Alpha B.1.1.7 Variant of COVID19 coronavirus thread

[Okieman]

New variant of Covid reported in three other European countries


There are also media reports of cases in two more EU nations

Cases of Covid-19 involving the new coronavirus variant observed in Britain have been reported in at least three other countries in Europe, the European Centre for Disease Prevention and Control said.

The Stockholm-based agency said in a “threat assessment” that while preliminary analysis in the UK suggests the new variant is “significantly more transmissible”, there is no indication that infections are more severe.

It said “timely efforts” to prevent and control the spread of cases of the new variant are needed.

The ECDC said a few cases with the new variant have been reported already by Iceland, Denmark and the Netherlands.

It also cited media reports of cases in Belgium and Italy.

<snip>

https://www.kentlive.news/news/uk-world-news/new-variant-covid-reported-three-4818916

 

[Okieman]

UK coronavirus variant may be more able to infect children - scientists

By Kate Kelland

LONDON (Reuters) - A new variant of the coronavirus spreading rapidly in Britain carries mutations that could mean children are as susceptible to becoming infected with it as adults - unlike previous strains, scientists said on Monday.

Briefing reporters on the latest findings, scientists from the government’s New and Emerging Respiratory Virus Threats Advisory Group (NERVTAG) who are tracking the variant said it had swiftly become the dominant strain in the south of Britain, and could soon do the same across the country.

“We now have high confidence that this variant does have a transmission advantage over other virus variants that are currently in the UK,” said Peter Horby, a professor of emerging infectious diseases at Oxford University and chair of NERVTAG.

“There is a hint that it has a higher propensity to infect children,” said Neil Ferguson, a professor and infectious disease epidemiologist at Imperial College London and also a member of NERVTAG.

“We haven’t established any sort of causality on that, but we can see it in the data,” Ferguson said. “We will need to gather more data to see how it behaves going forward.”

<snip>

https://www.reuters.com/article/uk-...e-to-infect-children-scientists-idUKKBN28V2EV

 

[gsgs]

WHO thinks the new mutation can be controlled
--------------------------------------
they don't say what it costs. They ignore the risk of another financial crisis with Country-defaults
and currency-turbolences. We can eliminate most diseases with money, but when the system
collapses we just cannot feed the populations and pay their health anymore.
It's an economical problem. It's an ethical problem : how much worth is our health as compared
to the health of our descendents, of future generations


WHO h?lt die entdeckte Mutation des Coronavirus f?r kontrollierbar.
--------------------------------
WHO has lost its scientific competence.
Remember Chen,Fukuda etc....
Now it's mainly ethical, almost religious with Tedros.
Where is Bruce Aylward ? Remember the China-mission in Feb.

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

there will be more and new mutations. We also have it in South Africa.
They do not understand it. WHO has no clue.
They _want_ it to be controllable, but the evidence is against it.
"out of control" says Hancock.

 

[gsgs]

the South Africa mutations are listed now !
https://twitter.com/Tuliodna/status/1340902851061673985

at least the nonsynonymous ones.
Rambaut speculates that they are all related to N501Y,
(supporting it, optimising it)

he posts a tree with >50 South Africa sequences, presumably from GISAID

-------------------------------------
they have intermediate mutations in SA, so not just one immunodeficient patient.

I speculate about some mechanism to increase mutations, to deactivate
the proofreading. Still puzzled, why 55% are nonsynonymous
while for flu it's <20% and the distance to RaTG13 is 13% nonsyn.

(maybe I said this already ? hard to check in this thread)

 

[gsgs]

Fauci warns against "overreacting" to new strain,
advises against banning UK flights
{so Countries who see this differently, like most of Europe would likely have to ban flights from US then ....}
-------------------------------------------------------------
08:30 WHO :
https://www.who.int/csr/don/21-decem...ed-kingdom/en/
Most B1.1.7 cases were <60
calibrating travel related risk mitigation measures in the context of international travel,.
-------------------------------------------------------------

 

[gsgs]

08:30 WHO :
https://www.who.int/csr/don/21-decem...ed-kingdom/en/
Most B1.1.7 cases were <60
calibrating travel related risk mitigation measures in the context of international travel,.
they don't mention the stop-codon and the possibly reduced virulence

 

[sharon sanders]

FDF
@Foodanddrinkfed
?
Dec 20
Responding to this evening's suspension of accompanied freight traffic from the UK to France, FDF's CEO Ian Wright said: “Tonight’s suspension of accompanied freight traffic from the UK to France has the potential to cause serious disruption to UK Christmas fresh food supplies /1
4
56
33
FDF
@Foodanddrinkfed
?
Dec 20
– and exports of UK food and drink. Continental truckers will not want to travel here if they have a real fear of getting marooned. The Government must very urgently persuade the French government to exempt accompanied freight from its ban.”

 

[Mary Wilson]

France and UK reach deal over border, Grant Shapps says

Tuesday 22 December 2020, 10:02pm

France and the UK have reached an agreement to reopen their border after it was closed amid concerns over a new strain of coronavirus.

... Transport Secretary Grant Shapps confirmed a deal had been struck to resume travel across the border, but he urged lorry drivers not to head to Kent in the hope of getting across the border soon.

He added: "We'll be saying more on hauliers who at the moment must stay put, they mustn't travel to Kent at this time."

https://www.itv.com/news/2020-12-22/france-and-uk-reach-deal-over-border-grant-shapps-says

 

[sharon sanders]

UK's port of Dover says reopening to outgoing traffic


Issued on: 23/12/2020 - 01:27

https://www.france24.com/en/live-ne...r-says-reopening-to-outgoing-traffic?ref=tw_i

 

[sharon sanders]

Dear travelers:


In accordance with the requirements of the epidemic prevention and control work, Sichuan Airlines will suspend the carriage of passengers from the UK (GB) transiting to China via a third country from the United Kingdom (GB) from 24:00 on December 22, 2020 Beijing time. The resumption time will be notified separately.


If you have already purchased the above-mentioned ticket, please contact the original issuing place for refund procedures as soon as possible.


Thank you for your understanding and cooperation.

https://www.bjnews.com.cn/detail/160868243315378.html

 

[gsgs]

there seems to be a pattern :
occasionally we have an increase in mutations, mostly nonsynonymous, also deletions. We don't understand, why
We now had it in South Africa and South-England, and probably other places.

Also, we had at least 2 times now mutations at 3 consecutive positions. Unusual. We don't understand, why.

Also we have 55% nonsynonymous mutations, while the difference to RaTG13 and other differences have only 15% nonsynonymous.
We don't understand why.

-----------------------------------------------------------
Anyway, the growth of strains with certain spike-protein mutations should be surveilled.
Other such strains like B.1.1.7 may emerge. We must identify them earlier:
I'm trying to start here :
https://ncovinfo.createaforum.com/ge...msg267/#msg267
hopefully others will also do it or even find it and help updating

-------------------------------------------------------------------
new analysis :
https://khub.net/documents/135939561...=1608569319930
owever this was prepared 11 days ago and the latest NERVTAG assessment is 'high confidence' of increased transmission
---------------------------------------------------------------------
Racaniello still sceptical :
https://twitter.com/theosanderson/st...66269421993987
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WHO-meeting about B.1.1.7 today
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[gsgs]

good dailymail article :
https://www.dailymail.co.uk/news/ar...-shot-foot-best-world-sequencing-viruses.html

> not completely fair to slap travel bans on the UK
that's a strange way to see it. UK by itself should stop travel as Wuhan should have done in Jan.
Exporting dangerous infectious disease is not nice.
Remember, what we had calling for the last decades with WHO,CDC,ECDC, ...wrt. H5N1,Ebola,MERS. etc.
Punishing countries with travel bans ?
China, so successful in containing it inside China, now gets back what it exported in Jan+Feb .
In a more transmissable form. Greatly amplified outside China.
They could not have expected that others would be able to eradicate it as they did ....
------------------------------------------------------------------------------------
full sequence of the Pfizer vax:
https://twitter.com/markwbudde/status/1341430999381495811
I don't understand, why there are phis in it and why it doesn't match the spike
---------------------------------------------------------------------------------------------

 

[sharon sanders]

bump this

 

[Okieman]

New ‘more transmissible’ coronavirus variant discovered in UK


New variant was brought in by travelers from South Africa.
BY WILLIAM ADKINS
December 23, 2020 5:44 pm

British Health Secretary Matt Hancock announced that a new “highly concerning” variant of the coronavirus has been discovered in two individuals returning from South Africa.

“It is yet more transmissible and it appeared to have mutated further than the new variant that has been discovered here,” Hancock said in Wednesday’s Downing Street news conference.

The government is also asking anybody that has been to South Africa in the past two weeks and their close contacts to quarantine immediately. “These measures are temporary, while we investigate this further new strain, which is currently being analyzed,” he added.

<snip>

https://www.politico.eu/article/new...scovered-uk-south-africa-travel-restrictions/

 

[Mary Wilson]

COVID-19: What do we know about the second coronavirus variant found in the UK?

...Mr Hancock said it was "highly concerning" that the variant was "yet more transmissible" than the original strain - and also that it "appears to have mutated further" than the first new variant, though to an unknown extent.

Public Health England's chief adviser Dr Susan Hopkins added that the two variants have different mutations.

https://flutrackers.com/forum/forum/...ound-in-the-uk

 

[Shiloh]

Source: https://www.cnn.com/2020/12/23/heal...es-less-effective-prevent-covid-19/index.html

Genetics experts worry coronavirus vaccines might not work quite as well against UK variant
By Elizabeth Cohen, CNN Senior Medical Correspondent
Updated 6:14 PM ET, Wed December 23, 2020

(CNN)Michael Worobey, a biologist at the University of Arizona, has seen more than 100,000 different strains of the virus that causes Covid-19. But when he saw the new variant from the UK, he noticed something different.

"This is the first variant I've seen during the whole pandemic where I took a step back and said: 'Whoa,' " he remembers.
Health officials have downplayed the possibility that the coronavirus vaccines won't work against the UK strain, but Worobey and other scientists thinks it's a possibility -- and it's just a possibility -- that this new variant might, to a small extent, outsmart the vaccines.

"This is the first variant I've seen where I think there is this burning question," said Worobey, head of the department of ecology and evolutionary biology at the University of Arizona...

 

[sharon sanders]

The UK has recorded 744 more deaths, the highest daily toll since last Spring, along with more than 39,000 new coronavirus cases - the highest case number yet.

The Government said a further 744 people had died within 28 days of testing positive for Covid-19 as of Wednesday, bringing the UK total to 69,051.

It is the highest deaths figure reported on one day since April 29 during the first peak of the virus.

more....

https://www.standard.co.uk/news/uk/uk-covid-death-toll-highest-cases-b460321.html

 

[gsgs]

UK coronavirus variant found in Malaysia and Singapore
---------------------------------------------------------
Estimated transmissibility and severity of novel SARS-CoV-2 Variant of Concern 202012/01 in England
https://cmmid.github.io/topics/covid...l-variant.html
56% more transmissible
found no evidence for greater or lesser severity
Our estimates suggest that control measures of a similar stringency to the national lockdown
implemented in England in November 2020 are unlikely to reduce the effective reproduction
number Rt to less than 1, unless primary schools, secondary schools, and universities are also closed.
-----------------------------------------------
there is another strain , B.1.1.70 with equally many mutations, again mostly nonsynonymous,
but not so many in spike, which grew remarcably. But only in Wales it rarely went to England.
http://magictour.free.fr/b117a.GIF
------------------------------------------
England bans flights and visitors from South Africa due to coronavirus mutation
in SA, cases are increasing at a slower rate since 1 week, still increasing a lot, though
http://magictour.free.fr/e-1222.GIF
--------------------------------------------------------
China bans flights to and from the UK due to coronavirus mutation
-----------------------------------------------------
Detection of SARS-CoV-2 P681H Spike Protein Variant in Nigeria
-------------------------------------------------

 

[gsgs]

TWiV 697:
https://www.microbe.tv/twiv/
NERVTAG meeting minutes (pdf)
NERVTAG
Preliminary genomic characterization of UK variant (virological.org)
PHE investigation of UK variant (pdf)
N501Y does not affect antibody neutralization (Science, eLife)
WHO notice on UK variant (WHO)
------------------------------------------------------------------------------
TWiV697 , recorded on Dec23
07:00 NERVTAG, 11:40 VR:can be misleading,
seem to accept somehow, that it's probably more transmissable
18:30 animal experiments --> increased transmissability of D614G
[gs: some paper got confusing results about several regions, which was it
maybe nervtag3.pdf]
23:00 , VR : (animals) wants to see human data
33:00 VR sees no big change of the situation now with B.1.1.7
plays down genomics 41:20 stop-codon
I stopped at 50:00
1:12 (Kathy Spindler ?) , general agreement
1:18 emails

------------------------------------
nervtag3 : New evidence on VUI-202012/01 and review
of the public health risk assessment
it's not the one, I was looking for

found it , b117h.pdf
Early Analysis of a potential link between viral load and the N501Y
mutation in the SARS-COV-2 spike protein
so , e) below makes some doubts

Summary
a) A new variant of SARS-CoV-2 has emerged which is increasing in frequency, primarily
in the South East of England (lineage B.1.1.7 ​(​1​)​; VUI-202012/01).
b) One potential hypothesis is that infection with the new variant results in higher viral
loads, which in turn may make the virus more transmissible.
c) We found higher (sequence derived) viral loads in samples from individuals infected with
the new variant. Median inferred viral loads were three-fold higher in individuals with the
new variant (Fig. 1).
d) Most of the new variants were sampled in Kent and Greater London. We observed
higher viral loads in Kent compared to Greater London for both the new variant and
other circulating lineages.
e) Outside Greater London, the variant has higher viral loads. Within Greater London, the
new variant does not have significantly higher viral loads compared to other circulating
lineages.
f) Higher variant viral loads outside Greater London could be due to demographic effects,
such as a faster variant growth rate compared to other lineages or concentration in
particular age-groups. Our analysis does not exclude a causal link between infection
with the new variant and higher viral loads.
g) This is a preliminary analysis and further work is needed to investigate any potential
causal link between infection with this new variant and higher viral loads, and whether
this results in higher transmissibility, severity of infection, or affects relative rates of
symptomatic and asymptomatic infection

 

[gsgs]

33 cases of B.1.1.7 SARS-CoV-2 in Denmark from 14 nov to 14 dec out
of 7805 genomes. 12 of these from contact tracing.
--------------------------------------------------

one "South-African" virus is now at cogconsortium.uk , it has these 24 mutations ::
>England/ALDP-C497BF/2020,UK,UK-ENG,2020-12-12,50,B.1.351,1.0,G,N,L,A,Y,Y,T,P,Q,ref,24
G174T,C241T,C1059T,A2692T,C3037T,C4202T,G5230T,T6106C,C9344T,A10323G,
C14408T,A21801C,A22206G,G22813T,G23012A,A23063T,A23403G,C23664T,G25563T,C25904T,
C26456T,T27193C,C28253T,C28887T
-----------------------------------------------------------------
@AineToole 1h
We're now hosting a daily global report tracking new variant #SARSCoV2 lineage B.1.1.7 and B.1.351 on
http://cov-lineages.org/global_report.html
Data displayed in the report pulled from GISAID this morning 2020-12-24 and pangolin was
run on the entire dataset.
--------------------------------------------------------------------
Introduction into the Marseille geographical area of a mild SARS-CoV-2 variant originating from
sub-Saharan Africa https://medrxiv.org/cgi/content/short/2020.12.23.20248758v1 #medRxiv
have been submitted to the GISAID database.
The Marseille-1 variant emerged in week 27, when it accounted for 100% of
sequenced genomes (Figure 1)
We obtained SARS-CoV-2 full-
length genome sequences from 916 patients (submitted to the GISAID database). These
included 429 genomes from episode 2, which were added to 487 genomes from episode 1 11.
we cannot rule out that the mutations observed in the Marseille-1 variant
... occurred in an animal population in sub-Saharan countries,
# they really should hve told us earlier. The strains in SA and UK may have been deteted earlier.
# This scientific process with publishing in papers and funding is unfortunate
# Why is it so bad for researchers to report about interesting facts directly ?
# Can't we protect their "copyright" if they do ?


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SAGE : The entire UK needs to go into Tier 4 *TODAY*