COVID-19 Viral Genome Analysis Pipeline
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Tables of mutating sites in Spike, updated daily
Last update: Oct 21, 2021
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Table 1A. Table of sites with common mutations, found with a frequency of >0.003. (Within the ACE2 contact region, the frequency threshold for inclusion is lower, >0.001.)
Note: The mutation D614G is not included in this summary; it is now the globally dominant form and can be readily tracked using many other tools at this site.
total # of seqs: 3246301
| ori | pos | mut | global count | global frequency |
|---|---|---|---|---|
| L | 5 | # | 435 | 0.0001340 |
| - | 147 | 0.0000453 | ||
| C | 1 | 0.0000003 | ||
| F | 96278 | 0.0296578 | ||
| I | 23 | 0.0000071 | ||
| P | 4 | 0.0000012 | ||
| R | 1 | 0.0000003 | ||
| V | 3 | 0.0000009 | ||
| X | 2232 | 0.0006876 | ||
| S | 13 | # | 4 | 0.0000012 |
| - | 2 | 0.0000006 | ||
| C | 28 | 0.0000086 | ||
| G | 97 | 0.0000299 | ||
| I | 32579 | 0.0100357 | ||
| N | 136 | 0.0000419 | ||
| R | 3 | 0.0000009 | ||
| T | 468 | 0.0001442 | ||
| V | 1 | 0.0000003 | ||
| X | 1252 | 0.0003857 | ||
| L | 18 | # | 2 | 0.0000006 |
| - | 45 | 0.0000139 | ||
| F | 157916 | 0.0486449 | ||
| H | 5 | 0.0000015 | ||
| I | 27 | 0.0000083 | ||
| K | 8 | 0.0000025 | ||
| P | 26 | 0.0000080 | ||
| R | 2770 | 0.0008533 | ||
| S | 1 | 0.0000003 | ||
| V | 7 | 0.0000022 | ||
| X | 951 | 0.0002929 | ||
| T | 19 | # | 3 | 0.0000009 |
| - | 7 | 0.0000022 | ||
| A | 75 | 0.0000231 | ||
| G | 56 | 0.0000173 | ||
| I | 2170 | 0.0006685 | ||
| K | 229 | 0.0000705 | ||
| P | 6 | 0.0000018 | ||
| Q | 1 | 0.0000003 | ||
| R | 1283554 | 0.3953897 | ||
| S | 43 | 0.0000132 | ||
| X | 1078 | 0.0003321 | ||
| T | 20 | - | 25 | 0.0000077 |
| A | 182 | 0.0000561 | ||
| F | 3 | 0.0000009 | ||
| I | 7799 | 0.0024024 | ||
| K | 10 | 0.0000031 | ||
| N | 75902 | 0.0233811 | ||
| P | 137 | 0.0000422 | ||
| S | 95 | 0.0000293 | ||
| X | 344 | 0.0001060 | ||
| P | 26 | # | 28 | 0.0000086 |
| - | 4 | 0.0000012 | ||
| A | 2 | 0.0000006 | ||
| F | 80 | 0.0000246 | ||
| H | 364 | 0.0001121 | ||
| L | 2183 | 0.0006725 | ||
| R | 124 | 0.0000382 | ||
| S | 83311 | 0.0256634 | ||
| T | 37 | 0.0000114 | ||
| X | 381 | 0.0001174 | ||
| Y | 5 | 0.0000015 | ||
| T | 29 | - | 3 | 0.0000009 |
| A | 6731 | 0.0020734 | ||
| H | 1 | 0.0000003 | ||
| I | 3190 | 0.0009827 | ||
| N | 1 | 0.0000003 | ||
| P | 2 | 0.0000006 | ||
| R | 1 | 0.0000003 | ||
| S | 111 | 0.0000342 | ||
| V | 7 | 0.0000022 | ||
| W | 1 | 0.0000003 | ||
| X | 181 | 0.0000558 | ||
| A | 67 | # | 2 | 0.0000006 |
| - | 16 | 0.0000049 | ||
| D | 207 | 0.0000638 | ||
| F | 1 | 0.0000003 | ||
| G | 20 | 0.0000062 | ||
| M | 1 | 0.0000003 | ||
| N | 5 | 0.0000015 | ||
| P | 13 | 0.0000040 | ||
| S | 3385 | 0.0010427 | ||
| T | 120 | 0.0000370 | ||
| V | 13788 | 0.0042473 | ||
| X | 553 | 0.0001703 | ||
| H | 69 | - | 988516 | 0.3045053 |
| A | 4 | 0.0000012 | ||
| D | 23 | 0.0000071 | ||
| I | 4 | 0.0000012 | ||
| L | 41 | 0.0000126 | ||
| M | 2 | 0.0000006 | ||
| N | 19 | 0.0000059 | ||
| P | 20 | 0.0000062 | ||
| Q | 140 | 0.0000431 | ||
| R | 78 | 0.0000240 | ||
| S | 312 | 0.0000961 | ||
| T | 2 | 0.0000006 | ||
| X | 18752 | 0.0057764 | ||
| Y | 1881 | 0.0005794 | ||
| V | 70 | # | 3098 | 0.0009543 |
| - | 984550 | 0.3032836 | ||
| A | 112 | 0.0000345 | ||
| D | 1 | 0.0000003 | ||
| E | 1 | 0.0000003 | ||
| F | 4699 | 0.0014475 | ||
| G | 195 | 0.0000601 | ||
| I | 6817 | 0.0020999 | ||
| K | 1 | 0.0000003 | ||
| L | 203 | 0.0000625 | ||
| M | 1 | 0.0000003 | ||
| X | 14621 | 0.0045039 | ||
| G | 75 | - | 61 | 0.0000188 |
| A | 320 | 0.0000986 | ||
| C | 75 | 0.0000231 | ||
| D | 144 | 0.0000444 | ||
| F | 3 | 0.0000009 | ||
| I | 1 | 0.0000003 | ||
| K | 6 | 0.0000018 | ||
| R | 2285 | 0.0007039 | ||
| S | 266 | 0.0000819 | ||
| T | 1 | 0.0000003 | ||
| V | 10055 | 0.0030974 | ||
| X | 641 | 0.0001975 | ||
| K | 77 | $ | 2 | 0.0000006 |
| - | 40 | 0.0000123 | ||
| E | 10 | 0.0000031 | ||
| F | 1 | 0.0000003 | ||
| I | 6 | 0.0000018 | ||
| M | 51 | 0.0000157 | ||
| N | 565 | 0.0001740 | ||
| R | 73 | 0.0000225 | ||
| T | 10039 | 0.0030924 | ||
| X | 290 | 0.0000893 | ||
| D | 80 | # | 2 | 0.0000006 |
| - | 6 | 0.0000018 | ||
| A | 12258 | 0.0037760 | ||
| C | 10 | 0.0000031 | ||
| E | 22 | 0.0000068 | ||
| F | 27 | 0.0000083 | ||
| G | 10553 | 0.0032508 | ||
| H | 95 | 0.0000293 | ||
| K | 1 | 0.0000003 | ||
| L | 1 | 0.0000003 | ||
| N | 301 | 0.0000927 | ||
| P | 1 | 0.0000003 | ||
| S | 3 | 0.0000009 | ||
| T | 1 | 0.0000003 | ||
| V | 11 | 0.0000034 | ||
| X | 449 | 0.0001383 | ||
| Y | 7324 | 0.0022561 | ||
| T | 95 | # | 10 | 0.0000031 |
| $ | 1 | 0.0000003 | ||
| - | 15 | 0.0000046 | ||
| A | 110 | 0.0000339 | ||
| F | 9 | 0.0000028 | ||
| I | 627833 | 0.1933995 | ||
| M | 6 | 0.0000018 | ||
| N | 229 | 0.0000705 | ||
| P | 1 | 0.0000003 | ||
| S | 88 | 0.0000271 | ||
| V | 43 | 0.0000132 | ||
| X | 2226 | 0.0006857 | ||
| S | 98 | - | 4 | 0.0000012 |
| A | 6 | 0.0000018 | ||
| C | 1 | 0.0000003 | ||
| F | 33578 | 0.0103435 | ||
| N | 1 | 0.0000003 | ||
| P | 92 | 0.0000283 | ||
| R | 1 | 0.0000003 | ||
| T | 11 | 0.0000034 | ||
| X | 662 | 0.0002039 | ||
| Y | 18 | 0.0000055 | ||
| S | 112 | $ | 2 | 0.0000006 |
| - | 11 | 0.0000034 | ||
| A | 19 | 0.0000059 | ||
| F | 29 | 0.0000089 | ||
| L | 26932 | 0.0082962 | ||
| M | 6 | 0.0000018 | ||
| P | 115 | 0.0000354 | ||
| T | 13 | 0.0000040 | ||
| X | 991 | 0.0003053 | ||
| D | 138 | # | 3 | 0.0000009 |
| - | 288 | 0.0000887 | ||
| A | 196 | 0.0000604 | ||
| E | 8 | 0.0000025 | ||
| G | 267 | 0.0000822 | ||
| H | 17480 | 0.0053846 | ||
| N | 379 | 0.0001167 | ||
| V | 27 | 0.0000083 | ||
| X | 1475 | 0.0004544 | ||
| Y | 82842 | 0.0255189 | ||
| G | 142 | # | 95 | 0.0000293 |
| - | 2823 | 0.0008696 | ||
| A | 49 | 0.0000151 | ||
| C | 70 | 0.0000216 | ||
| D | 976048 | 0.3006647 | ||
| E | 1 | 0.0000003 | ||
| F | 7 | 0.0000022 | ||
| H | 10 | 0.0000031 | ||
| I | 7 | 0.0000022 | ||
| K | 2 | 0.0000006 | ||
| L | 3 | 0.0000009 | ||
| N | 21 | 0.0000065 | ||
| P | 4 | 0.0000012 | ||
| R | 3 | 0.0000009 | ||
| S | 944 | 0.0002908 | ||
| T | 4 | 0.0000012 | ||
| V | 2843 | 0.0008758 | ||
| W | 2 | 0.0000006 | ||
| X | 82367 | 0.0253726 | ||
| Y | 66 | 0.0000203 | ||
| Y | 144 | # | 2189 | 0.0006743 |
| $ | 15 | 0.0000046 | ||
| - | 970760 | 0.2990357 | ||
| C | 20 | 0.0000062 | ||
| D | 4 | 0.0000012 | ||
| E | 2 | 0.0000006 | ||
| F | 1240 | 0.0003820 | ||
| G | 2 | 0.0000006 | ||
| H | 53 | 0.0000163 | ||
| K | 9 | 0.0000028 | ||
| L | 5 | 0.0000015 | ||
| N | 74 | 0.0000228 | ||
| S | 6841 | 0.0021073 | ||
| T | 170 | 0.0000524 | ||
| V | 320 | 0.0000986 | ||
| W | 4 | 0.0000012 | ||
| X | 24487 | 0.0075430 | ||
| Y | 145 | # | 82 | 0.0000253 |
| $ | 7 | 0.0000022 | ||
| - | 719 | 0.0002215 | ||
| C | 21 | 0.0000065 | ||
| D | 104 | 0.0000320 | ||
| F | 1 | 0.0000003 | ||
| G | 1 | 0.0000003 | ||
| H | 15175 | 0.0046746 | ||
| N | 7317 | 0.0022539 | ||
| P | 1 | 0.0000003 | ||
| S | 33 | 0.0000102 | ||
| T | 1 | 0.0000003 | ||
| X | 5431 | 0.0016730 | ||
| W | 152 | # | 2 | 0.0000006 |
| $ | 1 | 0.0000003 | ||
| - | 48 | 0.0000148 | ||
| C | 31640 | 0.0097465 | ||
| F | 4 | 0.0000012 | ||
| G | 96 | 0.0000296 | ||
| K | 1 | 0.0000003 | ||
| L | 10657 | 0.0032828 | ||
| Q | 2 | 0.0000006 | ||
| R | 18090 | 0.0055725 | ||
| S | 35 | 0.0000108 | ||
| X | 900 | 0.0002772 | ||
| Y | 1 | 0.0000003 | ||
| M | 153 | # | 9 | 0.0000028 |
| - | 42 | 0.0000129 | ||
| I | 3950 | 0.0012168 | ||
| K | 175 | 0.0000539 | ||
| L | 26 | 0.0000080 | ||
| R | 4 | 0.0000012 | ||
| T | 8747 | 0.0026945 | ||
| V | 279 | 0.0000859 | ||
| W | 8 | 0.0000025 | ||
| X | 422 | 0.0001300 | ||
| E | 156 | # | 43 | 0.0000132 |
| $ | 1 | 0.0000003 | ||
| - | 590 | 0.0001817 | ||
| A | 79 | 0.0000243 | ||
| D | 240 | 0.0000739 | ||
| F | 1 | 0.0000003 | ||
| G | 1255770 | 0.3868310 | ||
| K | 15 | 0.0000046 | ||
| Q | 143 | 0.0000441 | ||
| S | 1 | 0.0000003 | ||
| V | 745 | 0.0002295 | ||
| W | 1 | 0.0000003 | ||
| X | 20484 | 0.0063100 | ||
| Y | 2 | 0.0000006 | ||
| F | 157 | # | 5 | 0.0000015 |
| - | 1257927 | 0.3874955 | ||
| C | 15 | 0.0000046 | ||
| E | 1 | 0.0000003 | ||
| L | 2712 | 0.0008354 | ||
| S | 11058 | 0.0034063 | ||
| V | 3 | 0.0000009 | ||
| X | 24787 | 0.0076355 | ||
| Y | 14 | 0.0000043 | ||
| R | 158 | # | 147 | 0.0000453 |
| $ | 186 | 0.0000573 | ||
| - | 1252169 | 0.3857218 | ||
| G | 1224 | 0.0003770 | ||
| I | 29 | 0.0000089 | ||
| K | 39 | 0.0000120 | ||
| L | 3 | 0.0000009 | ||
| S | 2861 | 0.0008813 | ||
| X | 28801 | 0.0088719 | ||
| Y | 1 | 0.0000003 | ||
| G | 181 | # | 3 | 0.0000009 |
| $ | 2 | 0.0000006 | ||
| - | 2 | 0.0000006 | ||
| A | 724 | 0.0002230 | ||
| E | 886 | 0.0002729 | ||
| K | 1 | 0.0000003 | ||
| L | 48 | 0.0000148 | ||
| N | 4 | 0.0000012 | ||
| R | 1363 | 0.0004199 | ||
| V | 8215 | 0.0025306 | ||
| X | 353 | 0.0001087 | ||
| R | 190 | # | 10 | 0.0000031 |
| - | 40 | 0.0000123 | ||
| G | 44 | 0.0000136 | ||
| I | 12 | 0.0000037 | ||
| K | 284 | 0.0000875 | ||
| M | 298 | 0.0000918 | ||
| N | 14 | 0.0000043 | ||
| S | 75599 | 0.0232877 | ||
| T | 3 | 0.0000009 | ||
| W | 40 | 0.0000123 | ||
| X | 450 | 0.0001386 | ||
| D | 215 | # | 2 | 0.0000006 |
| - | 12 | 0.0000037 | ||
| A | 132 | 0.0000407 | ||
| C | 2 | 0.0000006 | ||
| E | 164 | 0.0000505 | ||
| G | 12313 | 0.0037929 | ||
| H | 2761 | 0.0008505 | ||
| L | 5 | 0.0000015 | ||
| N | 183 | 0.0000564 | ||
| V | 100 | 0.0000308 | ||
| X | 377 | 0.0001161 | ||
| Y | 4398 | 0.0013548 | ||
| A | 222 | # | 4 | 0.0000012 |
| - | 2 | 0.0000006 | ||
| D | 3 | 0.0000009 | ||
| F | 21 | 0.0000065 | ||
| G | 1 | 0.0000003 | ||
| I | 11 | 0.0000034 | ||
| L | 1 | 0.0000003 | ||
| N | 1 | 0.0000003 | ||
| P | 77 | 0.0000237 | ||
| R | 1 | 0.0000003 | ||
| S | 1515 | 0.0004667 | ||
| T | 64 | 0.0000197 | ||
| V | 291295 | 0.0897314 | ||
| W | 1 | 0.0000003 | ||
| X | 1668 | 0.0005138 | ||
| L | 242 | # | 6 | 0.0000018 |
| - | 12698 | 0.0039115 | ||
| F | 293 | 0.0000903 | ||
| H | 28 | 0.0000086 | ||
| I | 76 | 0.0000234 | ||
| P | 104 | 0.0000320 | ||
| Q | 8 | 0.0000025 | ||
| R | 3 | 0.0000009 | ||
| V | 5 | 0.0000015 | ||
| X | 845 | 0.0002603 | ||
| Y | 1 | 0.0000003 | ||
| A | 243 | # | 93 | 0.0000286 |
| - | 13387 | 0.0041238 | ||
| D | 7 | 0.0000022 | ||
| G | 33 | 0.0000102 | ||
| P | 34 | 0.0000105 | ||
| S | 2039 | 0.0006281 | ||
| T | 61 | 0.0000188 | ||
| V | 411 | 0.0001266 | ||
| X | 1134 | 0.0003493 | ||
| L | 244 | # | 10 | 0.0000031 |
| - | 13526 | 0.0041666 | ||
| F | 84 | 0.0000259 | ||
| S | 634 | 0.0001953 | ||
| V | 22 | 0.0000068 | ||
| X | 187 | 0.0000576 | ||
| T | 250 | - | 6122 | 0.0018858 |
| A | 56 | 0.0000173 | ||
| F | 1 | 0.0000003 | ||
| G | 4 | 0.0000012 | ||
| I | 7176 | 0.0022105 | ||
| N | 575 | 0.0001771 | ||
| P | 30 | 0.0000092 | ||
| S | 706 | 0.0002175 | ||
| X | 112 | 0.0000345 | ||
| P | 251 | # | 88 | 0.0000271 |
| - | 6111 | 0.0018825 | ||
| H | 458 | 0.0001411 | ||
| L | 12334 | 0.0037994 | ||
| R | 5 | 0.0000015 | ||
| S | 828 | 0.0002551 | ||
| T | 169 | 0.0000521 | ||
| X | 156 | 0.0000481 | ||
| D | 253 | - | 6127 | 0.0018874 |
| A | 1603 | 0.0004938 | ||
| E | 12 | 0.0000037 | ||
| G | 36786 | 0.0113317 | ||
| H | 10 | 0.0000031 | ||
| N | 177 | 0.0000545 | ||
| S | 12 | 0.0000037 | ||
| V | 64 | 0.0000197 | ||
| X | 272 | 0.0000838 | ||
| Y | 701 | 0.0002159 | ||
| A | 262 | # | 7 | 0.0000022 |
| - | 13 | 0.0000040 | ||
| D | 36 | 0.0000111 | ||
| F | 1 | 0.0000003 | ||
| G | 24 | 0.0000074 | ||
| K | 1 | 0.0000003 | ||
| P | 158 | 0.0000487 | ||
| S | 15817 | 0.0048723 | ||
| T | 124 | 0.0000382 | ||
| V | 573 | 0.0001765 | ||
| W | 1 | 0.0000003 | ||
| X | 2053 | 0.0006324 | ||
| Y | 6 | 0.0000018 | ||
| P | 272 | F | 31 | 0.0000095 |
| H | 95 | 0.0000293 | ||
| L | 9655 | 0.0029742 | ||
| Q | 2 | 0.0000006 | ||
| R | 6 | 0.0000018 | ||
| S | 350 | 0.0001078 | ||
| T | 42 | 0.0000129 | ||
| X | 433 | 0.0001334 | ||
| V | 289 | # | 1 | 0.0000003 |
| A | 5 | 0.0000015 | ||
| E | 1 | 0.0000003 | ||
| I | 17220 | 0.0053045 | ||
| L | 786 | 0.0002421 | ||
| T | 1 | 0.0000003 | ||
| X | 329 | 0.0001013 | ||
| R | 346 | $ | 1 | 0.0000003 |
| F | 2 | 0.0000006 | ||
| G | 109 | 0.0000336 | ||
| I | 307 | 0.0000946 | ||
| K | 8577 | 0.0026421 | ||
| S | 1639 | 0.0005049 | ||
| T | 93 | 0.0000286 | ||
| X | 460 | 0.0001417 | ||
| K | 417 | # | 2 | 0.0000006 |
| - | 1 | 0.0000003 | ||
| A | 3 | 0.0000009 | ||
| E | 11 | 0.0000034 | ||
| M | 14 | 0.0000043 | ||
| N | 15295 | 0.0047115 | ||
| Q | 3 | 0.0000009 | ||
| R | 189 | 0.0000582 | ||
| T | 73883 | 0.0227591 | ||
| X | 1121 | 0.0003453 | ||
| N | 439 | - | 2 | 0.0000006 |
| D | 1 | 0.0000003 | ||
| F | 1 | 0.0000003 | ||
| I | 7 | 0.0000022 | ||
| K | 26985 | 0.0083125 | ||
| S | 3 | 0.0000009 | ||
| T | 2 | 0.0000006 | ||
| X | 549 | 0.0001691 | ||
| Y | 1 | 0.0000003 | ||
| G | 446 | - | 1 | 0.0000003 |
| A | 53 | 0.0000163 | ||
| C | 1 | 0.0000003 | ||
| D | 26 | 0.0000080 | ||
| F | 1 | 0.0000003 | ||
| I | 2 | 0.0000006 | ||
| R | 9 | 0.0000028 | ||
| S | 265 | 0.0000816 | ||
| T | 2 | 0.0000006 | ||
| V | 3578 | 0.0011022 | ||
| X | 1034 | 0.0003185 | ||
| L | 452 | # | 12 | 0.0000037 |
| - | 2 | 0.0000006 | ||
| F | 1 | 0.0000003 | ||
| H | 1 | 0.0000003 | ||
| M | 1205 | 0.0003712 | ||
| P | 2 | 0.0000006 | ||
| Q | 6935 | 0.0021363 | ||
| R | 1341391 | 0.4132060 | ||
| V | 6 | 0.0000018 | ||
| W | 41 | 0.0000126 | ||
| X | 1066 | 0.0003284 | ||
| S | 477 | # | 3 | 0.0000009 |
| G | 457 | 0.0001408 | ||
| H | 1 | 0.0000003 | ||
| I | 2759 | 0.0008499 | ||
| K | 3 | 0.0000009 | ||
| N | 58398 | 0.0179891 | ||
| R | 1258 | 0.0003875 | ||
| T | 34 | 0.0000105 | ||
| V | 1 | 0.0000003 | ||
| X | 829 | 0.0002554 | ||
| T | 478 | - | 3 | 0.0000009 |
| A | 12 | 0.0000037 | ||
| E | 1 | 0.0000003 | ||
| I | 717 | 0.0002209 | ||
| K | 1304118 | 0.4017243 | ||
| L | 1 | 0.0000003 | ||
| N | 12 | 0.0000037 | ||
| R | 428 | 0.0001318 | ||
| S | 2 | 0.0000006 | ||
| X | 718 | 0.0002212 | ||
| E | 484 | # | 5 | 0.0000015 |
| - | 2 | 0.0000006 | ||
| A | 282 | 0.0000869 | ||
| D | 100 | 0.0000308 | ||
| G | 113 | 0.0000348 | ||
| K | 152249 | 0.0468992 | ||
| Q | 7329 | 0.0022576 | ||
| R | 19 | 0.0000059 | ||
| V | 41 | 0.0000126 | ||
| X | 704 | 0.0002169 | ||
| F | 490 | $ | 1 | 0.0000003 |
| A | 1 | 0.0000003 | ||
| I | 29 | 0.0000089 | ||
| L | 885 | 0.0002726 | ||
| N | 1 | 0.0000003 | ||
| S | 10544 | 0.0032480 | ||
| V | 109 | 0.0000336 | ||
| X | 239 | 0.0000736 | ||
| Y | 92 | 0.0000283 | ||
| S | 494 | # | 2 | 0.0000006 |
| $ | 1 | 0.0000003 | ||
| - | 1 | 0.0000003 | ||
| A | 51 | 0.0000157 | ||
| L | 700 | 0.0002156 | ||
| P | 9705 | 0.0029896 | ||
| Q | 1 | 0.0000003 | ||
| R | 5 | 0.0000015 | ||
| T | 12 | 0.0000037 | ||
| X | 254 | 0.0000782 | ||
| N | 501 | # | 5 | 0.0000015 |
| - | 17 | 0.0000052 | ||
| D | 1 | 0.0000003 | ||
| E | 1 | 0.0000003 | ||
| F | 2 | 0.0000006 | ||
| H | 38 | 0.0000117 | ||
| I | 47 | 0.0000145 | ||
| K | 13 | 0.0000040 | ||
| L | 1 | 0.0000003 | ||
| P | 2 | 0.0000006 | ||
| Q | 2 | 0.0000006 | ||
| R | 1 | 0.0000003 | ||
| S | 94 | 0.0000290 | ||
| T | 3737 | 0.0011512 | ||
| X | 1999 | 0.0006158 | ||
| Y | 1077303 | 0.3318555 | ||
| A | 570 | D | 972626 | 0.2996105 |
| E | 1 | 0.0000003 | ||
| G | 18 | 0.0000055 | ||
| H | 1 | 0.0000003 | ||
| N | 1 | 0.0000003 | ||
| S | 1843 | 0.0005677 | ||
| T | 30 | 0.0000092 | ||
| V | 531 | 0.0001636 | ||
| X | 1215 | 0.0003743 | ||
| Y | 121 | 0.0000373 | ||
| T | 572 | # | 4 | 0.0000012 |
| A | 29 | 0.0000089 | ||
| I | 10899 | 0.0033574 | ||
| N | 84 | 0.0000259 | ||
| S | 68 | 0.0000209 | ||
| X | 174 | 0.0000536 | ||
| Q | 613 | $ | 3 | 0.0000009 |
| - | 1 | 0.0000003 | ||
| E | 91 | 0.0000280 | ||
| H | 20022 | 0.0061676 | ||
| K | 32 | 0.0000099 | ||
| L | 9 | 0.0000028 | ||
| R | 50 | 0.0000154 | ||
| X | 198 | 0.0000610 | ||
| Y | 2 | 0.0000006 | ||
| H | 655 | - | 1 | 0.0000003 |
| D | 1 | 0.0000003 | ||
| E | 1 | 0.0000003 | ||
| L | 22 | 0.0000068 | ||
| N | 3 | 0.0000009 | ||
| P | 12 | 0.0000037 | ||
| Q | 20 | 0.0000062 | ||
| R | 87 | 0.0000268 | ||
| X | 373 | 0.0001149 | ||
| Y | 81887 | 0.0252247 | ||
| Q | 675 | $ | 2 | 0.0000006 |
| - | 67 | 0.0000206 | ||
| E | 2 | 0.0000006 | ||
| H | 23157 | 0.0071333 | ||
| K | 319 | 0.0000983 | ||
| L | 57 | 0.0000176 | ||
| P | 11 | 0.0000034 | ||
| R | 2048 | 0.0006309 | ||
| S | 2 | 0.0000006 | ||
| W | 2 | 0.0000006 | ||
| X | 227 | 0.0000699 | ||
| Y | 3 | 0.0000009 | ||
| Q | 677 | # | 1 | 0.0000003 |
| - | 73 | 0.0000225 | ||
| E | 3 | 0.0000009 | ||
| H | 35933 | 0.0110689 | ||
| K | 122 | 0.0000376 | ||
| L | 169 | 0.0000521 | ||
| P | 4065 | 0.0012522 | ||
| R | 484 | 0.0001491 | ||
| S | 1 | 0.0000003 | ||
| X | 506 | 0.0001559 | ||
| Y | 16 | 0.0000049 | ||
| P | 681 | # | 14 | 0.0000043 |
| - | 24 | 0.0000074 | ||
| A | 1 | 0.0000003 | ||
| C | 4 | 0.0000012 | ||
| H | 1029210 | 0.3170408 | ||
| L | 648 | 0.0001996 | ||
| Q | 1 | 0.0000003 | ||
| R | 1297787 | 0.3997741 | ||
| S | 78 | 0.0000240 | ||
| T | 4 | 0.0000012 | ||
| X | 2339 | 0.0007205 | ||
| Y | 105 | 0.0000323 | ||
| A | 688 | - | 10 | 0.0000031 |
| D | 27 | 0.0000083 | ||
| F | 5 | 0.0000015 | ||
| G | 8 | 0.0000025 | ||
| P | 14 | 0.0000043 | ||
| S | 757 | 0.0002332 | ||
| T | 439 | 0.0001352 | ||
| V | 12726 | 0.0039202 | ||
| X | 264 | 0.0000813 | ||
| A | 701 | # | 2 | 0.0000006 |
| - | 1 | 0.0000003 | ||
| E | 10 | 0.0000031 | ||
| G | 25 | 0.0000077 | ||
| I | 1 | 0.0000003 | ||
| K | 1 | 0.0000003 | ||
| L | 1 | 0.0000003 | ||
| P | 26 | 0.0000080 | ||
| Q | 1 | 0.0000003 | ||
| S | 1138 | 0.0003506 | ||
| T | 149 | 0.0000459 | ||
| V | 41651 | 0.0128303 | ||
| X | 333 | 0.0001026 | ||
| T | 716 | - | 2 | 0.0000006 |
| A | 12 | 0.0000037 | ||
| D | 1 | 0.0000003 | ||
| I | 978787 | 0.3015084 | ||
| K | 6 | 0.0000018 | ||
| L | 11 | 0.0000034 | ||
| M | 7 | 0.0000022 | ||
| N | 1 | 0.0000003 | ||
| P | 1 | 0.0000003 | ||
| Q | 1 | 0.0000003 | ||
| R | 3 | 0.0000009 | ||
| S | 11 | 0.0000034 | ||
| V | 334 | 0.0001029 | ||
| X | 1473 | 0.0004537 | ||
| T | 732 | - | 1 | 0.0000003 |
| A | 23710 | 0.0073037 | ||
| I | 1376 | 0.0004239 | ||
| N | 2 | 0.0000006 | ||
| S | 952 | 0.0002933 | ||
| V | 2 | 0.0000006 | ||
| X | 187 | 0.0000576 | ||
| G | 769 | $ | 1 | 0.0000003 |
| - | 1 | 0.0000003 | ||
| A | 171 | 0.0000527 | ||
| C | 1 | 0.0000003 | ||
| E | 25 | 0.0000077 | ||
| K | 10 | 0.0000031 | ||
| N | 2 | 0.0000006 | ||
| R | 319 | 0.0000983 | ||
| V | 12909 | 0.0039765 | ||
| X | 172 | 0.0000530 | ||
| A | 845 | # | 1 | 0.0000003 |
| - | 1 | 0.0000003 | ||
| D | 73 | 0.0000225 | ||
| G | 11 | 0.0000034 | ||
| P | 28 | 0.0000086 | ||
| R | 1 | 0.0000003 | ||
| S | 8930 | 0.0027508 | ||
| T | 89 | 0.0000274 | ||
| V | 1040 | 0.0003204 | ||
| X | 403 | 0.0001241 | ||
| T | 859 | # | 2 | 0.0000006 |
| - | 6 | 0.0000018 | ||
| A | 42 | 0.0000129 | ||
| C | 1 | 0.0000003 | ||
| I | 4563 | 0.0014056 | ||
| N | 17468 | 0.0053809 | ||
| S | 9 | 0.0000028 | ||
| X | 262 | 0.0000807 | ||
| D | 936 | - | 2 | 0.0000006 |
| A | 11 | 0.0000034 | ||
| E | 127 | 0.0000391 | ||
| G | 102 | 0.0000314 | ||
| H | 1355 | 0.0004174 | ||
| L | 1 | 0.0000003 | ||
| N | 3896 | 0.0012001 | ||
| T | 3 | 0.0000009 | ||
| V | 96 | 0.0000296 | ||
| X | 197 | 0.0000607 | ||
| Y | 5160 | 0.0015895 | ||
| S | 939 | # | 2 | 0.0000006 |
| - | 3 | 0.0000009 | ||
| A | 14 | 0.0000043 | ||
| C | 2 | 0.0000006 | ||
| F | 10029 | 0.0030894 | ||
| P | 1 | 0.0000003 | ||
| T | 3 | 0.0000009 | ||
| X | 208 | 0.0000641 | ||
| Y | 61 | 0.0000188 | ||
| D | 950 | # | 91 | 0.0000280 |
| - | 1 | 0.0000003 | ||
| A | 24 | 0.0000074 | ||
| E | 10 | 0.0000031 | ||
| G | 34 | 0.0000105 | ||
| H | 10170 | 0.0031328 | ||
| I | 8 | 0.0000025 | ||
| K | 4 | 0.0000012 | ||
| N | 1241458 | 0.3824223 | ||
| S | 17 | 0.0000052 | ||
| T | 3 | 0.0000009 | ||
| V | 2 | 0.0000006 | ||
| W | 1 | 0.0000003 | ||
| X | 32187 | 0.0099150 | ||
| Y | 188 | 0.0000579 | ||
| Q | 957 | $ | 1 | 0.0000003 |
| - | 1 | 0.0000003 | ||
| A | 2 | 0.0000006 | ||
| E | 15 | 0.0000046 | ||
| H | 38 | 0.0000117 | ||
| K | 3 | 0.0000009 | ||
| L | 1072 | 0.0003302 | ||
| N | 1 | 0.0000003 | ||
| R | 10604 | 0.0032665 | ||
| X | 1643 | 0.0005061 | ||
| S | 982 | # | 1 | 0.0000003 |
| A | 972807 | 0.2996663 | ||
| L | 108 | 0.0000333 | ||
| P | 1 | 0.0000003 | ||
| T | 5 | 0.0000015 | ||
| V | 1 | 0.0000003 | ||
| X | 1376 | 0.0004239 | ||
| T | 1027 | - | 1 | 0.0000003 |
| A | 27 | 0.0000083 | ||
| I | 84211 | 0.0259406 | ||
| N | 25 | 0.0000077 | ||
| S | 45 | 0.0000139 | ||
| V | 7 | 0.0000022 | ||
| X | 236 | 0.0000727 | ||
| A | 1078 | # | 1 | 0.0000003 |
| D | 1 | 0.0000003 | ||
| F | 1 | 0.0000003 | ||
| S | 9364 | 0.0028845 | ||
| T | 510 | 0.0001571 | ||
| V | 586 | 0.0001805 | ||
| X | 238 | 0.0000733 | ||
| V | 1104 | # | 4 | 0.0000012 |
| $ | 1 | 0.0000003 | ||
| - | 1 | 0.0000003 | ||
| A | 12 | 0.0000037 | ||
| E | 1 | 0.0000003 | ||
| I | 498 | 0.0001534 | ||
| L | 17571 | 0.0054126 | ||
| X | 175 | 0.0000539 | ||
| D | 1118 | # | 1 | 0.0000003 |
| A | 39 | 0.0000120 | ||
| E | 9 | 0.0000028 | ||
| G | 25 | 0.0000077 | ||
| H | 971746 | 0.2993395 | ||
| N | 2 | 0.0000006 | ||
| Q | 4 | 0.0000012 | ||
| R | 4 | 0.0000012 | ||
| V | 22 | 0.0000068 | ||
| X | 1547 | 0.0004765 | ||
| Y | 3231 | 0.0009953 | ||
| P | 1162 | A | 259 | 0.0000798 |
| L | 2822 | 0.0008693 | ||
| Q | 68 | 0.0000209 | ||
| R | 598 | 0.0001842 | ||
| S | 6848 | 0.0021095 | ||
| T | 59 | 0.0000182 | ||
| X | 298 | 0.0000918 | ||
| V | 1176 | - | 1 | 0.0000003 |
| A | 4 | 0.0000012 | ||
| D | 1 | 0.0000003 | ||
| F | 87007 | 0.0268019 | ||
| G | 3 | 0.0000009 | ||
| I | 32 | 0.0000099 | ||
| L | 10 | 0.0000031 | ||
| X | 229 | 0.0000705 | ||
| K | 1191 | - | 1 | 0.0000003 |
| D | 1 | 0.0000003 | ||
| E | 18 | 0.0000055 | ||
| M | 7 | 0.0000022 | ||
| N | 33827 | 0.0104202 | ||
| Q | 40 | 0.0000123 | ||
| R | 34 | 0.0000105 | ||
| T | 9 | 0.0000028 | ||
| X | 444 | 0.0001368 | ||
| G | 1219 | A | 30 | 0.0000092 |
| C | 4557 | 0.0014038 | ||
| D | 6 | 0.0000018 | ||
| F | 4 | 0.0000012 | ||
| L | 1 | 0.0000003 | ||
| R | 6 | 0.0000018 | ||
| S | 162 | 0.0000499 | ||
| V | 6939 | 0.0021375 | ||
| X | 242 | 0.0000745 | ||
| Y | 1 | 0.0000003 | ||
| V | 1264 | - | 1 | 0.0000003 |
| A | 60 | 0.0000185 | ||
| D | 3 | 0.0000009 | ||
| E | 5 | 0.0000015 | ||
| F | 62 | 0.0000191 | ||
| G | 4 | 0.0000012 | ||
| L | 34398 | 0.0105961 | ||
| M | 81 | 0.0000250 | ||
| S | 1 | 0.0000003 | ||
| X | 511 | 0.0001574 |
Table 1B. Details regarding common mutations listed in A and their geographic locations.
| ori | pos | mut | codon | mut | covariations | location | # of occurrences | #seqs from local | #seqs from state/province | #seqs from country | #seqs from continent |
|---|---|---|---|---|---|---|---|---|---|---|---|
| L | 5 | # | CTT | -TT | H69-,V70-,Y144-,N501Y,A570D,P681H,T716I,S982A,D1118H,D614G | Belgium_Ghent | 1 | 4462 | 39721 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | T19R,G142D,E156G,F157-,R158-,L452R,T478K,P681R,D950N,D614G | Belgium_Ghent | 2 | 4462 | 39721 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,P681R,D950N,D614G | Belgium_Ghent | 6 | 4462 | 39721 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,Q677H,P681R,D950N,D614G | Belgium_Ghent | 1 | 4462 | 39721 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | H69-,V70-,Y144-,N501Y,A570D,P681H,T716I,S982A,D1118H,D614G | Belgium_Luxembourg | 1 | 622 | 39721 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | E484K,V1176F,D614G | Brazil_Minas-Gerais_Desterro-do-Melo | 1 | 2 | 692 | 39661 | South-America 67618 |
| L | 5 | # | CTT | -TT | E484K,V1176F,D614G | Brazil_Rio-Grande-do-Sul_Candelaria | 1 | 2 | 1798 | 39661 | South-America 67618 |
| L | 5 | # | CTT | -TT | E484K,V1176F,D614G | Brazil_Santa-Catarina_Florianopolis | 1 | 206 | 931 | 39661 | South-America 67618 |
| L | 5 | # | CTT | -TT | T95I,Y144X,Y145N,R346K,E484K,N501Y,P681H,D950N,D614G | Colombia | 1 | 1890 | South-America 67618 | ||
| L | 5 | # | CTT | -TT | T95I,Y144X,Y145N,R346K,S477N,E484K,N501Y,P681H,D950N,D614G | Colombia | 1 | 1890 | South-America 67618 | ||
| L | 5 | # | CTT | -TT | T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,P681R,D950N,D614G | Czech-Republic_Usti-nad-Labem-Region_Litomerice_Lovosice | 1 | 3 | 52 | 6486 | Europe 1811060 |
| L | 5 | # | CTT | -TT | H69-,V70-,D614G | Denmark | 1 | 155577 | Europe 1811060 | ||
| L | 5 | # | CTT | -TT | H69-,V70-,F490S,N501Y,A570D,P681H,T716I,S982A,D1118H,D614G | Denmark | 1 | 155577 | Europe 1811060 | ||
| L | 5 | # | CTT | -TT | A222V,A262S,D614G | Denmark_Hovedstaden | 1 | 69833 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | A222V,D614G | Denmark_Hovedstaden | 2 | 69833 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | H69-,V70-,N439K,D614G | Denmark_Hovedstaden | 1 | 69833 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | H69-,V70-,Y144-,E484K,N501Y,A570D,P681H,T716I,S982A,D1118H,D614G | Denmark_Hovedstaden | 1 | 69833 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | H69-,V70-,Y144-,F490S,N501Y,A570D,P681H,T716I,S982A,D1118H,D614G | Denmark_Hovedstaden | 4 | 69833 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | H69-,V70-,Y144-,N501Y,A570D,P681H,T716I,S982A,D1118H,D614G | Denmark_Hovedstaden | 16 | 69833 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | H69-,V70-,Y144-,W152R,N501Y,A570D,P681H,T716I,S982A,D1118H,D614G | Denmark_Hovedstaden | 13 | 69833 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | H69-,V70-,Y144X,W152R,N501Y,A570D,P681H,T716I,S982A,D1118H,D614G | Denmark_Hovedstaden | 1 | 69833 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | L18F,A222V,D614G | Denmark_Hovedstaden | 1 | 69833 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | S477N,D614G | Denmark_Hovedstaden | 3 | 69833 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | A222V,D614G | Denmark_Midtjylland | 7 | 29028 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | H69-,V70-,Y144-,F490S,N501Y,A570D,P681H,T716I,S982A,D1118H,D614G | Denmark_Midtjylland | 13 | 29028 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | H69-,V70-,Y144-,N501Y,A570D,P681H,T716I,S982A,D1118H,D614G | Denmark_Midtjylland | 11 | 29028 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | H69-,V70-,Y144X,N501Y,A570D,P681H,T716I,S982A,D1118H,D614G | Denmark_Midtjylland | 1 | 29028 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | L18F,A222V,D614G | Denmark_Midtjylland | 1 | 29028 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | L18F,Y144-,A222V,D614G | Denmark_Midtjylland | 1 | 29028 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | S477R,D614G | Denmark_Midtjylland | 1 | 29028 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | A222V,D614G | Denmark_Nordjylland | 23 | 13856 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | A67S,H69-,V70-,Y144-,F490S,N501Y,A570D,P681H,T716I,S982A,D1118H,D614G | Denmark_Nordjylland | 2 | 13856 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | G181A,A222V,D614G | Denmark_Nordjylland | 1 | 13856 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | H69-,V70-,D614G | Denmark_Nordjylland | 1 | 13856 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | H69-,V70-,Y144-,F490S,N501Y,A570D,P681H,T716I,S982A,D1118H,D614G | Denmark_Nordjylland | 120 | 13856 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | L18F,A222V,D614G | Denmark_Nordjylland | 7 | 13856 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | A222V,D614G | Denmark_Sjaelland | 2 | 17300 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | A67V,H69-,V70-,Y144-,F490S,N501Y,A570D,P681H,T716I,S982A,D1118H,D614G | Denmark_Sjaelland | 1 | 17300 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | D614G | Denmark_Sjaelland | 3 | 17300 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | H69-,V70-,Y144-,E484K,N501Y,A570D,P681H,T716I,S982A,D1118H,D614G | Denmark_Sjaelland | 1 | 17300 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | H69-,V70-,Y144-,F490S,N501Y,A570D,P681H,T716I,S982A,D1118H,D614G | Denmark_Sjaelland | 6 | 17300 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | H69-,V70-,Y144-,N501Y,A570D,P681H,T716I,S982A,D1118H,D614G | Denmark_Sjaelland | 1 | 17300 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | H69-,V70-,Y144-,W152R,N501Y,A570D,P681H,T716I,S982A,D1118H,D614G | Denmark_Sjaelland | 2 | 17300 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | L452M,D614G | Denmark_Sjaelland | 1 | 17300 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | A222V,D614G | Denmark_Syddanmark | 2 | 23362 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | D614G | Denmark_Syddanmark | 3 | 23362 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | H69-,V70-,Y144-,E484K,N501Y,A570D,P681H,T716I,S982A,D1118H,D614G | Denmark_Syddanmark | 2 | 23362 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | H69-,V70-,Y144-,F490S,N501Y,A570D,P681H,T716I,S982A,D1118H,D614G | Denmark_Syddanmark | 6 | 23362 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | H69-,V70-,Y144-,N501Y,A570D,P681H,T716I,S982A,D1118H,D614G | Denmark_Syddanmark | 5 | 23362 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | H69-,V70-,Y144X,F490S,N501Y,A570D,P681H,T716I,S982A,D1118H,D614G | Denmark_Syddanmark | 1 | 23362 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | Q677H,D614G | Denmark_Syddanmark | 1 | 23362 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | T95I,D253G,S477N,Q957R,D614G | Denmark_Syddanmark | 4 | 23362 | 155577 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | A67V,H69-,V70#,Y144-,N501Y,A570D,P681H,T716I,S982A,D1118H,D614G | Ecuador_Carchi_Tulcan | 1 | 16 | 25 | 1439 | South-America 67618 |
| L | 5 | # | CTT | -TT | G75V,T95I,D253G,E484K,A701V,D614G | Ecuador_Carchi_Tulcan | 1 | 16 | 25 | 1439 | South-America 67618 |
| L | 5 | # | CTT | -TT | T95X,D253X,E484K,A701X,D614G | Ecuador_Esmeraldas_Esmeraldas | 1 | 18 | 32 | 1439 | South-America 67618 |
| L | 5 | # | CTT | -TT | T95I,D253G,E484K,A701X,D614G | Ecuador_Loja_Loja | 1 | 18 | 25 | 1439 | South-America 67618 |
| L | 5 | # | CTT | -TT | T95I,D253G,E484K,A701V,D614G | Ecuador_Los-Rios_Urdaneta | 1 | 1 | 77 | 1439 | South-America 67618 |
| L | 5 | # | CTT | -TT | T95I,D253G,E484K,A701V,D614G | Ecuador_Manabi_Portoviejo | 3 | 18 | 127 | 1439 | South-America 67618 |
| L | 5 | # | CTT | -TT | T95I,D253G,E484K,A701X,D614G | Ecuador_Manabi_Portoviejo | 1 | 18 | 127 | 1439 | South-America 67618 |
| L | 5 | # | CTT | -TT | T95I,D253G,E484K,A701V,D614G | Ecuador_Pichincha_Quito | 1 | 144 | 225 | 1439 | South-America 67618 |
| L | 5 | # | CTT | -TT | T95I,D253G,E484K,A701V,D614G | Ecuador_Portoviejo_Andres-de-Vera | 1 | 1 | 6 | 1439 | South-America 67618 |
| L | 5 | # | CTT | -TT | T95I,D253G,E484K,A701V,D614G | Ecuador_Portoviejo_Manabi | 1 | 2 | 6 | 1439 | South-America 67618 |
| L | 5 | # | CTT | -TT | T95X,D253X,E484K,A701X,D614G | Ecuador_Santo-Domingo_Santo-Domingo | 1 | 11 | 11 | 1439 | South-America 67618 |
| L | 5 | # | CTT | -TT | H69-,V70-,Y144-,E484K,N501Y,A570D,P681H,T716I,S982A,D1118H,D614G | France_Normandie | 1 | 1092 | 65761 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | H69-,V70-,Y144-,N501Y,A570D,Q677H,P681H,T716I,S982A,D1118H,D614G | France_Provence-Alpes-Cote-d-Azur | 1 | 11830 | 65761 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | H69-,V70-,Y144-,N501Y,A570D,P681H,T716I,S982A,D1118H,P1162S,D614G | Gabon_Lambarene | 5 | 90 | 142 | Africa 20313 | |
| L | 5 | # | CTT | -TT | S13I,H69-,V70-,Y144-,E484K,N501Y,A570D,P681H,T716I,S982A,D1118H,D614G | Gabon_Lambarene | 1 | 90 | 142 | Africa 20313 | |
| L | 5 | # | CTT | -TT | T95I,Y144-,E484K,P681H,P1162S,D614G | Gabon_Lambarene | 1 | 90 | 142 | Africa 20313 | |
| L | 5 | # | CTT | -TT | H69-,V70-,Y144-,N501Y,A570D,P681H,T716I,S982A,D1118H,D614G | Germany_Baden-Wurttemberg_Tuebingen | 1 | 117 | 17854 | 158834 | Europe 1811060 |
| L | 5 | # | CTT | -TT | A67T,D614G | Hong-Kong | 1 | 4417 | Asia 225073 | ||
| L | 5 | # | CTT | -TT | D614G | Hong-Kong | 1 | 4417 | Asia 225073 | ||
| L | 5 | # | CTT | -TT | D614G | India_Gujarat | 1 | 3341 | 31805 | Asia 225073 | |
| L | 5 | # | CTT | -TT | T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,P681R,D950N,D614G | Japan_Oita | 2 | 1063 | 126062 | Asia 225073 | |
| L | 5 | # | CTT | -TT | T95I,D138Y,R346K,E484K,N501Y,P681H,D950N,D614G | Mexico_Puebla | 1 | 894 | 23200 | North-America 1101562 | |
| L | 5 | # | CTT | -TT | T95I,Y144S,Y145N,R346K,E484K,N501Y,P681H,D950N,D614G | Mexico_Puebla | 1 | 894 | 23200 | North-America 1101562 | |
| L | 5 | # | CTT | -TT | T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,P681R,D950N,D614G | New-Zealand_Auckland | 1 | 549 | 2137 | Oceania 20675 | |
| L | 5 | # | CTT | -TT | Q677H,D614G | North-Macedonia | 3 | 606 | Europe 1811060 | ||
| L | 5 | # | CTT | -TT | T19R,G142D,E156G,F157-,R158-,L452R,T478K,N501-,P681R,D614G | Pakistan_Islamabad | 1 | 68 | 587 | Asia 225073 | |
| L | 5 | # | CTT | -TT | H69-,V70-,Y144-,N501Y,A570D,P681H,T716I,A845S,S982A,D1118H,D614G | Poland_Dolnoslakie_Bobolice | 1 | 1 | 843 | 17997 | Europe 1811060 |
| L | 5 | # | CTT | -TT | S98F,D614G | Poland_Zachodniopomorskie | 1 | 991 | 17997 | Europe 1811060 | |
| L | 5 | # | CTT | --T | H69X,Y144-,F490S,N501Y,A570D,P681H,T716I,S982A,D1118H,D614G | Slovakia_Komarno | 1 | 118 | 6853 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,P681R,D950N,D614G | Sri-Lanka_Bandaragama | 1 | 6 | 1066 | Asia 225073 | |
| L | 5 | # | CTT | -TT | H69-,V70-,Y144-,N501Y,A570D,P681H,T716I,S982A,D1118H,D614G | Sweden_Kalmar-lan | 1 | 131 | 99113 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | H69-,V70-,Y144-,N501Y,A570D,P681H,T716I,S982A,D1118H,D614G | Sweden_Uppsala | 8 | 1844 | 99113 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | H69-,V70-,Y144-,N501Y,A570D,P681H,T716I,S982A,D1118H,D614G | Switzerland_Bern | 2 | 5427 | 54367 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,Q677H,P681R,D950N,D614G | Switzerland_Bern | 1 | 5427 | 54367 | Europe 1811060 | |
| L | 5 | # | CTT | -TT | H69-,V70-,Y144-,N501Y,A570D,P681H,T716I,S982A,D1118H,D614G | USA_Colorado | 1 | 22343 | 931669 | North-America 1101562 | |
| L | 5 | # | CTT | -TT | L18F,T95I,D253G,S477N,Q957R,D614G | USA_Colorado | 2 | 22343 | 931669 | North-America 1101562 | |
| L | 5 | # | CTT | -TT | T95I,D253G,E484K,A701V,D614G | USA_Colorado | 1 | 22343 | 931669 | North-America 1101562 | |
| L | 5 | # | CTT | -TT | T95I,D253G,S477N,A701V,D614G | USA_Colorado | 1 | 22343 | 931669 | North-America 1101562 | |
| L | 5 | # | CTT | -TT | T95I,D253G,S477N,Q957R,D614G | USA_Colorado | 1 | 22343 | 931669 | North-America 1101562 | |
| L | 5 | # | CTT | -TT | L18F,T95I,D253G,E484K,A701V,D614G | USA_Idaho | 2 | 7501 | 931669 | North-America 1101562 | |
| L | 5 | # | CTT | -TT | T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,P681R,D950N,D614G | USA_Idaho | 1 | 7501 | 931669 | North-America 1101562 | |
| L | 5 | # | CTT | -TT | T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,P681R,D950N,V1264L,D614G | USA_Idaho | 1 | 7501 | 931669 | North-America 1101562 | |
| L | 5 | # | CTT | -TT | T19R,G142D,E156G,F157-,R158-,L452R,T478K,P681R,D950N,D614G | USA_Idaho | 6 | 7501 | 931669 | North-America 1101562 | |
| L | 5 | # | CTT | --T | T19R,G142D,E156G,F157-,R158-,L452R,T478K,P681R,D950N,D614G | USA_Idaho | 1 | 7501 | 931669 | North-America 1101562 | |
| L | 5 | # | CTT | -TT | D614G | USA_Idaho_Ada | 1 | 1377 | 7501 | 931669 | North-America 1101562 |
| L | 5 | # | CTT | -TT | T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,P681R,D950N,D614G | USA_Idaho_Ada | 1 | 1377 | 7501 | 931669 | North-America 1101562 |
| L | 5 | # | CTT | -TT | T19R,G142D,E156G,F157-,R158-,L452R,T478K,P681R,D950N,P1162L,D614G | USA_Idaho_Ada | 2 | 1377 | 7501 | 931669 | North-America 1101562 |
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