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genetics / Re: B.1.1.529 (=omicron)
« Last post by gsgs on November 30, 2021, 01:12:08 am »flutrackers-thread:
https://flutrackers.com/forum/forum/the-pandemic-discussion-forum/928700-omicron-covid-19-variant-b-1-1529-a-variant-of-concern/page2
----------------------------------------------------------------
Gauteng:
weekly hosp : 125,120,135,276,580,71(incomplete)
weekly cases : 593,547,426,737,2762
weekly pos.rates 0.9%,0.9%,0.7%,1.1%,4.3%
9,8,7,3,1,1,1,1,1,0 promille increase yesterday in hosp by age10group
{doesn't look milder than delta from these numbers}
------------------------------------------------------------------------------------------
> Israel is now reporting community transmission of Omicron from a cardiologist
> with 3 doses to another cardiologist with 3 doses Warning sign
--------------------------------------------------------------
2021-11-30 : 5 omicron sequences at cog-UK
@TWenseleers
But to explain the current growth rate advantage of Omicron over Delta one already
has to assume almost complete immune evasion even if one assumes an R0 that is
the same as Delta. R0 can't be much less than that of Delta then I would say...
---------------------------------------------------------------
cluster at TUT Nov.18
https://rekord.co.za/399202/concerns-over-rising-covid-19-cases-in-tshwane/
-------------------------------------------------------------------
Head of EU Public Health gives information that thus far
*ALL* (42) Omicron cases in EU are either mild or without symptoms.
----------------------------------------------------------------
On Monday, an NICD presentation a flagged a large number of COVID-19
admissions among infants aged under two years as an area of concern.
But von Gottberg cautioned against linking that with Omicron just yet.
"It looks like in fact some of those admissions might have started before
the emergence of Omicron. We are also seeing that there was an increase
in influenza cases just in the last month or so, and so we need to be really
careful to look at the other respiratory infections," she said.
----------------------------------------------------
... a report by Channel 12 said the Pfizer vaccine is just slightly less effective in
preventing infection with Omicron than with Delta – 90% as opposed to 95% –
while it is as effective – around 93% – in preventing serious symptoms at least
for those vaccinated with a booster.
According to the report, the ability of the variant to infect is higher than Delta but
not as much as feared – around 1.3 times higher...
-----------------------------------------------------------------
Minimum dose interval for booster jabs to be halved from 6 months to 3
months and all adults to be offered booster Covid vaccine,
UK Health Secretary Sajid Javid confirms
-----------------------------------------------------
@jburnmurdoch
So far admissions following ~same path as past waves.
------------------------------------------------------------
The earliest known cases are still from southern Africa. The first identified samples were
collected Nov. 9, from a 34-year-old man and a 23-year-old man in Johannesburg,
according to the GISAID global database. On Nov. 11, five samples of the variant were
collected in Botswana.
-----------------------------------------------------------
https://flutrackers.com/forum/forum/the-pandemic-discussion-forum/928700-omicron-covid-19-variant-b-1-1529-a-variant-of-concern/page2
----------------------------------------------------------------
Gauteng:
weekly hosp : 125,120,135,276,580,71(incomplete)
weekly cases : 593,547,426,737,2762
weekly pos.rates 0.9%,0.9%,0.7%,1.1%,4.3%
9,8,7,3,1,1,1,1,1,0 promille increase yesterday in hosp by age10group
{doesn't look milder than delta from these numbers}
------------------------------------------------------------------------------------------
> Israel is now reporting community transmission of Omicron from a cardiologist
> with 3 doses to another cardiologist with 3 doses Warning sign
--------------------------------------------------------------
2021-11-30 : 5 omicron sequences at cog-UK
Code: [Select]
B.1.1.529 w=9
ENG/MILK-2B987AD/2021,Y,2021-11-22,100, B.1.1.529,PLEARN-v1.2.97,0.0,0.9925692411619005, Omicron (B.1.1.529-like),0.851100,0.000000,X,X,T,A,H,del,Q,L, orf1ab:K856R, synSNP:C3037T, synSNP:T5386G, synSNP:G5515T, orf1ab:A2710T, orf1ab:T3255I, orf1ab:P3395H, orf1ab:I3758V,synSNP:T13195C, orf1ab:P4715L,synSNP:C15240T, orf1ab:I5967V, S:A67V, S:T95I, S:G339D, S:S371L, S:S373P, S:S375F, S:S477N, S:T478K, S:E484A, S:Q493R, S:G496S, S:Q498R, S:N501Y, S:Y505H, S:T547K, S:D614G, S:H655Y, S:N679K, S:P681H, S:N764K, S:D796Y, S:N856K, S:Q954H, S:N969K, S:L981F,synSNP:C25000T,synSNP:C25584T, E:T9I, M:D3G, M:Q19E, M:A63T,synSNP:A27259C, N:P13L, N:R203K, N:G204R, Y, G, A, ref, _
ENG/MILK-2B95A89/2021,Y,2021-11-22,100, B.1.1.529,PLEARN-v1.2.97,0.0,0.9964109466128309, Omicron (B.1.1.529-like),0.936200,0.000000,X,X,T,A,H,del,Q,L, orf1ab:K856R, synSNP:C3037T, synSNP:T5386G, orf1ab:T1822I, orf1ab:A2710T, orf1ab:T3255I, orf1ab:P3395H, orf1ab:I3758V,synSNP:T13195C, orf1ab:P4715L,synSNP:C15240T, orf1ab:I5967V, S:A67V, S:T95I, S:G339D, S:S371L, S:S373P, S:S375F, S:K417N, S:S477N, S:T478K, S:E484A, S:Q493R, S:G496S, S:Q498R, S:N501Y, S:Y505H, S:T547K, S:D614G, S:H655Y, S:N679K, S:P681H, S:N764K, S:D796Y, S:N856K, S:Q954H, S:N969K, S:L981F,synSNP:C25000T,synSNP:C25584T, E:T9I, M:D3G, M:Q19E, M:A63T,synSNP:A27259C, N:P13L, N:R203K, N:G204R, Y, G, A, ref, _
ENG/ALDP-2B4DF63/2021,Y,2021-11-20, 99, B.1.1.529,PLEARN-v1.2.97,0.0,0.9925692411619005, Omicron (B.1.1.529-like),0.851100,0.000000,X,X,T,A,H,del,Q,L, orf1ab:K856R, synSNP:C3037T, synSNP:T5386G, orf1ab:V1887I, orf1ab:A2710T, orf1ab:T3255I, orf1ab:P3395H, orf1ab:I3758V,synSNP:T13195C, orf1ab:P4715L,synSNP:C15240T, orf1ab:F5086Y, orf1ab:I5967V, S:A67V, S:T95I, S:G339D, S:S371L, S:S373P, S:S375F, S:S477N, S:T478K, S:E484A, S:Q493R, S:G496S, S:Q498R, S:N501Y, S:Y505H, S:T547K, S:D614G, S:H655Y, S:N679K, S:P681H, S:N764K, S:D796Y, S:N856K, S:Q954H, S:N969K, S:L981F,synSNP:C25000T,synSNP:C25584T, E:T9I, M:D3G, M:Q19E, M:A63T,synSNP:A27259C, N:P13L, N:R203K, N:G204R, Y, G, A, ref, _
ENG/MILK-2B67570/2021,Y,2021-11-21,100, B.1.1.529,PLEARN-v1.2.97,0.0,0.9925692411619005, Omicron (B.1.1.529-like),0.851100,0.000000,X,X,T,A,H,del,Q,L, orf1ab:K856R, synSNP:C3037T, synSNP:T5386G, orf1ab:V1887I, orf1ab:A2710T, orf1ab:T3255I, orf1ab:P3395H, orf1ab:I3758V,synSNP:T13195C, orf1ab:P4715L,synSNP:C15240T, orf1ab:I5967V, S:A67V, S:T95I, S:G339D, S:S371L, S:S373P, S:S375F, S:S477N, S:T478K, S:E484A, S:Q493R, S:G496S, S:Q498R, S:N501Y, S:Y505H, S:T547K, S:D614G, S:H655Y, S:N679K, S:P681H, S:N764K, S:D796Y, S:N856K, S:Q954H, S:N969K, S:L981F,synSNP:C25000T,synSNP:C25584T, E:T9I, M:D3G, M:Q19E, M:A63T,synSNP:A27259C, N:P13L, N:R203K, N:G204R, Y, G, A, ref, _
ENG/PHEC-3U06FU0A/2021,N,2021-11-23,100, B.1.1.529,PLEARN-v1.2.97,0.0,0.9247776976688296, Omicron (B.1.1.529-like),0.680900,0.000000,X,X,T,X,H,del,X,L, orf1ab:K856R, synSNP:C3037T, synSNP:T5386G, orf1ab:A2710T, orf1ab:T3255I, orf1ab:P3395H, orf1ab:I3758V,synSNP:T13195C, orf1ab:P4715L,synSNP:C15240T, orf1ab:I5967V, S:A67V, S:T95I, S:G339D, S:T547K, S:D614G, S:H655Y, S:N679K, S:P681H, S:N764K, S:D796Y, S:N856K, S:Q954H, S:N969K, S:L981F,synSNP:C25000T,synSNP:C25584T, E:T9I, M:Q19E, M:A63T,synSNP:A27259C, N:P13L, N:R203K, N:G204R, X, G, X, ref,
Code: [Select]
1 2 3 4 5 6
--------------------------------------------------
1 >Wuhan-Hu1 0 54 60 54 38 59
2 >England/MILK-2B987AD/202 54 0 9 4 3 10
3 >England/MILK-2B95A89/202 60 9 0 9 8 5
4 >England/MILK-2B67570/202 54 4 9 0 3 6
5 >England/PHEC-3U06FU0A/202 38 3 8 3 0 8
6 >England/ALDP-2B4DF63/202 59 10 5 6 8 0
---------------------------------------------------
1 2 3 4 5 6
0000000000111111111111112222222222222222222222222222222222222222
0233555588001344558999991122222233333333333333344445566667788888
2808357938045145251222227856666800000000245668914450525572823888
4337813293243905426011116488889200245678113016533710973816182999
1277650435997582013902472672385214297424124833793829399688600012
-codon-position---------- 1111 22 2122 21 1 22 2 2 1 2 22 21 1211121 21 1 2 12
Index--------------------CACTTGCGGTCCATCTCTATAAACCCGTCTCGGCAAGAATCACTCCGCATCCCCACGACACGGG
1 >Wuhan-Hu1 ................................................................
2 >ENG/MILK-2B987AD/202 TGTKGT..A.TAGCT.TWG.....TTACTCT-AACGAGTCAGTGAATATATTTTGGACTTTAAC
4 >ENG/MILK-2B67570/202 TGT.G..AAYTAGCT.TWG.....TTACTCT-AACGAGTCAGTGAATATATTTTGGACTTTAAC
5 >ENG/PHEC-3U06FU0A/202 TGT.G...A.TAGCT.T.G.....TTA-------------AGTGAATATATTTT-GACTTTAAC
3 >ENG/MILK-2B95A89/202 TGT.G.T.A.TAGCTYTWGKRRRMTTACTCTTAACGAGTCAGTGAATATATTTTGGACTTTAAC
6 >ENG/ALDP-2B4DF63/202 TGT.G..AAYTAGCT.TAGKRRRMTTACTCT-AACGAGTCAGTGAATATATTTTGGACTTTAAC
Index--------------------CACTTGCGGTCCATCTCTATAAACCCGTCTCGGCAAGAATCACTCCGCATCCCCACGACACGGG
-codon-position----------1 1111 22 2122 21 1 22 2 2 1 2 22 21 1211121 21 1 2 12
0000000000111111111111112222222222222222222222222222222222222222
0233555588001344558999991122222233333333333333344445566667788888
2808357938045145251222227856666800000000245668914450525572823888
4337813293243905426011116488889200245678113016533710973816182999
1277650435997582013902472672385214297424124833793829399688600012
@TWenseleers
But to explain the current growth rate advantage of Omicron over Delta one already
has to assume almost complete immune evasion even if one assumes an R0 that is
the same as Delta. R0 can't be much less than that of Delta then I would say...
---------------------------------------------------------------
cluster at TUT Nov.18
https://rekord.co.za/399202/concerns-over-rising-covid-19-cases-in-tshwane/
-------------------------------------------------------------------
Head of EU Public Health gives information that thus far
*ALL* (42) Omicron cases in EU are either mild or without symptoms.
----------------------------------------------------------------
On Monday, an NICD presentation a flagged a large number of COVID-19
admissions among infants aged under two years as an area of concern.
But von Gottberg cautioned against linking that with Omicron just yet.
"It looks like in fact some of those admissions might have started before
the emergence of Omicron. We are also seeing that there was an increase
in influenza cases just in the last month or so, and so we need to be really
careful to look at the other respiratory infections," she said.
----------------------------------------------------
... a report by Channel 12 said the Pfizer vaccine is just slightly less effective in
preventing infection with Omicron than with Delta – 90% as opposed to 95% –
while it is as effective – around 93% – in preventing serious symptoms at least
for those vaccinated with a booster.
According to the report, the ability of the variant to infect is higher than Delta but
not as much as feared – around 1.3 times higher...
-----------------------------------------------------------------
Minimum dose interval for booster jabs to be halved from 6 months to 3
months and all adults to be offered booster Covid vaccine,
UK Health Secretary Sajid Javid confirms
-----------------------------------------------------
@jburnmurdoch
So far admissions following ~same path as past waves.
------------------------------------------------------------
The earliest known cases are still from southern Africa. The first identified samples were
collected Nov. 9, from a 34-year-old man and a 23-year-old man in Johannesburg,
according to the GISAID global database. On Nov. 11, five samples of the variant were
collected in Botswana.
-----------------------------------------------------------