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21

Download and unzip https://storage.googleapis.com/ve-public/v1.4/data_package.json.gz
Then with node.js    (on my laptop the file is too big for chrome)


Code: [Select]


var t = require('./data_package.json');

var fr_loc = {};

var c =t["geo_select_tree"].children[2].children[15].children;  // list of French locations
for (var i=0;i<c.length;i++) {
if (c[i]) {
fr_loc[c[i].location_id]=c[i].label;
for  (var j=0;j<c[i].children.length;j++) {
if (c[i].children[j]) fr_loc[c[i].children[j].location_id]=c[i].label;
}
}
}

var fr_sequences=[];
for (var i = 0;i < t.case_data.length; i++) {
if (fr_loc[t.case_data[i].location_id]) fr_sequences.push(t.case_data[i]);
}

var lab_count = {};
for (var i =0;i < fr_sequences.length; i++) {
var l = t.metadata_map.submitting_lab[fr_sequences[i].submitting_lab];
if (!lab_count[l]) lab_count[l]=0;
lab_count[l]++;
}
lab_count;


var SNP= {};
for (var n in t.metadata_map.dna_snp) {
if (t.metadata_map.dna_snp.hasOwnProperty(n)) {
SNP[t.metadata_map.dna_snp[n]]=n;
}
}

for (var i =0;i < fr_sequences.length; i++) {
var mut = [];
for (var j =0; j<fr_sequences[i].dna_snp_str.length;j++) {
mut.push(SNP[fr_sequences[i].dna_snp_str[j]]);
}
fr_sequences[i].mut = mut;
fr_sequences[i].loc = fr_loc[fr_sequences[i].location_id];
}





output : a table of 2753 sequences, the first one is

Code: [Select]
> fr_sequences[0]
{ 'Accession ID': '2d58d2cd',
  collection_date: '2020-02-26',
  submission_date: '2020-03-14',
  gender: 0,
  age_start: 36,
  age_end: 37,
  patient_status: 0,
  passage: 0,
  specimen: 5,
  lineage: 'A.2',
  clade: 'S',
  sequencing_tech: 7,
  assembly_method: 23,
  comment_type: -1,
  authors: 39,
  originating_lab: 51,
  submitting_lab: 30,
  dna_snp_str: [ 28245, 28855, 4217, 14839, 15498, 18708, 19358, 19677 ],
  gene_aa_snp_str: [ 14838, 4890, 18663, 18297, 19910, 605 ],
  protein_aa_snp_str: [ 11687, 13956, 13590, 15422, 605, 15820 ],
  location_id: 1315,
  mut:
   [ '8782|C|T',
     '9477|T|A',
     '14805|C|T',
     '25553|C|T',
     '25979|G|T',
     '28144|T|C',
     '28657|C|T',
     '28863|C|T' ]
  loc:'Grand-Est'}
22
genetics / Re: B.1.1.7 (UK) and B.1.351(SA) and P1(Manaos) and 22033 ...)
« Last post by gsgs on January 13, 2021, 10:03:51 pm »
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: [Select]

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



Code: [Select]

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

24
actual epidemic charts / measures
« Last post by gsgs on January 09, 2021, 09:43:05 pm »
(incomplete)  list of measures in Europe since October




------------------------------------------------
Oct05,
new restrictions in Paris for two weeks
bars in Paris and suburbs closed starting Oct06
Restaurants : strict health protocols.
events < 1000 no alcohol >22:00
Public student, wedding, festive gathering forbidden.
Dance halls, game rooms, gyms and swimming pools closed
fairs, shows, and parks banned.
sricter guidelines for nursing home visits
------------------------------------------------
Denmark measures since mid-Sept :
restaurants,cafes,pubs close at 22:00
and masks are required there.
no gatherings >50 ,
homeoffice when possible,
avoid bus,train at main traffic hours
cases are declining since Sep27
up again since Oct18
----------------------------------------------
Since 2020/09/21 in Austria
private Feiern, Freizeitgestaltung, Gastronomie Märkte Messen
all private groups, except funerals, except dwellings : <10 instead <50
events : <100
masks on markets, exhibitions,gastro even outdoors
closed since 01:00
cases were plateauing in Austria since Sep21, up again since Sep28

Vienna measures : https://coronavirus.wien.gv.at/site/...tliches-leben/
since Sep27 Vienna surprisingly does better than Rest-Austria
Austria, Oct19, <7 on private meetings indoors and 13 outdoors
including weddings,clubs,birthday,gym
------------------------------------------
Montreal on 2020/10/08 released a breakdown
most have occurred in restaurants, bars, gyms and hotels.
------------------------------------------
Germany on 2020/10/07 detailed list, where people are infected
https://www.rki.de/DE/Content/Infekt...ublicationFile
mostly in dwellings
restaurants,bus,train : very rare
------------Oct07--------------------------------
Brussels closes all bars,cafes,restaurants
--------------------------------------------------------
Cataluna-Canovelles,Granollers,Franqueses, Aug25-Sep24
meetings<10 public and private, religious,bars,restaurants <50%
indoors and outdoors
cultural,recr.,sports special rules, <50%
cases are plateauing since Jul20, half of Madrid, deaths 1/3 of Spain
(why did it stop going up in July ? there must be other reasons)
Jul17 , Barcelona+Lleida, nightlife , masks required
https://web.gencat.cat/en/activem/re...als/catalunya/
https://portaljuridic.gencat.cat/ca/...ts/pjur_CoV-2/
----------------edit 2020/10/12---------------------------------------------
Quebec. The "red zone" limited closure strategy (close bars, restos, gyms,
restrict private gatherings, masks indoors in high schools) has knocked
R down from 1.4 two weeks ago to 0.9 today.
many clusters in Montreal are work-related.
Tele-work can prevent it
-----------------edit Oct14------------------
Netherlands partial lockdown since Oct14: Masks in public , asked to stay home
gatherings <5, no alcohol eve; bars, restaurants, cafes only takeout.
NL, bars restaurants closed no alcohol >20:00 , <3 private guests per day,
buses trains only if really necessary. Mask-rules (so far they had none).
Oct01 : After months of debate, NL issues 'urgent advice' for masks in public spaces
cases peak on Oct29
----Nov04
Netherlands, public buildings closed no foreign travel
----Nov19,
theaters museums,cinemas,libraries may re-open
bars,pubs,restaurants,cafes stay closed
3 (instead of 2) private guests per day allowed
---------------------edit Oct15-------------------------------------------------------
Czech builds field-hospitals
---------------------------------------------
curfew from 9pm-6am in Paris,St.Etienne,Lille,Lyon,Toulouse,Rouen
Grenoble,Montpellier,Marseille effective from 00:00 Saturday. Oct17
France bans all private parties at public venues, including weddings,
https://www.themayor.eu/en/france-en...rgency-tonight
https://www.connexionfrance.com/Fren...tions-answered
Oct17 , 19M , curfew , 21-06
no restrictions on public transport
€135fine , 12000 police officers
Bars closed , restaurants until 21:00.
IdF,Rouen,Lille,St.Etienne,Lyon,Grenoble,Toulouse, Montpellier,Marseille
----edit 1102 --- seems to be working ! cases down
especially in those 15 cities, but also elsewhere
but software bug, 60000 more cases since Oct28
http://magictour.free.fr/frci58b.GIF
-------------------------------------------------------
Oct16 , Lebanon closes bars, night clubs
------------------------------------------
Ontario, Sep.26 , bars restaurants, alcohol
week before : gatherings, events
screening business
"we can still prevent a staggering second wave in our city.”
Oct.16, York-region in modified stage 2 next week
------------------------------------------
Oct 17 The UK's new three-tier lockdown strategy won't stop the spread
according to former head of the WHO Professor Anthony Costello.
cases plateauing since Oct24
------------------------------------
Oct 19, lockdown in Berchtesgaden, Bavaria

=========================================
in Czechia Schools, bars, restaurants are closed,
public gatherings <7. Masks indoors
Full lockdown in two weeks.
--------------------------------------------------------------
Oct19
in Belgium bars cafes and restaurants close for 4 weeks,
curfew from 0-5, no alcohol > 8 pm. masks recommended
schools also closed (I think)
cases (MA3m) peak on Oct27 , full lockdown on Nov02
-------------------------------------------------
no gathering in London and 7 other ciies. bars, pubs and restaurants closed > 10 pm
“circuit breaker” , shutdown in Wales Oct23 , NI closed schools
--------------------------------------------------
Spain Oct09 , Madrid and 9 others in emergency. only essential travel,
reducing hotel and restaurant capacity, curfew >11 pm, gatherings <7
Catalonia closed bars and restaurants. Oct15 for 15d
------------------------------------------------------
Ireland lockdown:Oct21, only essential businesses asked to stay home.
Ireland is moving to level 5 from midnight on Wednesday, 21 October
cases peaked Oct19, 2 days before the lockdown
-----------------------------------------------------
Austria, gatherings <7 indoors <13 outdoors, local lockdown.
-------------------------------------------------------
Italy masks local 9 pm curfews restaurants )
-----------------------------------------------------------
Germany curfews, border checks, gatherings, local lockdown.
--------------------------------------------------
Greece masks
------------------------------------
Sweden encouraged to work from home.
-----------------------------------------------
2020/10/21 Radio Prague Int. @RadioPragueFr
New health measures in #Czechia from 10/22:
closure of all "non-essential" shops except food stores, pharmacies
and drugstores
Czech health secretary expects peak around Nov11
------------------------------------------
France , 15 departments under curfew from Oct25
---------------------------------------
Quebec, Oct01,no guests at home,
cases are plateauing
----------------------------------------------------
Oct23
Slovakia and Slovenia announce partial lockdowns
------------------------------
spanish government officials fail to agree on curfew measures
as health minister says epidemic is "out of control"
------------------------------------
France , the 9 p.m. curfew will be expanded to affect 46M people
----------------------------------------------------
Ireland,since Oct21: level5,lockdown {cases are going down since Oct19}
"we already have the strongest measures in Europe, but"
shops closed
Meet indoors only with people from same household
outdoors only <5km except work,school
schools and Kitas stay open
work from home, if possible
Oct 15 , budget , government members tested
5-level-plan
https://www.msn.com/en-ie/news/coron...ic/ar-BB194dlK
Oct15, Donegal, Monaghan and Cavan goto Level 4
---------------------------------------------------
Wales, lockdown since Oct30
--------------------------------------------------------
Bulgaria Oct 21
Oct 27 no entertainment , restrictions for bars etc.
cases plateauing since Nov05
------------------------------------------------------
Croatia, Oct 26
close events, gatherings<50,30,15 ; no alcohol>00:00, masks
https://www.thedubrovniktimes.com/ne...across-croatia
cases plateauing since Oct29 ... up again since Nov18
------------------------------------------------------
Northern Ireland {cases stable since Oct07}
lockdown on Oct.16, schools closed since Oct19
-------------------------------------
Germany since Nov02 :
only members from 2 household and max 10 people may meet in public
recreational and sports events cancelled
Bars,restaurants,clubs,discos,pubs, non-essential services closed. Take-away services allowed
Canteens stay open.
Financial support of $12B for companies that are affected
No Tourists
Asked to avoid private traveling
schools and shops stay open, only 1 customer per 10 squaremeters
Asked to work from home if possible
Churches stay open, but some measures are required
no curfew afaics
Bavaria orders contact reduction also for private rooms
(how to control ?)
Nov26:extended until Dec20 , plus private meetings<6,<3households
---------------------------------------------------
Oct29 , Macron announces nationwide lockdown, schools and work will continue
stay at home, except school, work, essential travel
Travel between regions prohibited
until 5000 cases/d
-------------------------------------------------
Oct31 ,
Belgium lockdown:
- All non-essential stores and some other businesses will close
- Bars and restaurants remain closed
- Working from home is mandatory, where possible
- People are still allowed to leave their home, but no visitors at home
- Measures will last at least 6 weeks
peak at Oct26, 5 daysl before the lockdown
----------------------------
Nov01 , UK nationwide lockdown
--------------------------------------
Oct29
measures in Switzerland
<11 friends+family
<50 events
<16 gatherings,sports
distance learning mandatory at > highschool
bars+ : <5 per table , sit for eat/drink
keep records , closed at 2300
nightclubs closed
masks in school , working indoors, bars+,shops,busy zones
Cantonal measures
no curfew, no travel restrictions, increased testing
cases down since ca. Nov05
-----------------------------------------
Oct15
Austria has ordered a full, three-week lockdown
shops (except food,drugs) and schools closed,
leave the home only for a good reason
---------------------------------------------
Nov11 , Sweden imposes partial lockdown on bars and restaurants ...
Nov20 , no alcohole in pubs after 22PM, closure 1/2hour earlier
------------------------------
Nov19 , Catalonia plans to open bars and restaurants at 30%
until five in the afternoon from Monday
The Government wants to carry out a de-escalation in four phases
that will have, at least, a duration of 15 days each
----------------------------------------------
Nov30 , Turkey announces weekend lockdown and 9 p.m. curfew on weekdays
Dec08,Bavaria, curfew in Hotspots , pupils change-lessons
Dec07 , Austria , reductions
Dec07 , Denmark is planning a partial lockdown in cities
Dec08 , Geneve opens restaurans
Dec08 , , Sachsen (SN) closes schools, most commerce
Dec08 , Bavaria in some days curfew21h , Thuringia maybe
Dec16 , hard lockdown in Germany and Netherlands
Dec15 , Italy increases measures (chart is down, looks good)
Dec17 , Germany-Saxony curfew in hotspots planned
Dec17, Denmark orders lockdown
Dec27,Czech lockdown #3

25
genetics / Re: spike-mutations
« Last post by gsgs on January 09, 2021, 09:46:50 am »
mutation table of the 27   C22033T viruses :

Code: [Select]

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


26
genetics / Re: spike-mutations
« Last post by gsgs on January 09, 2021, 12:39:11 am »

>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

27
genetics / Re: spike-mutations
« Last post by gsgs on January 08, 2021, 11:11:49 am »
Code: [Select]
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



Code: [Select]
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]
28
genetics / Re: B.1.1.7 and B.1.351 (and ...)
« Last post by gsgs on January 08, 2021, 11:09:31 am »
Code: [Select]
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

29
genetics / Re: B.1.1.7 and B.1.351 (and ...)
« Last post by gsgs on January 06, 2021, 01:26:47 am »
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.
----------------------------------------------
30
genetics / B.1.1.7 (UK) and B.1.351(SA) and P1(Brazil) and B.1.617(India) and ...
« Last post by gsgs on January 05, 2021, 12:52:36 am »
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
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2021/02/01  Cologne reports 9% B.1.1.7 and 5% B.1.351


Code: [Select]
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 ,

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