key: cord-342010-5mkf67os authors: Levasseur, Anthony; Delerce, Jeremy; Caputo, Aurelia; Brechard, Ludivine; Colson, Philippe; Lagier, Jean-Christophe; Fournier, Pierre-Edouard; Raoult, Didier title: Genomic diversity and evolution of coronavirus (SARS-CoV-2) in France from 309 COVID-19-infected patients date: 2020-09-04 journal: bioRxiv DOI: 10.1101/2020.09.04.282616 sha: doc_id: 342010 cord_uid: 5mkf67os The novel coronavirus (SARS-CoV-2) causes pandemic of viral pneumonia. The evolution and mutational events of the SARS-CoV-2 genomes are critical for controlling virulence, transmissibility, infectivity, severity of symptoms and mortality associated to this infectious disease. We collected and investigated 309 SARS-CoV-2 genomes from patients infected in France. Detailed genome cartography of all mutational events (SNPs, indels) was reported and correlated to clinical features of patients. A comparative analysis between our 309 SARS-CoV-2 genomes from French patients and the reference Wuhan coronavirus genome revealed 315 substitution mutations and six deletion events: ten were in 5’/3’ UTR, 178 were nonsynonymous, 126 were synonymous and one generated a stop codon. Six different deleted areas were also identified in nine viral variants. In particular, 30 substitution mutations (18 nonsynonymous) and one deletion (Δ21765-21770) concerned the spike S glycoprotein. An average of 7.8 mutational events (+/- 1.7 SD) and a median of 8 (range, 7-9) were reported per viral isolate. Comparative analyses and clustering of specific mutational signatures in 309 genomes disclose several divisions in groups and subgroups combining their geographical and phylogenetic origin. Clinical outcomes of the 309 COVID-19-infected patients were investigated according to the mutational signatures of viral variants. These findings highlight the genome dynamics of the coronavirus 2019-20 and shed light on the mutational landscape and evolution of this virus. Inclusion of the French cohort enabled us to identify 161 novel mutations never reported in SARS-CoV-2 genomes collected worldwide. These results support a global and continuing surveillance of the emerging variants of the coronavirus SARS-CoV-2. The new coronavirus SARS-CoV-2 has now spread to every country in the world. SARS-CoV-2 is 4 23248 26885 3924 7162 313 28881 28882 28883 11289 24998 29167 15324 19602 4761 24794 1942 3338 15438 21597 25731 25667 26718 3429 6636 27942 18175 20268 29745 18366 22346 24079 27641 4459 9652 27143 28628 10642 6032 11761 27208 10369 20199 26314 27494 20310 14228 21015 6082 10323 7728 12496 19368 21938 12334 15810 22480 9886 510 511 512 513 514 515 516 517 518 241 3037 14408 23403 1427 13693 27741 3784 537 10279 22550 6094 21618 10802 23191 24050 15327 28886 204 8676 19167 6762 28291 21369 24193 10681 21846 5336 9166 21778 28541 25776 25521 18259 19269 27874 11117 15021 9058 10480 11858 5806 12528 9246 12663 10228 15779 958 16289 1168 20808 7424 10252 20125 25782 27403 17104 27659 2065 16992 18495 27684 7393 353 710 834 1959 2037 2537 3478 3902 4800 5570 5869 6547 5365 10277 11152 12756 14857 8394 15277 16020 16226 16377 16816 18412 19488 19884 16386 19900 20401 12789 21225 23415 24904 25012 25047 25699 1736 25710 25720 26256 639 27002 27476 27256 28037 16089 28202 28311 28374 15120 28519 28775 541 28851 28957 4886 29179 1493 7521 10097 29206 29477 1361 26773 29527 18186 18904 25606 6531 14599 29744 21727 25825 6286 10262 21622 9996 29747 9891 29754 1059 2150 11083 16394 22458 28651 29363 20382 1198 6401 13458 20946 4655 27996 2189 4105 625 2578 13105 12513 20628 683 2602 3049 17808 27261 19160 28027 16045 21587 19518 28845 13132 14358 24867 4551 18351 5338 21364 28851 29171 6539 19999 26161 28690 29281 15368 28312 2676 8782 22606 28144 28878 29742 17541 24771 14391 13006 25688 9286 9360 12318 10582 16968 28253 14724 2062 18877 15579 26735 2086 23042 25909 2455 1440 2891 10626 27505 1515 9223 12565 17247 14805 26144 21765 21766 21767 21768 21769 21770 25433 686 687 688 689 690 691 692 693 694 12924 17125 27434 27435 27436 3328 28326 26622 29536 8179 8858 11540 25440 24095 1463 2480 2558 25933 29272 17964 23575 29555 4320 12439 3094 26907 29218 1605 1606 1607 2416 8371 25563 28682 3619 20294 29779 1 2 5 4 3 IHUCOVID-0116 IHUCOVID-0118 IHUCOVID-0017 IHUCOVID-0035 Wuhan IHUCOVID-0349 IHUCOVID-0031 IHUCOVID-0135 IHUCOVID-0497 IHUCOVID-0084 IHUCOVID-0195 IHUCOVID-0132 IHUCOVID-0347 IHUCOVID-0328 IHUCOVID-0028 IHUCOVID-0171 IHUCOVID-0475-PV IHUCOVID-0133 IHUCOVID-0158 IHUCOVID-0167 IHUCOVID-0250 IHUCOVID-0320 IHUCOVID-0073-PV IHUCOVID-0379 IHUCOVID-0225 IHUCOVID-0282 IHUCOVID-0242 IHUCOVID-0149 IHUCOVID-0136 IHUCOVID-0016 IHUCOVID-0391 IHUCOVID-0385 IHUCOVID-0368 IHUCOVID-0263 IHUCOVID-0213-PV IHUCOVID-0093-PV IHUCOVID-0026 IHUCOVID-0145 IHUCOVID-0439 IHUCOVID-0483 IHUCOVID-0063 IHUCOVID-0006 IHUCOVID-0069 IHUCOVID-0396 IHUCOVID-0501 IHUCOVID-0020 IHUCOVID-0395 IHUCOVID-0323-PV IHUCOVID-0259 IHUCOVID-0110 IHUCOVID-0120-PV IHUCOVID-0033-PV IHUCOVID-0445-PV IHUCOVID-0066 IHUCOVID-0407 IHUCOVID-0051 IHUCOVID-0480-PV IHUCOVID-0087 IHUCOVID-0054-PV IHUCOVID-0160 IHUCOVID-0012 IHUCOVID-0316 IHUCOVID-0241 IHUCOVID-0146 IHUCOVID-0128 IHUCOVID-0080 IHUCOVID-0055 IHUCOVID-0291 IHUCOVID-0338 IHUCOVID-0240 IHUCOVID-0194 IHUCOVID-0197 IHUCOVID-0198 IHUCOVID-0177 IHUCOVID-0276 IHUCOVID-0434 IHUCOVID-0200 IHUCOVID-0421 IHUCOVID-0222 IHUCOVID-0210-PV IHUCOVID-0168 IHUCOVID-0078 IHUCOVID-0038-PV IHUCOVID-0190 IHUCOVID-0024 IHUCOVID-0360 IHUCOVID-0065 IHUCOVID-0254 IHUCOVID-0070 IHUCOVID-0170 IHUCOVID-0485 IHUCOVID-0488 IHUCOVID-0141 IHUCOVID-0238-PC IHUCOVID-0351-PV IHUCOVID-0188 IHUCOVID-0155 IHUCOVID-0300 IHUCOVID-0075 IHUCOVID-0216 IHUCOVID-0411 IHUCOVID-0203 IHUCOVID-0337 IHUCOVID-0117 IHUCOVID-0040 IHUCOVID-0060 IHUCOVID-0139 IHUCOVID-0495 IHUCOVID-0491 IHUCOVID-0329 IHUCOVID-0094-PV IHUCOVID-0389 IHUCOVID-0296 IHUCOVID-0297 IHUCOVID-0083 IHUCOVID-0058 IHUCOVID-0433 IHUCOVID-0193 IHUCOVID-0082 IHUCOVID-0076 IHUCOVID-0032 IHUCOVID-0097 IHUCOVID-0086 IHUCOVID-0400 IHUCOVID-0050 IHUCOVID-0412 IHUCOVID-0430-PV IHUCOVID-0179 IHUCOVID-0047 IHUCOVID-0369 IHUCOVID-0199 IHUCOVID-0496 IHUCOVID-0345-PC IHUCOVID-0342 IHUCOVID-0131 IHUCOVID-0100 IHUCOVID-0062 IHUCOVID-0057-PV IHUCOVID-0046 IHUCOVID-0037 IHUCOVID-0030 IHUCOVID-0019 IHUCOVID-0281 IHUCOVID-0304 IHUCOVID-0409 IHUCOVID-0227-PV IHUCOVID-0061 IHUCOVID-0029 IHUCOVID-0251 IHUCOVID-0261 IHUCOVID-0371-PC IHUCOVID-0493 IHUCOVID-0417 IHUCOVID-0232 IHUCOVID-0290 IHUCOVID-0153 IHUCOVID-0107 IHUCOVID-0450 IHUCOVID-0435-PV IHUCOVID-0176 IHUCOVID-0233-PV IHUCOVID-0487 IHUCOVID-0344 IHUCOVID-0125 IHUCOVID-0119 IHUCOVID-0021 IHUCOVID-0049 IHUCOVID-0056 IHUCOVID-0151-PC-PV IHUCOVID-0039 IHUCOVID-0231-PV IHUCOVID-0252 IHUCOVID-0438 IHUCOVID-0376-PC IHUCOVID-0269 IHUCOVID-0129 IHUCOVID-0500 IHUCOVID-0440-PC IHUCOVID-0441 IHUCOVID-0280 IHUCOVID-0428-PV IHUCOVID-0079 IHUCOVID-0180-PV IHUCOVID-0274 IHUCOVID-0381 IHUCOVID-0405 IHUCOVID-0502 IHUCOVID-0121 IHUCOVID-0104 IHUCOVID-0071 IHUCOVID-0237 IHUCOVID-0306 IHUCOVID-0115 IHUCOVID-0479 IHUCOVID-0398 IHUCOVID-0256 IHUCOVID-0218 IHUCOVID-0192 IHUCOVID-0186 IHUCOVID-0147-PC-PV IHUCOVID-0074 IHUCOVID-0059 IHUCOVID-0178 IHUCOVID-0401-PV IHUCOVID-0481 IHUCOVID-0424-PV IHUCOVID-0366 IHUCOVID-0215 IHUCOVID-0354 IHUCOVID-0324 IHUCOVID-0217-PV IHUCOVID-0219 IHUCOVID-0451 IHUCOVID-0492 IHUCOVID-0326 IHUCOVID-0099 IHUCOVID-0494 IHUCOVID-0378 IHUCOVID-0126-PV IHUCOVID-0287 IHUCOVID-0211 IHUCOVID-0419 IHUCOVID-0196 IHUCOVID-0332 IHUCOVID-0336 IHUCOVID-0455 IHUCOVID-0309 IHUCOVID-0299 IHUCOVID-0303 IHUCOVID-0423 IHUCOVID-0499 IHUCOVID-0224 IHUCOVID-0191 IHUCOVID-0453 IHUCOVID-0226 IHUCOVID-0189 IHUCOVID-0247 IHUCOVID-0284 IHUCOVID-0286 IHUCOVID-0397 IHUCOVID-0308 IHUCOVID-0444 IHUCOVID-0446 IHUCOVID-0449 IHUCOVID-0490 IHUCOVID-0044 IHUCOVID-0045 IHUCOVID-0053 IHUCOVID-0081 IHUCOVID-0106 IHUCOVID-0108 IHUCOVID-0122 IHUCOVID-0201 IHUCOVID-0204-PV IHUCOVID-0206 IHUCOVID-0212 IHUCOVID-0221 IHUCOVID-0228 IHUCOVID-0229 IHUCOVID-0234 IHUCOVID-0235 IHUCOVID-0236 IHUCOVID-0239 IHUCOVID-0258 IHUCOVID-0266 IHUCOVID-0268 IHUCOVID-0271-PC IHUCOVID-0283 IHUCOVID-0293 IHUCOVID-0295 IHUCOVID-0298 IHUCOVID-0355 IHUCOVID-0365 IHUCOVID-0382 IHUCOVID-0386 IHUCOVID-0388 IHUCOVID-0416 IHUCOVID-0429 IHUCOVID-0431-PV IHUCOVID-0447 IHUCOVID-0456 IHUCOVID-0489 IHUCOVID-0498 IHUCOVID-0205 IHUCOVID-0248 IHUCOVID-0092 IHUCOVID-0288 IHUCOVID-0272-PC-PV IHUCOVID-0262 IHUCOVID-0257 IHUCOVID-0334 IHUCOVID-0109-PV IHUCOVID-0064 IHUCOVID-0243 IHUCOVID-0246-PV IHUCOVID-0319 IHUCOVID-0432 IHUCOVID-0208 IHUCOVID-0327 IHUCOVID-0249 IHUCOVID-0214 IHUCOVID-0333-PC IHUCOVID-0072 IHUCOVID-0361 IHUCOVID-0209-PV IHUCOVID-0095 IHUCOVID-0318-PC-PV IHUCOVID-0162 IHUCOVID-0375 IHUCOVID-0172 T R G > T 1 2 4 1 5 U T R C > T 2 9 7 3 1 3 n s p 1 C T C > C T T L 2 0 3 5 3 n s p T T L 1 6 2 5 n s p 1 A A G > A A T K 1 2 0 N 1 6 3 9 n s p 1 A A G > A G G K 1 2 5 R 1 6 8 3 n s p 1 C T A > T T A L 2 6 8 6 n s p 1 A A G > X 3 6 8 7 n s p 1 A A G > X 3 6 8 8 n s p 1 A A G > X 3 6 8 9 n s p 1 T C A > X 3 6 9 0 n s p 1 T C A > X 3 6 9 1 n s p 1 T C A > X 3 6 9 2 n s p 1 T T T > X 3 6 9 3 n s p 1 T T T > X 3 6 9 4 n s p 1 T T T > X 3 7 1 0 n s p 1 C T T > A T T L 1 4 9 I 1 8 3 4 n s p 2 T T C > T G C F 1 0 C 1 9 5 8 n s p 2 T G C > T G T C 1 1 0 5 9 n s p 2 A C C > A T C T 8 5 I 6 8 1 1 6 8 n s p 2 C G A > C G G R 1 1 1 9 8 n s p 2 G A A > G A G E 6 1 3 6 1 n s p 2 G T T > T T T V 1 8 T T V 1 1 9 5 9 n s p 2 G C C > G T C A 3 8 5 V 1 2 0 3 7 n s p 2 G C T > G T T A 4 1 1 V 1 2 0 6 2 n s p 2 G C C > G C T A 2 2 0 6 5 n s p 2 T A C > T A T Y 1 2 0 8 6 n s p 2 C A G > C A T Q 4 2 7 H 1 2 1 5 0 n s p 2 G A T > A A T D 4 4 9 N 2 2 1 8 9 n s p 2 C T T > T T T L 4 6 2 F 4 2 4 1 6 n s p 2 T A C > T A T Y 1 2 6 2 4 5 5 n s p 2 C T C > C T T L 1 2 4 8 0 n s p 2 A T T > G T T I 5 5 9 V 1 2 5 3 7 n s p 2 T T G > C T G L 1 2 5 5 8 n s p 2 C C A > T C A P 5 8 5 S 1 2 5 7 8 n s p 2 A G T > A G C S 3 2 6 0 2 n s p 2 G T T > G T G V 1 2 6 7 6 n s p 2 C C T > C T T P 6 2 4 L 2 2 8 9 1 n s p 3 G C A > A C A A 5 8 T 2 3 0 3 7 n s p 3 T T C > T T T F 3 0 3 3 0 4 9 n s p 3 G A T > G A C D 1 3 0 9 4 n s p 3 C C A > C C G P 1 3 3 2 8 n s p 3 C A G > C A T Q 2 0 3 H 2 3 3 3 8 n s p 3 G T G > T T G V 2 0 T C I 2 4 5 5 1 n s p 3 A C A > A T A T 6 1 1 I 3 4 6 5 5 n s p 3 C G G > T G G R 6 4 6 W 1 4 7 6 1 n s p 3 G A A > G G A E 6 8 1 G 1 4 8 0 0 n s p 3 A A A > A G A K 6 9 4 R 1 4 8 8 6 n s p 3 C C T > T C T P 7 2 3 S 1 5 3 3 6 n s p 3 A A T > G A T N 8 7 3 D 1 5 3 3 8 n s p 3 A A T > A A C N 2 5 3 6 5 n s p 3 T A C > T A T Y 1 5 5 7 0 n s p 3 A T G > G T G M 9 5 1 V 1 5 8 0 6 n s p 3 T G C > T G T C 1 5 8 6 9 n s p 3 T A C > T A T Y 1 6 0 3 2 n s p 3 G C A > A C A A 1 1 0 5 T 2 6 0 8 2 n s p 3 G A T > G A C D 1 6 0 9 4 n s p 3 C A G > C A T Q 1 1 2 5 H 1 6 2 8 6 n s p 3 A C C > A C T T 1 6 4 0 1 n s p 3 C C A > T C A P 1 2 2 8 S 1 1 6 5 3 1 n s p 3 G A G > G T G E 1 2 7 1 V 1 6 5 3 9 n s p 3 C A C > T A C H 1 2 7 4 Y 1 6 5 4 7 n s p 3 G A T > G A C D 1 6 6 3 6 n s p 3 A C T > A T T T 1 3 0 6 I 1 6 7 6 2 n s p 3 A C T > A T T T 1 3 4 8 I 1 7 1 6 2 n s p 3 G A C > G A T D 2 C T T 1 9 2 2 3 n s p 4 C A C > C A T H 1 9 2 4 6 n s p 4 G C T > G T T A 2 3 1 V 1 9 2 8 6 n s p 4 A A C > A A T N 5 9 3 6 0 n s p 4 A C A > A T A T 2 6 9 I 2 9 6 5 2 n s p 4 A T G > A T T M 3 6 6 I 2 9 8 8 6 n s p 4 T A C > T A T Y 2 9 8 9 1 n s p 4 G C T > G T T A 4 4 6 V 1 9 9 9 6 n s p 4 T C A > T T A S 4 8 1 L 1 1 0 0 9 7 n s p 5 G G T > A G T G 1 5 S 1 1 0 2 2 8 n s p 5 C T C > C T T L 1 1 0 2 5 2 n s p 5 T T C > T T T F 1 1 0 2 6 2 n s p 5 G C T > T C T A 7 0 S 1 1 0 2 7 7 n s p 5 C T C > T T C L 7 5 F 1 1 0 2 7 9 n s p 5 C T C > C T T L 1 1 0 3 2 3 n s p 5 A A G > A G G K 9 0 R 2 1 0 3 6 9 n s p 5 C G C > C G T R 1 1 0 T T > T T T V 1 9 0 F 1 1 1 7 6 1 n s p 6 A A G > A A T K 2 6 3 N 2 1 1 8 5 8 n s p 7 G T A > A T A V 6 I 1 1 2 3 1 8 n s p 8 T C T > T A T S 7 6 Y 1 1 2 3 3 4 n s p 8 G C A > G C T A 2 1 2 4 3 9 n s p 8 C C C > C C T P 1 1 2 4 9 6 n s p 8 T A T > T A C Y 1 1 2 5 1 3 n s p 8 A C G > A T G T 1 4 1 M 3 1 2 5 2 8 n s p 8 A C A > A T A T 1 4 6 I 1 1 2 5 6 5 n s p 8 C A G > C A T Q 1 5 8 H 1 1 2 6 6 3 n s p 8 G C C > G T C A 1 9 1 V 1 1 2 7 5 6 n s p 9 A C T > A T T T 2 4 I 1 1 2 7 8 9 n s p 9 A C A > A T A T 3 5 I 1 1 2 9 2 4 n s p 9 C C T > C T T P 8 0 L 2 1 3 0 0 6 n s p 9 G C T > G C C A 7 1 3 1 0 5 n s p 1 0 T A C > T A T Y 3 1 3 1 3 2 n s p 1 0 C A A > C A G Q 1 1 3 4 5 8 n s p 1 2 a T C G > T T G S 6 L 1 1 1 3 6 9 3 n s p 1 2 b A C A > T C A T 7 6 S 1 1 4 2 2 8 n s p 1 2 b A A G > A G G K 2 5 4 R 2 1 4 3 5 8 n s p 1 2 b T G C > T G T C 1 1 4 3 9 1 n s p 1 2 b T T C > T T T F 5 1 4 4 0 8 n s p 1 2 b C C T > C T T P 3 1 4 L 3 0 3 1 4 5 9 9 n s p 1 2 b C T A > T T A T G > G T A V 1 1 6 0 4 5 n s p 1 2 b C T T > T T T L 8 6 0 F 1 1 6 0 8 9 n s p 1 2 b T T G > T T A L 1 1 6 2 2 6 n s p 1 2 b A C A > A T A T 9 2 0 I 1 1 6 2 8 9 n s p 1 3 G C T > G T T A 1 8 V 1 1 6 3 7 7 n s p 1 3 C C G > C C T P 1 1 6 3 8 6 n s p 1 3 T G C > T G T C 1 1 6 3 9 4 n s p 1 3 C C A > C T A P 5 3 L 3 1 6 8 1 6 n s p 1 3 C A A > A A A Q 1 9 4 K 1 1 6 9 6 8 n s p 1 3 G A G > G A T E 2 4 4 D 2 1 6 9 9 2 n s p 1 3 T T A > T T G L 1 1 7 1 0 4 n s p 1 3 C A T > T A T H 2 9 0 Y 1 1 7 1 2 5 n s p 1 3 C T C > T T C L 2 9 7 F 2 1 7 2 4 7 n s p 1 3 C G T > C G C R 1 1 7 5 4 1 n s p 1 3 G A C > G A T D 1 1 7 8 0 8 n s p 1 3 A A G > A A T K 5 2 4 N 1 1 7 9 6 4 n s p 1 3 A T G > A T A M 5 7 6 I 1 1 8 1 7 5 n s p 1 4 C C T > T C T P 4 G T T V 1 1 9 5 1 8 n s p 1 4 T T G > T T T L 4 9 3 F 3 1 9 6 0 2 n s p 1 4 A A C > A A T N 9 1 9 8 8 4 n s p 1 5 T A C > T A T Y 1 1 9 9 0 0 n s p 1 5 G C A > A C A A 9 4 T 1 1 9 9 9 9 n s p 1 5 G T T > T T T V 1 2 7 F 3 2 0 1 2 5 n s p 1 5 G G A > C G A G 1 6 9 R 1 2 0 1 9 9 n s p 1 5 T A C > T A T Y 1 2 0 2 6 8 n s p 1 5 T T A > T T G L 3 2 0 2 9 4 n s p 1 5 T A T > T G T Y 2 2 5 C 4 2 0 3 1 0 n s p 1 5 T A T > T A C Y 2 2 0 3 8 2 n s p 1 5 C T A > C T T L 1 2 0 4 0 1 n s p 1 5 T C A > C C A S 2 6 1 P 1 2 0 6 2 8 n s p 1 5 G G C > G G T G 1 2 0 8 0 8 n s p 1 6 C T G > C T A L 1 2 0 9 4 6 n s p 1 6 G T C > G T T V 1 1 2 1 0 1 5 n s p 1 6 C A T > C A C H 2 2 1 2 2 5 n s p 1 6 T G G > T G T W 1 8 T > A T T T 9 5 I 1 2 1 9 3 8 S G T T > T T T V 1 2 6 F 1 2 2 3 4 6 S G C T > T C T A 2 6 2 S 1 2 2 4 5 8 S A C A > A T A T 2 9 9 I 2 2 2 4 8 0 S T T C > T T T F 1 2 2 5 5 0 S C C T > T C T P 3 3 0 S 1 2 2 6 0 6 S G C A > G C T A 2 2 3 0 4 2 S T C A > G C A S 4 9 4 A 1 2 3 1 9 1 S T T C > T T T F 1 2 3 2 4 8 S T T C > T T T F 3 2 3 4 0 3 S G A T > G G T D 6 1 4 G 3 0 3 2 3 4 1 5 S A C A > A T A T 6 1 8 I 1 2 3 5 7 5 S T G C > T G T C 1 2 4 0 5 0 S G A T > C A T D 8 3 0 H 1 2 4 0 7 9 S G A T > G A C D 2 2 4 0 9 5 S G C T > T C T A 8 4 5 S 2 2 4 1 9 3 S C T G > C T A L 1 2 4 T T C > T T T F 1 2 5 5 6 3 O R F 3 a C A G > C A T Q 5 7 H 2 1 1 2 5 6 0 6 O R F 3 a G C A > T C A A 7 2 S 1 2 5 6 6 7 O R F 3 a T C A > T T A S 9 2 L 1 2 5 6 8 8 O R F 3 a G C T > G T T A 9 9 V 8 2 5 6 9 9 O R F 3 a G C C > T C C A 1 0 3 S 1 2 5 7 1 0 O R F 3 a C T C > C T T L 1 2 5 7 2 0 O R F 3 a G C T > T C T A 1 1 0 S 1 2 5 7 3 1 O R F 3 a T A C > T A T Y 6 2 5 7 7 6 O R F 3 a T G G > T G T W 1 2 8 C 1 2 5 7 8 2 O R F 3 a T G C > T G T C 1 2 5 8 2 5 O R F 3 a T A T > C A T Y 1 4 5 H 1 2 5 9 0 9 O R F 3 a G A T > T A T D 1 7 3 Y 3 2 5 9 3 3 O R F 3 a G A A > A A A E 1 8 1 K 1 2 6 1 4 4 O R F 3 a G G T > G T T G 2 5 1 V 2 2 6 1 6 1 O R F 3 a A A T > X 1 2 6 2 5 6 E T T C > T T T F 1 2 6 3 1 4 E G T G > T T G V 2 4 L 1 2 6 6 2 2 M C T T > T T T L 3 4 F 2 2 6 7 1 8 M G T G > T T G V 6 6 L 4 2 6 7 3 5 M T A C > T A T Y 1 2 6 7 7 3 M A T G > A C G M 8 4 T 1 T C G > T C A S 1 2 8 2 5 3 O R F 8 T T C > T T T F 2 2 8 2 9 1 N C C C > C C T P 1 2 8 3 1 1 N C C C > C T C P 1 3 L 1 2 8 3 1 2 N C C C > C C T P 4 2 8 3 2 6 N G G T > G T T G 1 T > G C T T 2 0 5 A 1 2 8 9 5 7 N A A C > A A T N 1 2 9 1 6 7 N T A C > T A T Y 3 2 9 1 7 1 N C A T > T A T H 3 0 0 Y 1 2 9 1 7 9 N C C G > C C T P 1 2 9 2 0 6 N G C T > G C A A 1 2 9 2 1 8 N T T C > T T T F 1 2 9 2 7 2 N T A C > T A T Y 1 2 9 2 8 1 N G C C > G C T A 1 2 9 3 6 3 N C C A > T C A P 3 6 4 S 2 2 9 4 7 7 N G A T > T A T D 4 0 2 Y 1 2 9 5 2 7 N C A G > C A T Q 4 1 8 H 1 2 9 5 3 6 T > C 1 2 9 5 5 5 C > T 1 2 9 7 4 2 3 U T R G > A 1 2 9 7 4 4 3 U T R G > T 1 2 9 7 4 5 3 U T R G > T 1 2 9 7 4 7 3 U T R G > T 1 2 9 7 5 4 3 U T R C > T 1 2 9 7 7 9 3 U T R G > C 3 1 G G C > A G C G 3 0 S 1 5 1 0 n s p 1 G G T > X 1 5 1 1 n s p 1 G G T > X 1 5 1 2 n s p 1 C A T > X 1 5 1 3 n s p 1 C A T > X 1 5 1 4 n s p 1 C A T > X 1 5 1 5 n s p 1 G T T > X 1 5 1 6 n s p 1 G T T > X 1 5 1 7 n s p 1 G T T > X 1 5 1 8 n s p 1 A T G > X 1 5 3 7 n s p 1 G A A > G G A E 9 1 G 1 5 4 1 n s p 1 C T C > C6 F 1 1 4 2 7 n s p 2 C A T > T A T H 2 0 8 Y 1 1 4 4 0 n s p 2 G G C > G A C G 2 1 2 D 2 1 4 6 3 n s p 2 G G T > A G T G 2 2 0 S 1 1 4 9 3 n s p 2 G T G > A T G V 2 3 0 M 1 1 5 1 5 n s p 2 C A T > C G T H 2 3 7 R 1 1 6 0 5 n s p 2 A A T > X 2 1 6 0 6 n s p 2 A A T > X 2 1 6 0 7 n s p 2 G A C > X 2 1 7 3 6 n s p 2 G T G > A T G V 3 1 1 M 1 1 9 4 2 n s p 2 G T G > G7 L 6 3 4 2 9 n s p 3 A C A > A T A T 2 3 7 I 1 3 4 7 8 n s p 3 G T T > G T C V 1 3 6 1 9 n s p 3 G T C > G T T V 2 3 7 8 4 n s p 3 G T C > G T T V 2 3 9 0 2 n s p 3 C C A > T C A P 3 9 5 S 1 3 9 2 4 n s p 3 C C T > C T T P 4 0 2 L 1 4 1 0 5 n s p 3 A A G > A A T K 4 6 2 N 1 4 3 2 0 n s p 3 G C C > G T C A 5 3 4 V 2 4 4 5 9 n s p 3 A T A > A Netherland s/NA 93/2020 Netherland s/NA 42/2020