COVID-19 Viral Genome Analysis Pipeline
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Tables of mutating sites in Spike, updated daily
Last update: Jun 29, 2026
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Collection dates: 2026-03-31 - 2026-06-25
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.
# of seqs: 4,215
| ori | pos | mut | count | frequency |
|---|---|---|---|---|
| L | 5 | F | 21 | 0.0049822 |
| X | 67 | 0.0158956 | ||
| P | 9 | L | 757 | 0.1795967 |
| X | 68 | 0.0161329 | ||
| T | 19 | A | 1 | 0.0002372 |
| F | 2 | 0.0004745 | ||
| I | 2942 | 0.6979834 | ||
| L | 9 | 0.0021352 | ||
| V | 20 | 0.0047450 | ||
| X | 314 | 0.0744958 | ||
| R | 21 | - | 7 | 0.0016607 |
| F | 1 | 0.0002372 | ||
| K | 1 | 0.0002372 | ||
| T | 3649 | 0.8657177 | ||
| X | 405 | 0.0960854 | ||
| T | 22 | N | 3001 | 0.7119810 |
| X | 233 | 0.0552788 | ||
| L | 24 | - | 3042 | 0.7217082 |
| N | 1 | 0.0002372 | ||
| S | 1 | 0.0002372 | ||
| X | 259 | 0.0614472 | ||
| P | 25 | - | 3045 | 0.7224199 |
| N | 2 | 0.0004745 | ||
| Q | 1 | 0.0002372 | ||
| S | 1 | 0.0002372 | ||
| X | 265 | 0.0628707 | ||
| P | 26 | - | 3046 | 0.7226572 |
| F | 1 | 0.0002372 | ||
| L | 767 | 0.1819692 | ||
| N | 1 | 0.0002372 | ||
| Q | 2 | 0.0004745 | ||
| X | 256 | 0.0607355 | ||
| A | 27 | - | 1 | 0.0002372 |
| Q | 1 | 0.0002372 | ||
| S | 3221 | 0.7641756 | ||
| T | 1 | 0.0002372 | ||
| V | 3 | 0.0007117 | ||
| X | 117 | 0.0277580 | ||
| S | 31 | - | 116 | 0.0275208 |
| F | 3 | 0.0007117 | ||
| L | 2 | 0.0004745 | ||
| P | 1734 | 0.4113879 | ||
| X | 44 | 0.0104389 | ||
| S | 50 | L | 3140 | 0.7449585 |
| X | 286 | 0.0678529 | ||
| F | 59 | - | 1 | 0.0002372 |
| A | 1 | 0.0002372 | ||
| S | 1532 | 0.3634638 | ||
| X | 144 | 0.0341637 | ||
| A | 67 | S | 2 | 0.0004745 |
| V | 762 | 0.1807829 | ||
| X | 143 | 0.0339265 | ||
| H | 69 | - | 3995 | 0.9478055 |
| P | 1 | 0.0002372 | ||
| S | 1 | 0.0002372 | ||
| X | 213 | 0.0505338 | ||
| V | 70 | - | 3998 | 0.9485172 |
| I | 3 | 0.0007117 | ||
| X | 172 | 0.0408066 | ||
| T | 95 | - | 1 | 0.0002372 |
| I | 748 | 0.1774614 | ||
| X | 204 | 0.0483986 | ||
| E | 96 | D | 482 | 0.1143535 |
| X | 145 | 0.0344009 | ||
| S | 98 | F | 26 | 0.0061684 |
| X | 145 | 0.0344009 | ||
| I | 101 | - | 1 | 0.0002372 |
| T | 789 | 0.1871886 | ||
| X | 149 | 0.0353499 | ||
| A | 123 | T | 1 | 0.0002372 |
| V | 15 | 0.0035587 | ||
| X | 51 | 0.0120996 | ||
| V | 127 | F | 3360 | 0.7971530 |
| I | 1 | 0.0002372 | ||
| X | 54 | 0.0128114 | ||
| C | 136 | - | 562 | 0.1333333 |
| X | 202 | 0.0479241 | ||
| D | 138 | - | 562 | 0.1333333 |
| H | 2 | 0.0004745 | ||
| X | 201 | 0.0476868 | ||
| Y | 1 | 0.0002372 | ||
| P | 139 | - | 562 | 0.1333333 |
| S | 1 | 0.0002372 | ||
| T | 1 | 0.0002372 | ||
| X | 202 | 0.0479241 | ||
| F | 140 | - | 562 | 0.1333333 |
| X | 198 | 0.0469751 | ||
| L | 141 | - | 562 | 0.1333333 |
| V | 1 | 0.0002372 | ||
| X | 198 | 0.0469751 | ||
| G | 142 | - | 562 | 0.1333333 |
| D | 3388 | 0.8037960 | ||
| N | 2 | 0.0004745 | ||
| X | 203 | 0.0481613 | ||
| V | 143 | - | 562 | 0.1333333 |
| F | 1 | 0.0002372 | ||
| I | 2 | 0.0004745 | ||
| X | 202 | 0.0479241 | ||
| Y | 144 | - | 3936 | 0.9338078 |
| C | 2 | 0.0004745 | ||
| X | 211 | 0.0500593 | ||
| Y | 145 | - | 564 | 0.1338078 |
| F | 2 | 0.0004745 | ||
| X | 197 | 0.0467378 | ||
| H | 146 | - | 573 | 0.1359431 |
| Q | 7 | 0.0016607 | ||
| X | 200 | 0.0474496 | ||
| K | 147 | - | 581 | 0.1378410 |
| E | 8 | 0.0018980 | ||
| I | 2 | 0.0004745 | ||
| N | 2 | 0.0004745 | ||
| Q | 8 | 0.0018980 | ||
| X | 180 | 0.0427046 | ||
| N | 149 | - | 563 | 0.1335706 |
| X | 54 | 0.0128114 | ||
| K | 150 | - | 1 | 0.0002372 |
| E | 1 | 0.0002372 | ||
| I | 4 | 0.0009490 | ||
| N | 19 | 0.0045077 | ||
| R | 2 | 0.0004745 | ||
| X | 54 | 0.0128114 | ||
| M | 153 | I | 240 | 0.0569395 |
| T | 1 | 0.0002372 | ||
| V | 3 | 0.0007117 | ||
| X | 56 | 0.0132859 | ||
| E | 156 | D | 40 | 0.0094899 |
| G | 1 | 0.0002372 | ||
| V | 1 | 0.0002372 | ||
| X | 80 | 0.0189798 | ||
| F | 157 | L | 22 | 0.0052195 |
| P | 1 | 0.0002372 | ||
| S | 3987 | 0.9459075 | ||
| X | 182 | 0.0431791 | ||
| R | 158 | G | 3327 | 0.7893238 |
| I | 1 | 0.0002372 | ||
| V | 1 | 0.0002372 | ||
| X | 88 | 0.0208778 | ||
| N | 164 | K | 748 | 0.1774614 |
| X | 67 | 0.0158956 | ||
| S | 172 | F | 739 | 0.1753262 |
| X | 136 | 0.0322657 | ||
| Q | 173 | H | 16 | 0.0037960 |
| K | 1 | 0.0002372 | ||
| P | 3 | 0.0007117 | ||
| X | 133 | 0.0315540 | ||
| K | 182 | G | 2 | 0.0004745 |
| N | 1 | 0.0002372 | ||
| R | 1803 | 0.4277580 | ||
| X | 49 | 0.0116251 | ||
| G | 184 | S | 1553 | 0.3684460 |
| V | 1 | 0.0002372 | ||
| X | 49 | 0.0116251 | ||
| K | 187 | - | 1 | 0.0002372 |
| I | 3 | 0.0007117 | ||
| T | 750 | 0.1779359 | ||
| X | 52 | 0.0123369 | ||
| R | 190 | G | 1 | 0.0002372 |
| K | 1 | 0.0002372 | ||
| S | 1806 | 0.4284698 | ||
| T | 2 | 0.0004745 | ||
| X | 52 | 0.0123369 | ||
| N | 211 | - | 4016 | 0.9527877 |
| G | 1 | 0.0002372 | ||
| I | 5 | 0.0011862 | ||
| K | 2 | 0.0004745 | ||
| S | 1 | 0.0002372 | ||
| X | 123 | 0.0291815 | ||
| L | 212 | - | 1 | 0.0002372 |
| D | 1 | 0.0002372 | ||
| G | 2 | 0.0004745 | ||
| I | 4016 | 0.9527877 | ||
| R | 2 | 0.0004745 | ||
| S | 5 | 0.0011862 | ||
| X | 134 | 0.0317912 | ||
| V | 213 | - | 5 | 0.0011862 |
| D | 5 | 0.0011862 | ||
| E | 3 | 0.0007117 | ||
| G | 3401 | 0.8068802 | ||
| T | 1 | 0.0002372 | ||
| X | 68 | 0.0161329 | ||
| R | 214 | - | 3 | 0.0007117 |
| P | 14 | 0.0033215 | ||
| T | 5 | 0.0011862 | ||
| X | 84 | 0.0199288 | ||
| L | 216 | - | 1 | 0.0002372 |
| F | 3402 | 0.8071174 | ||
| X | 54 | 0.0128114 | ||
| G | 219 | - | 1 | 0.0002372 |
| D | 2 | 0.0004745 | ||
| S | 21 | 0.0049822 | ||
| V | 1 | 0.0002372 | ||
| X | 49 | 0.0116251 | ||
| A | 222 | T | 1 | 0.0002372 |
| V | 21 | 0.0049822 | ||
| X | 51 | 0.0120996 | ||
| A | 243 | - | 660 | 0.1565836 |
| N | 2 | 0.0004745 | ||
| S | 4 | 0.0009490 | ||
| V | 1 | 0.0002372 | ||
| X | 306 | 0.0725979 | ||
| L | 244 | - | 666 | 0.1580071 |
| F | 3 | 0.0007117 | ||
| X | 300 | 0.0711744 | ||
| H | 245 | - | 3 | 0.0007117 |
| N | 3236 | 0.7677343 | ||
| X | 231 | 0.0548043 | ||
| P | 251 | S | 738 | 0.1750890 |
| T | 2 | 0.0004745 | ||
| X | 236 | 0.0559905 | ||
| D | 253 | G | 250 | 0.0593120 |
| H | 1 | 0.0002372 | ||
| V | 1 | 0.0002372 | ||
| X | 224 | 0.0531435 | ||
| S | 255 | - | 3 | 0.0007117 |
| A | 2 | 0.0004745 | ||
| F | 9 | 0.0021352 | ||
| X | 221 | 0.0524318 | ||
| S | 256 | - | 3 | 0.0007117 |
| A | 1 | 0.0002372 | ||
| L | 54 | 0.0128114 | ||
| X | 221 | 0.0524318 | ||
| G | 257 | - | 11 | 0.0026097 |
| S | 2 | 0.0004745 | ||
| V | 18 | 0.0042705 | ||
| X | 222 | 0.0526690 | ||
| W | 258 | - | 10 | 0.0023725 |
| C | 1 | 0.0002372 | ||
| L | 8 | 0.0018980 | ||
| R | 3 | 0.0007117 | ||
| X | 222 | 0.0526690 | ||
| A | 262 | - | 8 | 0.0018980 |
| S | 2 | 0.0004745 | ||
| T | 4 | 0.0009490 | ||
| X | 238 | 0.0564650 | ||
| A | 263 | - | 8 | 0.0018980 |
| S | 1 | 0.0002372 | ||
| V | 11 | 0.0026097 | ||
| X | 239 | 0.0567023 | ||
| A | 264 | - | 8 | 0.0018980 |
| D | 3220 | 0.7639383 | ||
| X | 244 | 0.0578885 | ||
| G | 268 | C | 1 | 0.0002372 |
| S | 38 | 0.0090154 | ||
| X | 239 | 0.0567023 | ||
| T | 286 | I | 52 | 0.0123369 |
| X | 263 | 0.0623962 | ||
| I | 326 | V | 771 | 0.1829181 |
| X | 100 | 0.0237248 | ||
| I | 332 | V | 3369 | 0.7992883 |
| X | 63 | 0.0149466 | ||
| L | 335 | F | 210 | 0.0498221 |
| X | 62 | 0.0147094 | ||
| G | 339 | H | 3372 | 0.8000000 |
| Q | 1 | 0.0002372 | ||
| R | 1 | 0.0002372 | ||
| X | 68 | 0.0161329 | ||
| Y | 773 | 0.1833926 | ||
| R | 346 | - | 10 | 0.0023725 |
| I | 3 | 0.0007117 | ||
| K | 37 | 0.0087782 | ||
| T | 1793 | 0.4253855 | ||
| X | 67 | 0.0158956 | ||
| A | 348 | P | 778 | 0.1845789 |
| S | 1 | 0.0002372 | ||
| X | 64 | 0.0151839 | ||
| K | 356 | - | 1 | 0.0002372 |
| T | 4086 | 0.9693950 | ||
| X | 107 | 0.0253855 | ||
| S | 371 | F | 4103 | 0.9734282 |
| X | 101 | 0.0239620 | ||
| S | 373 | P | 4111 | 0.9753262 |
| Q | 1 | 0.0002372 | ||
| X | 102 | 0.0241993 | ||
| S | 375 | - | 2 | 0.0004745 |
| A | 17 | 0.0040332 | ||
| F | 4047 | 0.9601423 | ||
| X | 131 | 0.0310795 | ||
| T | 376 | - | 17 | 0.0040332 |
| A | 3274 | 0.7767497 | ||
| N | 32 | 0.0075919 | ||
| X | 125 | 0.0296560 | ||
| R | 403 | K | 3943 | 0.9354686 |
| X | 248 | 0.0588375 | ||
| D | 405 | N | 4075 | 0.9667853 |
| X | 137 | 0.0325030 | ||
| R | 408 | G | 5 | 0.0011862 |
| S | 3989 | 0.9463820 | ||
| X | 220 | 0.0521945 | ||
| K | 417 | I | 1 | 0.0002372 |
| N | 3773 | 0.8951364 | ||
| T | 239 | 0.0567023 | ||
| X | 200 | 0.0474496 | ||
| D | 420 | N | 427 | 0.1013049 |
| X | 185 | 0.0438909 | ||
| A | 435 | S | 2561 | 0.6075919 |
| X | 345 | 0.0818505 | ||
| N | 440 | K | 3149 | 0.7470937 |
| R | 736 | 0.1746145 | ||
| X | 314 | 0.0744958 | ||
| L | 441 | I | 99 | 0.0234875 |
| R | 287 | 0.0680902 | ||
| X | 311 | 0.0737841 | ||
| K | 444 | N | 1 | 0.0002372 |
| R | 1562 | 0.3705813 | ||
| T | 2 | 0.0004745 | ||
| X | 329 | 0.0780546 | ||
| V | 445 | - | 5 | 0.0011862 |
| A | 720 | 0.1708185 | ||
| D | 1 | 0.0002372 | ||
| H | 679 | 0.1610913 | ||
| L | 1 | 0.0002372 | ||
| P | 1583 | 0.3755635 | ||
| R | 884 | 0.2097272 | ||
| S | 2 | 0.0004745 | ||
| X | 333 | 0.0790036 | ||
| G | 446 | D | 721 | 0.1710558 |
| I | 2 | 0.0004745 | ||
| N | 134 | 0.0317912 | ||
| S | 3012 | 0.7145907 | ||
| T | 1 | 0.0002372 | ||
| X | 330 | 0.0782918 | ||
| N | 450 | D | 3203 | 0.7599051 |
| X | 283 | 0.0671412 | ||
| Y | 1 | 0.0002372 | ||
| L | 452 | M | 1 | 0.0002372 |
| R | 474 | 0.1124555 | ||
| W | 3450 | 0.8185053 | ||
| X | 288 | 0.0683274 | ||
| L | 455 | F | 1 | 0.0002372 |
| S | 3209 | 0.7613286 | ||
| X | 277 | 0.0657177 | ||
| F | 456 | L | 3212 | 0.7620403 |
| X | 276 | 0.0654804 | ||
| N | 460 | K | 3948 | 0.9366548 |
| X | 265 | 0.0628707 | ||
| A | 475 | S | 2 | 0.0004745 |
| V | 292 | 0.0692764 | ||
| X | 140 | 0.0332147 | ||
| S | 477 | D | 2 | 0.0004745 |
| K | 2 | 0.0004745 | ||
| N | 4066 | 0.9646501 | ||
| X | 141 | 0.0334520 | ||
| T | 478 | E | 25 | 0.0059312 |
| I | 492 | 0.1167260 | ||
| K | 1425 | 0.3380783 | ||
| L | 1 | 0.0002372 | ||
| N | 759 | 0.1800712 | ||
| V | 2 | 0.0004745 | ||
| X | 157 | 0.0372479 | ||
| N | 481 | K | 3267 | 0.7750890 |
| R | 3 | 0.0007117 | ||
| X | 148 | 0.0351127 | ||
| G | 482 | - | 3 | 0.0007117 |
| R | 2 | 0.0004745 | ||
| S | 13 | 0.0030842 | ||
| X | 145 | 0.0344009 | ||
| V | 483 | - | 3229 | 0.7660735 |
| G | 1 | 0.0002372 | ||
| K | 2 | 0.0004745 | ||
| N | 1 | 0.0002372 | ||
| X | 214 | 0.0507711 | ||
| E | 484 | - | 3 | 0.0007117 |
| A | 3 | 0.0007117 | ||
| K | 3983 | 0.9449585 | ||
| P | 1 | 0.0002372 | ||
| S | 2 | 0.0004745 | ||
| X | 151 | 0.0358244 | ||
| F | 486 | - | 2 | 0.0004745 |
| D | 1 | 0.0002372 | ||
| L | 3 | 0.0007117 | ||
| P | 3219 | 0.7637011 | ||
| S | 6 | 0.0014235 | ||
| X | 150 | 0.0355872 | ||
| N | 487 | - | 8 | 0.0018980 |
| D | 1348 | 0.3198102 | ||
| X | 135 | 0.0320285 | ||
| Q | 493 | E | 3017 | 0.7157770 |
| X | 110 | 0.0260973 | ||
| G | 496 | S | 770 | 0.1826809 |
| X | 157 | 0.0372479 | ||
| Q | 498 | R | 4057 | 0.9625148 |
| X | 157 | 0.0372479 | ||
| T | 500 | - | 1 | 0.0002372 |
| A | 5 | 0.0011862 | ||
| X | 153 | 0.0362989 | ||
| N | 501 | X | 151 | 0.0358244 |
| Y | 4063 | 0.9639383 | ||
| Y | 505 | H | 3281 | 0.7784104 |
| X | 152 | 0.0360617 | ||
| K | 529 | E | 1 | 0.0002372 |
| N | 784 | 0.1860024 | ||
| Q | 1 | 0.0002372 | ||
| T | 136 | 0.0322657 | ||
| X | 13 | 0.0030842 | ||
| N | 532 | D | 11 | 0.0026097 |
| K | 5 | 0.0011862 | ||
| S | 1 | 0.0002372 | ||
| X | 9 | 0.0021352 | ||
| T | 547 | I | 5 | 0.0011862 |
| K | 11 | 0.0026097 | ||
| X | 8 | 0.0018980 | ||
| E | 554 | D | 784 | 0.1860024 |
| K | 3413 | 0.8097272 | ||
| X | 13 | 0.0030842 | ||
| I | 569 | F | 1 | 0.0002372 |
| V | 16 | 0.0037960 | ||
| X | 8 | 0.0018980 | ||
| A | 570 | V | 3409 | 0.8087782 |
| X | 9 | 0.0021352 | ||
| T | 572 | I | 1498 | 0.3553974 |
| X | 11 | 0.0026097 | ||
| A | 575 | S | 786 | 0.1864769 |
| X | 11 | 0.0026097 | ||
| E | 583 | D | 749 | 0.1776987 |
| X | 191 | 0.0453144 | ||
| T | 604 | A | 1 | 0.0002372 |
| I | 116 | 0.0275208 | ||
| X | 185 | 0.0438909 | ||
| P | 621 | F | 4 | 0.0009490 |
| S | 3269 | 0.7755635 | ||
| X | 189 | 0.0448399 | ||
| H | 625 | R | 749 | 0.1776987 |
| X | 191 | 0.0453144 | ||
| N | 641 | K | 741 | 0.1758007 |
| T | 2 | 0.0004745 | ||
| X | 297 | 0.0704626 | ||
| Y | 5 | 0.0011862 | ||
| V | 642 | A | 2 | 0.0004745 |
| G | 738 | 0.1750890 | ||
| S | 1 | 0.0002372 | ||
| X | 297 | 0.0704626 | ||
| E | 654 | K | 734 | 0.1741400 |
| X | 312 | 0.0740214 | ||
| H | 655 | X | 315 | 0.0747331 |
| Y | 3899 | 0.9250297 | ||
| S | 673 | T | 32 | 0.0075919 |
| X | 347 | 0.0823250 | ||
| T | 676 | - | 1 | 0.0002372 |
| A | 1 | 0.0002372 | ||
| I | 2 | 0.0004745 | ||
| N | 1 | 0.0002372 | ||
| P | 17 | 0.0040332 | ||
| X | 353 | 0.0837485 | ||
| Q | 677 | E | 1 | 0.0002372 |
| H | 72 | 0.0170819 | ||
| R | 34 | 0.0080664 | ||
| X | 221 | 0.0524318 | ||
| N | 679 | K | 2784 | 0.6604982 |
| M | 1 | 0.0002372 | ||
| R | 1180 | 0.2799526 | ||
| T | 4 | 0.0009490 | ||
| X | 217 | 0.0514828 | ||
| S | 680 | - | 5 | 0.0011862 |
| A | 1 | 0.0002372 | ||
| F | 68 | 0.0161329 | ||
| P | 152 | 0.0360617 | ||
| X | 203 | 0.0481613 | ||
| Y | 111 | 0.0263345 | ||
| P | 681 | - | 39 | 0.0092527 |
| H | 780 | 0.1850534 | ||
| L | 1 | 0.0002372 | ||
| R | 3167 | 0.7513642 | ||
| X | 219 | 0.0519573 | ||
| R | 683 | L | 2 | 0.0004745 |
| Q | 5 | 0.0011862 | ||
| W | 11 | 0.0026097 | ||
| X | 219 | 0.0519573 | ||
| A | 684 | T | 16 | 0.0037960 |
| X | 260 | 0.0616845 | ||
| A | 688 | D | 733 | 0.1739027 |
| S | 3 | 0.0007117 | ||
| T | 2 | 0.0004745 | ||
| V | 90 | 0.0213523 | ||
| X | 258 | 0.0612100 | ||
| S | 704 | L | 778 | 0.1845789 |
| X | 244 | 0.0578885 | ||
| N | 764 | K | 3952 | 0.9376038 |
| X | 262 | 0.0621590 | ||
| T | 791 | A | 41 | 0.0097272 |
| I | 3 | 0.0007117 | ||
| X | 310 | 0.0735469 | ||
| K | 795 | T | 726 | 0.1722420 |
| X | 333 | 0.0790036 | ||
| D | 796 | H | 2 | 0.0004745 |
| X | 346 | 0.0820878 | ||
| Y | 3867 | 0.9174377 | ||
| A | 829 | S | 1 | 0.0002372 |
| T | 15 | 0.0035587 | ||
| X | 319 | 0.0756821 | ||
| A | 852 | K | 729 | 0.1729537 |
| S | 1 | 0.0002372 | ||
| X | 317 | 0.0752076 | ||
| S | 939 | F | 4023 | 0.9544484 |
| X | 186 | 0.0441281 | ||
| S | 943 | G | 129 | 0.0306050 |
| X | 182 | 0.0431791 | ||
| G | 946 | E | 1 | 0.0002372 |
| R | 13 | 0.0030842 | ||
| X | 181 | 0.0429419 | ||
| Q | 954 | H | 4017 | 0.9530249 |
| R | 1 | 0.0002372 | ||
| X | 187 | 0.0443654 | ||
| Y | 10 | 0.0023725 | ||
| A | 958 | S | 15 | 0.0035587 |
| X | 194 | 0.0460261 | ||
| N | 969 | K | 3996 | 0.9480427 |
| X | 207 | 0.0491103 | ||
| D | 1084 | G | 27 | 0.0064057 |
| X | 7 | 0.0016607 | ||
| Y | 2 | 0.0004745 | ||
| G | 1099 | D | 1 | 0.0002372 |
| S | 25 | 0.0059312 | ||
| X | 18 | 0.0042705 | ||
| V | 1104 | L | 88 | 0.0208778 |
| X | 17 | 0.0040332 | ||
| P | 1143 | F | 3 | 0.0007117 |
| L | 3412 | 0.8094899 | ||
| X | 16 | 0.0037960 | ||
| D | 1146 | G | 39 | 0.0092527 |
| X | 16 | 0.0037960 | ||
| A | 1174 | V | 215 | 0.0510083 |
| X | 31 | 0.0073547 | ||
| D | 1184 | E | 789 | 0.1871886 |
| X | 31 | 0.0073547 | ||
| Y | 1 | 0.0002372 | ||
| I | 1216 | T | 3 | 0.0007117 |
| V | 107 | 0.0253855 | ||
| X | 64 | 0.0151839 | ||
| V | 1264 | L | 357 | 0.0846975 |
| M | 2 | 0.0004745 | ||
| X | 52 | 0.0123369 |
Table 1B. Details regarding common mutations listed in A and their geographic locations.
| ori | pos | mut | covariations | location | # of occurrences | #seqs from local | #seqs from state/province | #seqs from country | #seqs from continent |
|---|---|---|---|---|---|---|---|---|---|
| L | 5 | F | L5F,T19X,R21X,T22X,L24X,P25X,P26X,A27S,S31P,S50L,H69-,V70-,V127F,G142D,Y144-,F157X,R158G,K182R,R190S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,T376A,R403K,D405N,R408S,K417N,N440K,K444R,V445R,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478K,N481K,V483-,N487D,Q493E,Q498R,N501Y,Y505H,E554K,A570V,T572I,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L,D614G | USA_New-York_Monroe | 1 | 68 | 328 | 919 | North-America 1827 |
| L | 5 | F | L5F,T19I,R21T,T22N,L24-,P25-,P26-,A27S,S31P,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,K182R,R190S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,T376A,R403K,D405N,R408S,K417N,N440K,V445R,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478E,N481K,V483-,E484K,F486P,Q493E,Q498R,N501Y,Y505H,T547I,E554K,A570V,P621S,H655Y,N679R,P681R,N764K,D796Y,S939F,Q954H,N969K,V1104L,P1143L,V1264L,D614G | USA_California | 1 | 120 | 919 | North-America 1827 | |
| L | 5 | F | L5F,T19I,R21T,T22N,L24-,P25-,P26-,A27S,S50L,F59S,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,G184S,N211-,L212I,V213G,L216F,A243X,L244X,H245X,P251X,D253X,S255X,S256X,G257X,W258X,A262X,A263X,A264X,G268X,T286X,I332V,G339H,K356T,S371F,S373P,T376A,R403K,D405N,R408X,K417X,D420X,A435X,N440X,L441X,K444X,V445X,G446X,N450X,L452X,L455X,F456X,N460X,S477N,T478I,N481K,V483X,E484X,F486P,Q493E,Q498R,N501Y,Y505H,E554K,A570V,P621S,H655Y,N679K,P681R,A684T,N764K,D796Y,S939F,Q954H,N969K,P1143L,D614G | Australia_Queensland | 1 | 332 | 864 | Oceania 991 | |
| L | 5 | F | L5F,T19I,R21T,T22N,L24-,P25-,P26-,A27S,S31P,S50L,H69-,V70-,V127F,G142D,Y144-,M153I,F157S,R158G,K182R,R190S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,T376A,R403K,D405N,R408S,K417N,A435S,N440K,L441R,K444R,V445P,G446S,N450D,L452W,L455S,F456L,N460K,A475V,S477N,N481K,V483-,E484K,F486P,Q498R,N501Y,Y505H,E554K,A570V,P621S,H655Y,N679R,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L,D614G | Singapore | 1 | 685 | Asia 886 | ||
| L | 5 | F | L5F,T19I,R21T,T22N,L24-,P25-,P26-,A27S,S50L,F59S,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,G184S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,K356T,S371F,S373P,T376A,R403K,D405N,R408S,K417N,A435S,N440K,V445H,G446S,N450D,L452W,L455S,F456L,N460K,S477N,N481K,V483-,E484K,F486P,Q493E,Q498R,N501Y,Y505H,E554K,A570V,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L,V1264L,D614G | Canada_Ontario | 1 | 618 | 887 | North-America 1827 | |
| L | 5 | F | L5F,T19I,R21T,T22N,L24-,P25-,P26-,A27S,S31P,S50L,H69-,V70-,E96D,V127F,G142D,Y144-,F157S,R158G,K182R,R190S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,T376A,R403K,D405N,R408S,K417N,N440K,K444R,V445P,G446S,N450D,L452R,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,N487D,Q493E,Q498R,N501Y,Y505H,E554K,A570V,T572I,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L,D614G | USA_California | 1 | 120 | 919 | North-America 1827 | |
| L | 5 | F | L5F,P9L,R21T,P26L,A67V,H69-,V70-,T95I,I101T,C136X,D138X,P139X,F140X,L141X,G142X,V143X,Y144X,Y145X,H146X,K147X,F157S,N164K,S172F,K187T,N211-,L212I,A243X,P251S,I326V,G339Y,A348P,K356T,S371F,S373P,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | Sweden_Vastmanland | 1 | 9 | 25 | Europe 435 | |
| L | 5 | F | L5F,T19I,R21T,T22N,L24-,P25-,P26-,A27S,S31P,S50L,H69-,V70-,E96D,V127F,G142D,Y144-,F157X,R158X,K182R,R190S,N211-,L212I,V213G,L216F,H245N,A264D,I326X,I332V,G339H,R346T,K356T,S373P,T376A,R403K,D405N,R408S,K417N,V445X,G446S,N450D,L452R,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,N487D,Q493E,Q498R,N501Y,Y505H,E554K,A570V,T572I,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L,D614G | USA_Arizona_Graham | 1 | 2 | 22 | 919 | North-America 1827 |
| L | 5 | F | L5F,T19I,R21T,T22N,L24-,P25-,P26-,A27S,S50L,F59S,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,G184S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,K356T,S371F,S373P,T376A,R403K,D405N,R408S,K417N,A435S,N440K,V445P,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478I,N481K,V483-,E484K,F486P,Q493E,Q498R,N501Y,Y505H,E554K,A570V,E583X,T604X,P621S,H655Y,N679K,S680X,P681X,R683X,A684X,A688X,N764K,K795X,D796X,S939F,S943G,Q954H,N969K,P1143L,D614G | Australia_New-South-Wales_Sydney | 1 | 265 | 265 | 864 | Oceania 991 |
| L | 5 | F | L5F,T19I,R21X,T22N,L24-,P25-,P26-,A27S,S31P,S50L,H69-,V70-,E96D,V127F,G142D,Y144-,F157S,R158G,K182R,R190S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,T376A,R403K,D405N,R408S,K417N,N440K,K444R,V445P,G446S,N450D,L452R,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,N487D,Q493E,Q498R,N501Y,Y505H,E554K,A570V,T572I,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L,D614G | USA_Minnesota_Minneota | 1 | 99 | 99 | 919 | North-America 1827 |
| L | 5 | F | L5F,S31P,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,K182R,R190S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,T376A,R403K,D405N,R408S,K417N,N440K,K444R,V445R,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,N487D,Q493E,Q498R,N501Y,Y505H,K529T,E554K,A570V,T572I,T604I,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L,V1264L,D614G | USA_New-York_New-York-City | 1 | 125 | 328 | 919 | North-America 1827 |
| L | 5 | F | L5F,T19I,R21T,T22N,L24-,P25-,P26-,A27S,S31P,S50X,F59X,A67X,H69X,V70X,T95X,E96X,S98X,I101X,V127F,G142D,Y144-,F157S,R158G,K182R,R190S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,L335F,G339H,R346T,K356T,S371F,S373P,T376A,R403K,D405N,R408S,K417T,N440K,K444R,V445R,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,N487D,Q493E,Q498R,N501Y,Y505H,E554K,A570V,T572I,P621S,N641X,V642X,E654X,H655X,S673X,T676X,N679K,P681R,N764K,T791X,K795X,D796X,A829X,A852X,S939X,S943X,G946X,Q954X,A958X,N969X,P1143L,I1216X,V1264X,D614G | USA_Colorado | 1 | 85 | 919 | North-America 1827 | |
| L | 5 | F | L5F,T19I,R21T,T22N,L24-,P25-,P26-,A27S,S31P,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,K182R,R190S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,T376A,R403K,D405N,R408S,K417N,N440K,K444R,V445R,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,N487D,Q493E,Q498R,N501Y,Y505H,E554K,A570V,T572I,P621S,H655Y,N679K,S680P,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L,D614G | France_Auvergne-Rhone-Alpes_Rhone | 1 | 17 | 23 | 63 | Europe 435 |
| L | 5 | F | L5F,P9L,R21T,P26L,A67V,H69-,V70-,T95I,I101T,C136-,D138-,P139-,F140-,L141-,G142-,V143-,Y144-,Y145-,H146-,K147-,N149-,F157S,N164K,S172F,K187T,N211-,L212I,A243-,L244-,P251S,I326V,G339Y,A348P,K356X,S371F,S373P,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | Australia_Victoria | 1 | 16 | 864 | Oceania 991 | |
| L | 5 | F | T19I,R21T,T22N,L24-,P25-,P26-,A27S,S31P,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,K182R,R190S,N211-,L212I,V213G,L216F,A243X,L244X,H245X,P251X,D253X,S255X,S256X,G257X,W258X,A262X,A263X,A264X,G268X,T286X,I332V,G339H,R346T,K356T,S371X,S373X,S375X,T376X,R403X,D405X,R408X,K417X,D420X,A435X,N440X,L441X,K444X,V445X,G446X,N450X,L452X,L455X,F456X,N460X,S477N,T478K,N481K,V483X,E484K,F486P,N487D,Q493E,Q498R,N501Y,Y505H,E554K,A570V,T572I,P621S,H655Y,N679K,S680P,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L,D614G | Australia_Queensland | 1 | 332 | 864 | Oceania 991 | |
| L | 5 | F | L5F,T19I,R21T,T22N,L24-,P25-,P26-,A27S,S50L,F59S,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,G184S,N211-,L212I,V213G,L216F,H245N,D253G,A264D,I332V,G339H,K356T,S371F,S373P,T376A,R403K,D405N,R408S,K417T,D420N,A435S,N440K,V445H,G446S,N450D,L452W,L455S,F456L,N460K,S477N,N481K,V483-,E484K,F486P,Q493E,Q498R,N501Y,Y505H,E554K,A570V,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L,I1216V,D614G | Singapore | 1 | 685 | Asia 886 | ||
| L | 5 | F | L5F,T19I,R21T,T22N,L24-,P25-,P26-,A27S,S50L,F59S,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,G184S,N211-,L212I,V213G,L216F,H245N,S256L,A264D,I332V,G339H,K356T,S371F,S373P,T376A,R403K,D405N,R408S,K417N,A435S,N440K,V445P,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478I,N481K,V483-,E484K,F486P,Q493E,Q498R,N501Y,Y505H,E554K,A570V,E583X,T604X,P621X,H625X,N641X,V642X,E654X,H655X,S673X,T676X,Q677X,N679X,S680X,P681X,R683X,A684X,A688X,S704X,N764X,T791X,K795X,D796X,A829X,A852X,S939F,Q954H,N969K,P1143L,D614X | Australia_New-South-Wales_Sydney | 2 | 265 | 265 | 864 | Oceania 991 |
| L | 5 | F | L5F,A27S,S31P,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,K182R,R190S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,T376A,R403K,D405N,R408S,K417N,N440K,L441I,K444R,V445R,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,N487D,Q493E,Q498R,N501Y,Y505H,E554K,A570V,T572I,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L,D614G | Poland_Malopolskie | 1 | 3 | 10 | Europe 435 | |
| L | 5 | F | L5F,A27S,S31P,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,K182R,R190S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,T376A,R403K,D405N,R408S,K417N,N440K,K444R,V445R,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,N487D,Q493E,Q498R,N501Y,Y505H,K529T,E554K,A570V,T572I,T604I,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L,V1264L,D614G | Poland_Pomorze | 1 | 3 | 10 | Europe 435 | |
| L | 5 | F | L5F,T19X,R21X,T22X,L24X,P25X,P26X,A27S,S31P,S50L,H69-,V70-,E96D,V127F,G142D,Y144-,F157X,R158G,K182R,R190S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,T376A,R403K,D405N,R408S,K417N,N440K,K444R,V445P,G446S,N450D,L452R,L455S,F456L,N460K,S477N,T478K,N481K,V483-,N487D,Q493E,Q498R,N501Y,Y505H,E554K,A570V,T572I,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L,D614G | USA_New-York_Monroe | 1 | 68 | 328 | 919 | North-America 1827 |
| L | 5 | X | L5X,T19A,R21X,T22X,L24X,P25X,P26X,A27X,S31X,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,K182R,N211-,L212I,V213G,H245N,A264D,I332X,G339X,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417X,D420X,N440K,K444R,V445R,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,N487D,Q493E,Q498R,N501Y,Y505H,E554K,A570V,T572I,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L,D614G | Uganda_Kampala | 1 | 1 | 1 | Africa 21 | |
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P25X,P26X,A27X,S31X,S50X,F59X,A67X,H69X,V70X,T95X,E96X,S98X,I101X,V127F,G142D,Y144-,F157S,R158G,G184S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,A435X,N440K,L441X,K444X,V445X,G446X,N450X,L452X,L455X,F456X,N460X,A475X,S477N,N481K,V483X,E484X,F486X,N487X,Q493X,G496X,Q498X,T500X,N501X,E554K,I569V,A570V,P621S,H655Y,N679K,S680P,P681R,N764K,D796Y,S939F,Q954Y,N969K,P1143L,D614G | Hong-Kong | 1 | 36 | Asia 886 | ||
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P25X,P26X,A27X,S31X,S50L,F59S,A67X,H69X,V70X,A123X,V127X,C136X,D138X,P139X,G142D,Y144-,M153T,F157S,R158G,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417T,A435S,N440K,V445R,G446I,N450D,L452W,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,Q493E,Q498R,N501Y,E554K,A570V,T572I,E583X,T604X,P621X,H625X,N641X,V642X,E654X,H655X,S673X,T676X,Q677X,N679X,S680X,P681X,R683X,A684X,A688X,S704X,N764X,T791X,D796X,A829X,A852X,S939F,Q954H,N969K,V1104L,P1143L,D614X | Australia_New-South-Wales_Sydney | 1 | 265 | 265 | 864 | Oceania 991 |
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P25X,P26X,A27X,S31P,S50L,H69X,V70X,T95X,E96X,S98X,I101X,A123X,V127X,C136X,D138X,P139X,F140X,L141X,G142X,V143X,Y144X,Y145X,H146X,K147X,N149X,K150X,M153X,E156X,F157X,R158X,K182R,R190S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,K444R,V445R,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,N487D,Q493E,Q498R,N501Y,Y505H,E554K,A570V,T572I,E583X,T604X,P621X,H625X,N641X,V642X,E654X,H655X,S673X,T676X,Q677X,N679X,S680X,P681X,R683X,A684X,A688X,S704X,N764X,T791X,D796X,A829X,A852X,S939F,Q954H,N969K,P1143L,D614X | Australia_New-South-Wales_Sydney | 1 | 265 | 265 | 864 | Oceania 991 |
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P25X,P26X,A27X,S31X,S50X,F59X,A67X,H69X,V70X,T95X,E96X,S98X,I101X,A123X,V127X,C136X,D138X,P139X,F140X,L141X,G142X,V143X,Y144X,Y145X,H146X,K147X,N149X,K150X,M153X,E156X,F157X,R158X,N164X,S172X,Q173X,K182R,R190S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,K444R,V445R,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,N487D,Q493E,Q498R,N501Y,Y505H,K529T,E554K,A570V,T572I,E583X,T604X,P621X,H625X,N641X,V642X,E654X,H655X,S673X,T676X,Q677X,N679X,S680X,P681X,R683X,A684X,A688X,S704X,N764X,T791X,D796X,A829X,A852X,S939F,Q954H,N969K,P1143L,V1264L,D614X | Australia_New-South-Wales_Sydney | 1 | 265 | 265 | 864 | Oceania 991 |
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P25X,P26X,A27X,S31X,S50X,F59X,A67X,H69X,V70X,T95X,E96X,S98X,I101X,A123X,V127X,C136X,D138X,P139X,F140X,L141X,G142X,V143X,Y144X,Y145X,H146X,K147X,N149X,K150X,F157X,R158X,N164X,S172X,Q173X,G184S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,D420N,A435S,N440K,V445P,G446S,N450D,L452W,L455S,F456L,N460K,S477N,N481K,V483-,E484K,F486P,Q493E,Q498R,N501Y,Y505H,E554K,A570V,E583X,T604X,P621X,H625X,N641X,V642X,E654X,H655X,S673X,T676X,Q677X,N679X,S680X,P681X,R683X,A684X,A688X,S704X,N764X,T791X,D796X,A829X,A852X,S939F,Q954H,N969K,P1143L,D614X | Australia_New-South-Wales_Sydney | 1 | 265 | 265 | 864 | Oceania 991 |
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P26X,A27X,S31P,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,K182R,R190S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,K444R,V445R,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,N487D,Q493E,Q498R,N501Y,Y505H,E554K,A570V,T572I,P621S,H655Y,N679K,S680P,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L,D614G | Brazil_Federal-District_Plano-Piloto | 1 | 3 | 6 | 49 | South-America 55 |
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P25X,P26X,A27X,S31X,S50L,H69-,V70-,T95I,I101T,F157X,N164X,S172X,K187T,R190X,N211-,L212I,A243-,L244-,P251S,A264X,I326X,G339X,A348X,K356T,S371F,S373P,S375F,T376X,R403K,D405N,R408X,K417N,A435X,K444X,V445X,G446X,N450X,L452W,L455X,F456X,N460K,S477N,T478X,E484K,G496X,Q498R,N501Y,K529X,A575X,E583D,N641X,V642X,H655Y,N679X,P681R,N764K,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | Italy_Torino | 1 | 4 | 29 | Europe 435 | |
| L | 5 | X | T19I,R21T,T22N,L24-,P25-,P26-,A27S,S31P,S50X,H69-,V70-,V127F,G142D,Y144-,M153I,F157S,R158G,K182R,R190S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,A435S,N440K,L441R,K444R,V445P,G446S,N450D,L452W,L455S,F456L,N460K,A475V,S477N,N481K,V483-,E484K,F486P,Q498R,N501Y,Y505H,E554K,A570V,P621S,H655Y,N679R,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L,D614G | Singapore | 1 | 685 | Asia 886 | ||
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P25X,P26X,A27X,S31X,S50X,F59X,A67X,H69X,V70X,T95X,E96X,S98X,I101X,A123X,V127X,C136X,D138X,P139X,F140X,L141X,G142X,V143X,Y144X,Y145X,H146X,K147X,N149X,K150X,M153X,E156X,F157X,R158X,N164X,S172X,Q173X,K182X,G184X,K187X,R190X,N211X,L212X,V213X,R214X,L216X,G219X,A222X,A243X,L244X,H245X,P251X,D253X,S255X,S256X,G257X,W258X,A262X,A263X,A264X,G268X,T286X,I326V,G339Y,A348P,K356X,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,S673X,T676X,Q677X,N679X,S680X,P681X,R683X,A684X,A688X,S704X,N764X,T791X,D796X,A829X,A852X,S939X,S943X,G946X,Q954X,A958X,N969X,D1184E,D614G | Spain_Catalunya_Pineda-de-Mar | 1 | 1 | 23 | 112 | Europe 435 |
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P26X,A67V,H69-,V70-,T95I,I101T,C136-,D138-,P139-,F140-,L141-,G142-,V143-,Y144-,Y145-,H146-,K147-,N149-,F157S,N164K,S172F,K187T,N211-,L212I,A243-,L244-,P251S,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | Spain_Catalunya_Santa-Coloma-de-Gramenet | 1 | 1 | 23 | 112 | Europe 435 |
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P25X,P26X,A27X,S31X,S50L,F59S,H69-,V70-,V127F,G142D,Y144-,F157S,R158X,G184S,N211-,L212I,V213G,L216F,A222X,H245N,A264D,I332V,G339H,R346K,K356X,S371X,S373X,S375X,T376X,R403X,R408X,K417N,A435S,N440K,V445P,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478I,N481K,V483-,E484K,F486P,Q493E,Q498R,N501Y,Y505H,E554K,A570V,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L,A1174X,D1184X,I1216X,D614G | Australia_Western-Australia | 1 | 44 | 864 | Oceania 991 | |
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P25X,P26X,A27X,S31X,S50L,F59S,H69-,V70-,V127F,G142D,Y144-,F157X,R158X,N164X,G184S,N211-,L212I,V213G,L216F,A243X,H245N,A264D,I332V,G339H,R346K,K356X,S371X,S373X,S375X,T376X,R403X,R408X,K417N,A435S,N440K,V445P,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478I,N481K,V483-,E484K,F486P,Q493E,Q498R,N501Y,Y505H,E554K,A570V,P621S,H655Y,N679K,P681R,R683Q,N764K,D796Y,S939F,Q954H,N969K,P1143L,A1174X,D1184X,I1216X,D614G | Australia_Western-Australia | 1 | 44 | 864 | Oceania 991 | |
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P25X,P26X,A27X,S31X,S50X,F59X,A67X,H69X,V70X,T95X,E96X,S98X,I101X,A123X,V127X,C136X,D138X,P139X,F140X,L141X,G142X,V143X,Y144X,Y145X,H146X,K147X,N149X,K150X,M153X,E156X,F157X,R158X,N164X,S172X,Q173X,K182X,G184X,K187X,R190X,N211X,L212X,V213X,R214X,L216X,G219X,A222X,A243X,L244X,H245X,P251X,D253X,S255X,S256X,G257X,W258X,A262X,A263X,A264X,G268X,T286X,I326X,I332X,L335X,G339X,R346X,A348X,K356X,S371X,S373X,S375X,T376X,R403X,D405X,R408X,K417X,D420X,A435X,N440X,L441X,K444X,V445X,G446X,N450X,L452X,L455X,F456X,N460X,A475X,S477X,T478X,N481X,G482X,V483X,E484X,F486X,N487X,Q493X,G496X,Q498X,T500X,N501X,Y505X,E554K,A570V,P621S,E654X,S673X,T676X,Q677X,N679X,S680X,P681X,R683X,A684X,A688X,S704X,N764X,D796Y,S939X,S943X,G946X,Q954H,N969K,D1084X,G1099X,V1104X,P1143X,D1146X,A1174X,D1184X,I1216X,D614G | Australia_Western-Australia | 1 | 44 | 864 | Oceania 991 | |
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P25X,P26X,A27X,S31X,S50X,F59X,A67X,H69X,V70X,T95X,E96X,S98X,I101X,V127F,G142D,Y144-,F157S,R158G,K182R,R190S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,S375F,T376A,R403X,D405N,R408S,K417N,N440K,K444X,V445X,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478K,N481X,G482X,V483X,E484X,F486X,N487X,Q493X,G496X,Q498X,T500X,N501X,Y505X,E554K,A570V,T572I,P621S,S673X,T676X,N679K,P681R,A688V,N764K,D796Y,S939X,S943X,G946X,Q954X,A958X,N969X,P1143L,D614G | USA_Utah | 1 | 6 | 919 | North-America 1827 | |
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P26X,A27X,S31X,S50X,H69-,V70-,E96D,V127F,G142D,Y144-,F157S,R158G,K182R,R190S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,K444R,V445P,G446S,N450D,L452R,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,N487D,Q493E,Q498R,N501Y,Y505H,E554K,A570V,T572I,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L,D614G | Canada_Ontario | 1 | 618 | 887 | North-America 1827 | |
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P26X,A27X,S50L,F59S,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,G184S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,A435S,N440K,V445P,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478I,N481K,V483-,E484K,F486P,Q493E,Q498R,N501Y,Y505H,E554K,A570V,P621S,H655Y,N679K,S680Y,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L,D614G | Canada_Ontario | 1 | 618 | 887 | North-America 1827 | |
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P26X,A27X,S31P,S50L,H69-,V70-,E96D,V127F,G142D,Y144-,F157S,R158G,K182R,R190S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,K444R,V445P,G446S,N450D,L452R,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,N487D,Q493E,Q498R,N501Y,Y505H,E554K,A570V,T572I,P621S,H655Y,N679K,P681-,A684X,A688X,S704X,N764K,D796Y,S939X,S943X,G946X,Q954X,A958X,N969X,P1143L,D614G | Canada_Ontario | 1 | 618 | 887 | North-America 1827 | |
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P26X,A27X,S50L,F59S,H69-,V70-,A123X,V127F,G142D,Y144-,F157S,R158G,G184S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,A435S,N440K,V445P,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478I,N481K,V483-,E484K,F486P,Q493E,Q498R,N501Y,Y505H,E554K,A570V,P621S,H655Y,N679K,S680Y,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L,D614G | Canada_Ontario | 1 | 618 | 887 | North-America 1827 | |
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P26X,A27X,S31P,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,K182R,R190S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339Q,R346T,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,K444R,V445R,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,N487D,Q493E,Q498R,N501Y,Y505H,E554K,A570V,T572I,P621S,H655Y,N679K,P681R,N764K,D796Y,S939X,S943X,G946X,Q954X,A958X,N969X,P1143L,D614G | Brazil_Rio-Grande-do-Norte_Sao-Goncalo-do-Amarante | 1 | 1 | 7 | 49 | South-America 55 |
| L | 5 | X | L5X,P9X,R21T,P26L,A67V,H69-,V70-,T95I,I101T,C136-,D138-,P139-,F140-,L141-,G142-,V143-,Y144-,Y145-,H146-,K147-,N149-,F157S,N164K,S172F,K182X,G184X,K187X,R190X,N211X,L212X,V213X,R214X,L216X,G219X,A222X,A243X,L244X,H245X,P251X,D253X,S256X,G257X,W258X,A262X,A263X,A264X,G268X,T286X,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | New-Zealand_Whanganui | 1 | 1 | 118 | Oceania 991 | |
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P25X,P26X,A27X,S31X,A67V,H69-,V70-,T95I,I101T,A123X,V127X,C136X,D138X,P139X,F140X,L141X,G142X,V143X,Y144X,Y145X,H146X,K147X,N149X,K150X,M153X,E156X,F157X,R158X,N164X,S172X,Q173X,K182X,G184X,K187X,R190X,N211X,L212X,V213X,R214X,L216X,G219X,A222X,A243X,L244X,H245X,P251X,D253X,S256X,G257X,W258X,A262X,A263X,A264X,G268X,T286X,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | New-Zealand_Canterbury | 1 | 2 | 118 | Oceania 991 | |
| L | 5 | X | L5X,P9X,R21T,P26L,A67V,H69-,V70-,T95I,I101T,C136-,D138-,P139-,F140-,L141-,G142-,V143-,Y144-,Y145-,H146-,K147-,N149-,F157S,N164K,S172F,K187T,R190X,N211X,L212X,V213X,R214X,L216X,G219X,A222X,A243X,L244X,H245X,P251X,D253X,S256X,G257X,W258X,A262X,A263X,A264X,G268X,T286X,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | New-Zealand_Waitemata | 1 | 1 | 118 | Oceania 991 | |
| L | 5 | X | P9X,R21T,P26L,A67V,H69-,V70-,T95I,I101T,C136-,D138-,P139-,F140-,L141-,G142-,V143-,Y144-,Y145-,H146-,K147-,N149-,F157S,N164K,S172F,G184V,K187T,N211-,L212I,R214X,A243-,L244-,P251S,T286X,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | New-Zealand_Northland | 1 | 10 | 118 | Oceania 991 | |
| L | 5 | X | P9X,R21T,P26L,A67V,H69-,V70-,T95I,I101T,F157S,N164K,S172F,K187T,N211-,L212I,A243-,L244-,P251S,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | New-Zealand_MidCentral | 1 | 16 | 118 | Oceania 991 | |
| L | 5 | X | L5X,P9X,R21T,P26L,A67V,T95I,I101T,F157S,N164K,S172F,K187T,N211X,L212X,V213X,R214X,L216X,G219X,A222X,A243X,L244X,H245X,P251X,D253X,S256X,G257X,W258X,A262X,A263X,A264X,G268X,T286X,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | New-Zealand_Southern | 1 | 13 | 118 | Oceania 991 | |
| L | 5 | X | P9X,R21T,P26L,A67V,H69-,V70-,T95I,I101T,F157S,N164K,S172F,K187T,N211-,L212I,R214X,A243-,L244-,P251S,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | New-Zealand_Waikato | 1 | 16 | 118 | Oceania 991 | |
| L | 5 | X | P9X,R21T,P26L,A67V,H69X,V70-,T95I,I101T,F157S,N164K,S172F,K187T,N211-,L212I,R214X,A243-,L244-,P251S,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | New-Zealand_Counties-Manukau | 1 | 10 | 118 | Oceania 991 | |
| L | 5 | X | L5X,P9X,R21T,P26L,A67V,H69-,V70-,T95I,I101T,C136-,D138-,P139-,F140-,L141-,G142-,V143-,Y144-,Y145-,H146-,K147-,N149-,F157S,N164K,S172F,K187T,N211-,L212I,R214X,A243X,L244X,H245X,P251X,D253X,S256X,G257X,W258X,A262X,A263X,A264X,G268X,T286X,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | New-Zealand_Waikato | 1 | 16 | 118 | Oceania 991 | |
| L | 5 | X | L5X,P9X,R21T,P26L,A67V,H69-,V70-,T95I,I101T,F157S,N164K,S172F,K187T,N211X,L212X,V213X,R214X,L216X,G219X,A222X,A243X,L244X,H245X,P251X,D253X,S256X,G257X,W258X,A262X,A263X,A264X,G268X,T286X,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | New-Zealand_Waikato | 1 | 16 | 118 | Oceania 991 | |
| L | 5 | X | P9X,R21T,P26L,A67V,H69-,V70-,T95I,I101T,C136-,D138-,P139-,F140-,L141-,G142-,V143-,Y144-,Y145-,H146-,K147-,N149-,F157S,N164K,S172F,K187T,N211-,L212I,A243-,L244-,P251S,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | New-Zealand_Northland | 1 | 10 | 118 | Oceania 991 | |
| L | 5 | X | P9X,R21T,P26L,A67V,H69-,V70-,T95I,I101T,C136-,D138-,P139-,F140-,L141-,G142-,V143-,Y144-,Y145-,H146-,K147-,N149-,F157S,N164K,S172F,K187T,N211-,L212I,A243-,L244-,P251S,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | New-Zealand_Taranaki | 1 | 17 | 118 | Oceania 991 | |
| L | 5 | X | L5X,P9X,R21T,P26L,A67V,H69-,V70-,T95I,I101T,C136-,D138-,P139-,F140-,L141-,G142-,V143-,Y144-,Y145-,H146-,K147-,N149-,F157S,N164K,S172F,K187T,N211-,L212I,R214X,A243X,L244X,H245X,P251X,D253X,S256X,G257X,W258X,A262X,A263X,A264X,G268X,T286X,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | New-Zealand_Taranaki | 1 | 17 | 118 | Oceania 991 | |
| L | 5 | X | L5X,P9X,R21T,P26L,A67V,H69-,V70-,T95I,I101T,C136-,D138-,P139-,F140-,L141-,G142-,V143-,Y144-,Y145-,H146-,K147-,N149-,F157S,N164K,S172F,N211X,L212X,V213X,R214X,L216X,G219X,A222X,A243X,L244X,H245X,P251X,D253X,S256X,G257X,W258X,A262X,A263X,A264X,G268X,T286X,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478X,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | New-Zealand_Taranaki | 1 | 17 | 118 | Oceania 991 | |
| L | 5 | X | L5X,P9X,R21T,P26L,A67V,H69-,V70-,T95I,I101T,C136-,D138-,P139-,F140-,L141-,G142-,V143-,Y144-,Y145-,H146-,K147-,N149-,F157S,N164K,S172F,K187T,N211-,L212I,R214X,A243X,L244X,H245X,P251X,D253X,S256X,G257X,W258X,A262X,A263X,A264X,G268X,T286X,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | New-Zealand_Canterbury | 1 | 2 | 118 | Oceania 991 | |
| L | 5 | X | L5X,P9X,R21T,P26L,A67V,H69-,V70-,T95I,I101T,F157S,N164K,S172F,K187T,N211-,L212I,R214X,A243X,L244X,P251X,A262X,A263X,A264X,G268X,T286X,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478X,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | New-Zealand_Nelson-Marlborough | 1 | 3 | 118 | Oceania 991 | |
| L | 5 | X | P9X,R21T,P26L,A67V,H69-,V70-,T95I,I101T,C136-,D138-,P139-,F140-,L141-,G142-,V143-,Y144-,Y145-,H146-,K147-,N149-,F157S,N164K,S172F,K187T,N211-,L212I,A243-,L244-,P251S,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478X,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | New-Zealand_Southern | 1 | 13 | 118 | Oceania 991 | |
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P25X,P26X,A27X,S31P,S50L,H69-,V70-,E96D,A123X,V127X,C136X,D138X,P139X,F140X,L141X,G142X,V143X,Y144X,H146X,K147X,N149X,K150X,M153X,E156X,F157X,R158X,N164X,S172X,Q173X,K182X,R190S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356X,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,K444R,V445P,G446S,N450D,L452R,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,N487D,Q493E,Q498R,N501Y,Y505H,E554K,A570V,T572I,P621S,H655Y,N679K,P681R,N764K,D796Y,S939X,S943X,G946X,Q954X,A958X,N969X,P1143L,D614G | USA_California | 1 | 120 | 919 | North-America 1827 | |
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P26X,A27X,S50L,F59S,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,G184S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,A435S,N440K,V445P,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478I,N481K,V483-,E484K,F486P,Q493E,Q498R,N501Y,Y505H,E554K,A570V,P621S,H655Y,N679K,P681R,N764K,D796Y,S939X,S943X,G946X,Q954X,A958X,N969X,P1143L,D614G | USA_California | 1 | 120 | 919 | North-America 1827 | |
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P25X,P26X,A27X,S31X,S50X,F59X,H69-,V70-,V127F,G142D,Y144-,F157X,N164X,S172X,Q173X,K182X,G184X,K187X,R190X,N211X,L212X,V213X,R214X,L216X,G219X,A222X,A243X,L244X,H245X,P251X,D253X,S255X,S256X,G257X,W258X,A262X,A263X,A264X,G268X,T286X,I326X,I332X,L335X,G339X,R346X,A348X,K356X,S371X,S373X,S375X,T376X,R403X,D405X,R408X,K417X,D420X,A435X,N440X,L441X,K444X,V445X,G446X,N450X,L452X,L455X,F456X,N460X,A475X,S477X,T478X,N481X,G482X,V483X,E484X,F486X,N487X,Q493X,G496X,Q498X,T500X,N501X,Y505X,K529X,N532X,T547X,E554X,I569X,A570X,T572X,A575X,E583X,T604X,P621X,H625X,N641X,V642X,E654X,N679K,S680P,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L,D614X | USA_Arizona_Maricopa | 1 | 11 | 22 | 919 | North-America 1827 |
| L | 5 | X | L5X,T19I,R21T,T22N,L24-,P25-,P26-,A27S,S31P,S50L,H69-,V70-,V127F,G142D,Y144X,F157X,K182R,R190S,N211-,L212I,V213G,A243X,L244X,H245X,P251X,D253X,S255X,S256X,G257X,W258X,A262X,A263X,A264X,G268X,T286X,I326X,I332X,L335X,G339X,R346X,A348X,K356X,S371X,S373X,S375X,T376X,R403X,D405X,R408X,K417X,D420X,A435X,N440X,L441X,K444X,V445X,G446X,N450X,L452X,L455X,F456X,N460X,A475X,S477X,T478X,N481X,G482X,V483X,E484X,F486X,N487X,Q493X,G496X,Q498X,T500X,N501X,Y505X,K529X,N532X,T547X,E554X,I569X,A570X,T572X,A575X,E583X,T604X,P621X,H625X,N641X,V642X,E654X,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L,V1264L,D614X | USA_Arizona_Maricopa | 1 | 11 | 22 | 919 | North-America 1827 |
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P25X,P26X,A27X,S31X,S50X,F59X,A67X,H69X,V70X,T95X,E96X,S98X,I101X,A123X,V127X,C136X,D138X,P139X,F140X,L141X,G142X,V143X,Y144X,Y145X,H146X,K147X,N149X,K150X,M153X,E156X,F157X,R158X,N164X,S172X,Q173X,K182X,G184X,K187X,R190X,N211X,L212X,V213X,R214X,L216X,G219X,A222X,A243X,L244X,H245X,P251X,D253X,S255X,S256X,G257X,W258X,A262X,A263X,A264X,G268X,T286X,I326X,I332X,L335X,G339X,R346X,A348X,K356X,S371X,S373X,S375X,T376X,R403X,D405X,R408X,K417X,D420X,A435X,N440X,L441X,K444X,V445X,G446X,N450X,L452X,L455X,F456X,N460X,A475X,S477X,T478X,N481X,G482X,V483X,E484X,F486X,N487X,Q493X,G496X,Q498X,T500X,N501X,Y505X,K529T,E554K,A570V,T572I,P621S,H655Y,N679K,P681R,N764X,T791X,D796X,A829X,S939F,Q954H,N969K,P1143L,A1174X,D1184X,I1216X,D614G | Ecuador_El-Oro | 1 | 1 | 6 | South-America 55 | |
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P25X,P26X,A27X,S31X,S50X,F59X,A67X,H69X,V70X,T95X,E96X,S98X,I101X,A123X,V127X,C136X,D138X,P139X,F140X,L141X,G142X,V143X,Y144X,Y145X,H146X,K147X,N149X,K150X,M153X,E156X,F157X,R158X,N164X,S172X,Q173X,G184S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,D420N,A435S,N440K,V445P,G446S,N450D,L452W,L455S,F456L,N460K,S477N,N481K,V483-,E484K,F486P,Q493E,Q498R,N501Y,Y505H,E554K,A570V,E583X,T604X,P621X,H625X,N641X,V642X,E654X,H655X,S673X,T676X,Q677X,N679X,S680X,P681X,R683X,A684X,A688X,S704X,N764X,T791X,D796X,A829X,A852X,S939F,Q954H,N969K,P1143L,D614X | Australia_New-South-Wales_Sydney | 1 | 265 | 265 | 864 | Oceania 991 |
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P25X,P26X,A27X,S50X,F59X,A67X,H69X,V70X,T95X,E96X,S98X,I101X,A123X,V127X,C136X,D138X,P139X,F140X,L141X,G142X,V143X,Y144X,Y145X,H146X,K147X,N149X,K150X,M153X,E156X,F157X,R158X,G184S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,D420N,A435S,N440K,V445P,G446S,N450D,L452W,L455S,F456L,N460K,S477N,N481K,V483-,E484K,F486P,Q493E,Q498R,N501Y,Y505H,E554K,A570V,E583X,T604X,P621X,H625X,N641X,V642X,E654X,H655X,S673X,T676X,Q677X,N679X,S680X,P681X,R683X,A684X,A688X,S704X,N764X,T791X,D796X,A829X,A852X,S939F,Q954H,N969K,P1143L,D614X | Australia_New-South-Wales_Sydney | 1 | 265 | 265 | 864 | Oceania 991 |
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P25X,P26X,A27X,S31X,S50L,F59S,A67X,H69X,V70X,I101X,V127F,C136X,D138X,P139X,G142D,Y144X,Y145X,H146X,K147X,N149X,K150X,M153X,E156X,F157X,R158X,N164X,G184S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,A435S,N440K,V445H,G446S,N450D,L452W,L455S,F456L,N460K,S477N,N481K,V483-,E484K,F486P,Q493E,Q498R,N501Y,Y505H,E554K,A570V,E583X,T604X,P621X,H625X,N641X,V642X,E654X,H655X,S673X,T676X,Q677X,N679X,S680X,P681X,R683X,A684X,A688X,S704X,N764X,T791X,D796X,A829X,A852X,S939F,Q954H,N969K,P1143L,D614X | Australia_New-South-Wales_Sydney | 1 | 265 | 265 | 864 | Oceania 991 |
| L | 5 | X | L5X,P9X,T19X,R21X,P26L,A67V,H69-,V70-,T95I,I101T,C136-,D138-,P139-,F140-,L141-,G142-,V143-,Y144-,Y145-,H146-,K147-,N149-,F157S,N164K,S172F,K187X,R190X,N211X,L212X,V213X,R214X,L216X,G219X,A222X,A243X,L244X,H245X,P251X,D253X,S256X,G257X,W258X,A262X,A263X,A264X,G268X,T286X,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | New-Zealand_Capital-and-Coast | 1 | 1 | 118 | Oceania 991 | |
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P25X,P26X,A27X,S31X,S50X,F59X,A67X,H69X,V70X,T95X,E96X,S98X,I101X,A123X,V127X,C136X,D138X,P139X,F140X,L141X,G142X,V143X,Y144X,Y145X,H146X,K147X,N149X,K150X,M153X,E156X,F157X,R158X,N164X,S172X,Q173X,K182X,G184X,K187X,R190X,N211X,L212X,V213X,R214X,L216X,G219X,A222X,A243X,L244X,H245X,P251X,D253X,S256X,G257X,W258X,A262X,A263X,A264X,G268X,T286X,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478X,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | New-Zealand_South-Canterbury | 1 | 1 | 118 | Oceania 991 | |
| L | 5 | X | L5X,P9X,R21T,P26L,A67V,H69-,V70-,T95I,I101T,C136-,D138-,P139-,F140-,L141-,G142-,V143-,Y144-,Y145-,H146-,K147-,N149-,F157S,N164K,S172F,K187X,R190X,N211X,L212X,V213X,R214X,L216X,G219X,A222X,A243X,L244X,H245X,P251X,D253X,S256X,G257X,W258X,A262X,A263X,A264X,G268X,T286X,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | New-Zealand_Northland | 1 | 10 | 118 | Oceania 991 | |
| L | 5 | X | L5X,P9X,R21T,P26L,A67V,H69-,V70-,T95I,I101T,C136X,D138X,P139X,F140X,L141X,G142X,V143X,Y144X,Y145X,H146X,K147X,F157S,N164K,S172F,G184X,K187X,R190X,N211X,L212X,V213X,R214X,L216X,G219X,A222X,A243X,L244X,H245X,P251X,D253X,S256X,G257X,W258X,A262X,A263X,A264X,G268X,T286X,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | New-Zealand_Counties-Manukau | 1 | 10 | 118 | Oceania 991 | |
| L | 5 | X | P9X,R21T,P26L,A67V,H69-,V70-,T95I,I101T,C136-,D138-,P139-,F140-,L141-,G142-,V143-,Y144-,Y145-,H146-,K147-,N149-,F157S,N164K,S172F,K187T,N211-,L212I,A243-,L244-,P251S,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | New-Zealand_Southern | 2 | 13 | 118 | Oceania 991 | |
| L | 5 | X | P9X,R21T,P26L,A67V,H69-,V70-,T95I,I101T,C136-,D138-,P139-,F140-,L141-,G142-,V143-,Y144-,Y145-,H146-,K147-,N149-,F157S,N164K,S172F,K187T,N211-,L212I,A243-,L244-,P251S,T286X,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | New-Zealand_Southern | 1 | 13 | 118 | Oceania 991 | |
| L | 5 | X | L5X,P9X,R21T,P26L,A67V,H69-,V70-,T95I,I101T,C136X,D138X,P139X,F140X,L141X,G142X,V143X,Y144X,Y145X,H146X,K147X,N149X,K150X,M153X,E156X,F157X,R158X,N164X,S172X,Q173X,K182X,G184X,K187X,R190X,N211X,L212X,V213X,R214X,L216X,G219X,A222X,A243X,L244X,H245X,P251X,D253X,S256X,G257X,W258X,A262X,A263X,A264X,G268X,T286X,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | New-Zealand_Bay-of-Plenty | 1 | 2 | 118 | Oceania 991 | |
| L | 5 | X | L5X,T19X,R21X,T22X,L24X,P25X,P26X,A27X,S31X,S50X,F59X,A67X,H69X,V70X,T95X,E96X,S98X,I101X,V127F,G142D,Y144-,F157S,R158G,G184S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,D420N,A435S,N440K,V445P,G446S,N450D,L452W,L455S,F456L,N460K,S477N,N481K,V483-,E484K,F486P,Q493E,Q498R,N501Y,Y505H,E554K,A570V,P621S,H655Y,N679K,S680F,P681R,N764K,T791X,D796X,A829X,A852X,S939F,Q954H,N969K,P1143L,D614G | USA_California | 1 | 120 | 919 | North-America 1827 | |
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P26X,A27S,S31P,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,K182R,R190S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,K444R,V445R,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,N487D,Q493E,Q498R,N501Y,Y505H,E554K,A570V,T572I,P621S,H655Y,N679R,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L,D614G | USA_New-York_New-York-City | 1 | 125 | 328 | 919 | North-America 1827 |
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P25X,P26X,A27X,S31X,S50X,F59X,A67X,H69X,V70X,T95X,E96X,S98X,I101X,A123X,V127X,C136X,D138X,P139X,F140X,L141X,G142X,V143X,Y144X,Y145X,H146X,K147X,N149X,K150X,M153X,E156X,F157X,R158X,N164X,S172X,Q173X,K182X,G184X,K187X,R190X,N211X,L212X,V213X,R214X,L216X,G219X,A222X,A243X,L244X,H245X,P251X,D253X,S255X,S256X,G257X,W258X,A262X,A263X,A264X,G268X,T286X,I332V,G339H,R346T,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445R,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478X,N481K,V483-,E484K,F486P,Q493E,Q498R,N501Y,Y505H,E554K,A570V,T572I,P621S,H655Y,N679R,P681-,A684X,A688X,S704X,N764X,T791X,D796X,A829X,A852X,S939X,S943X,G946X,Q954X,A958X,N969X,D614G | Norway | 1 | 26 | Europe 435 | ||
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P25X,P26X,A27X,S31X,S50X,F59X,A67X,H69X,V70X,T95X,E96X,S98X,I101X,A123X,V127X,C136X,D138X,P139X,F140X,L141X,G142X,V143X,Y144X,Y145X,H146X,K147X,N149X,K150X,M153X,E156X,F157X,R158X,N164X,S172X,Q173X,K182X,G184X,K187X,R190X,N211X,L212X,V213X,R214X,L216X,G219X,A222X,A243X,L244X,H245X,P251X,D253X,S255X,S256X,G257X,W258X,A262X,A263X,A264X,G268X,T286X,G339H,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,G446S,L452R,F456L,S477N,T478X,F486S,Q498R,N501Y,Y505H,H655Y,N679K,R683X,A684X,A688X,S704X,N764X,T791X,D796X,A829X,A852X,S939X,S943X,G946X,Q954X,A958X,N969X,D614G | Norway_Agder | 1 | 1 | 26 | Europe 435 | |
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P25X,P26X,A27X,S31X,S50X,F59X,A67X,H69X,V70X,T95X,E96X,S98X,I101X,A123X,V127X,C136X,D138X,P139X,F140X,L141X,G142X,V143X,Y144X,Y145X,H146X,K147X,N149X,K150X,M153X,E156X,F157X,R158X,N164X,S172X,Q173X,K182X,G184X,K187X,R190X,N211X,L212X,V213X,R214X,L216X,G219X,A222X,A243X,L244X,H245X,P251S,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,Q498X,N501Y,E554X,N641X,H655Y,N679X,P681H,R683X,A684X,A688X,S704X,N764X,T791X,D796X,A829X,A852X,S939X,S943X,G946X,Q954X,A958X,N969X,D614G | Norway_Trondelag | 1 | 2 | 26 | Europe 435 | |
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P25X,P26X,A27X,S31X,S50X,F59X,A67X,H69X,V70X,T95X,E96X,S98X,I101X,A123X,V127X,C136X,D138X,P139X,F140X,L141X,G142X,V143X,Y144X,Y145X,H146X,K147X,N149X,K150X,M153X,E156X,F157X,R158X,N164X,S172X,Q173X,K182X,G184X,K187X,R190X,N211X,L212X,V213X,R214X,L216X,G219X,A222X,A243X,L244X,H245X,P251X,D253X,S256X,G257X,W258X,A262X,A263X,A264X,G268X,T286X,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,R683X,A684X,A688X,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | Spain_Catalunya_Mataro | 1 | 1 | 23 | 112 | Europe 435 |
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P25X,P26X,A27X,S31X,S50X,F59X,A67X,H69X,V70X,T95X,E96X,S98X,I101X,A123X,V127X,C136X,D138X,P139X,F140X,L141X,G142X,V143X,Y144X,Y145X,H146X,K147X,N149X,K150X,M153X,E156X,F157X,R158X,N164X,S172X,Q173X,K182X,G184X,K187X,R190X,N211X,L212X,V213X,R214X,L216X,G219X,A222X,A243X,L244X,H245X,P251X,D253X,S256X,G257X,W258X,A262X,A263X,A264X,G268X,T286X,I326X,I332V,G339H,R346T,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,K444R,V445P,G446S,N450D,L452R,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,N487D,Q493E,Q498R,N501Y,Y505H,E554K,A570V,T572I,P621S,H655Y,N679K,P681X,R683X,A684X,A688X,S704X,N764K,D796Y,A852X,S939F,Q954H,N969K,P1143L,D614G | Canada_Nova-Scotia | 1 | 6 | 887 | North-America 1827 | |
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P26X,A27X,S31X,S50X,F59X,A67X,H69X,V70X,V127F,G142D,Y144-,E156X,F157X,K182R,R190S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,K444R,V445R,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,N487D,Q493E,Q498R,N501Y,Y505H,E554K,A570V,T572I,P621S,H655Y,Q677H,N679K,S680F,P681R,A688X,S704X,N764X,D796Y,S939F,Q954H,N969K,D1084X,G1099X,V1104X,P1143L,D614G | New-Caledonia_Houailou | 1 | 1 | 9 | Oceania 991 | |
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P26X,A27X,S50X,F59S,H69-,V70-,V127F,G142D,Y144-,E156X,F157X,G184S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,K356X,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,A435S,N440K,V445H,G446S,N450D,L452W,L455S,F456L,N460K,S477N,N481K,V483-,E484K,F486P,Q493E,Q498R,N501Y,Y505H,E554K,A570V,P621S,H655Y,N679R,P681R,A688X,S704X,N764K,D796Y,S939F,Q954H,N969K,D1084X,G1099X,V1104X,P1143L,D614G | New-Caledonia_Noumea | 1 | 3 | 9 | Oceania 991 | |
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P26X,A27X,S31X,A67V,H69-,V70-,T95I,I101T,C136-,D138-,P139-,F140-,L141-,G142-,V143-,Y144-,Y145-,H146-,K147-,N149-,F157S,N164K,S172F,K187T,N211-,L212I,A243-,L244-,P251S,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | New-Zealand_Waikato | 1 | 16 | 118 | Oceania 991 | |
| L | 5 | X | P9X,R21T,P26L,A67V,H69-,V70-,T95I,I101T,C136-,D138-,P139-,F140-,L141-,G142-,V143-,Y144-,Y145-,H146-,K147-,N149-,F157S,N164K,S172F,K187T,N211-,L212I,R214X,A243-,L244-,P251S,G268X,T286X,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | New-Zealand_Waikato | 1 | 16 | 118 | Oceania 991 | |
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P25X,P26X,A27X,S31X,S50X,F59X,A67X,H69X,V70X,T95X,E96X,S98X,I101X,V127F,G142D,Y144-,F157S,R158G,K182R,R190S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,A435X,N440X,L441X,K444X,V445X,G446X,N450X,L452X,L455X,F456X,N460X,A475X,S477X,T478X,N481X,G482X,V483X,E484X,F486X,N487X,Q493X,G496X,Q498X,T500X,N501X,K529T,E554K,A570V,T572I,T604I,P621S,H655Y,N679K,P681R,N764K,D796Y,S939X,S943X,G946X,Q954X,A958X,N969X,P1143L,V1264L,D614G | USA_Connecticut_New-Haven | 1 | 1 | 3 | 919 | North-America 1827 |
| L | 5 | X | L5X,P9X,T19X,R21X,T22X,L24X,P25X,P26X,A27X,S31X,S50X,F59X,A67X,H69X,V70X,T95X,E96X,S98X,I101X,V127F,G142D,Y144-,F157S,R158G,K182R,R190S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,A435X,N440X,L441X,K444X,V445X,G446X,N450X,L452X,L455X,F456X,N460X,A475X,S477X,T478X,N481X,G482X,V483X,E484X,F486X,N487X,Q493X,G496X,Q498X,T500X,N501X,E554K,A570V,T572I,P621S,H655Y,N679K,P681R,N764K,D796Y,S939X,S943X,G946X,Q954X,A958X,N969X,P1143L,D614G | USA_Connecticut_Hartford | 1 | 1 | 3 | 919 | North-America 1827 |
| L | 5 | X | T19I,R21T,T22N,L24-,P25-,P26-,A27S,S31P,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,K182R,R190S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,L441I,K444R,V445R,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,N487D,Q493E,Q498R,N501Y,Y505H,E554K,A570V,T572I,P621S,H655Y,N679K,S680P,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L,D614G | Canada_Ontario | 1 | 618 | 887 | North-America 1827 | |
| P | 9 | L | R21T,P26L,A67V,H69-,V70-,T95I,I101T,F157S,N164K,S172F,K187T,N211-,L212I,A243-,L244-,P251S,I326V,L335F,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | Australia_South-Australia | 1 | 207 | 864 | Oceania 991 | |
| P | 9 | L | R21T,P26L,A67V,H69-,V70-,T95I,I101T,C136X,D138X,P139X,F140X,L141X,G142X,V143X,Y144X,Y145X,H146X,K147X,F157S,N164K,S172F,K187T,N211-,L212I,A243-,L244-,P251S,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | USA_New-York_Monroe | 14 | 68 | 328 | 919 | North-America 1827 |
| P | 9 | L | R21T,P26L,A67V,H69X,T95I,I101T,C136X,D138X,P139X,F140X,L141X,G142X,V143X,Y144X,Y145X,H146X,K147X,F157S,N164K,S172F,K187T,N211X,L212X,A243X,L244X,P251S,W258L,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | Spain_Asturias | 1 | 53 | 112 | Europe 435 | |
| P | 9 | L | R21T,P26L,A67V,H69X,T95I,I101T,C136X,D138X,P139X,F140X,L141X,G142X,V143X,Y144X,Y145X,H146X,K147X,F157S,N164K,S172F,K187T,N211X,L212X,A243X,L244X,P251S,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | Spain_Asturias | 10 | 53 | 112 | Europe 435 | |
| P | 9 | L | R21T,P26L,A67V,H69X,T95I,S98F,I101T,C136X,D138X,P139X,F140X,L141X,G142X,V143X,Y144X,Y145X,H146X,K147X,F157S,N164K,S172F,Q173H,K187T,N211X,L212X,A243X,L244X,P251S,I332X,L335X,G339X,A348P,K356T,S371F,S373P,S375F,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641X,V642X,E654X,H655X,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | Spain_Asturias | 1 | 53 | 112 | Europe 435 | |
| P | 9 | L | R21T,P26L,A67V,H69X,T95I,I101T,C136X,D138X,P139X,F140X,L141X,G142X,V143X,Y144X,Y145X,H146X,K147X,F157S,N164K,S172F,K187T,N211X,L212X,R214P,A243X,L244X,P251S,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | Spain_Asturias | 7 | 53 | 112 | Europe 435 | |
| P | 9 | L | R21T,P26L,A67V,H69X,T95I,I101T,C136X,D138X,P139X,F140X,L141X,G142X,V143X,Y144X,Y145X,H146X,K147X,F157S,N164K,S172F,K187T,N211X,L212X,A243X,L244X,P251S,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | Spain_Asturias | 1 | 53 | 112 | Europe 435 | |
| P | 9 | L | R21T,P26L,A67V,H69X,T95I,I101T,C136X,D138X,P139X,F140X,L141X,G142X,V143X,Y144X,Y145X,H146X,K147X,F157S,N164K,S172F,K187T,N211X,L212X,A243X,L244X,P251S,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | Spain_Asturias | 1 | 53 | 112 | Europe 435 | |
| P | 9 | L | R21T,P26L,A67V,H69X,V70X,T95I,I101T,C136X,D138X,P139X,F140X,L141X,G142X,V143X,Y144X,Y145X,H146X,K147X,F157S,N164K,S172F,K187T,N211X,L212X,A243X,L244X,P251S,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641X,V642X,E654X,H655X,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | Spain_Asturias | 1 | 53 | 112 | Europe 435 | |
| P | 9 | L | R21T,P26L,A67V,H69-,V70-,T95I,I101T,C136-,D138-,P139-,F140-,L141-,G142-,V143-,Y144-,Y145-,H146-,K147-,N149-,F157S,N164K,S172F,K187T,N211-,L212I,A243-,L244-,P251S,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | USA_California | 1 | 120 | 919 | North-America 1827 | |
| P | 9 | L | R21T,P26L,A67V,H69-,V70-,T95I,I101T,C136-,D138-,P139-,F140-,L141-,G142-,V143-,Y144-,Y145-,H146-,K147-,N149-,F157S,N164K,S172F,K187T,N211-,L212I,A243-,L244-,P251S,I326V,G339Y,A348P,K356T,S371F,S373P,S375F,R403K,D405N,R408S,K417N,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | Singapore | 78 | 685 | Asia 886 | ||
| P | 9 | L | R21T,P26L,A67V,H69-,V70-,T95I,I101T,C136X,D138X,P139X,F140X,L141X,G142X,V143X,Y144X,Y145X,H146X,K147X,N149X,K150X,M153X,E156X,F157X,R158X,N164X,S172X,Q173X,K182X,G184X,K187X,R190X,N211X,L212X,V213X,R214X,L216X,G219X,A222X,A243X,L244-,P251S,I326V,G339Y,A348P,K356X,S371X,S373X,S375X,T376X,R403X,D405X,R408X,K417X,A435S,N440R,V445A,G446D,L452W,N460K,S477N,T478N,E484K,G496S,Q498R,N501Y,K529N,E554D,A575S,E583D,H625R,N641K,V642G,E654K,H655Y,N679R,P681H,A688D,S704L,N764K,K795T,D796Y,A852K,S939F,Q954H,N969K,D1184E,D614G | Japan_Hyogo | 1 | 10 | 25 | Asia 886 |
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