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61
genetics / Re: Coronaviruses
« Last post by gsgs on December 27, 2020, 12:52:33 am »

human non-sars-like Coronaviruses at genbank , release 239.0 :

   1394, Human coronavirus OC43
    907, Human coronavirus NL63
    424, Human coronavirus 229E
    415, Human coronavirus HKU1
    195, unidentified human coronavirus
      6, Human enteric coronavirus 4408
      4, Human coronavirus Feline-like Hu142
      2, Human betacoronavirus 2c Jordan-N3/2012
      2, Human betacoronavirus 2c EMC/2012
      1, Human group 1 coronavirus associated with pneumonia
      1, Human enteric coronavirus strain 4408
      1, Human coronavirus type 5
      1, Human coronavirus NO/2708/04
      1, Human coronavirus NO/1917/04
      1, Human coronavirus NO/1055/04
      1, Human coronavirus NO/0867/04
      1, Human coronavirus NO/0848/04
      1, Human coronavirus NO/0835/04
      1, Human coronavirus NO/0749/04
      1, Human coronavirus NO/0733/05
      1, Human coronavirus NO/0643/05
      1, Human coronavirus NO/0398/05
      1, Human coronavirus NO/0341/04
      1, Human coronavirus NO/0193/05
      1, Human coronavirus NO/0053/04
      1, Human coronavirus NO/0023/05
      1, Human coronavirus NO/0003/05
      1, Human coronavirus 3363/2000/NL
      1, Human coronavirus 1196/2001/NL
      1, Human betacoronavirus 2c England-Qatar/2012


62
genetics / spike-mutations
« Last post by gsgs on December 22, 2020, 12:42:56 pm »
Code: [Select]

  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)

Code: [Select]

    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


Code: [Select]

    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

63
nCoV - discussion / Re: B.1.1.7 = vui-202012/1
« Last post by gsgs on December 19, 2020, 04:41:18 am »
Boris Johnson calls crisis meeting over new Covid strain on Friday night  (Dec18)

rumors say it is 50% more transmissable

and now we also have a report from South Africa about a more transmissable strain,
also containing N501Y

64
nCoV - discussion / Re: updates
« Last post by gsgs on December 19, 2020, 04:37:16 am »
=======================================
2020/11/11,Wed
GER,16579,08%+0.4,13365+387,3064+57,201
GER,18487,261 = 138.1
BEL,04293,19.8%-2.5,7058-159,1470-4,345
USA,130989,10.6%+2.6,61964+2690,11952+419,1347
========================================
2020/11/12,Thu
USA,144270,10.4%-0.2,65368+3404,12518+566,1562
GER,21886,8.2%+0.2,13496+131,3150+86,221
===============================
2020/11/13,Fri
Code: [Select]
per million population : cases,hosp.,ICU,deaths
USA,+454,10.1%-0.3,202+5.21,39+0.84,+3.33
GER,+281,08.3%+0.1,170+7.12,39+0.69,+2.36
FRA,+510,18.7%-0.8,511+11.3,75+1.48,+6.54
UK-,+492,08.9%+1.4,216+10.5,19+0.72,+8.28
ITA,+633,28.8%+2.4,498+7.15,53+1.48,+10.6
========================================
2020/11/14
Code: [Select]
ITA--,+0682,28.2%-0.3,515+17.4,54+1.0,+09.1
US-IL,+1195,14.5%+1.9,416+08.1,77+2.6,+02.1
USA--,+0512,10.1%+0.0,206+04.3,39+1.0,+03.9
US-TX,+0390,--.-%+-.-,262+05.9,73+4.0,+06.4
FRA--,+0366,17.7%-1.0,503+00.4,75+0.1,+14.5


New Mexico to be put on lockdown
La baisse des cas à Paris est vraiment impressionnante
Effet des vacances ? Immunité Collective des lycéens et étudiants ?
Age differential analysis of COVID-19 second wave in Europe reveals
highest incidence among young adults
======================================
2020/11/15,Sun
Code: [Select]
USA,+0491,09.9%-0.2,209+2.82,40+0.6,04.0  Sunday
======================================
2020/11/16,Mon
USA,145670,09.9%+0.0,69987+532,13697+356,+672
FRA,+27228,16.9%-0.4,33081+582,4896+25,302


Michigan partial lockdown Nov18-Dec09
Boris Johnson told to self-isolate
===========================================
2020/11/17,Tue
FRA,09406,16.4%-0.5,33497+416,4919+23,508
USA,148532,10.0%+0.1,73014+3027,14313+616,581
8M to be tested in Catalunya , 2M? in Auvergne Rhone-Alpes,
0.5M in Liverpool, 6M in Slovakia
========================================
2020/11/18,Wed

USA,+155835,10.4%+0.4,76830+3816,14851+538,+1566
-TX,+10826,--.-%,+-.-,7841+373,2127+84,+117
FRA,45522,16.2%-0.2,33170-327,4854-65,+1228   incl. 32935 antigen since Oct
GER,+15971,09.3%,15649+852,3521+86,348

Latest positive rates in Asia:
Iran:28.9%Indonesia:14.8%Bangladesh:12.2%Japan:7.4%
Pakistan:6.2%Philippines:5.9%India:4.1%Turkey:2%


Tokyo, highest alert-level , South-Australia : lockdown
===========================================
2020/11/19,Thu
USA,+163975,10.6%+0.2,79410+2580,15350+499,+1869
-TX,+8489,11.5%+0.5,7958+117,2127,---,+187
FRA,+28383 (-b4219),16.2%+0.0,32842-328,4775-79,+427
POL,+19883,34.9%-10.7,22812-221,2117+3,+603
POL,+23975,41.3%+6.4,22536-276,2080-37,+637

NYC closes schools
Countries with the most daily new confirmed COVID-19 deaths per million:
Bosnia:16.9 Belgium:15.8 Czechia:15.6 Bulgaria:13 Macedonia:12.7
Slovenia:11.1 Hungary:10.2 Switzerland:10.1 Italy:10.1 Poland: 10
========================================
2020/11/20,Fri
USA,+182832,10.1%-0.5,80698+1288,15573+223,+1971
-TX,+12293,12.1%+0.6,7982+24,2154+17,+230
GER,+23504,9.3%+0.0,16115+27,3601+40,+285
FRA,+21150,15.5%-0.7,32345-497,4653-122,+436

masstesting in South-Tirol
107300 sequences from UK are available now at
https://www.cogconsortium.uk/data/

=======================================
2020/11/21,Sat
ITA,37242,--.-%+-.-,33957+347,3748+36,699
USA,+192805,10.1%-0.0,82178+1480,15915+342,+1862
FRA,+22882,15.0%-0.5,31906-439,4582-71,1138
lockdown in Toronto
============================================
2020/11/22,Sun
USA,+178309,09.0%-1.1,83227+1049,16054+139,+1506
-TX,+12597,11.8%-0.2,8245+81,2195-19,+171
FRA,+17881,14.8%,-0.2,31365-541,4493-89,+276 [h??]
==============================================
2020/11/23,Mon
USA,150098,8.7%-0.3,83870+643,16219+165,889
FRA,13157,906,190h

 
Los Angeles County bans all in-person dining at restaurants
================================================
2020/11/24,Tue
USA,+157252,8.7%-0.0,85836+1966,16811+592,+992
UK-,150975,8.6%-0.1,85836+1966,16811+592,956
FRA,+4452,13.3%-0.7,31449-73,4438-53,+501
============================================
2020/11/25,Wed
USA,+166672,9.3%+0.6,88080+2244,17127+316,+2028
FRA,+9155,13.1%-0.2,30594-855,4277-161,+1009

strong Sweden measures in effect
France reduced measures on Nov28
UK allows 3 households mixing at Xmas
=====================================
2020/11/26,Thu
Code: [Select]
USA,+553,10.7%+1.4,271+5.6,53+1.2,+06.9
-TX,+505,10.5%-0.1,296+3.1,81+0.9,+06.9
-NY,+313,03.6%+0.6,149+6.3,30+1.8,+02.1
GER,+248,09.5%+0.1,209+2.4,45+0.2,+04.9
FRA,+250,13.0%-0.1,461-9.9,64-2.5,+08.8
ITA,+431,11.1%+-.-,572-4.4,64+0.5,+12.0
UK-,+268,--.-%+-.-,240-0.6,22-0.1,+10.2
POL,+404,31.7%+1.6,582-7.5,55-0.6,+17.7
===================================
2020/11/27,Fri


CDC expects 20M vaccinations in Dec, then 25M each month
curfew in Passau
===================================
2020/11/28,Sat
Code: [Select]
USA,+610,09.1%-1.8,272+2.0,54+0.1,+04.2
ITA,+473,--.-%+-.-,561-5.9,63-1.0,+13.8
Argentina ends coronavirus lockdown nationwide, except for two small cities
: Los Angeles County issues 'Safer at Home' order, urging residents to
stay home as much as possible and banning most gatherings
Risk of infection was unchanged but symptom severity seems significantly
reduced in those with recent documented HCoV infection.
Italy loosens COVID restrictions in Lombardy and 4 other regions
=======================================
2020/11/29,Sun

Code: [Select]
Nov23,USA,+455,08.7%-0.3,254+1.9,49+0.5,+02.7
Nov24,USA,+477,08.7%-0.0,260+6.0,51+1.8,+03.0
Nov25,USA,+505,09.3%+0.6,267+6.8,52+1.0,+06.1
Nov26,USA,+553,10.7%+1.4,271+5.6,53+1.2,+06.9
Nov28,USA,+610,09.1%-1.8,272+2.0,54+0.1,+04.2
Nov29,USA,+445,09.0%-0.1,278+5.5,55+0.6,+03.6
Nov30,USA,+398,10.3%+1.3,283+4.9,55+0.5,+02.4
Dec01,USA,+446,09.2%-1.1,291+8.5,56+1.0,+03.4
Dec02,USA,+536,12.5%+3.3,299+8.0,58+1.5,+07.5
Dec03,USA,+593,13.5%+1.0,304+4.7,59+1.2,+08.3
Dec04,USA,+637,11.6%-1.9,305+1.3,59+0.2,+08.2
Dec05,USA,+681,12.4%+0.8,307+1.8,60+1.3,+07.7
Dec06,USA,+640,10.7%-1.7,307-0.3,60+0.3,+07.4
Dec07,USA,+536,10.8%+0.1,308+0.9,61+0.6,+03.4
Dec08,USA,+546,09.8%-1.0,310+2.0,61-0.1,+04.1
Dec09,USA,+647,13.0%+3.2,317+7.4,62+1.2,+07.9
Dec10,USA,+636,11.8%-1.2,323+6.3,63+1.3,+09.3
Dec11,USA,+649,11.1%-0.7,325+1.7,64+0.3,+09.3
Dec13,USA,+677,11.7%+0.6,329+1.3,64+0.5,+07.5
Dec14,USA,+566,10.7%-1.0,331+8.1.64+0.1,+04.5
Dec15,USA,+586,09.0%-1.7,335+3.7,65,+0.7,+04.1
Dec16,USA,+575,10.9%+1.9,342+6.9,66+1.3,+08.8
Dec17.USA,+699,13.1%+2.2,343+0.82,66+1.1,+10.3
Dec18,USA,+732,12.9%-0.2,346+3.5,66-0.1,+10.4

89,106,114

Dec02,GER,+187,09.4%+0.1,220+4.5,47-0.1,+6.0
Dec09,GER,+220,10.3%+1.0,242+10.7,51,0.9,+7.5
====================================
2020/11/30,Mon
Scots mass testing in universities and poor communities
 Spain bans travel between regions from December 23 until January 6;
holiday gatherings limited to 10 people


Code: [Select]
Oct20,FRA,+313,13.6%+-.-,191+12.5,33+1.3,+04.0
Oct27,FRA,+410,17.8%+-.-,272+20.4,42+3.0,+04.0
Oct20,UK-,+314,08.2%+-.-,102+07.5,10+0.4,+03.5
Oct27,UK-,+308,06.5%+-.-,137+03.4,12+0.3,+01.5
Oct20,ITA,+180,12.4%+-.-,140+12.9,14+1.2,+01.5
Oct27,ITA,+282,21.6%+-.-,215+16.4,21+1.3,+02.3
BEL,
Oct20,CZE,+755,29.6%+-.-,348+18.9,55+0.2,+08.5
Oct27,CZE,+960,34.4%+-.-,525+25.0,77+2.6,+15.3
Oct20,GER,+084,--.-%+-.-,050+04.0,10+0.3,+00.7
Oct27,GER,+136,06.4%+-.-,077+08.9,16+0.9,+00.5
Nov03,GER,+190,08.1%+-.-,---+10.3,27+2.4,+01.3
Dec02,GER,+187,09.4%+0.1,220+04.5,47-0.1,+06.0
Dec11,Ger,+337,10.3%+0.0,253+05.3,52+0.7,+06.3
Dec16,Ger,+252,11.6%+1.3,282,+09.0,56+0.6,+09.6
Dec17,Ger,+343,11.6%+0.0,296+13.8,58+1.2,+09.1
Dec18,GER,+368,11.6%+0.0,299,+03.5,58+0.3,+08.8



Oct28,USA,+222,06.9%,134,27,+02.8
Nov04,USA,+262,07.7%,153,31,+03.3
Nov10,USA,+359,08.0%,180,35,+01.8
Nov17,USA,+450,10.0%,221,43,+01.8
Nov24,USA,+477,08.7%,260,51,+03.0
Dec01,USA,+446,09.2%,291,56,+03.4
Dec08,USA,+546,09.8%,310,61,+04.1
Dec15,USA,+586,09.0%,335,65,+04.1

cases,positive-rate,hospital,ICU,deaths
per million population
Dec03 : Czech reduces measures

Dec03, IdF=21.3%,Grand Est=15.2%,AuvergneRhoneAlpes=14.3%
US Life Expectancy at Birth down >1 year
ICU capacity falls below 15% in S-CA , meeting threshold for SHO
900 staff positive at Mayo clinic,Rochester,MN
exposure mostly happened in rest rooms and lunchrooms
76% infected in Manaos,Brazil
UK advises against Pfizer/BioNTech vaccine because of allergical reactions
Dec11, Mueller expects hard lockdown in Germany on Dec20
US-MA:12.5% infected , 0.16% dead
Dec13: hard lockdown in Germany on Dec16
Macron tests positive
weekly 418 EU : http://magictour.free.fr/euw50.GIF
51-US-States : http://magictour.free.fr/rt1215.GIF
euromomo week 50 : http://magictour.free.fr/eumo50.GIF
last ECDC-205 daily from Dec.14 : http://magictour.free.fr/e-1214.GIF
now weekly, maybe I switch to daily 185-OWID
Pfizer vax efficacy was 52% after 1st dose and 95% after 2nd
22% with antibodies in Geneva

501.V2 Variant in South Africa
65
nCoV - discussion / Re: updates
« Last post by gsgs on December 19, 2020, 04:36:06 am »
http://magictour.free.fr/e-1007.GIF


2020/06/29
China,12+4+6,7Beijing ; Korea,41 ; Germany,262,4,R=0.71,0.71 ;
India,39 ; Brazil,30 ; Mexico,19 ; TX,37 ; AZ,55 ; FL,64 ; Pakistan,21 ; Russia,11
ALB,31;AZE,35;BGR,25;BUH,--;CRO,26;ROM,11;UKR,28; POL,06;ISR,27;GRC,05;SLN,07
MDA,19;ARM,31;MKD,30;HUN,01;CYP,--;TUR,07;SRB,18; K OS,38;CZE,#306 !! ;SLK,#14
Czech,#40,47,51,118,126,42,50,63,89,127,93,168,260,305
Slovakia,#1,3,3,4,0,9,0,14,11,0,0,0,18,23,13,14
picture : http://magictour.free.fr/cz-0628.GIF
no 2nd wave, they say. Miners tested.
post-peak in Florida ? http://magictour.free.fr/us-fl.GIF
=================================================
2====================
2020/10/15,Thu
GER,6638,128,33; SPA,11970,991,189; FRA,22591,1116,95,ITA,7332,43; UK,19724,680,137
ISR,1848,43,ARG,DNK,492,1; CZE,9543,66;NLD,7287,32;ROM,4016,66;BEL,8271,34
Wien,8.7,Aragon,13.2,Spain,11.8,Madrid,14.9
Dow=28240,Biden=65.5,US-CDS=16.1
Czech builds emergency field hospitals
===========================================
2020/10/16,Fri
GER,7334,136,24;SPA,13318,1052,140;FRA,30621,-,88;ITA,8803,83;UK,18978,792,138
ISR,1002,11;DNK,490,2;CZE,9720,58;NLD,7791,29;BEL,10448,49;ROM,4013,73
Dow=28494,Biden=65.1,gold=1913,US-CDS=16.0,USA national debt=$24T
Wien,4.9%,Aragon,17.1,Madrid,15.0,Spain,12.5
Argentina,pop=45.3M , @BNODesk , 2h ago (02:30 UTC)
cases=949063(+17096),hosp.=28987(+180),
ICU=4278(+38),deaths=25342(+421),pr=61.8%;
Belgium,pop=11.6M,10448,1949+172,327+14,49,pr=12.7
NLD,pop=19.2M,7997,1553+27,345+32,18
Health workers in France go on strike
===============================================
2020/10/17,Sat
GER,7830,111,33;SPA,15186,838,222;FRA,25086,1202,178;ITA,10009,55;UK,15635,844,136
ISR,2394,32 lockdown continued;ARG,16546,60.4%,368,68,381
CZE,11105,pr=29%,3120+200,551+8,1283+53
DNK,418,0;BEL,10448,49;NLD,7984,16;ROM,4026,75
Dow=28606,Biden=63.5,gold=1906,US-CDS=16.2
Wien,14.7,Aragon,20.1,Spa,11.7,Mad,14.7,Cat,15.6
the 2nd wave peaked in fall already in [DNK,MDA,EST,MNE ? , fill in]
Manaos,66% infected, 0.2% died
==================================================
2020/10/18,Sun
GER,5587,141,10;FRA,32427,964,89;ITA,10925,47;UK,16171,987,150
ISR,874,49;ARG,BEL,10192,32;NLD,8141,28;CZE,14152,80;
ROM,3952,63;CHE,POL,9622,84;
Wien,16.3,Aragon,17.0
Dow=28419,Biden=62.3,gold=1903,US-CDS=16.2
=================================================
2020/10/19,Mon
GER,4915,105,17;FRA,29837,13.2%,10897+498,1939+71,+85; ITA,11705,69;UK,16981,924,67
ISR,379,42;BEL,10964,33;NLD,8155,15;CZE,7065,64;ROM,3920,60;POL,8536,49
Wien,10.4,Aragon,18.0
ARG,10561,76%,29436+124,4387+1,+161
CZE,+5059,30.2%,3519+104,587-9,+70  {3104,39 last Mon}
DOW=28419,Biden=60.8,gold=1926,US-CDS=16.2
=================================================
2020/10/20,Thu
GER,6868,66,47;SPA,37889,1699,217; FRA,13243,1417, 146,ITA,9337,73; UK,18803,988,80
ISR,1767,54;ARG,12982,449; BEL,8227,30;NLD,CZE,8077,29.6%,3721+202,91; ROM,2466,59; POL,7482,41
Wien,Aragon,19.1,Madrid,15.1,Spain,12.3 ; no peak in Spain,France or elsewhere yet
Dow,28195,Biden,59.9,gold,1906,US-CDS=16.2,ITA-CDS=124.7,VIX=30

peak in Ile de France ?  https://raw.githubusercontent.com/rozierguillaume/covid-19/master/images/charts/france/departements_dashboards/dashboard_jour_Ile-de-France.jpeg

=================================================
2020/10/21,Wed
GER,-,117,-;SPA,13873,1222,218;FRA,20468,1924,262; ITA,10874,89; UK,21330,860,241
ISR,2239,59,ARG,16347,384;CZE,10799,99;BEL,-,-;NLD,8165,46;ROM,3400,65;POL,9291,107
Wien,6.7,Aragon,17.8,Spain,13.0,Madrid,17.4,Cata,11.5
Dow=28309,Biden=61.8,gold=1913,US-CDS=16.1,ITA-CDS=127.5,VIX=29
NZ has 25 new Covid-19 cases today
ARG,+16337,43.6%,29867(+253),4451(+59),+384
CZE,+11984,26.3%,4064+343,634+45,+106
GER,+7032,4163+337,880+25,+56
POL,+10040,16.9%,9439+477,757+25,+130

=============================================
2020/10/22,Thu
Italy,+15199,14.3%,9057+603,926+56,+127
GER,10463,55;SPA,16973,156;FRA,26676,1754,164;ITA,15199,127;UK,26688,193
CZ,14969,120;ARG,BEL,9679,46;
Dow=28211,Biden=63.4,gold=1928,CDS=16.1,125.5,VIX=29
ARG,+18326,47.8%,30067+,4573+122,+423
Wien,9.2,Aragon,17.1;Cataluna,13.2
================================================
2020/10/23/Fri
GER,SPA,20986,185;FRA,41622,152;ITA,16078,136;UK,21238,189
CZ,14150,106;BEL,13227,50;ARG,15928,344;ROM,4902,98
NLD,9271,46;CH,5256,11
DOW=28364,Biden=66.3,gold=1908,CDS=16.7,125.4
Wien,08.1,Aragon,20.9
=============================================
2020/10/24,Sat
GER,14714,46;SPA,19851,231;FRA,42032,298;ITA,19143,91;UK,,20530,224
CZE,15258,126;BEL,16746,49;NLD,9996,45;ROM,5028,82;POL,13632,153
CH,6634,15;ISR,593,10;ARG,15718,381,US,79219,894;CDN=2584,26
DOW=28336,Biden=65.4,gold=1903,CDS=16.1,125.1
BEL,+17568,18.8%,4061+412,632+59,+70
CZE+15252,30.8%,5044+267,751+16,+126
ARG,+15718,44.0%,30405+158,4696+85,+382
Czech health secretary Prymula forced to withdraw for being photographed
 leaving a restaurant without mask
=============================================
2020/10/25,Sun
FRA,+45422,16.0%,15637+629,2491+50,+138
BEL,+17709,20.0%,4401+340,708+76,+079
CZE,+12472,34.5%,5314+270,772+21,+106
USA-IL,+6169,7.4%,2616+118,560+49,+063

CZE,Sun/Sat : 0.63,1.06,0.97,0.67,0.67,0.54,0.78,0.82
Biden,65.8,CDS,16.0,122.0,DOW,28336,gold,1903
Spain declares national health emergency
==========================================
2020/10/26,Mon
China,137Xinjiang
FRA,52010;CZE,4576;
USA,+65413,5.9%,41753-129,8488-71,+337
FRA,+52010,17.0%,16454+817,2575+84,+116
CZE,+7301,34.4%,5345+31,800+28,+124
BEL,+15622,20.5%,4827+426,757+49,+73
 Macron predicts 9 more months of COVID-19 agony
# that would be an estimated 20M cases and 200000 deaths in France
# in 9 months without lockdown
1st phase of mass-testing in Slovakia finished
6000 new positives , (usually 2500 positives/d)
 antigen - quicktest , 3 weekends , 5 million people
El Paso, Texas, issues stay-at-home order
Dow=28056,Biden=66.2,gold=1900,CDS=,VIX=29
Dow=27641
--------------------------------------------------------
2020/10/27,Tue,

Code: [Select]
Oct27,FRA,+26771,17.8%,17784+1330,2770+195,258
Oct20,FRA,+20468,13.6%,12458+0818,2177+087,262
Oct27,UK-,+20890,06.5%,09296+0229,0823+019,102
Oct20,UK-,+21331,08.2%,06899+0506,0654+030,241
Oct27,ITA,+17012,21.6%,12997+0991,1284+076,141
Oct20,ITA,+10874,12.4%,08454+0778,0870+073,089
BEL,
Oct27,CZE,+10273,34.4%,05613+0268,0828+028,164
Oct20,CZE,+08076,29.6%,03721+0202,0589+002,+091
Oct27,GER,+11409,06.4%,06481+0748,1371+075,044
Oct20,GER,+07032,--.-%,04163+0337,0880,+025,056
Oct28,USA,+73096,06.9%,44212+1295,8909+067,931

Wien,Spain,13.1,Madrid,11.1,Catalunya,13.3%,Aragon,21.9%
   going down in Madrid ?
deaths continue to go up in CZE {FRA} to 14/M/d {4/M/d}
will it go to >50/M/d as in wave1 without measures ?
Dow=27685,Biden=64.6,gold=1905,VIX=31
Oct27,Moderna=71,Novavax=87,Inovio=11,BioNTech=70
Mar12,Novavax=9.59,Moderna=22.51,Inovio=9.83,BioNTech=29
BioNTech-7% yesterday (there had been speculation about
a German vaccine by end 2020 recently)
---------------------------------------------------------
2020/10/28,Wed
Code: [Select]
USA,73096,06.9%,44212+1295,8909+067,931
GER,13071,06.9%,07060+579,1476+105,82
FRA,33417,18.4%,18978+1194,2918+148,527
SPA,18418,13.8%,16696+688,2292+129,267
ITA,21994,20.7%,13955+958,1411+127,221
UK-,22885,08.7%,09502+206,0852+029,367
BEL,13571,26.4%,05554+294,0911+102,139
CZE,15663,29.4%,06191+578,0893+065,182
TX-,07055,08.1%,05512+234,1601+56,81

Dow=27220,Biden=63.9,gold=1909,CDS=16.0,118.1,VIX=32
jg:60% of Madrid infected  https://twitter.com/ChGefaell/status/1321204081227083777
France considers 30d lockdown, BFM TV {most watched, 10M daily}
intense lobbying from advisers for a new lockdown in UK
Germany,meeting today,"lockdown light" suggested
(not a lockdown,IMO, others had stricter measures without success)
-------------------------------------------------------------
2020/10/29,Thu
Code: [Select]
USA,78661,07.4%,45045+0833,9034+125,1025
GER,16282,06.5%,07684+0624,1577+101,097
FRA,36437,18.6%,20207+1229,3045+127,244
SPA,19765,13.5%,17073+0377,2368+076,168
ITA,24991,20.5%,14981+1026,1536+125,205
UK-,24701,08.8%,10316+0814,0902+050,310
BEL,21048,27.6%,05924+0370,0993+082,132
CZE,12980,--.-%,-----+----,----+---,128


nationwide semi-lockdown in Germany and France
Macron says up to 400000 people will die {in France} if no action is taken,
Dow=26520,Dax=11513,Biden=64.0,gold=1878,VIX=35,CDS=16,119,crude-oil=37.5
Italien plant neue Beschränkungen
BioNTech Aktie: Ganz wichtige News stehen an!

------------------------------------------------------
2020/10/30,Fri
Code: [Select]
USA,88452,06.7%,46095+1050,9208+174,1049
GER,18526,07.0%,08121+437,1700+123,077 ; 464300 in Quarantine
FRA,47637,19.4%,21183+976,3156+111,235h ; lockdown
SPA,23580,13.3%,17520+447,2404+36,173
ITA,26831,22.6%,15964,+983,1651+115,217
UK-,23065,07.5%,10699+383,957+55,280
BEL,23921,31.1%,06187+263,1057+64,138
CZE,13051,34.4%,06604-020,1031+069,187
IL,6363,07.7%,3030+169,643+43,56

Dow=26126,Dax=11402,Biden=63.5,gold=1869,oil-WTI=36.3,VIX=36,CDS=15.8,127.7
BioNTech,+9%;

shutdown in El Paso (against State-order)
---------------------------------------------------
2020/10/31,Sat
Code: [Select]
USA,97080,07.1%,46688+593,9437+229,933
GER,19059,07.4%,8707+586,1858+158,103
FRA,49215,20%,22153+0970,3368+212,545 (256h
SPA,25595,12.8%,18162+0642,2482+078,239
ITA,31084,24.0%,16994+1030,1746+095,199
UK-,24405,274
BEL,20056,32.1%,06438+0251,1105+048,144
CZE,13605,33.5%,07281+0677,1068+037,216

Boris Johnson considering nationwide lockdown
Slovakia test all people>10 this weekend
lockdown Barcelona,Belgium,

Dow=26500,Dax=11620,Biden=64.0,gold=1879,oil-WTI=35.7,VIX=34,CDS=16.0,124.7
Wien,weekly pr : 5.71%,5.92%,7.85%,7.62%,9.99%
last days : 7.5%,8.5%,11.2%,14.2%,14.2%
-----------------------------------------------------------
2020/11/01,Sun
Code: [Select]
USA,90058,06.6%,47374+686,9495+58,960
GER,14177,29
FRA,35641,20.2%,23036+883,3453+85,224h
UK-,21915,06.3%,11108+183,978+03,326
ITA,31758,24.0%,17966+972,1843+97,297
BEL,16915,30.7%,6497+59,1160+55,173
CZE,11429,173
Wien,16.7%,

DOW=26522,DAX=11622,Biden=64.9,gold=1880,CDS=15.8,124,VIX=34
England lockdown,shops closed,
Austria lockdown (curfew 20-06,recreation.closed)
Portugal partial lockdown from Nov04 on
-------------------------------------------------------------------
2020/11/02,Mon
GER,12097,49
FRA,46290,20.4,24031+995,3578+125,231
UK-,23254,162
ITA,29907,208
BEL,16915,173
CZE,3905,97

Dow=26451,Dax=11609,Biden=64.4;gold=1882,VIX=34,oil=34.5,CDS=15.8,124

half of Slovakia population tested in one day
decline in French cities
---------------------------------------------------
2020/11/03,Tue
USA,76031,447
FRA,52518,20.6%,17683,2678,418
GER,15945,08.1%,+869,2265+204,110
UK-,18950,136
ITA,22253,233
SPA,50019,379, weekend , 18340,127
BEL,11789,112
CZE,04055,174
CHE,21926,078 , pop=8.7M

Biden=63.8,DOW=27020,DAX=11900,gold=1893,oil=36.9,VIX=33,CDS=15.8,124

 mass testing in Liverpool , 18:00,Biden=60.4,Dow=27544
----------------------------------------------------------------
2020/11/04,Wed
USA,86507,07.7%,50340+1870,10105+247,1079
GER,16498,08.4%,10979+972,2397+132,152, 546400 quarantined
FRA,36330,20.6%,26265+1122,3878+148,858
SPA,18669,13.9%,19943+773,2754+104,238
ITA,28244,25.7%,21114+1274,2225+203,353
CZE,6803,205
BEL,5186,26.9%,7485+254,1371+49,268
CHE,6126,67
NLD,7743,113

Biden=30,Dow=27237,DAX=11952,Euro=1.165,gold=1894,VIX=31.6
--============================================
2020/11/05,Thu
USA,103087,08.5%+0.8,52049+1709,10445+340,1116
GER,20087,07.5%,11865+886,2575+178,145
UK-,25177,09.5%,12944+97,1142-2,492
FRA,40558,??,?%,27,534+1269,4089+211,394  incomplete
SPA,25042,11.9%,20325+382,2786+32,297 (+1326 backlog)
ITA,30550,24.0%,22116+1002,2292+67,352
UK-,25177,09.5%,12944+97,1142-02,492
BEL,5955,268
CZE,15731,220

----------------------------------------------
DOW=27655,DAX=12251,gold=1906,oil=39.0,VIX=29, Biden=76%,CDS=15.8,121
Biden=86% at 00:00UTC,90% at 05:00,85% at 07:00
Greece preparing nationwide lockdown, l
Lithuania partial lockdown
Italy curfew 22-05
===========================================
2020/11/06,Fri
USA,116255,07.6%,53322+1273,10583+138,1124
FRA,58046,??,?,28426+892,4230+141,367 incomplete
ITA,34505,25.6%+1.6,23256+1140,2391,+99,428
POL,27143,40.4%,19114+460,1615-10,367
POL,27086,32.7%,19479+365,1703+88,445
SPA,17908,368
CZE,13231,107
BEL,11128,209

Dow=28300,Dax=12515,Biden=92,gold=1946,VIX=28,oil=38.6,CDS=15.7,120

Denmark puts 7 municipalities on lockdown amid concern over
coronavirus mutation found in at least 12 people
15% of COVID-deaths related to air-pollution
rumors that Putin will quit, has Parkinson
==========================================
2020/11/07,Sat
FRA,60486,??.?,28979+553,4331+101,835=405h
USA,125552,08.2%,54824,+1502,11085+502,1186
ITA,37809,28.1%+2.5,24005+749,2515+124,446
BEL,11128,189 ; per week:14937,12440 daily cases ; 097,173 daily deaths
CZ,05846,154 ; per week : 10411,10588 daily cases , 143,201 daily deaths
=========================================
2020/11/08,Sun
USA,128396,09.5%+1.3,55817+993,11078-7,1097
FRA,86852,20.6% -,29421+442,4421,+90,306
ITA,39811,28.9%+0.8,25109+1104,2634+119,425
POL,27875,41.7%+9,20249+770,1813+110,349
[@BNODesk gives these numbers, but regularly, I don't know the source]

Code: [Select]
CZE,10716,411220+13429,4681+197
BEL,11607,488044+8703,12708+188
HUN,9652,104943+5318,2357+107
BIH,3273,61212+1785,1498+41
ARM,2965,104249+2476,1533+27
SVN,2079,44270+1612,531+34,
MKD,2083,38782+1283,1110+14
MNE,628,22379+300,333+5
ARG,45342,1236851+8037,33348+212
country,population,cases,death

night curfew in Portugal in 121/308 communes including Lisboa
Spain now gives cases since Jan01
========================================
2020/11/09,Mon
FRA,38619,20.3%-0.3,30243+822,4539+118,271
ITA,32616,27.4%-1.5,26440+1331,2749+115,331
=========================================
2020/11/10,Tue
USA,118497,08%-0.8,59274+2481,11533+419,580
FRA,20155,19.8%-0.5,31125+882,4690+151,551
SPA,52386,13.5%+0.2,21029+790,3007+144,512
ITA,25271,28.5%+1.1,27636+1196,2849+100,356
POL,21713,50%+9.4,20967+753,1804-37,173
BELw,10223,204 [17689,127][13185,49]
CZEw,10791,228 [11935,175][12030,111]
66
nCoV - discussion / B.1.1.7 = vui-202012/1
« Last post by gsgs on December 17, 2020, 10:48:12 pm »
https://flutrackers.com/forum/forum/europe-aj/europe-covid-19-sept-13-2020-may-31-2021/901351-england-new-variant-of-covid19-coronavirus-may-be-causing-faster-spread-in-some-areas-december-14-2020-wales-scotland-denmark






twitter-thread from @Chjulian , translated from Spanish :

 Update: Headlines announce the identification of a "new variant" of the coronavirus in the UK.
 It is not clear if the new variant is responsible for the increase in cases.
However, this variant is interesting. And here I tell you why 37 / n
@Chjulian
·
First, we need to understand that our immune system uses specialized mechanisms
to recognize and eliminate the virus, preventing its spread and ending disease.
The infectious period is the time in which we can transmit SARS-CoV-2 to another person

In the case of COVID19, the infectious period begins a couple of days before symptoms
develop and can last up to a couple of weeks (more details here https://bmjopen.bmj.com/content/10/8/e039856
). The disease is generally acute, short-lived bone 39 / n

An Immunocompetent individual has a normal
immune response. When our immune
system is weakened, we say it is immunosuppressed. Immunosuppressed individuals
may have persistent infections that last for longer periods of time (months!) 40 / n

Under these conditions, SARS-CoV-2 can accumulate many more mutations than we
would expect (in a single individual) and which could be transmitted if the transmission
is successful after a long time 41 / n

Remember that it is normal for viruses to mutate and SARS-CoV-2 accumulates
(on average) one or two mutations per month at the population level 42 / n
[##  1.43 per month , ua5m1.gif {gsgs} ]

The new variant (named B.1.1.7) has 17 mutations (woah!). And it is speculated that
it could have originated in an individual with a persistent infection (for example,
an immunosuppressed individual, but we have no information about it) 43 / n

It is important to mention that our immune system goes to the battlefield as quickly
 as possible to avoid an arms race at the molecular level, reducing the chances that
the virus will produce a mutation that allows it to evade our immune response 44 / n

If the hypothesis turns out to be true, it can have important consequences for treatment.
 A persistent infection accumulates diversity and depending on how we treat it, we may
or may not cause an arms race at the molecular level 45 / n

That is, to select mutations with unknown epidemiological potential. There is no need
 to be alarmed, I just want to show how we scientists must think and articulate our strategy
to face the battle in the short, medium and long term 46 / N

Nor can we say that a persistent infection in an immunosuppressed individual is a
greater problem than infections in immunocompetent individuals. Definitely the
evolutionary forces that "moderate" the evolution of the virus are different and ... 47 / n

... we hope that the origin of B.1.1.7 was somewhat unusual and had nothing to do
 with the increase in cases (studies continue). There is also a second hypothesis
(with less support) to explain why this variant has so many 48 / n mutations

Are you sure they remember minks? there is always the slim chance that SARS-CoV-2
will adapt to other mammals (By the way, there are no minks on farms in the UK),
but a prolonged epidemic ... 49 / n

... in the fauna around us it could result in new genetic variants that could (after a while)
jump to humans with various mutations. For this and other reasons, it is important to
evaluate what is happening at the level of the fauna around us 50 / n

t really amazes me how much we learn and the twists and turns a sprout can take! 51 / n

Fortunately, there is no evidence (to date) that this variant has an impact on the severity
of the disease or on the effectiveness of 52 / n vaccines.


67
actual epidemic charts / USA-deaths
« Last post by gsgs on December 14, 2020, 01:35:49 am »
Code: [Select]
2453229, 2774641 ,04,All Cause
 2234697, 2550736 ,05,Natural Cause
   32960,   33776 ,06,Septicemia (A40-A41)
  518136,  512577 ,07,Malignant neoplasms (C00-C97)
   75070,   84086 ,08,Diabetes mellitus (E10-E14)
  103200,  111955 ,09,Alzheimer disease (G30)
   42979,   46919 ,10,Influenza and pneumonia (J09-J18)
  135074,  130283 ,11,Chronic lower respiratory diseases (J40-J47)
   37774,   38305 ,12,Other diseases of respiratory system (J00-J06,J30-J39,J67,J70-J98)
   44132,   44405 ,13,Nephritis, nephrotic syndrome and nephrosis (N00-N07,N17-N19,N25-N27)
   27040,   52927 ,14,Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified (R00-R99)
  565959,  582547 ,15,Diseases of heart (I00-I09,I11,I13,I20-I51)
  128206,  134272 ,16,Cerebrovascular diseases (I60-I69)
       0,  236985 ,17,COVID-19 (U071, Multiple Cause of Death)
       0,  216748 ,18,COVID-19 (U071, Underlying Cause of Death)
----------------------------------------------------------------------
    2019,    2020 ,  weeks 1-45
68
nCoV - discussion / Re: Apr07 model UofWA
« Last post by gsgs on December 09, 2020, 05:54:09 am »
2020/12/09, death forecasts per 2021/04/01 by IHME :
USA=538893,GER=108119,FRA=93581,ITA=101176,UK=118674,BRA=217147,IRN=94389

2021-06-13, death forecasts per 2021-10-01 by IHME :
USA=950337,GER=133026,FRA=143473,ITA=164264,UK=153761,BRA=727083,IND=1198621,all,9505216

69
genetics / release 240.0
« Last post by gsgs on November 03, 2020, 01:19:51 am »
2020/11/03 , genbank release 240 , Oct.15 is available

https://ftp.ncbi.nlm.nih.gov/genbank/gbrel.txt

release 239 from Aug2020 had 39 virus files with 17491 MB and 3161686 sequences and 5824026918 Bases
   and 50462 coronavirus nucleotide sequences
release 240 from Oct2020 has 44 virus files with 18889 MB and 3223498 sequences and 6442230159 Bases
   and 68651 coronavirus nucleotide sequences 33844 of which are SARS2
70
genetics / Re: genbank 04/11
« Last post by gsgs on October 28, 2020, 10:19:00 pm »
2020/10/29 , 36846 sequences



----------------------------------------
    Charite has 544 German sequences now,
    36 from October , all with the D614G mutation
    https://civnb.info/sequences/

    the most frequent mutations from October are :

    36,C3037T,C241T,C14408T,A23403G
    14,G28883C,14,G28882A,14,G28881A

    10,G21255C
    9,T445C
    9,G29645T
    9,G25563T
    9,C6286T
    9,C28932T
    9,C22227T
    8,G27870T
    8,C6040T
    8,C27944T
    8,C26801T
    8,C21614T
    7,C28854T

    27 (10 from October) are the new Spanish strain "20A.EU1" from this paper :
    https://www.medrxiv.org/content/10.1...063v1.full.pdf
    mutation picture : http://magictour.free.fr/sars2de5.GIF
   
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