nCoV_info
General Category => genetics => Topic started by: gsgs on December 22, 2020, 12:42:56 pm
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29, 26, 1,C21575T, L5F,
937, 435, 36,C21614T, L18F,20A.EU1=B.1.177
9, 10, 0,C21627T, T22I,
31, 11, 0,A21631T, Q23H,
41, 17, 7,C21637T, ,
6, 7, 0,C21638T, P26S,
2, 6, 0,C21727T, ,
30, 6, 5,G21800T, D80Y,
9, 10, 0,C21855T, S98F,
0, 6, 0,C22000T, ,
2, 6, 0,T22016A, W152R,
81, 6, 0,G22051T, ,
15, 6, 8,A22053C, N164T,
7, 8, 3,C22075T, ,
18, 7, 0,C22088T, L176F,
7, 9, 3,G22131T, R190M,
15, 19, 0,G22205C, D215H,
16, 11, 0,C22224T, S221L,
1584, 908, 73,C22227T, A222V,20A.EU1=B.1.177
13, 10, 0,C22329T, S256L,
58, 52, 3,G22346T, A262S, B.1.177
39, 39, 0,C22377T, P272L,
20, 13, 1,C22388T, ,
0, 19, 0,C22432T, ,
63, 47, 2,C22444T, , B.1.36
1, 8, 0,C22530T, T323I,
1, 7, 1,A22546G, ,
36, 33, 3,C22879A, N439K, B.1.5
2, 13, 1,G22918T, ,
43, 16, 0,G22992A, S477N,
6, 10, 0,T23042C, S494P,
423, 880, 12,A23063T, N501Y, B.1.1.7
406, 885, 14,C23271A, A570D, B.1.1.7
42, 25, 4,G23311C, E583D,
6, 19, 3,T23323C, ,
9, 6, 0,G23401T, Q613H,
2344,2015, 104,A23403G, D614G,
409, 889, 14,C23604A, P681H, B.1.1.7
1, 6, 0,G23608T, ,
12, 10, 0,C23625T, A688V,
28, 24, 0,C23644T, ,
11, 11, 0,C23679T, A706V,
407, 883, 14,C23709T, T716I, B.1.1.7
0, 6, 0,T23866C, ,
5, 14, 1,G23873T, A771S,
21, 10, 0,T24088C, ,
19, 35, 1,C24106T, ,
1, 6, 0,C24130T, ,
1, 6, 0,C24138A, T859N,
4, 9, 0,C24138T, T859I,
347, 235, 16,C24334T, ,
7, 15, 0,C24378T, S939F,
32, 9, 0,C24382T, ,
406, 885, 14,T24506G, S982A, B.1.1.7
11, 8, 0,G24620T,A1020S,
14, 10, 0,T24769C, ,
3, 8, 0,G24781T,K1073N,
30, 19, 1,T24910C, ,
406, 887, 14,G24914C,D1118H, B.1.1.7
1, 8, 1,T24979C, ,
4, 6, 0,C25000T, ,
2, 7, 0,G25049K, ,
45, 71, 0,G25049T,D1163Y, B.1.177
46, 76, 0,G25062T,G1167V, B.1.177
12, 14, 0,C25096T, ,
4, 14, 1,C25349A,P1263T,
-----------------------------------------------------
2345,2027,0104,total genomes
0049,0050,0051,week
frequency of spike-mutations in 133277 full genomes
in week 50 from cogconsortium , 2020/12/22
831,45416,151499
checking for the new strain B.1.1.7 = VUI202012/01 = VOC2020
prevalence in UK : http://magictour.free.fr/b117a.GIF
2020/12/08 , genbank=5/44708 , UK=1203(1050)/131631
2020/12/15 , DE=0/747 , UK=1289/133960
2020/12/17 , DE=0/764 , UK=141600 new strain-names
2020/12/20 , UK=2100/146416
2020/12/21 , DE=0/834,UK=3042/150173
2020/12/22 , DE=834,genbank=,UK=3063/150399
2020/12/23 , DE=0/831,genbank=45416,UK=3094/151499,RKI:0/1742
I downloaded the 133277 aligned sequences from cogconsortium (3.9GB)
and processed/converted them into a better format :
http://magictour.free.fr/sars2uk8.7z (2MB)
this takes many hours each day for me , because of the big files.
Is someone else doing this ?
Can we coordinate, exchange the processed/improved data ?
-------------------------------------------
viruses with many spike-amino-acid mutations :
genbank, USA,CA : S13I,C136G,W152C,L452R
UK, B.1.1.7 , B.1.258 , B.1.37 , B.1.315 , B.1.177 , B.1.160 , B.1.5 , B.1.351 (SA)
file spisur.12a : sequences with >=5? spike-amino-acid-mutations (2020/12/28)
182,B.1.177.9
55,B.1.177
31,B.1.258.4
25,B.1.1.37
14,B.1.177.6
11,B.1.177.17
4,B.1.1
3,B.1.160.7
1,B.1.5.34
1,B.1.351
1,B.1.1.194
329,D614G
286,A222V
222,A262S
184,D80Y
183,N164T
127,E583D
57,L5F
46,L18F
40,P272L
32,G1219V
31,V772I
31,N439K
31,L189F
28,H655Y
27,T95I
25,D574Y
18,V308L
15,Q23H
15,A1020S
12,I1216V
11,L176F
8,N536S
8,G446V
8,D796H
8,A520S
7,G1167V
7,D1163Y
6,Q613H
6,D215H
5,S98F
5,S477N
5,R346K
4,K1205N
4,A1226V
3,W152R
3,T678I
3,S884F
3,S221L
3,R21K
3,P681L
3,L244F
3,G482S
3,F329L
3,A871S
2,T716I
2,S982A
2,R190K
2,Q677H
2,Q675R
2,Q218H
2,P681H
2,P384L
2,N501Y
2,L552F
2,L1141F
2,K1191N
2,H146Y
2,E484K
2,E1150D
2,D936Y
2,D215Y
2,D215V
2,D138Y
2,D1118H
2,A845S
2,A783T
2,A771S
2,A706V
2,A688V
2,A570D
2,A522V
2,A522S
2,A1174V
2,A1078S
1,Y269C
1,Y266C
1,Y200C
1,Y145N
1,V687L
1,V539I
1,V445I
1,V36L
1,V367F
1,V213A
1,V1230A
1,V1104L
1,T768N
1,T63N
1,T51I
1,T307N
1,T22I
1,T20I
1,T19K
1,S937L
1,S813I
1,S735A
1,S691F
1,S659L
1,S50L
1,S494P
1,S151T
1,S12F
1,S1261F
1,S1242I
1,S1175P
1,R765L
1,R214L
1,Q314K
1,P9L
1,P681R
1,P561T
1,P384S
1,P1079S
1,N925S
1,N556Y
1,N211T
1,L822F
1,L455F
1,L216F
1,L141F
1,K444R
1,K417N
1,K1181I
1,K1073N
1,I468V
1,I210T
1,I1179V
1,H146Q
1,G482A
1,G476F
1,G181V
1,G181A
1,G142V
1,G1124V
1,F2L
1,F157S
1,F157L
1,E484R
1,E1182Q
1,D80A
1,D215G
1,D1257Y
1,D1153Y
1,D1084Y
1,A924V
1,A924S
1,A879V
1,A846V
1,A701V
1,A668S
1,A653V
1,A647S
1,A27S
1,A243S
1,A163V
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D00614G,135340,143930,8590
A00222V, 56710, 60647,3937
N00501Y, 6060, 9928,3868
P00681H, 5659, 9517,3858
T00716I, 5624, 9471,3847
D01118H, 5576, 9422,3846
S00982A, 5568, 9413,3845
A00570D, 5569, 9413,3844
L00018F, 31126, 33762,2636
A00262S, 2873, 3053, 180
E00583D, 1929, 2091, 162
N00439K, 3669, 3794, 125
L00005F, 2270, 2394, 124
P00272L, 1896, 2008, 112
S00477N, 2928, 3034, 106
D00080Y, 1134, 1227, 93
Q00023H, 591, 660, 69
G00181V, 248, 317, 69
N00164T, 648, 708, 60
S00256L, 743, 800, 57
A00706V, 141, 196, 55
S00098F, 809, 859, 50
D00215H, 883, 930, 47
A01020S, 227, 269, 42
Q00613H, 210, 252, 42
S00494P, 101, 143, 42
L00176F, 886, 924, 38
D01163Y, 1730, 1766, 36
P01069S, 173, 209, 36
G01167V, 1704, 1738, 34
A00688V, 833, 863, 30
A00701V, 81, 111, 30
S00939F, 246, 274, 28
H00655Y, 1078, 1104, 26
Q00675H, 215, 240, 25
N00185S, 101, 126, 25
P00026S, 307, 331, 24
S00254F, 124, 147, 23
D00138Y, 76, 98, 22
H00049Y, 93, 114, 21
E00484K, 23, 44, 21
Q00677H, 198, 218, 20
D00080A, 24, 44, 20
P00681R, 21, 41, 20
A00831V, 18, 38, 20
K00417N, 13, 33, 20
-------------------------------
spike amino-acid mutations at cog-uk
A:mutation
B:occurrances Jan03
C:occurrances Jan07
D:occurrances between Jan03 and Jan07
B.1.351 9, 29, 20
B.1.1.7 5579, 9432,3853
B.1.177 42296,46609,4313
B.1.1.7 5579, 9432,3853
B.1.177.7 2313, 2768, 455
B.1.177.4 3488, 3795, 307
B.1 5562, 5833, 271
B.1.1.37 4374, 4590, 216
B.1.177.15 1226, 1422, 196
B.1.1.315 4081, 4257, 176
B.39 183, 343, 160
B.1.1 11496,11650, 154
B.1.177.16 898, 1032, 134
B.1.160 1924, 2048, 124
B.1.1.311 2469, 2584, 115
B.1.36.17 1915, 2010, 95
B.1.36 652, 744, 92
B.1.177.6 604, 695, 91
B.1.177.9 647, 732, 85
B.1.160.7 596, 681, 85
B.1.177.18 459, 544, 85
B.1.1.1 5470, 5553, 83
B.1.1.307 2015, 2098, 83
B.1.177.5 479, 545, 66
B.1.1.301 700, 763, 63
B.1.1.71 23, 86, 63
B.1.258.7 418, 477, 59
B.1.177.10 348, 405, 57
B.1.160.1 96, 152, 56
B.1.1.70 666, 721, 55
B.1.258.11 2, 57, 55
B.1.1.279 1041, 1095, 54
B.1.177.20 453, 507, 54
B.1.1.300 36, 90, 54
B.1.177.17 827, 878, 51
B.1.221 667, 712, 45
B.1.177.22 76, 120, 44
B.1.258.10 41, 85, 44
B.1.160.6 129, 169, 40
B.1.36.6 99, 136, 37
B.1.1.125 60, 96, 36
B.1.177.8 870, 903, 33
B.1.247 118, 151, 33
B.1.258 1787, 1819, 32
B.1.258.3 406, 437, 31
B.1.222 170, 200, 30
B.1.1.130 78, 108, 30
B.1.177.19 445, 474, 29
B.1.1.10 469, 497, 28
B.1.1.49 33, 61, 28
B.1.1.238 0, 28, 28
B.1.254 26, 52, 26
A 66, 91, 25
B.1.177.2 182, 204, 22
B.1.1.286 323, 344, 21
B.1.1.196 153, 173, 20
B.1.104 96, 116, 20
B.1.351 9, 29, 20
B.1.1.240 176, 194, 18
B.1.177.26 129, 147, 18
B.1.246 21, 39, 18
B.1.1.282 11, 29, 18
B.1.1.5 6, 24, 18
B.1.1.101 0, 16, 16
B.1.235 859, 874, 15
B.1.1.105 4, 19, 15
B.1.1.236 90, 104, 14
B.1.177.11 564, 577, 13
B.1.141 59, 72, 13
B.26 29, 42, 13
B.1.1.197 7, 20, 13
B.1.1.303 350, 362, 12
B.48 147, 159, 12
B.1.258.4 205, 216, 11
B.1.36.9 203, 214, 11
B.1.1.204 68, 79, 11
B.54 65, 76, 11
B.52 59, 70, 11
B.47 5, 16, 11
B.1.362 204, 214, 10
B.1.1.234 47, 57, 10
B.32 25, 35, 10
B.1.36.1 25, 35, 10
B.1.1.316 8, 18, 10
B.3 508, 517, 9
B.18 11, 20, 9
B.1.1.304 139, 147, 8
B.1.1.264 136, 144, 8
B.1.131 28, 36, 8
B.1.1.190 10, 18, 8
B.1.1.285 0, 8, 8
B.1.258.12 101, 108, 7
B.1.1.43 49, 56, 7
B.1.1.292 46, 53, 7
B.1.1.46 10, 17, 7
B.1.5.34 6, 13, 7
B.1.111 3, 10, 7
B.1.1.198 418, 424, 6
B.1.1.44 340, 346, 6
B.1.160.2 121, 127, 6
B.1.1.232 88, 94, 6
B.1.1.170 65, 71, 6
B.1.353 1, 7, 6
B.1.1.4 473, 478, 5
B.1.98 461, 466, 5
B.1.367 268, 273, 5
B.1.1.217 251, 256, 5
B.1.177.13 106, 111, 5
B.1.1.12 77, 82, 5
B.1.1.50 53, 58, 5
B.1.240 49, 54, 5
B.1.1.159 42, 47, 5
B.1.1.153 30, 35, 5
B.1.248 28, 33, 5
B.1.2 25, 30, 5
B.1.1.248 25, 30, 5
B.1.1.106 9, 14, 5
B.1.1.103 5, 10, 5
B.1.35 217, 221, 4
B.1.160.4 179, 183, 4
B.1.146 159, 163, 4
B.10 118, 122, 4
B.1.1.189 76, 80, 4
B.1.1.274 69, 73, 4
B.1.201 64, 68, 4
B.1.36.16 62, 66, 4
B.1.258.6 46, 50, 4
B.1.229 29, 33, 4
B.1.1.20 11, 15, 4
B.1.36.3 0, 4, 4
B.1.1.126 0, 4, 4
B.1.1.255 294, 297, 3
B.1.1.3 103, 106, 3
B.1.236 74, 77, 3
B.1.1.39 65, 68, 3
B.1.1.54 24, 27, 3
B.1.11 19, 22, 3
B.1.5.33 18, 21, 3
B.1.1.114 3, 6, 3
C.14 1, 4, 3
B.1.102 0, 3, 3
B.1.1.62 0, 3, 3
B.1.1.239 0, 3, 3
B.1.1.89 146, 148, 2
B.31 132, 134, 2
B.1.36.12 100, 102, 2
B.1.1.294 96, 98, 2
B.1.1.299 73, 75, 2
B.1.1.15 69, 71, 2
B.1.3 26, 28, 2
B.1.1.86 26, 28, 2
B.1.1.288 23, 25, 2
B.1.1.163 22, 24, 2
B.1.77 21, 23, 2
B.1.275 20, 22, 2
B.1.1.133 17, 19, 2
B.1.1.131 16, 18, 2
B.6 11, 13, 2
B.1.1.162 4, 6, 2
B.1.1.182 3, 5, 2
B.1.213 2, 4, 2
B.1.334 0, 2, 2
B.1.260 0, 2, 2
B.1.5 2890, 2678,-212
B.40 2168, 1987,-181
B.1.1.291 145, 1,-144
B.1.255 162, 50,-112
B 1743, 1678, -65
B.1.1.206 45, 1, -44
B.1.1.257 218, 179, -39
B.1.223 231, 198, -33
B.1.1.25 41, 15, -26
B.1.1.207 33, 9, -24
B.1.1.47 29, 9, -20
B.1.1.151 256, 238, -18
B.1.88 138, 121, -17
B.1.1.195 59, 42, -17
B.1.1.253 371, 355, -16
B.23 112, 98, -14
B.1.1.53 15, 1, -14
B.1.1.216 52, 40, -12
B.1.1.273 27, 15, -12
B.1.177.14 14, 2, -12
B.1.1.152 13, 1, -12
A.1 31, 20, -11
B.1.1.64 129, 119, -10
B.1.178 18, 8, -10
B.1.182 10, 1, -9
B.1.1.31 11, 2, -9
B.1.1.80 18, 10, -8
B.1.1.237 352, 345, -7
H.1 14, 7, -7
B.1.1.104 31, 25, -6
B.1.1.164 161, 156, -5
B.1.1.245 299, 295, -4
B.1.215 95, 91, -4
B.1.75 90, 86, -4
B.1.1.165 69, 65, -4
B.1.1.127 33, 29, -4
B.1.1.243 26, 22, -4
B.1.3.1 20, 16, -4
B.1.1.161 9, 5, -4
B.29 159, 156, -3
B.1.1.29 140, 137, -3
B.1.258.5 105, 102, -3
B.1.1.193 65, 62, -3
B.1.173 29, 26, -3
B.1.5.12 22, 19, -3
B.1.186 7, 4, -3
B.1.212 5, 2, -3
B.3.1 555, 553, -2
B.1.1.38 223, 221, -2
B.1.252 133, 131, -2
B.34 73, 71, -2
B.1.1.95 30, 28, -2
B.4 26, 24, -2
B.1.1.261 13, 11, -2
B.1.36.13 10, 8, -2
B.1.277 9, 7, -2
B.1.358 4, 2, -2
B.1.1.297 4, 2, -2
B.1.1.296 232, 231, -1
B.1.1.59 156, 155, -1
B.1.1.250 88, 87, -1
B.1.1.313 71, 70, -1
B.1.1.123 63, 62, -1
B.1.81 33, 32, -1
B.1.1.166 23, 22, -1
B.1.1.260 20, 19, -1
B.1.1.187 20, 19, -1
B.1.1.266 17, 16, -1
B.1.108 16, 15, -1
B.1.177.21 12, 11, -1
B.1.1.281 6, 5, -1
B.1.177.25 4, 3, -1
B.1.1.211 4, 3, -1
C.13 3, 2, -1
B.1.190 3, 2, -1
B.1.324 2, 1, -1
B.1.1.99 2, 1, -1
B.1.1.84 2, 1, -1
B.1.1.135 2, 1, -1
strain
occurrance Jan03
occurrance Jan07
occurrance between Jan03 and Jan07
(report date ... ahh, this is useless since we have the sampling dates]
-
>4 spike mutations surveilance picture
Jan03 :
Jan08 : http://magictour.free.fr/s2ukc-sp.GIF
growing mutations : A701V , Q23H , L18F , F157L (selected list)
growing strains : B.1.1.7 , B.1.351 , B.1.177.7 , B.1.177.6
and one ancient strain "A" appeared without D614G ,
mutations : F157L , V367F , Q613H , P681R R102I , (L141F)
22 sequences from mid-Dec
Jan03 :
s2ukb1.GIF , aa-mutation-picture of 2443 randomly selected spike proteins
s2ukb-s4.GIF , 676 spike aa
s2ukb-s5.GIF
s2ukb-s5b.GIF big , with strain+mutation time-charts
Jan08 :
s2ukc-sp.GIF , mutation picture of 2912 spike aa sequences
no time-charts of mutations and strains yet
-
mutation table of the 27 C22033T viruses :
po 00001221011221101122222212202212022
si 00124888438716781122233418848808015
ti 39361286968985772200646051153870997
on 32198787468967486303600924677747080
75453818077475526003114714738879158
--Index--------------------------------------------------------------------
1 >Wuhan-Hu-1 ,2019-12-01,00 ...................................
3 >England/MILK-CB1C77,2020-12-06,50 TTATTAA......TTTTTTATTGCTCATCAT....
4 >England/MILK-CB1C86,2020-12-06,50 TTATTAA......TTTTTTATTGCTCATCAT....
5 >England/MILK-CB1C68,2020-12-06,50 TTATTAA......TTTTTTATTGCTCATCAT....
2 >England/MILK-C53AC8,2020-12-12,50 ......A......TTTTTTATTGCTCATCAT....
6 >England/ALDP-C3D88E,2020-12-10,50 -...........TTTTTTTATTGCTCATCA-....
7 >England/MILK-C91897,2020-12-12,50 ............TTTTTTTATTGCTCATCAT....
8 >England/CAMC-C70D53,2020-12-16,51 ...........-TTTTTTTATTGCTCATCAT-...
9 >England/ALDP-C8B57B,2020-12-16,51 ............TTTTTTTATTGCTCATCAT....
10 >England/ALDP-CB55B4,2020-12-20,52 ........T...TTTTTTTATTGCTCATCAT....
11 >England/LIVE-DCFF7C,2020-12-26,52 ........T..-TTTTTT-ATTGCTCATCAT-...
21 >England/CAMC-BD17BD,2020-11-27,48 .............TTTTTTATTGCTCATCATTTTT
20 >England/CAMC-C4380D,2020-12-10,50 ...........-.TTTTTTATTGCTCATCAT-TTT
14 >England/CAMC-C470E3,2020-12-10,50 .............TTTTTTATTGCTCATCATTTTT
22 >England/QEUH-C3151A,2020-12-11,50 .............TTTTTTATTGCTCATCATTTTT
12 >England/QEUH-C53F05,2020-12-11,50 ...........--TTTTT-ATTGCTCATCAT-T-T
23 >England/QEUH-C5C7B9,2020-12-14,51 .............TTTTTTATTGCTCATCATTTTT
25 >England/ALDP-C8DE41,2020-12-15,51 .............TTTTTTATTGCTCATCATTTTT
17 >England/QEUH-C93640,2020-12-16,51 .............TTTTTTATTGCTCATCATTTTT
18 >England/ALDP-C8A0A8,2020-12-16,51 .............TTTTTTATTGCTCATCATTTTT
19 >England/ALDP-C88D1C,2020-12-16,51 .............TTTTTTATTGCTCATCATTTTT
24 >England/QEUH-C7F8BD,2020-12-16,51 .............T-TTTTATTGCTCATCATTTTT
26 >England/ALDP-CBF602,2020-12-20,52 .............TTTTTTATTGCTCATCATTTTT
29 >England/QEUH-CC37F9,2020-12-21,52 .............TTTTTTATTGCTCATCATTTTT
13 >England/ALDP-C3A168,2020-12-08,50 .........TG..TTTTTTATTGCTCATCATTTTT
28 >England/ALDP-C8B432,2020-12-16,51 .........TG-.TTTTTTATTGCTCATCAT-TTT
27 >England/OXON-F43F7E,2020-12-18,51 .........TG..TTTTTTATTGCTCATCATTTTT
15 >England/ALDP-C8CD72,2020-12-14,51 .......A...R.TTTTTTATTGCTCATCATTTTT
16 >England/ALDP-C8CD72,2020-12-14,51 .......A...R.TTTTTTATTGCTCATCATTTTT
po 00001221011221101122222212202212022
si 00124888438716781122233418848808015
ti 39361286968985772200646051153870997
on 32198787468967486303600924677747080
75453818077475526003114714738879158
-
RBD:319-541
RBR:395-518
Bloom : 346,378,417,444,447,455f,484,490,486f
383f,452,419,384,475,472f
--------------------------------------------
(1) mutation in the RBD
(2) 1000*(4)/(3)
(3) number of sequences 0324 at cog-UK
(4) number of sequences 0324 at cog-UK
(5) #=match in the Bloom-picture
(1), (2), (3), (4) (5)
E484K,1178,000965,001137 #
L452R,1330,000263,000350 #
F490S,1326,000202,000268 #
P384L,1308,000269,000352 #
K417N,1243,000393,000489 #
L455F,1176,000090,000106 #
S477R,1149,000113,000130
P384S,1148,000241,000277 #
T385N,1122,000212,000238
K458N,3223,000012,000039
Y449H,2624,000014,000037
Y449D,1900,000012,000023
G496S,1464,000032,000047
A372V,1390,000015,000021
K417T,1365,000027,000037 #
F490Y,1304,000016,000021 #
K529R,1286,000031,000040
N370H,1277,000032,000041
R346S,1270,000018,000023 #
L335F,1258,000042,000053
E484Q,1238,000079,000098 #
Q321R,1232,000021,000026
E324K,1187,000026,000031
P322S,1183,000032,000038
Q493K,1160,000018,000021
K444N,1160,000018,000021 #
V483F,1155,000070,000081