genetics > genetics

B.1.1.7 (UK) and B.1.351(SA) and P1(Brazil) and B.1.617(India) and ...

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gsgs:
2021/03/02 : wikipedia has a good table : https://en.wikipedia.org/wiki/Lineage_B.1.1.7

variant charts by country :
https://covariants.org/per-country

genbank :  https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ss=SARS-CoV-2,%20taxid:2697049
UK-cog : https://www.cogconsortium.uk/tools-analysis/public-data-analysis-2/
Germany : https://civnb.info/sequences/
Denmark : https://www.covid19genomics.dk/statistics   (Jan15)

Brazil : https://github.com/CADDE-CENTRE/Novel-SARS-CoV-2-P1-Lineage-in-Brazil
sequences no longer available (? they claim it's there, but I couldn't find it - edit: found ir here:),
https://github.com/CADDE-CENTRE/Novel-SARS-CoV-2-P1-Lineage-in-Brazil/blob/main/virological_post/CADDE_B.1.1.28_P1.fas
here is a nice overview:
https://cov-lineages.org/global_report_P.1.html
https://cov-lineages.org/global_report_B.1.351.html
https://cov-lineages.org/global_report_B.1.1.7.html
https://cov-lineages.org/global_report_B.1.525.html
https://cov-lineages.org/global_report_B.1.617.2.html   {old, not updated}







RKI : https://www.rki.de/DE/Content/InfAZ/N/Neuartiges_Coronavirus/Virologische_Basisdaten.html


genbank old : https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?VirusLineage_ss=Severe%20acute%20respiratory%20syndrome%20coronavirus%202,%20taxid:2697049&SeqType_s=Nucleotide
UK , old  : https://www.cogconsortium.uk/data/  {no longer available 2021/02/26)


checking for the new strains B.1.351 and B.1.1.7 = VUI202012/01 = VOC2020

prevalence in UK :
2020/12/24 : http://magictour.free.fr/b117a.GIF
2020/12/31 : http://magictour.free.fr/s2ua5spa.GIF
2011/01/09 : http://magictour.free.fr/s2ukc-sp.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
DE,genbank,UK,RKI , 3rdcov(F157L,614D),B.1.351(South Africa),B.1.1.7,all
2020/12/21 , 0,0,0,834 , 0,0,0,45416 , 03,01,3042,150173 , 02,01,0958,3757
2020/12/22 , 0,0,0,834 , 0,0,0,45416 , 03,01,3063,150399 , 00,00,0021,0226
2020/12/23 , 0,0,0,831 , 0,0,0,45416 , 03,01,3094,151499 , 00,00,0031,1100 ,RKI:0/1742
2020/12/24 , 0,0,0,831 , 0,0,0,45660 , 06,01,3478,153115 , 03,00,0384,1616
2020/12/25 , 0,0,0,831 , 0,0,?,45690 , 06,01,3786,154728 , 00,00,0308,1613
2020/12/26 , 0,0,0,831 , 0,0,?,45690 , 07,01,4171,156089 , 01,00,0385,1362
2020/12/27 , 0,0,0,831 , 0,0,?,45802 , 08,01,4599,157340 , 01,00,0428,1251
2020/12/28 , 0,0,0,831 , 0,0,0,46123 , 08,01,4637,157550 , 00,00,0038,0210
2020/12/29 , 0,0,0,831 , 0,0,0,46123 , 09,02,4722,157828 , 01,01,0085,0278
2020/12/30 , 0,0,0,915 , 0,0,?,47112 , 09,02,4745,158072 , 00,00,0023,0248
2020/12/31 , 0,0,0,914 , 0,0,2,47316 , 09,02,4745,158072 , 00,00,0000,0000
2021/01/01 , ?,0,?,916 , 0,0,3,47364 , 12,06,5478,160174 , 03,04,0733,2102
2021/01/02 , ?,0,?,916 , 0,0,?,47375 , 12,09,5579,160683 , 00,03,0101,0509
2021/01/03 , ?,0,?,916 , 0,0,?,47375 , 12,10,5598,160953 , 00,01,0019,0270
2021/01/04 , ?,0,?,916 , 0,0,?,47405 , 20,19,7145,164105 , 08,09,0547,3152
2021/01/05 , ?,0,?,916 , 0,0,?.47405 , 20,19,7145,164105 , 00,00,0000,0000
2021/01/06 , ?,0,?,916 , 0,0,?,47405 ,       7145,19,0,0,57678,667,3171,675,0,0
2021/01/07 , ?,0,?,916 , 0,0,?,47996 , 32,29,9425,170346 , 12,10,2280,6241
2021/01/08 , ?,0,?,916 , 0,0,?,48034 , 32,29,9425,170346 , 00,00,0000,0000
2021/01/09 , ?,0,?,916 , 0,?,?,48038 , 32,29,9425,170346 , 00,00,0000,0000
2021/01/10 , ?,0,?,916 , 0,?,?,48063 , 32,29,9425,170346 , 00,00,0000,0000
2021/01/11 , ?,0,?,916 , 0,0,12,48451 ,   13620,36,0,0,64210,703,3386,703,0,0
2021/01/12 , 0,0,3,960,48602,179932  ,  13620,36,0,0,64210,703,3386,703,0,0
2021/01/13 , 0,0,3,960,49010,179932,24(cadde,Brazil,B.1.1.28 )
2021/01/14,960,49124,179932,24
2021/01/15 , 0,1,5,1042 , 49807 . 179932 , 24
2021/01/16 , 1042,50006,179932,24
2021/01/17 , 1042,50008,179932,24 ,
2021/01/18 , 1042,50326,179932,24
2021/01/19 , 0,1,8,1126 , 50886 , 179932 , 24
2021/01/20 , 1129,51594,179932,24
2021/01/21 , 1129 , 52058 , 179932 , 24
2021/01/22 , 1129 , 52636 , 179932 , 24
2021/01/23 , 1129 , 52969 . 179932 , 24
2021/01/24 , 1210 , 52969 , 179932 , 24
2021/01/25 , 1272 , 53630 , 179932 , 24
2021/01/26 , 1272 , 54758 , 179932 , 24   (PHE:214159)
2021/01/27 , 1272 , 56592 , 179932 , 24 ,
2021/01/28 , 1274 , 57355 , 179932 , 24
2021/01/29 , 1274 , 57693 , 179932 , 24
2021/01/30 , 1274 , 57706 , 179932 , 24
2021/01/31 , 1274 , 57806 , 179932 , 24
2021/02/01 , 1356 , 57806 , 179932 , 24
2021/02/02 , 1397 , 59644 , 224820 , 24  {format-change at cog-uk,}
2021/02/03 , 1397 , 60084 , 224820 , 24  , 42108,132,0,36,73752,876,3723,764,1,0
2021/02/04 , 1397 , 60084*, 224820 , 24
2021/02/05 , 1397 , 61835 , 229120 , 24
2021/02/06 , 1397 , 61835 , 229120 , 24
2021/02/09 , 1397 , 62467 , 242926 , 24   , { 60543,170,129,0,81227,656,4136,839,1,26 }
2021/02/10 , 1397 , 62827 , 242926*, 24 , 55405,156,0,36,76299,878,3780,772,1,0,10
2021/02/11 , 1397 , 63956 , 242926 , 24
2021/02/12 , 1397 , 65743 , 249523 , 24
2021/02/13 , 1397 , 65745 , 254045 , 24
2021/02/14 , 1397 , 66036 , 257782 , 24
2021/02/15 , 1397 , 66044 , 257782 , 24
2021/02/16 , 1397 ,
2021/02/17 , 1397 , 66781 , 267131 , 24    , 75194,205,30,36,78074,880,3817,778,1,0
2021/02/18 , 1397 , 66785 , 271789 , 24    , 79138,218,31,36,78354,888,3821,779,1,0
2021/02/19 , 1397 , 66785 , 271789 , 24
2021/02/20 , 1397 , 66785 , 271789 , 24
2021/02/21 , 1397 , 66785 , 271789 , 24
2021/02/22 , 1397 , 76163 , 271789 , 24    ,  big genbank update, all from USA
2021/02/22 , 1397 , 79179 , 271789 , 24    , 
2021/02/25 , 1397 , 80086 , 271789 , 24
2021/03/01 , 1397 , 84277 , 297806 , 24    , 101496,256,44,37,79650,885,3845,783,1,17
2021/03/06 , 1397 , 91705 , 313258 , 24    , 113272,282,48,38,80487,890,3866,789,1,34,1
2021/03/10 , 1397 , 98768 , 313652 , 24    ,  116531,278,47,37,80204,880,3856,787,1,43,1
2021/03/12 , 1397, 103388 , 322717 , 24   ,  124917,295,47,37,80336,880,3859,787,1,54,1
2021/03/17 , 1397, 107850 , 332354 , 24   ,  133622,308,47,38,80494,880,3864,788,1,77,2  ; B.1.525 to 77

2021/04/22 , 1397 , 242752 , 387173 , 24 ,  suddenly there are 242752 sequences at genbank !
--------------------------------------
first B.1.1.7 at genbank : MW422255,MW422256,MW423686
San Diego, USA , Italy
Italy,12mut., no deletions !
https://www.ncbi.nlm.nih.gov/nuccore/MW422255

-------------------------------------------
https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?VirusLineage_ss=Severe%20acute%20respiratory%20syndrome%20coronavirus%202,%20taxid:2697049&SeqType_s=Nucleotide
https://www.cogconsortium.uk/data/
https://civnb.info/sequences/

---------------------------------------------------
weekly % of B.1.1.7 in Denmark week 46 - 04 : redoubles every 8 days
0.3,0.0,0.2,0.2,0.4,0.8,2.1,2.3,4.0,7.5,12.8,19.1
Germany, week 4, B.1.1.7 = 5.8%
--------------------------------------------------------
ONS, Jan05

ttps://www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/conditionsanddiseases/adhocs/12722estimatesofcovid19casesto02januaryforenglandregionsofenglandandbycasescompatiblewiththenewvariant
--------------------------------------------------------------------------
2021/02/01  Cologne reports 9% B.1.1.7 and 5% B.1.351



--- Code: ---2020/12/23 , 151499,03094,001,00,00,51701,628,3000,652,0,0
2020/12/30 , 158072,04745,002,00,00,55287,661,3122,663,0,0
2021/01/06 , 164104,07145,019,00,00,57678,667,3171,675,0,0
2021/01/11 , 179931,13620,036,00,00,64210,703,3386,703,0,0
2021/02/03 , 224820,42108,132,00,36,73752,876,3723,764,1,0
2021/02/10 , 242925,55405,156,00,36,76299,878,3780,772,1,0
2021/02/17 , 267131,75194,205,30,36,78074,880,3817,778,1,0
------------------------------------------------------------------------------------
          A        ,           B,    C,  D, E, F, G,  H,  I,  J,  ,  L,M

all,
A , B.1.1.7,SE-England
B , B.1.351,South Africa
C , A.23,Uganda
D , B.1.1.28,Brazil-Manaos
E , B.1.177,Spain-Aragon
F , B.1.1.70,Wales
G , B.1.258 , Ireland ?
H , B.1.221 , Belgium
I , B.1.375 , USA - S-drop-out
J , B.1.525 ,


--- End code ---

gsgs:
400 Austria , 4*B117 , 1*B351
196 US-LA  Nov25-Dec18. 0*B117
Denmark ,86*B117
 India,76
Ireland, weeks 51,52,53 : 09%,13%,25%
Luxembourg: 2% (3/141) Dec20-Dec29
Belgium, Jan25, 25% are B117

2020-01-06,Cape Town The Western Cape government said its Garden Route district has passed
its Covid-19 peak and the rate of infections was significantly decreasing in the area.
----------------------------------------------

gsgs:

--- Code: ---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


--- End code ---

gsgs:
Germany updates :

2020/10/18 ,  496 , http://magictour.free.fr/sars2de4.GIF
2020/10/28 ,  546 , http://magictour.free.fr/sars2de5.GIF
2020/11/01 ,  576 , http://magictour.free.fr/sars2de6.GIF
2020/11/04 ,  619 , http://magictour.free.fr/sars2de7.GIF
2020/11/24 ,  658 , http://magictour.free.fr/sars2de8.GIF
2020/12/08 ,  713 , http://magictour.free.fr/sars2dea.GIF
2020/12/15 ,  747 , http://magictour.free.fr/sars2deb.GIF
2020/12/21 ,  835 , http://magictour.free.fr/sars2ded.GIF
2020/12/30 ,  917 , http://magictour.free.fr/sars2dee.GIF
2021/01/13 ,  960 , http://magictour.free.fr/sars2def.GIF
2021/01/16 , 1042 , http://magictour.free.fr/sars2deg.GIF
2021/01/20 , 1126 , http://magictour.free.fr/sars2deh.GIF
2021/01/25 , 1210 , http://magictour.free.fr/sars2dei.GIF
2021/01/26 , 1272 , http://magictour.free.fr/sars2dej.GIF
2021/02/02 , 1356 , http://magictour.free.fr/sars2dek.GIF
2021/02/03 , 1397 , http://magictour.free.fr/sars2del.GIF


--- Code: ---
=============Germany===============
00,0,0,0,013,0, 4 , 0, 505,4,2010-10-18
00,0,0,0,030,0,12 , 2, 572,6,2020-11-01
00,0,0,0,076,0,32 ,11, 710,a,2020-12-07
00,0,0,0,084,0,35 ,11, 745,b,2020-12-15
00,0,0,0,092,0,37 ,15, 764,c,2020-12-18
00,0,0,0,117,0,57 ,16, 835,d,2020-12-21
00,0,0,0,137,0,62 ,16, 915,e,2020-12-30
03,0,0,0,145,1,65 ,22, 992,f,2021-01-13
05,1,0,0,188,2,71 ,26,1042,g,2021-01-16
08,1,0,0,247,2,75 ,29,1127,h,2021-01-20
14,4,0,0,288,2,79 ,38,1210,i,2021-01-25
49,4,0,0,308,2,82 ,39,1273,j,2021-01-25
59,5,0,0,352,2,97 ,46,1356,k,2021-02-01
66,5,0,0,372,2,101,50,1397,l,2021-02-03
--------------------------------------
 A,B,C,D,  E,F, G , H,   I,J,    K

A , B.1.1.7,SE-England
B , B.1.351,South Africa
C , A-old,Uganda
D , B.1.1.28,Brazil-Manaos
E , B.1.177,Spain-Aragon
F , B.1.1.70,Wales
G , B.1.258 , Ireland ?
H , B.1.221 , Belgium
I , -,all,World
J , filename
K , date


--- End code ---



--- Code: ---
==================UK==================
    0,  0, 0,0,    0,  0,   0,  5, 42102,2020-10-18
   66,  0, 0,0,26660,230,2021,520,107132,2010-11-23
  963,  0, 0,0,43679,353,2697,647,131386,2020-12-07
09418,029,26,0,60484,560,3326,688,151280,2021-01-08
42130,132,94,0,74966,619,3818,779,201894,2021-02-03
---------------------------------------------------
    A,  B, C,D,    E,  F,   G,  H,     I,     J

A , B.1.1.7,SE-England
B , B.1.351,South Africa
C , A-old,Uganda
D , B.1.1.28,Brazil-Manaos
E , B.1.177,Spain-Aragon
F , B.1.1.70,Wales
G , B.1.258 , Ireland ?
H , B.1.221 , Belgium
I , -,all,World
J , date


--- End code ---

gsgs:
Feb20 , % sequences with N501Y:
UK:53,DK:22,US:08,CH:20,NL:27,F:53,E:26,B:35,ICE:15,LUX:20,
I:69,IRE:79,DE:13,POR:33,SW:42,AUT:27,N:26,SA:37,
LIT:00,AUS:60,ISR:27,FIN:38,CZ:25,CDN:56,
TUR:03,POL:11,HUN:99,IND:33,BRA:00:,SLK:79
EGY:03,NIG:68,MAC:00,SGP:18,GHA:46,ARU:49
https://covariants.org/per-country

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