,P26H,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.112 85 36 42.4% 0 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.112 85 6 7.1% 1 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D936G,D950N] AY.112 85 5 5.9% 1 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,E1207D] AY.112 85 4 4.7% 1 [T19R,T95I,E156G,F157-,R158-,S254F,L452R,T478K,D614G,P681R,D950N] AY.112 85 3 3.5% 1 [T19R,T76A,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.5.2 85 66 77.6% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.5.2 85 9 10.6% 1 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.5.2 85 7 8.2% 1 [T19R,G142D,S155I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.5.2 85 1 1.2% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,S875F,D950N] AY.5.2 85 1 1.2% 1 [L5F,T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.87 78 59 75.6% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.87 78 5 6.4% 1 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.87 78 5 6.4% 2 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,N679T,S680-,P681R,D950N] AY.87 78 2 2.6% 2 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.87 78 1 1.3% 3 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,T678I,P681R,L822F,D950N] AY.68 75 29 38.7% 0 [T19R,E156G,F157-,R158-,A222V,D253A,L452R,T478K,D614G,P681R,D950N,D979E] AY.68 75 20 26.7% 1 [T19R,G142D,E156G,F157-,R158-,A222V,D253A,L452R,T478K,D614G,P681R,D950N,D979E] (consensus) AY.68 75 5 6.7% 2 [T19R,G142D,E156G,F157-,R158-,A222V,D253A,L452R,T478K,D614G,P681R,P809S,D950N,D979E] AY.68 75 5 6.7% 1 [T19R,E156G,F157-,R158-,A222V,D253A,L452R,T478K,D614G,R646L,P681R,D950N,D979E] AY.68 75 3 4.0% 2 [T19R,G142D,E156G,F157-,R158-,A222V,D253A,L452R,T478K,D614G,R646L,P681R,D950N,D979E] B.1.621 71 21 29.6% 0 [T95I,+143T,Y144S,Y145N,R346K,E484K,N501Y,D614G,P681H,D950N] (consensus) B.1.621 71 7 9.9% 5 [T95I,Y144N,Y145-,R346K,Y449N,E484K,N501Y,E583D,D614G,P681H,D950N] B.1.621 71 5 7.0% 2 [T95I,+143T,Y144S,Y145N,R346K,Y449N,E484K,N501Y,E583D,D614G,P681H,D950N] B.1.621 71 4 5.6% 1 [T95I,+143T,Y144S,Y145N,R346K,K417N,E484K,N501Y,D614G,P681H,D950N] B.1.621 71 4 5.6% 1 [T95I,+143T,Y144S,Y145N,R346K,E484K,N501Y,D614G,P681H,S939F,D950N] AY.77 70 23 32.9% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.77 70 13 18.6% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.77 70 7 10.0% 1 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.77 70 5 7.1% 2 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.77 70 4 5.7% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,Q628H,P681R,D950N] AY.75.1 66 16 24.2% 0 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] (consensus) AY.75.1 66 9 13.6% 1 [T19R,G142D,N148T,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] AY.75.1 66 9 13.6% 2 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.75.1 66 4 6.1% 1 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,P812S,D950N] AY.75.1 66 3 4.5% 1 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,Q613H,D614G,P681R,D950N] AY.4.1 65 52 80.0% 0 [T19R,T95I,G142D,E156G,F157-,R158-,G446V,L452R,T478K,D614G,P681R,D950N] (consensus) AY.4.1 65 5 7.7% 1 [T19R,T95I,G142D,E156G,F157-,R158-,G446V,L452R,T478K,D614G,P681R,D950N,V1122L] AY.4.1 65 2 3.1% 1 [T19R,T95I,G142D,E156G,F157-,R158-,G446V,L452R,T478K,D614G,P681R,Q836L,D950N] AY.4.1 65 1 1.5% 3 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,E484A,D614G,P681R,D950N] AY.4.1 65 1 1.5% 2 [L5F,T19R,T95I,G142D,E156G,F157-,R158-,G446V,L452R,T478K,D614G,P681R,D950N,V1122L] AY.56 64 16 25.0% 0 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,S680F,P681R,D950N] AY.56 64 9 14.1% 3 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.56 64 5 7.8% 4 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,T1117I,C1243F] AY.56 64 5 7.8% 1 [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,S680F,P681R,D950N] AY.56 64 4 6.2% 4 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,S939F,D950N] C.37 60 15 25.0% 0 [G75V,T76I,R246N,S247-,Y248-,L249-,T250-,P251-,G252-,D253-,L452Q,F490S,D614G,T859N] (consensus) C.37 60 5 8.3% 1 [G75V,T76I,R246N,S247-,Y248-,L249-,T250-,P251-,G252-,D253-,L452Q,F490S,D614G,P792L,T859N] C.37 60 5 8.3% 1 [A27S,G75V,T76I,R246N,S247-,Y248-,L249-,T250-,P251-,G252-,D253-,L452Q,F490S,D614G,T859N] C.37 60 4 6.7% 1 [G75V,T76I,V120A,R246N,S247-,Y248-,L249-,T250-,P251-,G252-,D253-,L452Q,F490S,D614G,T859N] C.37 60 3 5.0% 5 [T20I,H66Q,G75V,T76I,R246N,S247-,Y248-,L249-,T250-,P251-,G252-,D253-,L452Q,F490S,D614G,Q675H,Q677H,T859N,D950N] AY.22 60 35 58.3% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] (consensus) AY.22 60 8 13.3% 5 [T19R,L54F,T95I,G142D,E156G,F157-,R158-,M177I,Q218H,L452R,T478K,D614G,P681R,D950N,V1104L] AY.22 60 8 13.3% 3 [T19R,T95I,G142D,E156G,F157-,R158-,Q218H,L452R,T478K,D614G,P681R,D950N,V1104L] AY.22 60 3 5.0% 4 [T19R,T95I,E156G,F157-,R158-,Q218H,L452R,T478K,D614G,P681R,D950N,V1104L] AY.22 60 2 3.3% 1 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] P.1 59 27 45.8% 0 [L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] (consensus) P.1 59 16 27.1% 1 [L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,P681H,T1027I,V1176F] P.1 59 2 3.4% 2 [L5F,L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,P681H,T1027I,V1176F] P.1 59 2 3.4% 3 [L18F,T20N,P26S,D138Y,R190S,K417T,K444N,E484K,N501Y,A522V,D614G,H655Y,P681H,T1027I,V1176F] P.1 59 1 1.7% 1 [L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,Q613H,D614G,H655Y,T1027I,V1176F] AY.60 59 15 25.4% 0 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] AY.60 59 11 18.6% 1 [T19R,G72W,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] AY.60 59 10 16.9% 1 [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] (consensus) AY.60 59 7 11.9% 2 [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,L821I,D950N] AY.60 59 3 5.1% 2 [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,C1243F] P.1.12 54 23 42.6% 0 [L18F,T20N,P26S,D138Y,R190S,R246G,T284I,K417T,E484K,N501Y,D614G,H655Y,N679K,T1027I,V1176F] P.1.12 54 16 29.6% 1 [L18F,T20N,P26S,D138Y,R190S,R246G,K417T,E484K,N501Y,D614G,H655Y,N679K,T1027I,V1176F] (consensus) P.1.12 54 4 7.4% 3 [L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] P.1.12 54 3 5.6% 2 [L18F,T20N,P26S,D138Y,R190S,R246G,K417T,E484K,N501Y,D614G,H655Y,N679K,T961M,T1027I,V1176F] P.1.12 54 2 3.7% 2 [L18F,T20N,P26S,D138Y,L176F,R190S,R246G,K417T,E484K,N501Y,D614G,H655Y,N679K,T1027I,V1176F] AY.29 53 22 41.5% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.29 53 8 15.1% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,S494L,D614G,P681R,D950N] AY.29 53 4 7.5% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,E465D,T478K,D614G,P681R,D950N] AY.29 53 2 3.8% 2 [T19R,T95I,Y144-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.29 53 2 3.8% 2 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.24 49 25 51.0% 0 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] (consensus) AY.24 49 7 14.3% 1 [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] AY.24 49 3 6.1% 1 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,D1153Y] AY.24 49 2 4.1% 1 [T19R,H69Y,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] AY.24 49 2 4.1% 5 [T19R,I128V,E156G,F157-,R158-,L452R,T478K,Q607H,D614G,P681R,Q949L,D950N] B.1.1.529 47 37 78.7% 0 [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] (consensus) B.1.1.529 47 2 4.3% 3 [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] B.1.1.529 47 2 4.3% 3 [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] B.1.1.529 47 1 2.1% 1 [A67V,H69-,V70-,T95I,L141F,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] B.1.1.529 47 1 2.1% 1 [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,V367F,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] AY.81 41 15 36.6% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,A694V,D950N,D1260Y] (consensus) AY.81 41 7 17.1% 3 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.81 41 4 9.8% 6 [T19R,D138Y,G142D,L452R,T478K,D614G,P681R,D1260Y] AY.81 41 4 9.8% 1 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,A694V,D950N,D1260Y] AY.81 41 2 4.9% 2 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,D1260Y] AY.21 37 19 51.4% 0 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.21 37 11 29.7% 2 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,S494P,D614G,P681R,G946R,D950N] AY.21 37 2 5.4% 3 [T19R,T95I,E156G,F157-,R158-,L452R,T470I,T478K,P479S,D614G,P681R,D950N,C1254F] AY.21 37 2 5.4% 1 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,P1079S] AY.21 37 2 5.4% 2 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,E702Q,D950N,L1063F] AY.71 36 10 27.8% 0 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,S1252F] (consensus) AY.71 36 5 13.9% 1 [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,S1252F] AY.71 36 4 11.1% 2 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,S1252F] AY.71 36 2 5.6% 1 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,N460S,T478K,D614G,P681R,D950N,S1252F] AY.71 36 2 5.6% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,S1252F] AY.99 36 21 58.3% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.99 36 3 8.3% 2 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.99 36 1 2.8% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,Q677R,P681R,D950N] AY.99 36 1 2.8% 2 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,E1202Q] AY.99 36 1 2.8% 1 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.52 36 29 80.6% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,L1141W] (consensus) AY.52 36 2 5.6% 1 [T19R,G142D,E156G,F157-,R158-,A262S,L452R,T478K,D614G,P681R,D950N,L1141W] AY.52 36 1 2.8% 4 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] AY.52 36 1 2.8% 5 [T19I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,A845S] AY.52 36 1 2.8% 3 [T19R,F59S,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] P.1.15 34 13 38.2% 0 [L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] (consensus) P.1.15 34 3 8.8% 1 [L18F,T20N,P26S,D138Y,M153T,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] P.1.15 34 3 8.8% 2 [L18F,T20N,P26S,T95S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,G1085E,V1176F] P.1.15 34 2 5.9% 3 [L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,A623S,H655Y,E780Q,A845V,T1027I,V1176F] P.1.15 34 2 5.9% 2 [L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,Q675H,T1027I,G1085E,V1176F] AY.95 33 5 15.2% 0 [T19R,G142D,E156G,F157-,R158-,L244S,L452R,T478K,T572I,D614G,P681R,D950N] AY.95 33 4 12.1% 1 [T19R,G142D,E156G,F157-,R158-,L244S,L452R,T478K,D614G,P681R,D950N] AY.95 33 3 9.1% 1 [T19R,E156G,F157-,R158-,L244S,L452R,T478K,T572I,D614G,P681R,D950N] AY.95 33 3 9.1% 5 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,G1219V] AY.95 33 2 6.1% 1 [T19R,G142D,E156G,F157-,R158-,L244S,L452R,T478K,T572I,D614G,P681R,D950N,V1189I] B.1.640 33 12 36.4% 0 [P9L,E96Q,C136-,N137Y,D138-,P139-,F140-,L141-,G142-,V143-,Y144-,Y145-,R190S,I210T,R346S,N394S,Y449N,F490R,N501Y,D614G,P681H,T859N,D936H] (consensus) B.1.640 33 11 33.3% 1 [P9L,E96Q,C136-,N137Y,D138-,P139-,F140-,L141-,G142-,V143-,Y144-,Y145-,R190S,I210T,R346S,N394S,Y449N,F490R,N501Y,D614G,P681H,T859N,D936H,K1191N] B.1.640 33 4 12.1% 1 [P9L,E96Q,C136-,N137Y,D138-,P139-,F140-,L141-,G142-,V143-,Y144-,Y145-,R190S,I210T,R346S,N394S,Y449N,F490R,N501Y,D614G,P681H,T859N,D936H,D1259H] B.1.640 33 2 6.1% 1 [L5F,P9L,E96Q,C136-,N137Y,D138-,P139-,F140-,L141-,G142-,V143-,Y144-,Y145-,R190S,I210T,R346S,N394S,Y449N,F490R,N501Y,D614G,P681H,T859N,D936H] B.1.640 33 2 6.1% 10 [P9L,E96Q,Y144F,R190S,I210T,R346S,N394S,Y449N,F490R,N501Y,D614G,P681H,T859N,D936H] AY.89 33 12 36.4% 0 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.89 33 3 9.1% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.89 33 3 9.1% 2 [T19R,T95I,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] AY.89 33 2 6.1% 2 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,Q675H,P681R,D950N] AY.89 33 2 6.1% 3 [T19R,T95I,L452R,T478K,D614G,P681R,D950N] AY.16 33 10 30.3% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.16 33 9 27.3% 2 [T19R,G142D,Y144-,E156G,F157-,R158-,D215H,L452R,T478K,D614G,P681R,D950N] (consensus) AY.16 33 3 9.1% 3 [T19R,Y144-,E156G,F157-,R158-,D215H,L452R,T478K,D614G,P681R,D950N] AY.16 33 2 6.1% 4 [T19R,Y144-,E156G,F157-,R158-,D215H,L452R,T478K,D614G,P681R,R682L,D950N] AY.16 33 1 3.0% 4 [T19R,D80Y,E156G,F157-,R158-,L452R,T478K,D614G,P681R,T1117I] AY.97 33 27 81.8% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.97 33 5 15.2% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,T1160I] AY.97 33 1 3.0% 3 [T19R,G142D,E156G,F157-,R158-,A348V,L452R,T478K,Q613H,D614G,P681R,D950N,N1187Y] AY.53 32 5 15.6% 0 [T19R,G142D,E156G,F157-,R158-,G181V,L452R,T478K,D614G,P681R,D950N] AY.53 32 4 12.5% 3 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.53 32 3 9.4% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.53 32 3 9.4% 5 [T19R,T95I,E156G,F157-,R158-,E281Q,L452R,T478K,D614G,P681R,I850L,D950N] AY.53 32 2 6.2% 2 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.17 26 20 76.9% 0 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.17 26 2 7.7% 3 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] AY.17 26 1 3.8% 3 [L5F,T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.17 26 1 3.8% 1 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R] AY.17 26 1 3.8% 3 [T19R,E156G,F157-,R158-,V433I,L452R,T478K,D614G,P681R,F782Y,D950N,C1250F] AY.38 25 6 24.0% 0 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] (consensus) AY.38 25 3 12.0% 1 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] AY.38 25 3 12.0% 3 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,H655Y,P681R,D950N] AY.38 25 2 8.0% 2 [T19R,E156G,F157-,R158-,A222V,T250S,L452R,T478K,D614G,P681R,D950N] AY.38 25 2 8.0% 1 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,V785I,D950N] AY.82 25 7 28.0% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.82 25 3 12.0% 2 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.82 25 2 8.0% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.82 25 2 8.0% 2 [T19R,T95I,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] AY.82 25 1 4.0% 2 [T19R,G142D,E156G,F157-,R158-,G257V,L452R,T478K,S494L,D614G,P681R,D950N] AY.120.2 24 6 25.0% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.120.2 24 3 12.5% 4 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,N1074S,V1264L] AY.120.2 24 3 12.5% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,S689N,D950N] AY.120.2 24 2 8.3% 5 [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,N1074S,V1264L] AY.120.2 24 2 8.3% 2 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.20.1 22 13 59.1% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1104L] (consensus) AY.20.1 22 1 4.5% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,M731I,D950N,V1104L] AY.20.1 22 1 4.5% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.20.1 22 1 4.5% 2 [T19R,T95I,E156G,F157-,R158-,G446V,L452R,T478K,D614G,P681R,D950N,V1104L] AY.20.1 22 1 4.5% 2 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,S640-,N641Y,P681R,D950N,V1104L] AY.76 22 7 31.8% 0 [T19R,E156G,F157-,R158-,L452R,T478K,T573I,D614G,P681R,D950N] AY.76 22 5 22.7% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,T573I,D614G,P681R,D950N] (consensus) AY.76 22 2 9.1% 2 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.76 22 2 9.1% 2 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,G946V,D950N] AY.76 22 1 4.5% 6 [T19R,L54F,D80Y,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R] AY.11 20 7 35.0% 0 [T19R,T95I,N148Y,E156G,F157-,R158-,L452R,T478K,D614G,P681R,A701V,D950N] AY.11 20 4 20.0% 6 [T19R,E156G,F157-,R158-,A222V,D253A,L452R,T478K,Q613H,D614G,P681R,D950N] AY.11 20 3 15.0% 3 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.11 20 1 5.0% 3 [T19R,T95I,N148Y,E156G,F157-,R158-,T376S,L452R,T478K,D614G,P681R,I850L,D950N] AY.11 20 1 5.0% 4 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.48 19 4 21.1% 0 [T19R,K77T,G142D,E156G,F157-,R158-,L452R,T478K,T547I,D614G,P681R,D950N] AY.48 19 2 10.5% 5 [T19R,E156G,F157-,R158-,A222V,L452R,S477I,T478K,D614G,P681R,D950N] AY.48 19 2 10.5% 1 [T19R,K77T,E156G,F157-,R158-,L452R,T478K,T547I,D614G,P681R,D950N] AY.48 19 1 5.3% 3 [T19R,K77T,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,P809S,D950N,N1187D] AY.48 19 1 5.3% 6 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L] B.1.177 18 6 33.3% 0 [A222V,D614G,Q675H] B.1.177 18 5 27.8% 1 [A222V,D614G] (consensus) B.1.177 18 2 11.1% 3 [A222V,A262S,P272L,D614G] B.1.177 18 1 5.6% 1 [A222V,D614G,Q675H,D1199N] B.1.177 18 1 5.6% 5 [L5F,A222V,T572I,D614G,D936H,T1027I] AY.19 17 6 35.3% 0 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,S680F,P681R,D950N,D1153Y] AY.19 17 3 17.6% 5 [T19R,Y144-,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] AY.19 17 2 11.8% 3 [T19R,T95I,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] AY.19 17 1 5.9% 4 [T19R,T95I,E156G,F157-,R158-,E281Q,L452R,T478K,D614G,P681R,I850L,D950N,D1153Y,V1264L] AY.19 17 1 5.9% 4 [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] AZ.5 16 9 56.2% 0 [D80Y,T95I,Y144-,W258L,E484K,D614G,P681H,D796H] (consensus) AZ.5 16 2 12.5% 2 [D80Y,T95I,Y144-,A243S,W258L,E484K,D614G,P681H,D796H,T859I] AZ.5 16 1 6.2% 1 [D80Y,T95I,Y144-,W258L,E484K,D614G,P681H,D796H,P1263L] AZ.5 16 1 6.2% 2 [Y144-,W258L,E484K,D614G,P681H,D796H] AZ.5 16 1 6.2% 1 [D80Y,T95I,Y144-,W258L,E484K,Q607H,D614G,P681H,D796H] AY.50 13 9 69.2% 0 [T19R,G142D,E156G,F157-,R158-,V308L,L452R,T478K,D614G,P681R,D950N] (consensus) AY.50 13 2 15.4% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.50 13 1 7.7% 2 [T19R,P26L,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.50 13 1 7.7% 2 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,Y508H,D614G,P681R,D950N] P.1.7 13 10 76.9% 0 [L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,P681H,T1027I,V1176F] (consensus) P.1.7 13 1 7.7% 1 [L18F,T20N,P26S,T95I,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,P681H,T1027I,V1176F] P.1.7 13 1 7.7% 4 [L5F,L18F,T20N,P26S,D138Y,V143D,Y144-,Y145-,R190S,K417T,E484K,N501Y,D614G,H655Y,P681H,T1027I,V1176F] P.1.7 13 1 7.7% 2 [L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,P681H,T747I,T1027I,V1176F,L1265P] AY.2 11 3 27.3% 0 [T19R,V70F,G142D,E156G,F157-,R158-,A222V,K417N,L452R,T478K,D614G,P681R,D950N] (consensus) AY.2 11 3 27.3% 1 [T19R,V70F,G142D,E156G,F157-,R158-,A222V,K417N,L452R,T478K,D614G,P681R,D950N,V1228L] AY.2 11 2 18.2% 4 [T19R,T95I,G142D,E156G,F157-,R158-,W258L,K417N,L452R,T478K,D614G,P681R,D950N] AY.2 11 1 9.1% 1 [T19R,V70F,E156G,F157-,R158-,A222V,K417N,L452R,T478K,D614G,P681R,D950N] AY.2 11 1 9.1% 3 [T19R,V70F,Y144-,E156G,F157-,R158-,A222V,K417N,L452R,T478K,E484G,D614G,P681R,D950N] B 11 6 54.5% 0 [] (consensus) B 11 1 9.1% 5 [G142D,L452R,T478K,D614G,V1264L] B 11 1 9.1% 3 [T19R,L452R,T478K] B 11 1 9.1% 5 [G142D,L452R,T478K,D571G,D614G] B 11 1 9.1% 1 [S247R] AY.15 11 8 72.7% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.15 11 2 18.2% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,G769V,D950N] AY.15 11 1 9.1% 3 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,A701S,D950N,A1078S] AY.16.1 10 7 70.0% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.16.1 10 1 10.0% 2 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,V615I,P681R,D950N,C1236F] AY.16.1 10 1 10.0% 1 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,V615I,P681R,D950N] AY.16.1 10 1 10.0% 2 [T19R,G142D,E156G,F157-,R158-,G446S,L452R,T478K,D614G,V615I,P681R,D950N] C.1.2 8 3 37.5% 0 [P9L,P25L,C136F,Y144-,W152R,R190S,D215G,A243-,L244-,Y449H,T478K,E484K,N501Y,D614G,H655Y,N679K,T716I,T859N,A879T] C.1.2 8 1 12.5% 4 [P9L,C136F,Y144-,R190S,D215G,A243-,L244-,Y449H,E484K,N501Y,D614G,H655Y,N679K,T716I,T859N] C.1.2 8 1 12.5% 4 [P9L,P25L,C136F,Y144-,R190S,D215G,A243-,L244-,P384L,Y449H,E484K,N501Y,D614G,H655Y,N679K,T716I,T859N] C.1.2 8 1 12.5% 4 [P9L,P25L,C136F,Y144-,R190S,D215G,A243-,L244-,Y449H,T478K,E484K,N501Y,D614G,T630A,H655Y,N679K,T716I,T859N,H1101Q] C.1.2 8 1 12.5% 1 [P9L,P25L,W64L,C136F,Y144-,W152R,R190S,D215G,A243-,L244-,Y449H,T478K,E484K,N501Y,D614G,H655Y,N679K,T716I,T859N,A879T] P.1.2 7 3 42.9% 0 [L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,Q675H,T1027I,V1176F] P.1.2 7 2 28.6% 1 [L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] (consensus) P.1.2 7 1 14.3% 2 [L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,P807L,T1027I,V1176F] P.1.2 7 1 14.3% 4 [L18F,T20N,T22I,P26S,D138Y,R190S,T323I,K417T,E484K,N501Y,D614G,H655Y,T791I,T1027I,V1176F] B.1 7 2 28.6% 0 [P9L,W152R,N501T,T572I,D614G,H655Y,E1111Q,G1124V] B.1 7 2 28.6% 11 [T19R,L452R,T478K,D614G,D950N] B.1 7 1 14.3% 11 [T19R,L452R,T478K] B.1 7 1 14.3% 29 [T33K,H66Q,E132A,F140L,L141-,Y144-,S151R,D215G,V367F,A372T,Y449H,N450D,L452R,S477N,Q493K,N501Y,D571G,D614G,P681S,L828F,K854E,S939F,V1176F,R1185H] B.1 7 1 14.3% 10 [T19R,L452R,T478K,D614G] (consensus) AY.40 6 2 33.3% 0 [T19R,T95I,G142D,E156G,F157-,R158-,E281Q,L452R,T478K,D614G,P681R,I850L,D950N] AY.40 6 1 16.7% 4 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D574Y,D614G,P681R,D950N] AY.40 6 1 16.7% 5 [T19R,G142D,E156G,F157-,R158-,A222V,V289I,L452R,T478K,D614G,P681R,D950N] AY.40 6 1 16.7% 3 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,N1187H] AY.40 6 1 16.7% 5 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] B.1.639 5 3 60.0% 0 [H69-,V70-,M153T,+214QAS,R246N,S247-,Y248-,T478K,E484K,A520S,D614G,Q677R,T859N,D936Y] (consensus) B.1.639 5 2 40.0% 1 [N30K,H69-,V70-,M153T,+214QAS,R246N,S247-,Y248-,T478K,E484K,A520S,D614G,Q677R,T859N,D936Y] B.1.2 5 2 40.0% 0 [D614G] (consensus) B.1.2 5 1 20.0% 2 [T95I,D614G,D950H] B.1.2 5 1 20.0% 3 [Y144-,E484R,D574N,D614G] B.1.2 5 1 20.0% 2 [N501T,D614G,T859I] P.1.4 5 3 60.0% 0 [L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,N679K,T1027I,V1176F] (consensus) P.1.4 5 1 20.0% 1 [L18F,T20N,P26S,D138Y,Y144-,R190S,K417T,E484K,N501Y,D614G,H655Y,N679K,T1027I,V1176F] P.1.4 5 1 20.0% 7 [L18F,T20N,P26S,T95N,D138Y,Y144-,R190S,L216F,P322S,D405G,K417T,E484K,F490L,Q498R,N501Y,D614G,H655Y,N679K,T1027I,V1176F] B.1.351 5 2 40.0% 0 [A27S,D80A,D215G,L242-,A243-,L244-,K417N,E484K,N501Y,D614G,A701V] B.1.351 5 1 20.0% 2 [D80A,D215G,L242-,A243-,L244-,K417N,E484K,N501Y,E516Q,D614G,A701V] B.1.351 5 1 20.0% 7 [P25S,D80A,L141-,G142-,V143-,D215G,L242-,A243-,L244-,R346T,K417N,V483F,E484K,N501Y,D614G,A701V] B.1.351 5 1 20.0% 1 [D80A,D215G,L242-,A243-,L244-,K417N,E484K,N501Y,D614G,A701V] (consensus) AY.49 4 1 25.0% 0 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,K854N,D950N] (consensus) AY.49 4 1 25.0% 1 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,Q675H,P681R,K854N,D950N] AY.49 4 1 25.0% 2 [T19R,E156G,F157-,R158-,L452R,T478K,Q493E,D614G,P681R,K854N,D950N] AY.49 4 1 25.0% 4 [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Q.2 4 4 100.0% 0 [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] (consensus) AY.55 4 3 75.0% 0 [T19R,K77T,G142D,E156G,F157-,R158-,D215Y,L452R,T478K,D614G,P681R] (consensus) AY.55 4 1 25.0% 5 [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] AY.91.1 4 3 75.0% 0 [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.91.1 4 1 25.0% 1 [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] AY.115 3 2 66.7% 0 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.115 3 1 33.3% 1 [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,A879S,D950N] AY.5.1 3 3 100.0% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) B.1.637 3 2 66.7% 0 [H69-,V70-,D80G,E96Q,Y144-,F157S,L244-,H245Y,R246-,S247-,Y248-,A264V,G446R,L452R,T478R,D614G,P681R,T859N,D936H,D950H,N978S] (consensus) B.1.637 3 1 33.3% 7 [R78S,D80G,Y144-,F157S,D215H,L244-,H245Y,R246-,S247-,Y248-,G446R,L452R,T478R,D614G,P681R,T859N,D950H,N978S] B.1.621.1 3 3 100.0% 0 [T95I,+143T,Y144S,Y145N,R346K,E484K,N501Y,D614G,P681H,D950N] (consensus) A.2.5 2 2 100.0% 0 [S13I,L141-,G142-,V143-,Y144-,+214AAG,D215Y,L452R,D614G] (consensus) AY.29.1 2 1 50.0% 0 [T19R,T95I,G142D,E156G,F157-,R158-,Q173H,L452R,T478K,D614G,P681R,D950N,M1237I] (consensus) AY.29.1 2 1 50.0% 5 [T19R,T95I,G142D,L452R,T478K,D614G,P681R,D950N] B.1.351.2 2 1 50.0% 0 [L18F,D80A,D215G,L242-,A243-,L244-,K417N,E484K,N501Y,D614G,A701V] (consensus) B.1.351.2 2 1 50.0% 1 [L18F,D80A,D215G,L242-,A243-,L244-,K417N,E484K,N501Y,D614G,A701V,A1020V] B.1.1.318 2 1 50.0% 0 [T95I,Y144-,E484K,D614G,P681H,D796H] (consensus) B.1.1.318 2 1 50.0% 3 [D80Y,T95I,Y144-,W258L,E484K,D614G,P681H,D796H,D936Y] C.36.3 2 2 100.0% 0 [S12F,H69-,V70-,W152R,R346S,L452R,D614G,Q677H,A899S] (consensus) B.1.626 2 1 50.0% 0 [L18F,A67V,I68-,H69-,V70-,G257S,E484K,F490S,N501T,D614G,T859N,M1237I] (consensus) B.1.626 2 1 50.0% 1 [L18F,A67V,I68-,H69-,V70-,G257S,E484K,F490S,N501T,D614G,T859N,P1162A,M1237I] B.1.429 2 1 50.0% 0 [S13I,W152C,A372T,L452R,S494L,T573I,D614G] (consensus) B.1.429 2 1 50.0% 3 [S13I,W152C,L452R,D614G] AY.18 2 1 50.0% 0 [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (consensus) AY.18 2 1 50.0% 5 [T19R,A67S,T95I,G142D,E156G,F157-,R158-,E281Q,L452R,T478K,D614G,P681R,I850L,D950N,G1251V] P.1.1 2 1 50.0% 0 [L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,P681H,T1027I,V1176F] (consensus) P.1.1 2 1 50.0% 2 [L18F,T20N,P26S,D138Y,R190S,E224Q,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] B.1.315 2 2 100.0% 0 [D614G,N856S] (consensus) B.1.234 2 1 50.0% 0 [D614G] (consensus) B.1.234 2 1 50.0% 2 [Y144-,D614G,A942T] C.18 2 1 50.0% 0 [F59L,D614G] (consensus) C.18 2 1 50.0% 1 [D614G] P.1.10 2 1 50.0% 0 [L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,A845S,T1027I,V1176F] (consensus) P.1.10 2 1 50.0% 2 [L5F,L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] B.1.525 2 1 50.0% 0 [Q52R,A67V,H69-,V70-,Y144-,E484K,D614G,Q677H,P681L,F888L] (consensus) B.1.525 2 1 50.0% 1 [Q52R,A67V,H69-,V70-,Y144-,E484K,D614G,Q677H,F888L] B.1.177.75 2 1 50.0% 0 [A222V,D614G,V1104L] (consensus) B.1.177.75 2 1 50.0% 2 [A222V,D614G,P1112Q] P.2 1 1 100.0% 0 [E484K,D614G,V1176F] (consensus) B.1.1.397 1 1 100.0% 0 [L5F,D80N,D138Y,G142S,M153T,L244S,G261D,S477N,F490Y,N556K,D614G,A1020V,I1114V] (consensus) B.1.258.17 1 1 100.0% 0 [H69-,V70-,L189F,N439K,D614G,V772I] (consensus) B.1.1 1 1 100.0% 0 [Y144-,L452R,T478K,F565L,A570D,D614G,P681R,S982A] (consensus) B.1.395 1 1 100.0% 0 [N74K,T95I,T250N,E484D,D614G,H655Y] (consensus) B.1.517 1 1 100.0% 0 [Q493R,N501T,Q613H,D614G,S939F,E1111K] (consensus) B.1.466.2 1 1 100.0% 0 [N439K,D614G,P681R,V1104L] (consensus) Q.7 1 1 100.0% 0 [H69-,V70-,Y144-,A163V,M177T,P251L,L303F,V308L,K444E,Y449H,Y453F,N460K,G485V,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] (consensus) B.1.177.18 1 1 100.0% 0 [T20I,I68T,Y144-,A222V,Q493L,T573I,E583D,D614G,A1087S] (consensus) B.1.617.3 1 1 100.0% 0 [T19R,K417N,L452R,E484Q,D614G,P681R,D950N] (consensus) A.2.5.2 1 1 100.0% 0 [L141-,G142-,V143-,+214AAG,D215Y,L452R,D614G] (consensus) B.1.177.51 1 1 100.0% 0 [A222V,F543L,D614G] (consensus) B.1.1.37 1 1 100.0% 0 [T19I,L24S,P25-,P26-,A27-,G142D,V213G,G339D,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,S477N,T478K,E484A,Q493R,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] (consensus) B.1.469 1 1 100.0% 0 [D614G,P681H] (consensus) B.1.1.113 1 1 100.0% 0 [D614G] (consensus) B.1.1.46 1 1 100.0% 0 [D614G] (consensus) B.1.9 1 1 100.0% 0 [D614G] (consensus) B.1.177.33 1 1 100.0% 0 [A222V,D614G,G639S] (consensus) B.1.160.22 1 1 100.0% 0 [Y144-,T385I,S477N,D614G] (consensus) B.1.575 1 1 100.0% 0 [S494P,D614G,P681H,T716I] (consensus) P.1.14 1 1 100.0% 0 [L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,T572I,D614G,H655Y,T1027I,V1176F] (consensus) B.1.177.28 1 1 100.0% 0 [A222V,D614G] (consensus) B.1.509 1 1 100.0% 0 [H245Y,D364N,Q493R,S494A,D614G] (consensus) B.1.240 1 1 100.0% 0 [D614G,A852S] (consensus) B.1.630 1 1 100.0% 0 [P9L,C136F,Y144-,A222V,A243-,L244-,D427N,L452R,T478R,E484Q,D614G,H655Y,D950N] (consensus) C.37.1 1 1 100.0% 0 [G75V,T76I,R246N,S247-,Y248-,L249-,T250-,P251-,G252-,D253-,L452Q,F490S,D614G,T859N] (consensus) B.1.1.242 1 1 100.0% 0 [D614G] (consensus) B.1.219 1 1 100.0% 0 [E281V,D614G] (consensus) AY.8 1 1 100.0% 0 [T19R,T95I,G142D,E156G,F157-,R158-,E281Q,L452R,T478K,D614G,P681R,I850L,D950N] (consensus) B.1.22 1 1 100.0% 0 [P26S,D614G] (consensus) B.1.1.263 1 1 100.0% 0 [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,L981F] (consensus) B.1.343 1 1 100.0% 0 [S13I,C136F,D215G,S254F,F486L,N501T,A520S,D614G,V622A,I805V] (consensus) B.1.1.385 1 1 100.0% 0 [D614G,Q675H] (consensus) B.1.629 1 1 100.0% 0 [C15F,H69-,V70-,K77E,T95I,P139T,R190K,L242-,A243P,R357I,A372T,A475V,T478K,E484K,T572N,T573I,D614G,N764K] (consensus) B.1.177.52 1 1 100.0% 0 [A222V,D614G,P1162R] (consensus) B.1.160 1 1 100.0% 0 [L5F,P9S,S477N,D614G,Q675R] (consensus)
last modified: Sun Aug 29 01:25 2021
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Questions or comments? Contact us at seq-info@lanl.gov.
Questions or comments? Contact us at seq-info@lanl.gov.
