Covid Mutations

[2hats]

B.1.351 clearly circulating in the community in the UK.

South African variant of Covid found in eight areas of England

Door-to-door testing launched as cases found in Hertfordshire, Surrey, Kent, Walsall, Sefton and three London boroughs

www.theguardian.com

 

[weltweit]

If the SA variant is here they had better be sure it is affected by the vaccines otherwise the vaccines will clear out the existing variant leaving the SA variant free to run riot.

 

[2hats]

I put this in the other thread but it makes more sense as a a reply here


Let's hope gaps longer than three weeks give similar results.

 

[2hats]

PHE update on VOC 202012/01 - technical briefing 5 - notes that genomic data indicates independent incidences of B.1.1.7 acquiring the E484K mutation (as seen in B.1.351, P.1 'escape' variants) in some wild samples recently collected in the UK. This is suggestive of convergent evolution which separately has recently been observed in vitro in cell cultures of recovered patient sera with antibodies (DOI: 10.1101/2020.12.28.424451) where E484K spontaneously arose after around 80 days incubation.

 

[2hats]

More contagious mutation causes half of new Dutch virus cases

The coronavirus mutation first detected in Britain caused half of all new infections in the Netherlands by Jan. 26, Dutch health minister Hugo de Jonge said on Monday.

www.reuters.com

 

[2hats]

B.1.1.7 outbreak in Vietnam.

Vietnam confirms latest virus outbreak is more contagious UK variant

Vietnam's health minister said on Tuesday a newly detected coronavirus outbreak, which has infected 301 people and spread to 10 provinces and cities, is caused by the more contagious British variant of the coronavirus.

www.reuters.com

 

[sptme]

Hi 2hats any chance you could summarise these last couple of days posts into simple English for us less scientifically minded folk. Thanks

 

[wayward bob]

am i reading it right that the bristol/liverpool cases mentioned by hancock today are the b.1.1.7 variant with added mutations that are the same as (but independent from) the SA variant? (as mentioned in your post last night 2hats)

Public Health England's team said they have identified 11 cases of the variant of Concern VOC202012/01, which genomic sequencing has shown to feature the spike protein mutation E484K, predominantly situated within the South West.

Everything we know as 'mutations of concern' found in Bristol

It is not yet known whether the new coronavirus mutation is more dangerous

www.bristolpost.co.uk

 

[wayward bob]

A separate variant featuring E484K (with potential for natural immunity/vaccine escape) may have independently arisen in Liverpool, where PHE are investigating a cluster. Lacking in detail somewhat right now.

Covid mutation cluster traced back to Liverpool

Cluster of cases involving mutation located among staff from Liverpool Women's Hospital

www.liverpoolecho.co.uk

okay reading back, it's this? apols doing my thinking out loud

 

[2hats]

am i reading it right that the bristol/liverpool cases mentioned by hancock today are the b.1.1.7 variant with added mutations that are the same as (but independent from) the SA variant? (as mentioned in your post last night 2hats)

Correct. Well, at least the cases in Bristol, to the best of my knowledge (e2a: 11 VOC202012/01+E484K reported thus far and in the genomic databases right now and 11 Bristol cases according to PHE via media).

e2a: Suspect the Liverpool cases are other E484K (B.1.351, or, less likely, P.1), probably related to this.
2e2a: Genomic database indicates earliest sighting of this was mid-December.

 

[2hats]

Hi 2hats any chance you could summarise these last couple of days posts into simple English for us less scientifically minded folk. Thanks ☺

The virus has 'discovered' [*] a handy couple of mutations that together [**] gain it an advantage, to varying degrees, in both transmission and evasion of previously acquired immunity (whether via infection or vaccination) to varying degrees.

* Of course, nothing has been discovered and the virus isn't intelligent; it's a selection effect.
** There are actually a couple of other changes which are almost certainly helping too.

 

[sptme]

The virus has 'discovered' [*] a handy couple of mutations that together [**] gain it an advantage, to varying degrees, in both transmission and evasion of previously acquired immunity (whether via infection or vaccination) to varying degrees.

* Of course, nothing has been discovered and the virus isn't intelligent; it's a selection effect.
** There are actually a couple of other changes which are almost certainly helping too.

Is this the Kent evolved virus or the South African one or the Brazil one or something new again?

 

[2hats]

Is this the Kent evolved virus or the South African one or the Brazil one or something new again?

All of the above. Convergent evolution.

 

[Doodler]

Dido Harding is quoted in the news today as stating:

We have seen the new variant emerge, which was something that none of us were able to predict.

If her advisory staff are all creationists that's possibly true.

 

[Doodler]

Surely it's not unreasonable to expect that a virus long adapted to animals which spend a lot of time being this close . . .



. . might experience selection pressures for increased transmissibility on crossing to a species influenced by concepts of personal space.

 

[2hats]

Dido Harding is quoted in the news today as stating:

We have seen the new variant emerge, which was something that none of us were able to predict.

If her advisory staff are all creationists that's possibly true.

 

[2hats]

Multiple B.1.351 introductions seen in Ireland and clusters of the same likely indicating local transmission in the Netherlands. Multiple clusters of P.2 in the UK might point to ongoing community transmission.

The E484K variant associated with a number of cases in/around Liverpool has been labelled A.23.1 (it did not arise from B.1.1.7).

 

[Doodler]

I hope they throw the book at him. That's recklessness.

The Japanese would be well entitled to make him the subject of one of their more interesting TV game shows.

 

[2hats]

Looks like B.1.351 is a growing problem in Austria.

After Travel Warning: Further Restrictions for Tyrol

Austria's federal government has decided to further tighten the measures for the province of Tyrol, excluding East Tyrol. After announcing a non-binding travel…

www.vindobona.org

 

[2hats]

Interesting case of a 45 year old immunocompromised patient (Boston, MA) who was infected for 155 days with SARS-CoV-2 until death. Accelerated exploration of mutations during that time was observed, including a number of the current ones in variants of concern, for example E484K by day 75, N501Y by day 128.

DOI: 10.1056/NEJMc2031364.

 

[2hats]

NERVTAG have declared the "Bristol" variant (B.1.1.7+E484K) to be a Variant Of Concern and the "Liverpool" variant (A.23.1+E484K) to be a Variant Under Investigation.

 

[weltweit]

NERVTAG have declared the "Bristol" variant (B.1.1.7+E484K) to be a Variant Of Concern and the "Liverpool" variant (A.23.1+E484K) to be a Variant Under Investigation.

More VOI, this isn't good news.

 

[2hats]

New work attempting to map various RBD mutations and their proclivity towards reducing binding by human convalescent plasma. Whilst E484K is the flavour of the moment there are other mutations to keep an eye on. Notably in the 443-450 loop and along the RBD receptor binding ridge (eg locations such as L455, F456, G485, F486, and F490). Though it should be noted that there can be quite a variation across individuals and relevance of mutations (or combinations thereof) can change during the course of an infection.

Most frequent mutations:

Mutation	Cumulative prevalence (%)
S477N	5.69
N439K	1.49
N501Y	1.39
Y453F	0.36

Mutations at key sites:

Mutation	Cumulative prevalence (%)
E484K	0.11
K417N	0.07
S494P	0.06
L452R	0.02
G446V	0.02
F490S	0.02
L452M	0.02
L455F	0.02
E484Q	0.02
F486L	0.01
G485R	0.01

DOI: 10.1016/j.chom.2021.02.003.

 

[2hats]

NERVTAG have declared the "Bristol" variant (B.1.1.7+E484K) to be a Variant Of Concern and the "Liverpool" variant (A.23.1+E484K) to be a Variant Under Investigation.

To clarify: "Bristol" variant (B.1.1.7+E484K) labelled VOC-202102/02, "Liverpool" variant (A.23.1+E484K) labelled VUI-202102/01.

 

[William of Walworth]

Ian Sample, Guardian Science Editor, suggests +early+ signs in the UK of limited spread of the SA variant -- for now

UK total of 170 cases of South Africa Covid variant 'reassuring'

Public Health England expert says figure suggests B1351 has not taken hold in Britain

Public Health England has uncovered a total of 170 confirmed or probable cases of the South Africa variant of coronavirus that appears less susceptible to vaccines.
Routine and surge testing revealed 151 cases in England, six in Scotland and 13 in Wales, according to Dr Susan Hopkins, PHE’s strategic response director, who described the numbers as “reassuring” because they suggest the variant has not taken hold in the UK.

Scientists are keeping a watchful eye on the South Africa variant, named B1351 or 501YV2, because it could undermine efforts to contain the epidemic with vaccines should it spread more widely. Of the 170 cases, 18 are not linked to international travel, suggesting they were caught in the community.

 

[2hats]

A.23.1 (same lineage as the "Liverpool" variant) recorded in some 12 countries now and quite likely to be the dominant variant in Uganda.
DOI: 10.1101/2021.02.08.21251393.

New variant, coined B.1.525, with mutations E484K, Q677H, F888L plus deletions 69-70, 144 (cf B.1.1.7) and the nsp6 deletion (cf B.1.1.7, B.1.351, P.1). Geographically widespread.

 

[nyxx]

WRT naming variants of concern - there was a lot of pushback against calling the virus after the place it was first identified, and this made sense given that various people were attacked because of their perceived ethnicity. How does that map across to naming these variants? I don’t think the general public are going to remember the number/letter combos, I’m certainly struggling with it. Is naming them for the places they were identified the generally accepted method? What other method would there be, realistically?

 

[2hats]

New variant, coined B.1.525, with mutations E484K, Q677H, F888L plus deletions 69-70, 144 (cf B.1.1.7) and the nsp6 deletion (cf B.1.1.7, B.1.351, P.1). Geographically widespread.

Another new coronavirus variant seen in the UK

It has similar mutations to the South Africa variant, so how worrying is it?

www.bbc.co.uk

 

[2hats]

As anticipated, and now if verified, potentially the real fun begins.

Exclusive: Two variants have merged into heavily mutated coronavirus

The UK and California variants of coronavirus appear to have combined into a heavily mutated hybrid, sparking concern that we may be entering a new phase of the covid-19 pandemic

www.newscientist.com

 

[Mr.Bishie]

Depressing.