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11
vaccine / Re: omicron vaccine effectiveness
« Last post by gsgs on February 04, 2022, 11:37:44 pm »

Paul Mainwood makes these nice weekly updated computer-readable data files for UK-VE ,
since 22 weeks
https://github.com/PaulMainwood/vaccine-surveillance-reports/blob/main/assortment%20of%20denominators.csv
https://github.com/PaulMainwood/vaccine-surveillance-reports/blob/main/vaccine%20surveillance.csv

that gives VE(UK,3dose)=
40,93,98%  for case,hosp,death

while figures 1-2 and table 8 suggest 
65,85,88% (7weeks) for symp,hosp,death
https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1052353/Vaccine_surveillance_report_-_week_5.pdf


average of age10grougs40-80,
boost 0%-50% Oct01-Jan01 average 7 weeks ago
average of AZ+AZ+BNT and BNT+BNT+BNT
wanes 2% per week for VE(case) and 1.2% per week for VE(hosp)

Germany : 75,91,98%   
(1*[18-59]+2*[>65])/3,3dose,clinical symp,hosp,death)

Italy :

12
vaccine / omicron vaccine effectiveness
« Last post by gsgs on December 31, 2021, 10:22:03 pm »
scroll down for the most actual numbers

actual numbers on hospitalisations and positive-rates here:
https://ncovinfo.createaforum.com/genetics/b-1-1-529-(nu-)/msg320/#msg320

: https://ourworldindata.org/grapher/united-states-rates-of-covid-19-deaths-by-vaccination-status


https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1044481/Technical-Briefing-31-Dec-2021-Omicron_severity_update.pdf

UK,symp,  http://magictour.free.fr/tb34a.GIF
UK,hosp:
VE(UK,h,1d, 7w,O)=52
VE(UK,h,2d,11w,O)=72
VE(UK,h,2d,30w,O)=52
VE(UK,h,3d, 4w,O)=88



Ontario , VE(case),1129-1231
76,76,74,74,72,73,72
71,70,69,67,67,64,63
59,53,47,40,32,25,16
+08,+01,-05,-12,-18,-25,-28
-31,-33,-29,-32,-38

Ontario , VE(hosp),1213-1231
84,84,83,82,82,81,81
79,78,77,75,73,70,66
63,60,56,54,47






---------------------------------------------------------
Robert Koch Institute report released today states that 95.58% of the #Omicron cases
in Germany are fully vaccinated (28% of those had a "booster"), 4.42% are unvaccinated.
--------------------------------------------------------
 the 2nd dose mRNA vaccine given to someone who also had past infection
did not further increase antibodies
---------------------------------------------------
> One of the studies shows omicron is 89% as severe in people with no vax, never infected
------------------------------------------------------


vaccine effectiveness

AZ,BNT,Mod
D,2,h,78,91
D,3,h,98,98
O,2,h,51,75
O,3,h,90,86
O,2,h,ar,54,77
O,3,h,ar,92,88


O,2,s,--,55,37

ar:adjusted for reinfections
s: symptomatic disease
h:hospitalisation
O:omicron
D:delta
w:weeks

https://twitter.com/freja_kirsebom/status/1474070653326270473

O,2AZ+BNT,s,3w,60
O,2AZ+BNT,s,10w,35
O,2AZ+Mod,s,10w,45
O,3BNT,s,1w,70
O,3BNT,s,10w,45
O,2BNT+Mod,9w,72
O,2Mod,3w,50
O,2Mod,22w,0

---------------------------------------------------------------------------

DNK,VE : https://www.medrxiv.org/content/10.1101/2021.12.20.21267966v2.full.pdf

---------------------------------------------------------------------

VE(3*BNT,omicron,symp)=75%
-----------------------------------------------------------------
SinoVac doesn’t provide sufficient antibodies to neutralize omicron
------------------------------------------------------
VE(2xBNT,omicron,hosp)=70%
VE(2xBNT,omicron,inf)=33%

wanes
1. 2-4 wks after 2nd dose: 56%
2. 3-4 mnths after 2nd dose: 25%

VE(delta-->omicron,inf)=60%
----------------------------------------------------------------
VE(symp,2AZ,omicron,5m?,UK)=0
VE(symp,2BNT,omicron,5m?,UK)~30%
VE(symp,3BNT,omicron,1m,UK)=72%
https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1040076/Technical_Briefing_31.pdf
https://twitter.com/kallmemeg/status/1469351833416122369
------------------------------------------------
current vaccine effectivity in Iceland
see  https://www.covid.is/data
VE(2shots,case) = -88% (Jan02)
VE(3shots,case) = 38% (Jan02)
VE(2shots,hosp) = 71% (Dec28)
VE(3shots,hosp) = 84% (Dec28)
------------------------------------------------


Iceland : http://magictour.free.fr/ice1228.GIF
VE(ICE,case,3d,5w,O)=48
VE(ICE,case,2d,20w,O)=-82%

Washington : http://magictour.free.fr/wa-1229.GIF
VE(WA,case,omicron)=60%

New York : http://magictour.free.fr/ny-1222.GIF
VE(NY,case,omicron)=75

Virginia : http://magictour.free.fr/va-1225.GIF 
VE(VA,case,omicron)=92%

UK,symp,  http://magictour.free.fr/tb34a.GIF

Ontario :  VE(case)= -31%  VE(hosp)=45% , VE(ICU)=84%    (was 73%,82%,90% 5  weeks ago)
http://magictour.free.fr/ont-0105.GIF

California : VE(case)=75% (-1% per day) , VE(hosp)=87% (-0.5% per day)  , VE(death)=95% (stable)
http://magictour.free.fr/ca-1226.GIF

Oregon, Dec30 : http://magictour.free.fr/or-1230.GIF
VE(case)=66%

Germany, Jan06 : http://magictour.free.fr/rki2w01.GIF
VE(case,2dose,18-59)= 53 , VE(hosp,18-59)=76  , VE(ICU)=89
VE(case,3dose,18-59) = 82 , VE(hosp,3dose,18-59)=92
(it's for the last 4 weeks , still mostly delta, the omicron wave is just starting,
mainly young people get it early in the wave, so I took 18-59 and not 60+)
----------------------------------------
USA-CA :
VE(Mod,case,O,2dose,14-90d)=30    quickly declining
VE(Mod,case,O,3dose,)=63
https://www.medrxiv.org/content/10.1101/2022.01.07.22268919v1
----------------------------------------

vaccine effectiveness in UK with 2-3 doses ,
4-week average
average of 4-5 highest from 7 agegroups
ONS-denumerators
reported in weeks 1,2 of 2022

VE(case) , av(5)=26.1% , 22.8%
VE(admis) , av(5)=+91.5%  ,  +89.1%
VE(death) , av(4)=+92.4% , +93.2%

-----------------------------------------------------------
VE-numbers in % for case/symp , hosp , ICU , death

ONT,0112 , VE(2+dose)=-25,40,77,--

ICE,0105 , VE(2dose) = 00,66,--,--
ICE,0105 , VE(3dose) = 32,68,--,--

Germany actual estimates from 4-week-period-numbers
DEU,0113 , VE(2dose) = 00,59,76,82
DEU,0113 , VE(3dose) = 40,83,86,89

----------------------------------------------------------------
Italy :
https://www.epicentro.iss.it/coronavirus/bollettino/Bollettino-sorveglianza-integrata-COVID-19_12-gennaio-2022.pdf

fig.A10,A11
VE much better in old people ? I assume it's because omicron infects young people first
 and the VE(old) will go down to the VE(young) in some weeks

Ontario, 01-25  : http://magictour.free.fr/ont-0125.GIF
VE(2+dose,case)=15%    , VE(2+dose,hosp)=50%   VE(2+dose,ICU)=80%
but these are lower numbers in the decreasing wave , VE was lower at the peak of the wave

DE : 2d:30,55,90,90  ;  3d : 65,84,90,90   (symp,hosp,ICU,death)
http://magictour.free.fr/rki2-w03.GIF

ITA : 2dl : 08,84 ; 2ds : 31,89 ; 3d : 46,94    (case,severe case) 2d >/< 120days ago

Iceland , VE(3dose,case) = 40% , VE(3dose,hosp) = 65%

California :VE(case)= 76% , VE(hosp) = 85% , VE(death) = 95%
http://magictour.free.fr/ca-0109.GIF

New York City : VE(case)=60% , VE(hosp)=88%
(NY-State gives 78% and 92%)
http://magictour.free.fr/nyc-21.GIF

France , 2022-01-01 , 2dose : -25% , 57% , 72%  (case,hosp,ICU)
France , 2022-01-01 , 3dose :  48% , 74% , 85%  (case,hosp,ICU)

Iceland, 2022-01-25  :  VE(2dose,case)=-35% , VE(2dose,hosp)=60% ,
VE(3dose,case)=40% , VE(3dose,hosp)=80%
http://magictour.free.fr/ice-0125.GIF

Germany, 2022-01-27 , http://rki2w04.GIF    40,70,80,85   ,   75,90,96,94

Israel, 2022-01-27 , average of 5 oldest age10groups
2dose>6m : 45,63 ; 2d>6m or 3dose : 45,88     for inf.,severe

UK,3dose : http://magictour.free.fr/3dosek.GiF

2022-01-16 , California : http://magictour.free.fr/ca-0116.GIF
68,80,87,93   2,3dose ; case,hosp


( how can it be 76% in CA and NY  but 10% in ONT and 40% in ICE ? )
46 in ITA , 30 in UK , 70% in DE


s also the effect that unvaccinated people are more likely to have natural immunity
and this increasing over time. Countries/States rarely report cases nd hospitalisations by
vaccination status _and_ status of previous infection
13
genetics / Re: B.1.1.529 (=omicron)
« Last post by gsgs on December 27, 2021, 09:09:53 pm »
London, admissions dec06-jan09
111,148,132,142,162,166,157
169,199,201,220,193,210,245
301,307,386,390,278,364,374
437,456,511,450,319,316,347
401,367,366,310,312,307,277

London, in hospital dec06-jan11
1102,1134,1136,1163,1193,1185,1253
1666,1573,1534,1460,1372,1349,1360
1819,1904,2036,2097,2260,2295,2425
2640,3024,3310,3457,3636,3666,3744
3848,3993,4074,4053,3989,3819,3867
3930,,3826
(max. was 7840)
boroughs : http://magictour.free.fr/lo-0107.GIF
https://data.london.gov.uk/download/coronavirus--covid-19--cases/151e497c-a16e-414e-9e03-9e428f555ae9/phe_cases_london_boroughs.csv

2022-01-02 : ZOE COVID Study shows infections in London dropping
 and appear to have reached an R rate of 1.0. 

2022-01-08 :
The median R-value across England is below 1 (0.98) Also true in East, London, SE, NW and E Midlands, although NE England is on 1.3

Denmark, 1216-0110    (max was 964 on 2021-01-04)
hospi,517,517,517,560,
581,554,553,570,538,522,579
608,666,675,665,665,665,709
770,794,784,756,755,730,723
777,754
positive-rate,480,502,368,429,
496,537,517,485,422,461,748
1188,1152,1162,0989,0792,1069,1156
1084,1242,1133,1074,0862

NY, in hospital, 11-22 ... 01-09
2756,2718,2978,2904,2832,2911,2459
2558,3265,3272,3473,3541,3598,3577
3599,3515,3898,3959,4432,3998,3906
3406,3610,4232,4250,4296,4400,4334
4397,4818,5006,5047,5524,5505,5519
5772,6525,7160,7772,8260,8451,8773
9563,10713,11194,11878,12395,12515

Israel, cases , Nov29-Jan03
 766, 684, 443, 565, 415, 359, 473,
 755, 804, 755, 571, 585, 356, 474,
 800, 761, 627, 878, 720, 696, 794,
1356,1120,1200,1745,1351,1455,1241,
3046,2995,3446,5600,3886,6121,5060
9803

Israel, positive-rate Nov29-Jan02
0032,0063,0060,0058,0057,0056,0058,
0057,0058,0062,0061,0064,0065,0065,
0066,0066,0064,0069,0069,0074,0078,
0085,0090,0098,0107,0114,0123,0128,
0145,0160,0177,0210,0229,0265,0294

Ontario , VE(case),1129-1231
76,76,74,74,72,73,72
71,70,69,67,67,64,63
59,53,47,40,32,25,16
+08,+01,-05,-12,-18,-25,-28
-31,-33,-29,-32,-38

Ontario , VE(hosp),1213-1231
84,84,83,82,82,81,81
79,78,77,75,73,70,66
63,60,56,54,47


in hospital in 51 US-States , change last 3 weeks , and number per M. population in the last 22 days
Code: [Select]
DC,138,150,247,,976,893,825,745,610,526,459,394,361,336,327,310,259,272,261,263,242,220,200,200,197,189
OH,106, 97,119,,510,502,491,475,462,436,423,428,432,439,439,442,430,427,437,436,434,433,437,424,414,410
DE,109,112,116,,500,485,479,443,432,428,432,430,432,401,387,389,391,388,382,374,379,374,339,343,348,349
NJ,115,136,167,,455,433,406,346,269,301,284,272,223,244,237,230,216,207,199,198,195,191,162,180,170,173
IL,116,112,133,,444,444,444,427,405,371,333,333,333,333,326,312,309,295,295,295,290,282,283,274,254,254
IN,108, 95,103,,440,443,442,440,442,433,425,424,416,433,425,436,431,430,443,441,439,442,427,426,426,410
NY,110,125,153,,418,408,384,354,322,285,273,272,273,249,247,238,217,214,217,212,210,209,178,168,193,197
MI, 92, 83,112,,409,401,390,380,380,371,361,365,373,387,382,406,407,415,435,446,456,465,469,471,465,470
PA,101, 95,120,,405,403,384,369,357,346,335,335,340,343,352,349,347,347,352,354,357,357,360,349,345,346
WV,103, 94,117,,400,374,375,382,355,335,332,340,330,339,344,354,363,376,358,355,362,368,367,363,362,346
GA,115,121,198,,347,327,294,254,230,186,171,175,176,173,154,142,141,136,144,139,134,131,130,122,123,125
MD,121,118,141,,343,343,343,331,295,277,256,243,243,243,237,225,217,203,205,194,188,186,189,182,169,169
WI,100, 93,109,,322,321,317,310,299,284,284,293,297,304,307,313,306,308,313,315,310,319,307,316,318,310
AZ, 92, 92, 96,,319,322,324,318,327,325,323,329,341,342,348,355,349,346,354,359,375,380,386,375,376,384
CT,125,113,137,,319,319,319,308,267,256,232,232,232,232,227,231,232,204,204,204,196,198,188,178,162,162
KY,105, 96,118,,318,318,318,318,295,271,268,268,268,268,268,267,267,278,278,278,274,277,269,278,264,264
KS,109, 96,116,,313,303,303,267,281,267,263,269,273,281,280,275,273,278,280,276,272,266,251,256,255,256
RI,120,104,121,,303,301,299,270,278,249,249,249,249,241,242,242,239,239,239,212,253,249,243,198,198,198
NH,101, 81,102,,290,290,290,286,294,301,283,283,283,283,306,327,324,347,347,347,347,354,349,339,343,343
MA,121,106,125,,284,277,258,243,242,232,226,226,226,232,230,229,215,213,213,213,209,200,200,192,176,176
NV, 97,101,129,,283,283,283,252,254,240,218,218,218,218,217,225,214,214,214,214,218,226,222,212,220,220
NE, 96, 79,107,,270,272,267,256,247,240,238,251,262,256,279,268,292,297,317,311,328,338,320,320,325,328
OK,105,108,120,,267,271,265,241,217,216,219,222,220,216,206,198,196,202,205,212,212,201,197,198,196,194
SD, 89, 96, 97,,259,268,271,266,256,258,266,265,275,268,269,269,256,263,275,281,298,299,320,307,304,307
TN,107,103,138,,253,254,234,219,199,187,176,183,181,174,169,175,178,174,177,167,164,164,162,159,159,164
ME,103, 88, 93,,253,248,254,250,261,264,261,272,281,290,308,309,309,309,306,309,306,306,297,293,287,296
MN, 90, 94, 94,,250,250,249,255,258,265,265,265,265,268,266,274,278,278,279,290,294,304,309,309,310,310
IA, 98, 90,107,,249,252,236,236,226,228,225,232,237,239,240,246,249,258,257,263,286,265,260,261,257,261
VA,110,111,133,,243,252,243,233,220,193,189,182,182,175,179,175,166,164,163,162,165,162,154,148,147,148
NM, 89, 88, 94,,242,242,242,222,218,215,257,257,257,257,264,261,254,291,291,312,289,289,314,288,326,326
FL,107,150,232,,242,229,205,178,146,111,106,104,101, 88, 85, 76, 70, 70, 69, 70, 72, 72, 65, 65, 64, 64
TX,101,111,164,,230,220,201,178,160,143,140,140,140,139,131,127,125,125,126,120,128,125,121,123,124,124
NC,105,105,142,,228,228,216,203,190,160,160,160,160,160,160,161,156,151,151,151,153,149,150,148,143,143
MS,104,112,204,,221,209,195,164,143,110,108,108,102,104,107, 99, 93, 95, 96,100,102,124, 95, 89, 90, 92
AR,108, 90,138,,214,207,194,194,189,172,160,155,163,164,164,164,170,171,171,178,175,171,172,169,161,157
CO, 87, 87,111,,206,206,201,201,197,187,184,184,184,187,187,190,211,211,211,211,218,222,228,231,240,240
SC,113,108,165,,202,191,168,160,132,121,121,122,122,114,109,104,108,110,112,111,116,113,108, 98, 99, 99
AL,115,110,209,,176,157,143,121,105,105, 74, 84, 86, 85, 82, 78, 76, 72, 76, 74, 75, 73, 71, 68, 66, 66
LA,102,147,250,,163,163,163,141,110, 96, 65, 65, 65, 65, 58, 56, 51, 44, 44, 44, 42, 43, 42, 42, 43, 43
CA,103,101,160,,160,147,139,131,120,111,105,100,102,101,100, 97, 97, 97, 99, 99,100, 99, 99, 96, 96, 96
ND, 84, 78,114,,157,163,163,138,139,133,137,137,148,155,152,154,180,178,175,187,201,202,209,211,211,206
WA, 99, 98,125,,143,143,126,124,112, 98,116,114,115,115, 95,105,111,111,116,112,115,129,110,116,117,117
UT, 94, 83,114,,143,136,135,133,131,130,127,125,125,133,134,131,146,147,149,155,152,159,154,154,155,157
ID, 90, 81,107,,134,134,133,135,127,121,120,125,130,129,134,140,151,151,154,161,161,166,167,171,173,171
WY, 90, 76, 84,,116,114,114,128,112,138,138,138,138,138,142,142,142,180,180,171,171,183,187,199,199,199
HI,117,148,186,,114,110,103, 86, 74, 58, 59, 61, 52, 49, 44, 45, 39, 38, 41, 34, 34, 31, 34, 35, 34, 35
MT, 80, 81,108,,113,113,113,111,111,103,104,104,104,104,115,117,116,128,128,128,140,140,143,151,160,160
OR, 96, 89,132,,110,110,110,104, 98, 93, 83, 83, 83, 83, 82, 83, 85, 93, 93, 93, 97, 96, 96,101, 96, 96
VT, 73, 94,106,, 87, 87, 87, 83, 85, 96, 82, 82, 82, 82, 82, 85, 85, 91, 87, 93, 93,108,119,119,111,118
AK, 79, 86, 93,, 74, 74, 74, 74, 80, 80, 79, 79, 79, 79, 79, 95, 95, 91, 91, 91, 98, 98, 92, 92,115,115
-------------------------------------------------------------------------------------------------------------------------------
01, 02, 03, 04,  05, 06,... , 26


the 26 columns are :

01,State
02,100 * (in_hospital_dec18) / (in_hospital_dec11)
03,100 * (in_hospital_dec25) / (in_hospital_dec18)
04,100 * (in_hospital_jan01) / (in_hospital_dec25)
05, in_hospital_per_million_population_jan01
06, in_hospital_per_illion_population_dec31
...
26,in_hospital_per_million_population_dec11

(in_hospital always means  : in_hospital_with_COVID )


(MO=Missouri removed - to_be_corrected)

data from newsnodes
https://newsnodes.com/us_state/DC
click "show hospital data"

charts for this , update 0108 : http://magictour.free.fr/hosp0108.GIF


the hospital trend is about 5 days behind the cases-trend ,
but more reliable especially on weekends and holidays

--------update-----------------------------------------
NY,(418),434,473,530,554,588,613,619,614,616
NJ,(455),478,471,557,579,561,641,657,682,676
DC,(976),970,1015,1134,1207,1228,1249,1285,1317,1311
TX(230),
CA(160),
FL(242),
GA(347),
PA(405),
IL(444),,

charts for this :  https://pbs.twimg.com/media/FIc6FqLWQAQh90r?format=jpg&name=4096x4096


--------------------------------------------------------------------

South Africa , weekly cases,hospitalisations and deaths by week of occurance :
http://magictour.free.fr/zaf-w02.GIF

14
genetics / Re: B.1.1.529 (=omicron)
« Last post by gsgs on December 23, 2021, 06:35:29 am »
early omicron severety studies :

ZAF : https://t.co/g24KTGU7Io
DNK : https://t.co/pQnetTf7IP
ENG : https://t.co/chqPEhph3p
SCO : https://t.co/CMv2zkG2sh

DNK,VE : https://www.medrxiv.org/content/10.1101/2021.12.20.21267966v2.full.pdf


-------------------------------------------------------------------------
vaccine effectiveness

AZ,BNT,Mod
D,2,h,78,91
D,3,h,98,98
O,2,h,51,75
O,3,h,90,86
O,2,h,ar,54,77
O,3,h,ar,92,88


O,2,s,--,55,37

ar:adjusted for reinfections
s: symptomatic disease
h:hospitalisation
O:omicron
D:delta
w:weeks

https://twitter.com/freja_kirsebom/status/1474070653326270473

O,2AZ+BNT,s,3w,60
O,2AZ+BNT,s,10w,35
O,2AZ+Mod,s,10w,45
O,3BNT,s,1w,70
O,3BNT,s,10w,45
O,2BNT+Mod,9w,72
O,2Mod,3w,50
O,2Mod,22w,0

-------------------------------------------------------------------------
=============================================
 SARS CoV-2 entry into a cell can occur via two routes: one that only needs ACE2 and
another that needs ACE2 and TMPRSS2.
TMPRSS2 (T2) is higher in the lower airways and so virus goes the second route in those areas.
Omicron spike has reduced ability to use the ACE2+T2 route and doesn't respond to higher
T2 levels, unlike Delta
==========================================================

TB33 : risk(EC or hosp,omicron)=0.62*risk(EC,delta)
risk(hosp,omicron)=0.38*risk(hosp,delta)
This effect is still present when stratified by vaccination status

Using a very similar data set, Imperial College, provided estimates that Omicron cases had a 15
to 25% (Hazard ratio 0.8; 95% CI 0.75-85) reduced risk of emergency department attendance
(hospitalisations in their data set) and 40 to 49% (HR 0.55, 95% CI 0.51-59) reduced risk of a
hospitalisation with a stay of one or more nights. Importantly, this group attempt to impute the
effect of prior infection, highlighting that while 17% of the population have tested positive for
COVID-19, this is likely to capture only one-third of total infections that have occurred in
England. Including the likelihood of previous infection, in addition to vaccination in their model,
they have estimated the intrinsic risk difference between Delta and Omicron as between 0 to
30% and the reduced risk of hospitalisation in those previously infected estimated as 55 to 70%.
===========================================================
The Sato Lab (Kei Sato)  @SystemsVirology
Japan - #Omicron is less infectious and pathogenic than #Delta and even an early pandemic
SARS-CoV-2 in infected hamster model. 1/5
-----------------------------------------------
Omicron infection enhances neutralizing immunity against Delta
------------------------------------------------
> One of the studies shows omicron is 89% as severe in people with no vax, never infected
-----------------------------------------------------------------
Coetzee :
"And their symptoms don't seem to get any worse than that. After about five
days they clear up, and that's it."
-------------------------------------------------------------------------
Omicron appears to have switched cell entry preference to endosomal fusion
(rather than ACE2+TMPRSS2 mediated cell surface fusion
like previous variants, incl. the well adapted Delta)
----------------------------------------------------------------------
Robert Koch Institute report released today states that 95.58% of the #Omicron cases
in Germany are fully vaccinated (28% of those had a "booster"), 4.42% are unvaccinated.
--------------------------------------------------------
 the 2nd dose mRNA vaccine given to someone who also had past infection
did not further increase antibodies
---------------------------------------------------
---------------------------------------------------------------
    Daily modelled estimates produced by the ONS showed around 9.5% of Londoners had
COVID-19 as of Sunday
    Report also showed a record 1 in 35 people in England had COVID-19 between Dec.
13 and Dec. 19
The ONS report also showed a record 1 in 35 people in England had COVID-19 between Dec. 13 and Dec. 19 — compared with a previous estimate published on Thursday of 1 in 45 in the week to Dec. 16.
7% infected in London during Christmas
-----------------------------------------------------------------
Study estimates nation’s Omicron outbreak grew 70% in a week to hit one in 25 people – as data shows infections are now rising quickest in over-65s

The Office for National Statistics swabbing estimates that 2.03 million people had the virus
on any given day in the week before Christmas
2022-01-01 , granthshala.com
The ONS conducts weekly surveillance tests
----------------------------------------------------------------------
2022-01-04 , Neil Ferguson warns of 5,000 Omicron deaths a DAY in UK
ahh, seems to be old news (I had missed it)
Published: 15:38 GMT, 17 December 2021 | Updated: 23:58 GMT, 17 December 2021
---------------------------------------------------------------------
@IHME_UW
 new projections show that daily estimated #COVID19 infections has peaked at 6.2 million
on 1/6 in the US, but daily cases will rise to nearly 1.2 million by 1/19, 2022.
80-90% asymptomatic
---------------------------------------------------------------
intrinsically reduced virulence may account for an approx 25%

15
genetics / Re: B.1.1.529 (=omicron)
« Last post by gsgs on December 19, 2021, 12:23:56 am »
==============================
SA , netcare-CEO , 12-13 : it's mild
------------------------------------------
neue Studie Imperial College, von Lauterbach vor 14h zitiert , als wahrscheinlich eingestuft
"Omnikron tellt alles in den Schatten, was wir bisher in Pandemie gesehen haben"
Katastrophenfall in London ausgerufen
hard lockdown in Netherlands at 2021-12-19, 5 AM
Denmark hospitalisations remain low
Lauterbach schliesst Lockdown ueber Weihnachten aus
Bund und Länder beraten am Dienstag (2021-12-21) über omicron
2021-12-20 , Ireland strengthens lockdown
Denmark re-introduces restrictions
Sachsen verschaeft Corona Massnahmen
----------------------------
in Thueringen ab 2021-12-20
Sobald eine ungeimpfte Person an einem Treffen teilnimmt,
dürfen nur noch zwei Personen aus einem weiteren Haushalt dabei sein.
Bisher galt diese Regel nicht für Geimpfte und Genesene.
--------------------------------
Der neue Expertenrat der Bundesregierung spricht sich für Kontaktbeschränkungen "bereits für
die kommenden Tage" aus. Es gehe um "wirksame bundesweit abgestimmte Gegenmaßnahmen",
heißt es in der Stellungnahme, die dem ARD-Hauptstadtstudio vorliegt
 Einschätzung der Wissenschaftler
Bisher sei nicht davon auszugehen, dass im Vergleich zur Delta-Variante Menschen
ohne Immunschutz einen milderen Krankheitsverlauf hätten
-------------------------------
It is obvious we are far from 95 per cent effectiveness that we obtained against the initial virus,"
Ugur Sahin told on 2021-12-20
VE(omicron,2BNT,hosp)=70%
-----------------------------------------------
Zoe :    Runny nose,  Headache , Fatigue , Sneezing ,   Sore throat
------------------------------------------------------------------
HALF of patients in London hospitals 'with Covid' were only diagnosed AFTER arriving
with another ailment https://trib.
-----------------------------------------------------------------------------
https://metro.co.uk/2021/12/16/omicron-may-be-milder-but-we-should-all-listen-to-chris-whitty-15782431/
Chris Whitty : "slightly milder than delta"
Omicron may be ‘intrinsically milder’,  but there is still not yet ‘clear evidence’.
--------------------------------------------
https://datakingz.com/2021/12/22/london-playbook-scoop-omicron-milder-in-uk-new-years-fireworks-liz-vs-no-10/
SCOOP: The Omicron coronavirus variant is causing a milder disease than the Delta
strain in most Britons, U.K. government scientists are set to conclude. The U.K.
Health Security Agency is due to publish its early real-world data on the severity
of the disease before Christmas, and Playbook is told the experts are likely to offer
a mixed outlook, with some positives and some negatives
---------------------------------------------
risk of hospitalisation from omicron is 1/3 of the delta risk
https://www.research.ed.ac.uk/en/pub...effectiveness-
-------------------------------------------
new data from @IHME_UW predict nearly 3 billion COVID-19 infections globally
in the next 2 months
----------------------------------------
16
genetics / Re: B.1.1.529 (=omicron)
« Last post by gsgs on December 09, 2021, 10:23:49 pm »
"in the South African city of Tshwane, 70% of those aged 50-69 and 90% of over-80s
had severe cases during the Delta wave. This share is now around 30% for all ages."
----------------------------------------------------------------------
2021-12-09 , Alarm as almost 20% of South Africa’s healthcare workers contract Covid
Richard Lessels,
Victor Khanyile, the deputy director of human resources at the department of health,
said there were 72 678 public sector healthcare workers infected as of 6 December,
representing 18% of the entire public healthcare workforce — 403 443 clinical and support staff.
Gauteng, at 17 008, has the highest number of healthcare workers infected followed by
the Eastern Cape with 11 975 and KwaZulu-Natal with 11 246.
shorter-lived than previous variants
https://mg.co.za/coronavirus-essentials/2021-12-09-alarm-as-almost-20-of-south-africas-healthcare-workers-contract-covid/
--------------------------------------------------------------------
update week 48 , comparing hospital surveillance in Tshwane waves 2,3,4
https://www.nicd.ac.za/wp-content/uploads/2021/12/COVID-19-HOSPITAL-SURVEILLANCE-UPDATE_WEEK-48-2021_rev.pdf
http://magictour.free.fr/tshh48.GIF

-----------------------------------------------------------------
 Selbst Booster scheinen keinen Schutz (oder nur geringen) vor Infektion und leichtem Verlauf zu bieten.
43% with dyspnaea (shortness of breath) despite 3 shots
--------------------------------------------------------
18/1280=1.4% of Omicron cases in Denmark are hospitalized. Delta was 2%
-------------------------------------------------------
2021-12-11 : 30% of (COVID)-infections in London are omicron
----------------------------------------------------
VE(symp,2AZ,omicron,5m?,UK)=0
VE(symp,2BNT,omicron,5m?,UK)~30%
VE(symp,3BNT,omicron,1m,UK)=72%
https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1040076/Technical_Briefing_31.pdf
https://twitter.com/kallmemeg/status/1469351833416122369
-----------------------------------------------------------

https://twitter.com/BallouxFrancois/status/1469733674426023936
also thread by Tom Moultre
-------------------------------------------------------
backlog now, the decrease was not real
----------------------------------------------------------------------------
Current earliest detection of omicron in South Africa: 8 November, Gauteng
------------------------------------------------------------------------------
South African president tests positive for Covid-19
------------------------------------------------------------------
https://www.dailymail.co.uk/news/article-10299773/South-Africas-Omicron-outbreak-slows-figures-suggest.html
--------------------------------------------------------------------
VE(2xBNT,omicron,hosp)=70%
VE(2xBNT,omicron,inf)=33%

wanes
1. 2-4 wks after 2nd dose: 56%
2. 3-4 mnths after 2nd dose: 25%

VE(delta-->omicron,inf)=60%

Adults (18+) infected with #Omicron  = 29% less likely to be hospitalised (than with Wuhuan-Hu1)
https://twitter.com/miamalan/status/1470684351151157252
------------------------------------------------------------------
VE(3*BNT,omicron,symp)=75%
-----------------------------------------------------------------
CDC; Omicron = 2.9% of cases in USA in week 49 , CDC; 13% in NY,NJ
-------------------------------------------------------------------
SinoVac doesn’t provide sufficient antibodies to neutralize omicron
-----------------------------------------------------------------------
HKUMed shows Omicron infects and multiplies 70X faster than Delta in the
human bronchus, which may explain why it transmits faster, BUT also shows
Omicron infection in the lung is significantly LOWER than the original virus,
which may be an indicator of lower disease severity.
-----------------------------------------------------------------
17
genetics / Re: B.1.1.529 (=omicron)
« Last post by gsgs on December 08, 2021, 10:21:11 pm »
https://www.capetalk.co.za/articles/434212/2-weeks-of-omicron-it-looks-like-people-don-t-get-as-sick-as-with-delta
3/4 of Covid patients were in the hospital for other conditions, and only found out they
had Covid-19 upon arrival.
Hospital stays seem considerably shorter (2.8 days, on average) than during
the pre-Omicron pandemic (8.5 days, on average).
------------------------------------------------------------------
https://www.citizen.co.za/news/vaccine-info/2937972/majority-of-tshwane-patients-unvaccinated/
24/38 adults in the Covid wards on 2 December, 24 were unvaccinated,
eight had unknown vaccination status and only six had had the jabs.
8/9 of hospitalised for Covid pneumonia,  were unvaccinated
80% of admissions were below the age of 50.
---------------------------------------------------------------------
@K_G_Andersen
I think it's likely VE against hospitalization will be relatively well-preserved (~50%?)
with 2x vax, increasing to >75% with boost.
I don't expect much VE to be preserved against infection.
------------------------------------------------------------------------------
sister lineage , BA.1 , BA.2
https://github.com/cov-lineages/pango-designation/issues/361
https://user-images.githubusercontent.com/686405/145027666-318a51b4-0053-4150-a2fc-783752442ae3.png
18
genetics / Re: B.1.1.529 (=omicron)
« Last post by gsgs on December 07, 2021, 11:48:51 pm »
https://drive.google.com/file/d/1bBO3DLrvVMYYMDg5CKUBVaunyKvOVfhv/view
Alex Sigal    @sigallab   7h
There are a few results:
1. Omicron still uses ACE2
2. There is a very large drop in neutralization of Omicron by BNT162b2 (2 doses) immunity
relative to ancestral virus
3. Omicron escape from BNT162b2 neutralization is incomplete.
Previous infection + vaccination still neutralizes
------------------------------------
 this was better than I expected of Omicron.
-----------------------------
Chise
Reduction in nAbs was even LESS in those who had a previous infection & two
doses of Pfizer’s vaccine. Boosters should be able to take this on!
------------------------------------
right thing to do to switch vaccine between prime and boost
=====================================
@BenjMurrell
https://drive.google.com/file/d/1CuxmNYj5cpIuxWXhjjVmuDqntxXwlfXQ/view
Omicron antibody neutralization thread, with preliminary results, and substantial caveats.
our first results were read this afternoon (1/n).

=====================================================
@CiesekSandra  2021-12-08,06:20UTC
2x Biontech, 2x Moderna, 1xAZ/1x Biontech  nach 6 Monaten 0% Neutralisation bei Omicron,
auch 3x Biontech 3 Monate nach Booster nur 25% NT versus 95% bei Delta.
Bis zu 37fache Reduktion Delta vs. Omicron
https://twitter.com/CiesekSandra/status/1468465347519041539/photo/1

Die monoklonalen AK imdevimab und casirivimab sind - wie erwartet- bei Omicron wirkungslos



19
genetics / Re: B.1.1.529 (=omicron)
« Last post by gsgs on December 03, 2021, 11:40:52 pm »
2021-12-04
BioNTech-Chef sieht Notwendigkeit Impfstoff-Anpassung
-------------------------------------
Risk Assessment for Omicron has been published.
Everything is still uncertain, but it doesn't look good.
https://twitter.com/Dr_D_Robertson/status/1466807346487869445/photo/1
---------------------------------------
first time we've seen data on vaccination status of hospitalised covid patients in Gauteng

vaccination status of in-hospital patients (n=1351) public and private
total:1121+230
unknown : 814 ; 190
no : 286 ; 31
yes : 21 ; 9

general wards  ; ICU/HC

VE(hosp)=86% , VE(ICU)=46%(low numbers)

--------------------------------------------------------------------
In France the numbers have been inverting for a few months now (then again,
it's winter now over here)
Some regions show up to 76% vaccinated in ICU, despite 94%
vaccination status (12+yo)
-------------------------------------------------------------------
What the CDC in Europe reported today is 50% of the cases they've seen outside
South Africa have been asymptomatic, 50% have just presented with mild symptoms,"
says @ScottGottliebMD on Omicron. "The vaccines--seem to be protective against more severe disease."
---------------------------------------------------------------
https://twitter.com/jburnmurdoch/status/1467270450111787012
------------------------------------------------------
2021-12-06, 183 confirmed omicron-cases in Denmark
-----------------------------------------------------
J.Ward estimates the impact of omicron :
https://twitter.com/JamesWard73/status/1467631048267866117
--------------------------------------------------------
Data from @nicd_sa
 show that in Gauteng province, the share of Covid-positive patients in ICU or on
ventilators is somewhere between 2-3x lower than it was at the same stage of
the Delta wave
------------------------------------------------------
 In southern New England, it turns out that ~27% of vaccines were given to
previously infected individuals. Pre-print below. 1/ https://medrxiv.org/content/10.110
20
genetics / Re: B.1.1.529 (=omicron)
« Last post by gsgs on December 01, 2021, 05:48:49 am »
2021-12-01
-----------------------------------------------------------------------
Botswana :  15 more cases (+4=19)
14 in the Greater Gaborone DHMT area,
4 in the Serowe/Palapye DHMT area, Truck drivers
1 in Kgatleng DHMT   from ZA
3 mild , 12 none  11 vaxed 4 not (asym)
--------------------------------------------------------------------
map of the initial omicron-wave in ZA :
http://magictour.free.fr/o-1201.GIF
------------------------------------------------------------------------------
On Omicron, for people with prior Covid but unvaccinated:
“In our population…where many people have had previous infection,
we believe that that previous infection doesn’t provide them with
protection from infection due to Omicron”
------------------------------------------------------------------
https://www.centerforhealthsecurity.org/our-work/publications/to-stop-a-pandemic--a-better-approach-to-global-health-security
To Stop a Pandemic - A Better Approach to Global Health Security
cited by 5 :
https://scholar.google.de/scholar?cites=12966832627588286534&as_sdt=2005&sciodt=0,5&hl=de

-----------------------------------------------------------------------
what was that organisation, created last year, dedicated to find and stop new outbreaks like omicron ?
Head was Ian Lipkin, I remember how I applauded at twitter. But now I can't find it.
Only nichtssagende stetments by Lipkin now, no reference to that task.

We were asking for it here since 2006's H5N1

China stopped Wuhan-Hu-1 in Feb.2020
But they let it escape to other countries
and most of the rest of the world didn't stop it

Alpha, Delta were detected too late.

Omicron was detected early but spreads better and faster, but i think we should try to stop it to contain it now.,
support ZA's measures financially. Although it's probably invain and too late.
https://www.chinadaily.com.cn/a/202103/10/WS604819fda31024ad0baae175.html
The key to global public health is global cooperation, transparency and investment."
the lack of international, inter-institutional and interpersonal trust, respect and collaboration,
[not the project that I had in mind. It was rather about early stopping emerging pandemics]
------------------------------------------------------------------------
https://twitter.com/PPI_Insights
--------------------------------------------------------------------------
Epidemiological data from South Africa shows a 3-fold increase in risk for reinfection
due to Omicron vs. Beta and Delta.
------------------------------------------------------------------------
Eine Überstandene Corona-Infektion schützt laut WHO offenbar nicht vor Omikron-Variante
SUBSTANTIAL population-level evidence for evasion of immunity from prior infection
https://www.medrxiv.org/content/10.1101/2021.11.11.21266068v2

------------------------------------------------------------------
67 omicrons at cog-uk on 1202
---------------------------------------------------------

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