Covid Mutations
- Thread starter Supine
- Start date
2hats
Dust.
SA variant (501Y.V2) a source of concern for Bell. All of its spike mutations (10) have the potential to undermine T cell recognition and reduce vaccine efficacy. A South African research group is investigating its ability to evade T cell response and the Oxford team is assessing the implications for AZD1222.
www.telegraph.co.uk
South African variant may evade vaccines and testing, warn scientists
Former health secretary, Jeremy Hunt, voices fears over mutation and calls for a 12-week lockdown
www.telegraph.co.uk
South African variant could be resistant to vaccine, expert suggests, but new jab could be made in 'weeks'
By Lizzie Roberts 3 January 2021 • 7:00pm
The coronavirus variant currently circulating in South Africa could be resistant to the vaccine, a leading expert has suggested, but cautioned it could take just six weeks to develop a new jab if needed.
Sir John Bell, Regius Professor of Medicine at the University of Oxford, said his “gut feeling” was that the vaccines already on stream would be effective against the new UK strain, which was first identified in Kent.
But he said: “I don't know about the South African strain, I think that's a big question mark.”
South Africans were placed on lockdown last week after President Cyril Ramaphosa said that a new variant - 501.V2 - appeared to be “more contagious” than the virus which circulated during the first wave.
Matt Hancock, the Health Secretary, said on December 23 that two cases of the South African strain had been identified in the UK.
The cases and their contacts were quarantined and the Government placed strict restrictions on travel from South Africa.
Anyone who had been in contact with someone who had been in the country within the last two weeks were told they must quarantine.
Speaking to Times Radio, Sir John said he was more concerned about this strain compared to the UK one “by some margin”.
“The mutations associated with the South African form are really pretty substantial changes in the structure of the protein,” he said.
He added that the strain had mutated in the part of the virus which allows antibodies to stick to it.
He added that although there was no data yet on whether it increases severity, “it's increased the infectiousness, probably by increasing its ability to bind to the human cells”.
Asked whether the current Covid-19 vaccines will be able to tackle both the UK and South African variant, he said the Oxford University team are currently assessing this possibility.
Sir John said there was still “room to maneuver” in relation to the vaccines as they worked “much better than any of us thought they were going to”.
“I think it's unlikely that these mutations will turn off the effects of vaccines entirely, I think they’ll still have a residual effect,” he said.
He added it was “perfectly possible” to make new vaccines in a matter of weeks if necessary.
“It might take a month, or six weeks, to get a new vaccine, so everybody should stay calm. It's going to be fine,” he added.
“But we're now in a game of cat and mouse, because these are not the only two variants we're gonna see, we’re going to see lots of variants.”
As of December 27, 944,539 people in the UK have received their first dose of the Pfizer vaccine. From Monday, the first doses of the Oxford AstraZeneca jab will be administered.
By Lizzie Roberts 3 January 2021 • 7:00pm
The coronavirus variant currently circulating in South Africa could be resistant to the vaccine, a leading expert has suggested, but cautioned it could take just six weeks to develop a new jab if needed.
Sir John Bell, Regius Professor of Medicine at the University of Oxford, said his “gut feeling” was that the vaccines already on stream would be effective against the new UK strain, which was first identified in Kent.
But he said: “I don't know about the South African strain, I think that's a big question mark.”
South Africans were placed on lockdown last week after President Cyril Ramaphosa said that a new variant - 501.V2 - appeared to be “more contagious” than the virus which circulated during the first wave.
Matt Hancock, the Health Secretary, said on December 23 that two cases of the South African strain had been identified in the UK.
The cases and their contacts were quarantined and the Government placed strict restrictions on travel from South Africa.
Anyone who had been in contact with someone who had been in the country within the last two weeks were told they must quarantine.
Speaking to Times Radio, Sir John said he was more concerned about this strain compared to the UK one “by some margin”.
“The mutations associated with the South African form are really pretty substantial changes in the structure of the protein,” he said.
He added that the strain had mutated in the part of the virus which allows antibodies to stick to it.
He added that although there was no data yet on whether it increases severity, “it's increased the infectiousness, probably by increasing its ability to bind to the human cells”.
Asked whether the current Covid-19 vaccines will be able to tackle both the UK and South African variant, he said the Oxford University team are currently assessing this possibility.
Sir John said there was still “room to maneuver” in relation to the vaccines as they worked “much better than any of us thought they were going to”.
“I think it's unlikely that these mutations will turn off the effects of vaccines entirely, I think they’ll still have a residual effect,” he said.
He added it was “perfectly possible” to make new vaccines in a matter of weeks if necessary.
“It might take a month, or six weeks, to get a new vaccine, so everybody should stay calm. It's going to be fine,” he added.
“But we're now in a game of cat and mouse, because these are not the only two variants we're gonna see, we’re going to see lots of variants.”
As of December 27, 944,539 people in the UK have received their first dose of the Pfizer vaccine. From Monday, the first doses of the Oxford AstraZeneca jab will be administered.
2hats
Dust.
2hats
Dust.
No recent travel history.
www.bloomberg.com
New York State Reports First Case of U.K. Covid-19 Variant
New York state has found its first case of the U.K. variant of coronavirus, Governor Andrew Cuomo said.
www.bloomberg.com
2hats
Dust.
More in vitro neutralising studies of the new variants starting to come in. Here in particular mapping of the effect on neutralisation of the various changes in the receptor binding domain.
Comprehensive mapping of mutations to the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human serum antibodies, Greaney, Loes, Crawford, Starr, Malone, Chu, Bloom, DOI: 10.1101/2020.12.31.425021.
Essentially E484K found (eg) in N501Y.V2 (B.1.351) is of most concern. It demonstrated a ten fold reduction in activity in neutralising assays in convalescent polyclonal human sera from a number of individuals (note: reduces neutralisation, does not fully undermine).
N501Y seen in (eg) VOC202012/01 (501Y.V1/B.1.1.7) was not found to have a strong effect on neutralising sera.
There are additional mutations in some variants (eg G446V and in the 443-450 loop) that appeared to reduce neutralisation in a subset of individuals and/or at particular stages of the infection cycle (ie degree of compromise of neutralisation varied with individuals and over time for any given individual). Effects of most mutations vary across individuals and thus may have a reduced impact across large populations.
This work tallies with the behaviour of E484K seen in DOI: 10.1101/2020.12.28.424451, mentioned in the vaccines/treatment thread, where several fold reductions in neutralising effect were seen in a number of sera.
Studies on vaccine sera yet to be completed.
(PS thread title is technically incorrect
)
Comprehensive mapping of mutations to the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human serum antibodies, Greaney, Loes, Crawford, Starr, Malone, Chu, Bloom, DOI: 10.1101/2020.12.31.425021.
Essentially E484K found (eg) in N501Y.V2 (B.1.351) is of most concern. It demonstrated a ten fold reduction in activity in neutralising assays in convalescent polyclonal human sera from a number of individuals (note: reduces neutralisation, does not fully undermine).
N501Y seen in (eg) VOC202012/01 (501Y.V1/B.1.1.7) was not found to have a strong effect on neutralising sera.
There are additional mutations in some variants (eg G446V and in the 443-450 loop) that appeared to reduce neutralisation in a subset of individuals and/or at particular stages of the infection cycle (ie degree of compromise of neutralisation varied with individuals and over time for any given individual). Effects of most mutations vary across individuals and thus may have a reduced impact across large populations.
This work tallies with the behaviour of E484K seen in DOI: 10.1101/2020.12.28.424451, mentioned in the vaccines/treatment thread, where several fold reductions in neutralising effect were seen in a number of sera.
Studies on vaccine sera yet to be completed.
(PS thread title is technically incorrect
)
Last edited:
wayward bob
i ate all your bees
"an escaped mutant" is the technical term?? (per whitty on the telly) they could find a more reassuring phrasing, no?
SpookyFrank
A cheap source of teeth for aquarium gravel
Yes, 'antigenic escape' is a technical term. Refers to a mutation or set of mutations which allow a pathogen to evade an acquired response while still able to function.
elbows
Well-Known Member
Yes the term is used in this NERVTAG document from September, a document which is now out of date in some regards since it came before UK and South Africa new variant concerns emerged properly.
I imagine the term vaccine escape mutants is even less reassuring. Official experts are probably wary about giving false reassurances on these fronts, they want the detail to demonstrate any legitimately reassuring aspects, not to soften the language and terminology for the sake of it, especially if nobody else has taken the time to create different terminology for them to use.
I wonder if I was overly reassuring when at various stages of this pandemic I kept going on about the press reaching for their book of tired 1918 pandemic mutation cliches, and how the evolution of this pandemic virus was unlikely to stick to some holywood script and pop notion about the 2nd wave being more deadly to young people etc etc. Hopefully I remembered not to be too reassuring, by pointing out that pressures on the virus might be expeted to be more likely to lead to it developing greater transmissibility/infectiousness rather than some other characteristic which was not a great advantage, such as causing more severe illness in younger people. Nut Im not sure how much I did, I was probably more interested in moaning about some of the tired cliches and assumptions, and that will bite me on the arse if the evolution of this virus turns out to resemble any of those cliches.
I imagine the term vaccine escape mutants is even less reassuring. Official experts are probably wary about giving false reassurances on these fronts, they want the detail to demonstrate any legitimately reassuring aspects, not to soften the language and terminology for the sake of it, especially if nobody else has taken the time to create different terminology for them to use.
I wonder if I was overly reassuring when at various stages of this pandemic I kept going on about the press reaching for their book of tired 1918 pandemic mutation cliches, and how the evolution of this pandemic virus was unlikely to stick to some holywood script and pop notion about the 2nd wave being more deadly to young people etc etc. Hopefully I remembered not to be too reassuring, by pointing out that pressures on the virus might be expeted to be more likely to lead to it developing greater transmissibility/infectiousness rather than some other characteristic which was not a great advantage, such as causing more severe illness in younger people. Nut Im not sure how much I did, I was probably more interested in moaning about some of the tired cliches and assumptions, and that will bite me on the arse if the evolution of this virus turns out to resemble any of those cliches.
elbows
Well-Known Member
Ah I just got round to watching that press conference and I think the problem is more that the likes of Whitty and Vallance dont always notice when they are throwing jargon around without explaining it to the wider audience. Sometimes they notice and add proper explanations, but they arent always good at that side of things. There have been press conferences where Whitty has spent loads of time explaining all sorts of stuff for far longer than is typical of that press conference format, but today wasnt one of those days.
The likes of JVT are more likely to avoid the jargon and put planning into explanations that may serve a broad audience, but nobody is perfect and sometimes his attempts dont necessarily hit the mark either. I know the feeeling, I'm not always happy with my attempts at explainations on this forum, its one of the reasons I often repeat the same point a lot, seeking to put it slightly differently each time in case I can improve the points ability to resonate.
The likes of JVT are more likely to avoid the jargon and put planning into explanations that may serve a broad audience, but nobody is perfect and sometimes his attempts dont necessarily hit the mark either. I know the feeeling, I'm not always happy with my attempts at explainations on this forum, its one of the reasons I often repeat the same point a lot, seeking to put it slightly differently each time in case I can improve the points ability to resonate.
He got taken to task about this the other day on TWIV. He's more concerned about bad science than anything else. He pretty much ssid in reality it could be a problem and mote transmissible though it is not proven however it should be treated as such for public health reasons. Fortunately the measures are similar to those for existing variants and they should be followed.
elbows
Well-Known Member
I end up using place names for strains when thats the language many are using in the mainstream to reference particular strains, but I would support efforts to use names that arent linked to places.
It seems to me that the overly technical naming of these strains doesnt help the chances of this happening. B.1.1.7 doesnt do the job, although I had a similar complaint about Covid-19 when that term didnt seem to be catching on well at all, and yet eventually that name did gain more of a foothold.
Maybe we need a more imaginitive naming committee or perhaps a public naming contest. Mutatey McMutantFace entries may yet subvert such plans though.
It seems to me that the overly technical naming of these strains doesnt help the chances of this happening. B.1.1.7 doesnt do the job, although I had a similar complaint about Covid-19 when that term didnt seem to be catching on well at all, and yet eventually that name did gain more of a foothold.
Maybe we need a more imaginitive naming committee or perhaps a public naming contest. Mutatey McMutantFace entries may yet subvert such plans though.
prunus
Tick tock.
B117 works for me. Less key presses and traceable to the science.
I suppose we could call it Dave if Mutanty McMutant Face is too long a name
How about we call it Boris?
Supine
Newt Member
wouldnt be fair for the virus
elbows
Well-Known Member
Could someone who doesnt mind messing around with spreadsheets and graphs take a look at this data?
Its the same data release that was used today to say that they estimate 1 in 50 people have been infected recently. But it also includes data relating to the different regions in England and the percentages testing positive in a way thats compatible with the new variant (s-gene dropout) as the percentages testing positive for other strains. Im tired so when I had a quick go some of the results looked somewhat interesting for the more recent days, I didnt trust myself to present this data at the moment, I wanted other opinions before making comment. And I was being a bit sloppy when I had a go so I just threw all the columns relating to upper and lower 95% credible interval figures away and graphed the basics.
The data in question is in tab 4 of the spreadheet that can be downloaded here:
Also the graphs of that data probably featured in the press conference today as well, but I wasnt paying enough attention at the time and when I went to the website where the slides are normally made available to download, I dont think todays stuff was there.
Its the same data release that was used today to say that they estimate 1 in 50 people have been infected recently. But it also includes data relating to the different regions in England and the percentages testing positive in a way thats compatible with the new variant (s-gene dropout) as the percentages testing positive for other strains. Im tired so when I had a quick go some of the results looked somewhat interesting for the more recent days, I didnt trust myself to present this data at the moment, I wanted other opinions before making comment. And I was being a bit sloppy when I had a go so I just threw all the columns relating to upper and lower 95% credible interval figures away and graphed the basics.
The data in question is in tab 4 of the spreadheet that can be downloaded here:
Also the graphs of that data probably featured in the press conference today as well, but I wasnt paying enough attention at the time and when I went to the website where the slides are normally made available to download, I dont think todays stuff was there.
elbows
Well-Known Member
And without attempting a proper explanation because I am too tired, I am interested in the regions where the new variant percentage is now falling while the other variants percentage is increasing, or where the other variants trajectory seems currently steeper than the new variant trajectory.
Combustible
Well-Known Member
On this last point, the authors of the preprint are confident that the vaccines are still effective for the time being.
I can see there being years of arguments over how much the spread of the new variant is due to beneficial mutations and how much is down to being in the right place at the right time.
Indeliblelink
\......👁&👁......./
update twitter thread from Dr Hodcroft at Nextstrain -
2hats
Dust.
#torymutantvirusI suppose we could call it Dave if Mutanty McMutant Face is too long a name
2hats
Dust.
Sera from participants in Pfizer BNT162b2 trials confirmed to be effective in neutralising the N501Y mutation, so likely effective against B.1.1.7.. Less clear regarding B.1.351 as E484K is key there. Investigations continue into that and other mutations.
DOI: 10.1101/2021.01.07.425740.
news.trust.org
DOI: 10.1101/2021.01.07.425740.
Pfizer/BioNTech vaccine appears effective against mutation in new coronavirus variants -study
HEALTH-CORONAVIRUS/PFIZER-VACCINE (PIX):Pfizer/BioNTech vaccine appears effective against mutation in new coronavirus variants -study
elbows
Well-Known Member
If people are interested in how genomic data studies have now been used to analyse further the initial importations of the virus into the UK in the first place, this study looks pretty detailed, though I have absolutely no brain power left to read it properly myself right now.
Favelado
J'adore South Shore
It's called the British variant in Spain and there'll be no going back from that.
Mr.Bishie
pickled egg
Similar threads
