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Table 2 Quantitative monitoring of SARS-CoV-2 strains with specific mutations

From: Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein

Mutant strains Collected locations Onset date Numbers before onset (%§) Numbers till deadline# (%§) P*
(total numbers)
E484K USA 2020/8/10 15/60 253 (0.02) 37 830/519 493 (7.28)  < 0.001
(86 585) Brazil 2020/10/14 15/3104 (0.48) 8001/12 725 (62.88)  < 0.001
  Japan 2020/12/8 16/17 633 (0.09) 5849/46 122 (12.68)  < 0.001
  Germany 2020/12/28 15/7313 (0.21) 3679/119 793 (3.07) 1.67E−73
  France 2021/1/6 19/5299 (0.36) 3114/37 205 (8.37) 2.72E−155
  South Africa 2020/10/10 15/2451 (0.61) 2675/6329 (42.27)  < 0.001
  Sweden 2021/1/18 15/3656 (0.41) 2351/54 991 (4.28) 6.95E−47
  Belgium 2021/1/10 16/3952 (0.4) 2187/22 666 (9.65) 8.51E−133
  United Kingdom 2020/12/12 16/145 591 (0.01) 2071/421 559 (0.49) 1.81E−237
  Canada 2020/12/14 20/16 160 (0.12) 1644/27 996 (5.87) 4.20E−296
S477N** USA 2020/8/21 15/63 825 (0.02) 12 772/519 495 (2.46)  < 0.001
(55 442) Australia 2020/5/28 17/3447 (0.49) 10 090/17 811 (56.65)  < 0.001
  Denmark 2020/8/17 33/3015 (1.09) 6194/101 999 (6.07) 6.24E−43
  Switzerland 2020/8/24 16/2422 (0.66) 5701/40 653 (14.02) 1.16E−126
  France 2020/7/29 19/2537 (0.75) 3853/37 205 (10.36) 1.64E−87
  United Kingdom 2020/4/12 15/20 890 (0.07) 3318/421 559 (0.79) 2.10E−49
  Germany 2020/9/10 15/3474 (0.43) 3191/119 797 (2.66) 3.40E−23
  Luxembourg 2020/10/7 15/423 (3.55) 1445/8248 (17.52) 4.51E−18
  Sweden 2020/8/11 16/876 (1.83) 1232/54 991 (2.24) 0.488828411
  Belgium 2020/9/15 22/1862 (1.18) 1229/22 666 (5.42)  < 0.001
T478K USA 2020/11/23 16/43 020 (0.04) 13 072/519 493 (2.52)  < 0.001
(31 516) United Kingdom 2020/12/31 15/172 126 (0.01) 10 085/421 559 (2.39)  < 0.001
  Mexico 2020/11/30 17/2845 (0.6) 4876/14 372 (33.93)  < 0.001
  India 2021/3/1 16/11 429 (0.14) 1719/22 009 (7.81) 7.92E−292
  Germany 2021/2/4 16/16 175 (0.1) 566/119 793 (0.47) 1.56E−15
  Canada 2021/1/19 16/19 501 (0.08) 374/27 996 (1.34) 4.64E−65
  Denmark 2021/4/5 15/79 383 (0.02) 258/101 999 (0.25) 2.80E−46
  Switzerland 2020/12/25 17/12 385 (0.14) 244/40 653 (0.6) 6.06E−13
  Sweden 2021/1/25 17/4328 (0.39) 182/54 991 (0.33) 0.493286089
  Japan 2021/4/16 18/40 879 (0.04) 154/46 122 (0.33) 9.30E−25
N439K Denmark 2020/8/24 21/3277 (0.64) 5599/101 999 (5.49) 1.46E−51
(27 987) Slovenia 2020/8/15 16/350 (4.57) 4555/11 747 (38.78) 4.87E−50
  United Kingdom 2020/3/24 16/8202 (0.2) 4459/421 559 (1.06) 3.11E−20
  Germany 2020/8/25 15/3338 (0.45) 3217/119 793 (2.69) 3.83E−22
  Sweden 2020/11/23 16/1325 (1.21) 1459/54 991 (2.65) 0.000464083
  Switzerland 2020/8/21 15/2355 (0.64) 1334/40 653 (3.28) 2.11E−17
  Austria 2020/11/2 18/1085 (1.66) 1302/15 060 (8.65) 1.29E−21
  Italy 2020/10/14 15/2291 (0.65) 972/28 589 (3.4) 1.97E−17
  Netherlands 2020/10/15 18/3257 (0.55) 468/33 758 (1.39) 1.63E−05
  Indonesia 2020/12/30 19/623 (3.05) 467/1773 (26.34) 2.40E−45
S494P USA 2020/7/18 15/52 902 (0.03) 6420/519 493 (1.24) 8.00E−243
(8638) United Kingdom 2020/8/14 15/49 206 (0.03) 937/421 559 (0.22) 1.60E−27
  Spain 2020/12/20 15/9540 (0.16) 376/29 902 (1.26) 1.90E−28
  Germany 2021/2/5 18/16 737 (0.11) 150/119 793 (0.13) 0.637633683
A520S** USA 2020/6/9 21/35 378 (0.06) 2867/519 493 (0.55) 8.67E−55
(4113) United Kingdom 2020/6/24 16/43 220 (0.04) 238/421 559 (0.06) 0.105089403
  Denmark 2020/8/31 91/3996 (2.28) 199/101 999 (0.2) 7.18E−57
F490S Denmark 2021/3/29 25/76 052 (0.03) 650/101 999 (0.64) 5.25E−122
(3954) USA 2020/12/7 15/109 237 (0.01) 632/519 493 (0.12) 2.62E−34
  Germany 2021/2/22 17/27 057 (0.06) 601/119 793 (0.5) 2.88E−33
  United Kingdom 2020/12/15 15/150 582 (0.01) 418/421 559 (0.1) 3.21E−37
  Israel 2021/1/7 18/2706 (0.67) 378/11 835 (3.19) 6.52E−17
  Chile 2021/3/7 15/1454 (1.03) 273/2193 (12.45) 6.14E−45
  Poland 2021/3/3 15/2917 (0.51) 267/12 832 (2.08) 1.04E−10
  Argentina 2021/2/26 16/2115 (0.76) 136/3148 (4.32) 2.71E−16
  Netherlands 2021/3/31 18/23 847 (0.08) 116/33 758 (0.34) 2.98E−12
N501T** USA 2020/8/28 15/65 569 (0.02) 2339/519 494 (0.45) 2.85E−97
(3288) France 2021/1/9 23/5626 (0.41) 200/37 177 (0.54) 0.233423368
  Australia 2020/12/16 15/16 685 (0.09) 170/17 811 (0.95) 1.47E−32
A522S** Germany 2020/12/10 15/6881 (0.22) 846/119 793 (0.71) 6.05E−08
(3275) USA 2020/8/26 16/65 058 (0.02) 654/519 493 (0.13) 2.63E−17
  France 2021/1/27 23/7974 (0.29) 344/37 205 (0.92) 2.22E−10
  Denmark 2020/11/23 35/12 200 (0.29) 231/101 999 (0.23) 0.19572294
  United Kingdom 2020/8/31 20/54 038 (0.04) 231/421 559 (0.05) 0.091287615
  Russia 2020/11/9 17/1896 (0.9) 182/3962 (4.59) 1.05E−15
  Italy 2021/3/13 16/15 095 (0.11) 147/28 589 (0.51) 3.09E−13
  Austria 2021/1/18 19/2638 (0.72) 122/15 060 (0.81) 0.722036891
V367F** United Kingdom 2020/4/17 15/24 276 (0.06) 391/421 559 (0.09) 0.126000419
(1886) USA 2020/6/1 15/33 267 (0.05) 358/519 493 (0.07) 0.125838334
  Canada 2021/1/2 17/17 660 (0.1) 275/27 996 (0.98) 5.81E−39
  Uganda 2020/8/15 22/95 (23.16) 220/428 (51.4) 4.08E−07
A522V** USA 2020/7/13 15/51 506 (0.03) 365/519 493 (0.07) 0.000214014
(1012) United Kingdom 2020/4/7 15/17 505 (0.09) 197/421 559 (0.05) 0.03237495
  1. *Fisher's exact test was used to compare proportion of mutant strains among all uploaded isolates which were collected between before onset date and till deadline
  2. **These mutations are with increasing predicted affinity to receptor
  3. The onset date listed in the table was the time when more than 15 mutants were uploaded locally
  4. §Proportion referred to the ratio of numbers of specific mutations among all uploaded sequences
  5. #Deadline referred to 30 May, 2021