B.1.1.7 (UK) and B.1.351(SA) and P1(Brazil) and B.1.617(India) and BA (South Africa) and BA.2 (Denmark) ...

genetics > genetics

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gsgs:

--- Code: --->B.1.1.7 ,28,C00241T,C00913T,C03037T,C03267T,C05388A,C05986T,T06954C,C14408T,C14676T,C15279T,T16176C,A23063T,C23271A,A23403G,C23604A,C23709T,T24506G,G24914C,C27972T,G28048T,A28111G,G28280C,A28281T,T28282A,G28881A,G28882A,G28883C,C28977T
>B.1.351 ,19,C00241T,C01059T,A02692T,C03037T,G05230T,A10323G,C14408T,A21801C,A22206G,G22813T,G23012A,A23063T,A23403G,C23664T,G25563T,C25904T,C26456T,C28253T,C28887T
>A.23 ,22,A00901T,C04573T,C08782T,C10747T,G11230T,G11266T,G11521T,C16575T,C17745T,G21985T,C22000T,C22033A,G22661T,G23401T,C23604G,T24097C,C25708T,G28079T,T28144C,G28167A,G28378C,G28878A
>B.1.1.28,25,C00241T,T00733C,C03037T,A05648C,A06319G,A06613G,C14408T,G17259T,C21614T,C21621A,C21638T,G21974T,A22812C,G23012A,A23403G,C24642T,G25088T,T26149C,G28167A,C28512G,A28877T,G28878C,G28881A,G28882A,G28883C
>B.1.177 ,13,C00241T,T00445C,C03037T,C06286T,C14408T,G21255C,C21614T,C22227T,A23403G,C26801G,C27944T,C28932T,G29645T
>B.1.1.70,25,C00214T,C03037T,C03096T,G04255A,C07334T,G10265A,C10449T,A12103G,C14408T,A15972G,C19374T,C19718T,C20270T,G20433A,A23063T,A23403G,A25859G,T26504C,C26858T,C27434T,G28300C,T28759C,G28881A,G28882A,G28883C
>B.1.258 , 6,T07767C,C08047T,C17104T,A20268G,C22879A,G29734C
>B.1.221 ,13,C00241T,C03037T,C03602T,C06941T,C14408T,C15324T,C21855T,A23403G,A25505G,G25906C,G25996T,C28651T,C28869T
>B.1.375 ,14,C00241T,C03037T,A23403G,C14408T,C01059T,T01171C,A05747G,C10789T,G17259T,G24007A,G25563T,C25844T,A26664G,C28887T
>B.1.525 ,18,C01498T,A01807G,T08593C,C09565T,9-11288,C14407T,C18171T,A20724G,A21717G,G23012A,G23593C,T24224C,C24748T,C26305T,T26767C,3-28278,A28699G,G29543T
>B.1.526 ,15,C00241T,C01059T,C03037T,T09867C,9-11288,C14408T,A16500C,C21575T,C21846T,A22320G,A23403G,C25517T,G25563T,C28869T,G28975A
>P.1 ,31,G28883C,G28882A,G28881A,G21974T,C14408T,C03037T,A23403G,C21614T,T26149C,T00733C,G28878C,G28167A,G25088T,G23012A,G22132T,G17259T,C28512G,C24642T,C23525T,C21638T,C21621A,C13860T,C12778T,C02749T,A28877T,A23063T,A22812C,A06613G,A06319G,A05648C,C03828T

--- 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
3092, 1, 3, 0,49129,465,2912,650, , , , , ,133277,2020-12-22
5575, 1, 11, 0,56531,539,3088,668, , , , , ,142672,2021-01-03
9418, 29, 26, 0,60484,560,3326,688, , , , , ,151280,2021-01-08
42130,132, 94, 0,74966,619,3818,779,1, , , , ,201894,2021-02-03
60543,170,129, 0,81227,656,4136,839,1, 28, , , ,242925,2021-02-09
101496,256, 44,37,79650,885,3845,703,1, 17,0, 5,42,297806,2021-02-28-
139044,324,167,10,80844,625,3904,796,1,149,3,15,53,306229,2021-03-18
162568,380,167,51,80322,770,3891,804,1,240,8,27,55,329268,2021-03-24
--------------------------------------------------------------------
A, B, C, D, E, F, G, H,I, J,K, L, M, N, O

A , B.1.1.7,SE-England
B , B.1.351,South Africa
C , A.23,Uganda
D , B.1.1.28,Brazil-Manaos 1176
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 477
J , B.1.525 , 52,67,484,677,888
K , B.1.526 , 5,95,253,701
L , P.1 , 18,20,26,138,190,417,484,N501,655,1176,1027
M , P.2 , 484,859,1176
N , -,all,World
O , date

--- End code ---

--- 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.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 , -,all,World
J , filename
K , date

--- End code ---

gsgs:

--- Code: ---date, all, 1.7, 351,A23,1.28, 177,1.70, 258,221,375,525,526, P1,P2,E484K
--------------------------------------------------------------------------------------------------
0202,224821, 42108, 132, 0, 36,73752, 876,3723,764, 1, 0, 0, 0,21,238
0214,257783, 67110, 197, 20, 36,77610, 880,3805,777, 1, 0, 0, 0,33,384
0228,297806,101496, 256, 44, 37,79650, 885,3845,783, 1, 17, 0, 5,42,532
0312,322718,124919, 295, 47, 37,80336, 880,3859,787, 1, 54, 1, 14,51,661
0327,358209,157497, 363, 51, 41,80721, 882,3881,791, 1,174, 6, 33,56,985
-----------------------------------------------------------------------------------------------------------
date, all, 1.7, 351,A23,1.28, 177,1.70, 258,221,375,525,526, P1,P2,E484K

--- End code ---

===============================================================

weeks 61,...,69 , from cog_0427.lw1

--- Code: ---
B.1.351 , 29,38,38,63,90,68,71,54,09
B.1.617 , 02,05,14,18,21,50,91,198,42
B.1.525 , 43,56,45,48,27,26,13,18,03
B.1.1.318, 08,24,18,11,27,14,13,04,01
A , 13,10,08,19,43,14,18,09,03
C.36 , 03,15,16,11,09,11,14,24,03
P.1 , 04,06,10,08,02,11,11,17,05
B.1.36.31, 02,08,25,14,05,04,01,00,00
B.1.177. ,105,46,27,13,12,04,00,01,00
B.1.177 ,162,84,69,28,28,04,11,05,00
B.1.36. , 07,04,15,07,02,01,01,08,00
B.1.36 , 06,11,11,07,02,01,00,00,00
B.1.1. , 19,24,23,04,13,03,08,06,01
B.1. , 37,35,48,22,19,16,13,16,05
B.1.1.7,15991,13973,16496,16091,17073,12456,7619,6553,742

--- End code ---

gsgs:
weekly promille of B.1.617 in cog-UK-sequences by lab per 2021-06-15

--- Code: ---oth-,000,003,011,033,046,089,270,432,611,795,837,000
HSLL,000,000,068,232,212,392,470,664,807,893,919,000
RAND,000,032,048,136,228,229,000,160,000,000,000,000
PHEC,000,015,061,083,217,291,380,379,691,795,878,000
MILK,001,004,026,086,160,273,416,602,766,892,899,000
ALDP,000,002,016,049,141,306,507,750,857,929,919,000
CAMC,021,041,081,046,000,000,000,000,000,000,000,000
NORT,000,049,008,020,030,023,089,222,455,650,710,000
LOND,000,000,000,103,117,299,547,672,746,892,895,000
QEUH,000,002,005,009,024,379,706,782,840,906,897,000
CAMB,000,000,041,393,136,331,360,440,968,000,914,000
all-,001,007,022,057,113,227,374,564,752,866,883,000

weekly numbers of all sequences by nation :
all-,2868,8746,7965,7998,7528,7055,7930,9994,13063,19521,4140
SCT,2060,1263,1204,1053,0990,1048,1356,1698,2531,3272,0005
WLS,0364,0351,0262,0205,0190,0162,0181,0175,0139,0272,0212
WLS,0142,0111,0091,0084,0014,0038,0099,0359,0206,0009,0000

weekly promille of B.1.617 by nation :
all,001,007,022,057,113,227,374,564,752,866,883
SCT,000,003,007,027,048,088,313,539,644,755,980
WLS,000,003,004,034,026,111,210,126,503,680,802
WLS,000,000,011,107,142,026,020,053,082,879,000

--- End code ---

gsgs:
delta with N501Y in Germany
https://outbreak.info/situation-reports?muts=S%3AN501Y
As of 4 November 2021 07:26 AM, 1,266,536
https://outbreak.info/situation-reports?muts=S%3AN501Y&selected=DEU&loc=DEU

https://outbreak.info/location-reports?loc=DEU

Theo Sanderson replied
Future
@UseBy2022
·
Nov 5
Message from @Unusual_Times

AY.39 is driving growth in Belgium and the Netherlands

But in Germany you have a potentially HUGE problem with the convergent evolution
of B.1.617.2 carrying the N501Y mutation - as yet unclassified in GISAID/PANGO.

RamalamaKlingelingelingDingdong
@shisha_de 2021-11-07
Die Deutschen haben sich wohl eine eigene Variante gezüchtet: B.1.617.2 mit N501Y
Mutation, die sonst nur in B1351 und P1 vorkommt. Anteil nun 6% und schnell steigend.
---------------------------------
https://twitter.com/SimonReiss3/status/1457149720514732036
---------------------------------------------

gsgs:
weekly AY.4.2 at cog_UK , weeks 76-98

AY.4.2 weeks 76-98
16, 11, 82, 132, 155,
188, 323, 389, 429, 603, 892,1395,1615,1823,2306,
2799,3178,3797,3844,4725,5377,5340, 51,
-----------------------------------
Using the surveillance case definition. sequences are identified from Germany (493),
Denmark (413), Poland (203), United States (128), Italy (117), Ireland (96), Belgium (95),
Romania (79), France (68), Spain (55), Switzerland (53), Netherlands (49), India (24),
Norway (24), Bulgaria (16), Slovakia (14), Canada (13), Czechia (11), Portugal (10),
Lithuania (10) and 21 other countries with fewer than 10 sequences.
------------------------------------------

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