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Alpha B.1.1.7 Variant of COVID19 coronavirus thread

kiwibird

kiwibird

Editor, Senior Moderator
https://news.sky.com/story/new-varia...-says-12161416

New variant' of coronavirus identified in UK, health secretary says
It is "highly unlikely" the new mutation would not respond to a coronavirus vaccine, Mr Hancock told the Commons today.

More than 1,000 cases of the new variant have been found, "predominantly in the south of England", Mr Hancock told the House of Commons this afternoon.

It is spreading faster than the existing strain of the virus and believed to be fuelling the "very sharp, exponential rises" in cases across the South East, he said.
Click to expand...
 
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Is the vaccine effective against the new coronavirus strain? Everything you need to know

More than 1,000 infections related to new variant reported across nearly 60 different local authorities in England, says government

Samuel Lovett
54 minutes ago

... That particular strain has shown “moderately decreased sensitivity” to the body’s neutralising antibodies, but there have been no indications it could impact the effectiveness of a vaccine, despite apparent genetic changes to the virus’ spike protein.

The UK’s new strain contains similar mutations to the spike receptor, which is the target of the majority of vaccines currently in development, but Dr Andrew Davidson, a reader in virology at the University of Bristol, does not believe this will present a significant issue.
...

https://www.independent.co.uk/news/...=Social&utm_source=Twitter#Echobox=1607971775
 
Update on new SARS-CoV-2 variant and how COG-UK tracks emerging mutations

COG-UK 14 Dec 2020

Since its creation COG-UK has been supporting genomic surveillance efforts to identify variants of the SARS-CoV-2 virus in the genome sequencing data from the UK.

New SARS-CoV-2 variant

The variant described today in the House of Commons contains a novel set of mutations associated with a lineage spreading rapidly in the South East of England (and more widely) that is the subject of ongoing investigations by the UK Public Health Agencies, coordinated by Public Health England and supported by COG-UK. This variant carries a set of mutations including an N501Y mutation in the receptor binding motif of the Spike protein that the virus uses to bind to the human ACE2 receptor.

Efforts are under way to confirm whether or not any of these mutations are contributing to increased transmission. There is currently no evidence that this variant (or any other studied to date) has any impact on disease severity, or that it will render vaccines less effective, although both questions require further studies performed at pace. We will provide further updates as our investigations proceed.

https://www.cogconsortium.uk/news_i...ant-and-how-cog-uk-tracks-emerging-mutations/
 
New coronavirus strain spreading in UK has key mutations, scientists say

LONDON (Reuters) - British scientists are trying to establish whether the rapid spread in southern England of a new variant of the virus that causes COVID-19 is linked to key mutations they have detected in the strain, they said on Tuesday.
 
I think, the deletion happened independently
at least 4 times in different strains,
even in the original with 614D.
The Danish strain with N439K is one of them.
The B.1.1.7 with N501Y and many mutations
of unclear origin is another.
http://magictour.free.fr/s2uk6-d6.GIF
http://magictour.free.fr/sars2deb.GIF

37 (out of 40000) at genbank with N501Y , mainly Australia, different strain.

That B1.1.7 has 25 Mutations ! It suddenly appeared in UK in Sept., it's unclear where it came from,
where it achieved these 25 mutations.

strange are also these mutations at 3 consecutive positions : 28280-2 and 28881-3 (ORF8)
I don't remember having seen that before

ORF8 is a rapidly evolving accessory protein that has been proposed to interfere with immune responses.

----------------edit---------------------
@arambaut 1h
Our current hypothesis is a substantial role for a chronically infected individual
(unsampled) with a transmission late in the infection.
In fact, personally I think it is the only likely explanation.

https://twitter.com/arambaut/status/1339139131029467138
 
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there are 2 other deletions in B.1.1.7 :
9 nucleotides : 11288-11296
3 nucleotides : 21991-21993

and from the 25 (new) mutations 19 (!) are nonsynonymous
 
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Fast-spreading strain of mutated coronavirus is found in Wales and Scotland

Scientists warn the VUI – 202012/01 variant appears to be spreading faster than other forms and is appearing most in areas of the country where infection rates are rising quickest

15:46, 15 DEC 2020
UPDATED19:31, 15 DEC 2020
By Martin Bagot Health and Science editor

The new mutated form of coronavirus has now spread to Wales and Scotland.
Experts analysing the genetic code of the variant say it is believed to have originated in South East England and was not imported from abroad.

Scientists contributing to the Government surveillance programme warn the VUI – 202012/01 variant appears to be spreading faster than other forms.

... The network of experts said VUI – 202012/01 has caused concern because it is appearing most in areas of the country where infection rates are rising quickest.

They were also concerned because it displays 17 changes to the original virus - many more than previous variants detected by their surveillance.

... The Mirror reported today how one in ten Londoners who caught the novel coronavirus last month were infected with the new strain, according to an expert.

Dr Andrew Page, who is at the forefront of research work into Covid-19, has said the virus's new strain "came out of nowhere".

In the month since detection in October the mutated virus, which has been named VUI – 202012/01, has infected 19.2% of all new Covid-19 patients in Norfolk.

https://www.mirror.co.uk/news/politi...covid-23172171
 
Major patient backlog at Medway Maritime Hospital, Gillingham

Emergency planners in Kent have met over concerns ambulances won't be able to get some patients into hospitals.

Increasing Covid numbers have seen casualty departments stretched to their limits.

<snip>
A Medway hospital worker, who asked to remain anonymous, said how at one point yesterday they counted 18 ambulances outside.

This meant an average of six-hour waits to get people in to be seen.

They also confirmed that Covid patients were now commonplace in every ward, including children's wards.

Also a "high number" of teenagers had been admitted with the illness.

<snip>

https://www.kentonline.co.uk/medway/news/major-backlog-as-hospital-reaches-capacity-239362/
 
We must stop/contain/eliminate B.1.1.7 , it could be dangerous.
17 aa-mutations plus 3 deletions and most in spike.
See how quickly it emerged from zero to widespread.
The world hopes that Britain won't export it .
The EU should contribute to the costs.

---------------------------------------
who are MILK-9E05B3 and MILK-9E2FE0 from Sep20 ?
Where did they get it from ?
-----------------------------------------
 
I have personal feedback from front line medics who are noting more extreme lactic acid build ups in patients from new variant (marker for septic shock). Too early to say about effects on mortality etc.
 
More lactic acid doesn't sound good. Any chance those cases are from a further mutation of the new variant?
 
one of these mutations in B.1.1.7 makes a stop-codon in ORF8,
thus effectively stopping the virus from using that protein.
Just as in the 382-deletion variant early in Singapore.

> After adjusting for age and presence of comorbidities,
> infection with the ∆382 variant only was associated
> with lower odds of developing hypoxia requiring
> supplemental oxygen (adjusted odds ratio
> 0?07 [95% CI 0?00–0?48]) compared with infection
> with wild-type virus only.
https://www.thelancet.com/action/showPdf?pii=S0140-6736(20)31757-8
----------------------------------------------
>, none of the patients in which the Δ382
> variant were detected required intensive care unit admission or invasive mechanical
> ventilation, compared to 16% and 11%, respectively, for the wild-type strain


so, that might be good.
While I just tweeted this were potentially dangerous and should be stopped
 
Also in Denmark -


snip


The new variant is currently present in the UK and Denmark only, according to European scientists tracking the genetic mutations of the virus.

Dr de Gascun said this highlighted the continued importance of surveillance and maintaining public health measures.

Immunologist Prof Paul Moynagh said people should not rush to be concerned over the newly identified mutation.

https://www.irishtimes.com/news/hea...in-uk-has-not-been-found-in-ireland-1.4437398
 
that's how Public Health England (PHE) called it.
https://www.gov.uk/government/news/phe-investigating-a-novel-strain-of-covid-19

cogconsortium called it B.1.1.7 , I keep searching twitter for B.1.1.7

GISAID also has a good short article now :
https://www.gisaid.org/references/gisaid-in-the-news/uk-reports-new-variant-termed-vui-20201201/

they also mention the stop-codon

we must have had a thread here about the 382 deletion,
it was also at TWiV , afair
https://flutrackers.com/forum/forum...mation/gsgs-s-workroom/848556-382-nt-deletion


I'm looking forward to the data whether it's less lethal now
and a discussion whether we may let it spread or even import and spread it
deliberately in some countries.

(why can't I find that already ?)

-------------------------------------------------------------------------
this German article mentions (summarises ?) a recent article in "British Medical Journal"
quotes from Nick Loman ,Sharon Peacock
https://www.heilpraxisnet.de/naturh...s-variante-in-grossbritannien-20201217529795/
B.1.1.7 reached 20% of sequences in Norfolk
no mentioning of the stop-codon in ORF8
----------------------------------------------------------------------------
I ound it : https://www.bmj.com/content/371/bmj.m4857
 
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Emily - too early to say. New variant is currently entered in the south east and appears to be responsible for an explosion in case numbers, and pressures are escalating in hospitals. Also some reported change in profiles of hospitalised patients, yet to be verified. We will have to be patient before we have accurate facts and more work done to assess the impacts of the changes. 17 mutations is quite significant, with the majority on the spike, there has to be some effects.
 
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