COVID-19: Vaccine and testing procedures Megathread Part 2 [Mod Warning - Post #1]

stephenjmcd · 18-12-2020 11:57pm

Azatadine wrote: »

Is this a concern in terms of vaccines (or just scaremongering)?

https://twitter.com/BNODesk/status/1340055216239030274?s=19

Multiple mutains have been reported and this one isn't that new. The UK wasn't the first to report it

https://twitter.com/firefoxx66/status/1338535621636333569?s=19

Azatadine · 18-12-2020 11:59pm

stephenjmcd wrote: »

Multiple mutains have been reported and this one isn't that new. The UK wasn't the first to report it

https://twitter.com/firefoxx66/status/1338535621636333569?s=19

Thanks. The fact that the new strain had mutations in the spike concerned me.

Goldengirl · 19-12-2020 12:06am

Azatadine wrote: »

Thanks. The fact that the new strain had mutations in the spike concerned me.

From reading of that article sounds like a more virulent strain , even in younger people.
Let's hope it doesn't turn up here too soon.

stephenjmcd · 19-12-2020 12:07am

Azatadine wrote: »

Thanks. The fact that the new strain had mutations in the spike concerned me.

Yeah can see how it would cause concern to people. See tweet below with link to BMJ. Vaccines aren't just targeting one area of spike, if they were then it would be a concern.

https://twitter.com/RolandBakerIII/status/1340054618445737984?s=19

hmmm · 19-12-2020 12:08am

Azatadine wrote: »

Thanks. The fact that the new strain had mutations in the spike concerned me.

A UK scientist quoted this week said they had seen around 4,000 spike mutations already. We just haven't heard about the previous 3,998.

Great news on the Oxford vaccine if it's to be approved. Themselves and J&J are the ones that have the production capacity to possibly get out of this by Summer.

stephenjmcd · 19-12-2020 12:13am

hmmm wrote: »

A UK scientist quoted this week said they had seen around 4,000 spike mutations already. We just haven't heard about the previous 3,998.

Great news on the Oxford vaccine if it's to be approved. Themselves and J&J are the ones that have the production capacity to possibly get out of this by Summer.

On that heres a good thread with paper attached, 12,706 mutations.
"We developed a framework to analyse the contribution of #SARSCoV2 mutations to the virus' transmissibility. We applied it to nearly 50k genomes and we found none (zero, zilch, nada) that increases transmission"

https://twitter.com/BallouxFrancois/status/1331669107062747137?s=19

Denny61 · 19-12-2020 12:23am

Its not looking good..these mutations are developing rapidly..and one vaccine is only enough to deal with a strain ..full stop ..the full force of whats waiting for is isn't too far away ..god help us all....scientists will not tell us the truth as economies will fall...be prepared..and pray

stephenjmcd · 19-12-2020 12:24am

Denny61 wrote: »

Its not looking good..these mutations are developing rapidly..and one vaccine is only enough to deal with a strain ..full stop ..the full force of whats waiting for is isn't too far away ..god help us all....scientists will not tell us the truth as economies will fall...be prepared..and pray

So much wrong with this post not even worth a dignified reply

Sconsey · 19-12-2020 12:25am

Denny61 wrote: »

Its not looking good..these mutations are developing rapidly..and one vaccine is only enough to deal with a strain ..full stop ..the full force of whats waiting for is isn't too far away ..god help us all....scientists will not tell us the truth as economies will fall...be prepared..and pray

How much wrong can you get in single short post? See above for the answer.

Azatadine · 19-12-2020 12:26am

Denny61 wrote: »

Its not looking good..these mutations are developing rapidly..and one vaccine is only enough to deal with a strain ..full stop ..the full force of whats waiting for is isn't too far away ..god help us all....scientists will not tell us the truth as economies will fall...be prepared..and pray

I was hesitant to ask about the spike mutation for exactly this reason.....people jump on genuine questions and run with it like its doomsday......

See posts above explaining why this is not a huge concern.

Hmmzis · 19-12-2020 12:32am

Azatadine wrote: »

Thanks. The fact that the new strain had mutations in the spike concerned me.

The 501 site appears to be not among the conserved ones and the substitution is synonymous, so no expected change to the protein structure. Some mouse studies have found no change in antibody affinity with that change (as would be expected). The deletions in the NTD are more interesting as they appear to shorten a small loop of amino acids on the edge of the NTD. That could impact antibody binding for that site, if it is part of a neutralizing site (I don't know of it is).

This is the reason our antibodies undergo affinity maturation in germinal centers so that single point mutations and trivial deletions can't so easily escape them. In addition to creating lots of them for all the possible sites on the presented antigen surface.

As to regards T cells this would be close to irrelevant. They recognize much larger epitopes and can tolerate quite a bit of point mutations and deletions before they don't bind anynore.

Goldengirl · 19-12-2020 12:56am

Hmmzis wrote: »

The 501 site appears to be not among the conserved ones and the substitution is synonymous, so no expected change to the protein structure. Some mouse studies have found no change in antibody affinity with that change (as would be expected). The deletions in the NTD are more interesting as they appear to shorten a small loop of amino acids on the edge of the NTD. That could impact antibody binding for that site, if it is part of a neutralizing site (I don't know of it is).

This is the reason our antibodies undergo affinity maturation in germinal centers so that single point mutations and trivial deletions can't so easily escape them. In addition to creating lots of them for all the possible sites on the presented antigen surface.

As to regards T cells this would be close to irrelevant. They recognize much larger epitopes and can tolerate quite a bit of point mutations a5nd deletions before they don't bind anynore.

I don't understand most of that but love the way you talk

Last paragraph I do get and that is good news, thankyou .

Van.Bosch · 19-12-2020 1:30am

Denny61 wrote: »

Its not looking good..these mutations are developing rapidly..and one vaccine is only enough to deal with a strain ..full stop ..the full force of whats waiting for is isn't too far away ..god help us all....scientists will not tell us the truth as economies will fall...be prepared..and pray

If we take your theory as correct, the mutations are developing rapidly so the vaccine is only good against one strain. Yet scientists would give up on science to protect the economy???

Also, why would you pray, if you believe in God, then this is the work of god, so it’s what God wants?

Deeper Blue · 19-12-2020 1:38am

Denny61 wrote: »

Its not looking good..these mutations are developing rapidly..and one vaccine is only enough to deal with a strain ..full stop ..the full force of whats waiting for is isn't too far away ..god help us all....scientists will not tell us the truth as economies will fall...be prepared..and pray

I've always wondered if people that post drivel like the above sit at home chuckling to themselves after writing it. What exactly do they get out of it? I find it sad tbh

ACitizenErased · 19-12-2020 1:48am

Moderna approved in the US just now

markodaly · 19-12-2020 4:43am

"General Population in Ireland will not get Vaccine till August, says MM" as per the Irish Examiner

Goodbye summer 2021 so, if that is the case.

schmoo2k · 19-12-2020 8:08am

markodaly wrote: »

"General Population in Ireland will not get Vaccine till August, says MM" as per the Irish Examiner

Goodbye summer 2021 so, if that is the case.

Why? The at risk groups will have been vaccinated by then (the minority) and we saw last year that the infection rates drop during the summer anyway.

Further - once the at risk folks are vaccinated, then the Covid hospital admissions will be insignificant.

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Wanderer78 · 19-12-2020 8:32am

schmoo2k wrote:

Further - once the at risk folks are vaccinated, then the Covid hospital admissions will be insignificant.

So hospital admissions will be done for the Craic?

funnydoggy · 19-12-2020 10:11am

Wanderer78 wrote: »

So hospital admissions will be done for the Craic?

That's not what the OP meant.

schmoo2k · 19-12-2020 10:20am

Wanderer78 wrote: »

So hospital admissions will be done for the Craic?

Insignificant numbers wise, IOW low numbers of people being admitted to hospital I am not suggesting the symptoms would be insignificant.

funnydoggy · 19-12-2020 10:42am

markodaly wrote: »

"General Population in Ireland will not get Vaccine till August, says MM" as per the Irish Examiner

Goodbye summer 2021 so, if that is the case.

Hmmm..

That isn't hugely surprising, because the general public will tolerate COVID much better than the more at risk groups who'll be vaccinated up to their eyeballs by then anyway.

I have a feeling he's tempering expectations though, I think many of us expect it to be sooner than that, especially with more vaccines being approved and distributed.

antiskeptic · 19-12-2020 11:02am

Although I won't be taking the vaccine my question isn't an anti-vaccine (or pro-safe vaccined as some of us prefer to be called). I'd just like to understand the basis for deciding it's effective/works at all

Its been pointed out elsewhere that 95% efficacy doesn't, and isn't intended to say
that it's 95% effective (where 95% effective would mean that if you exposed yourself to Covid post-vaccination, there's a 95% chance you'd be protected against contracting Covid.)

Question 1.

How effective is the vaccine, given the definition of effective above. If that's known?

Question 2:

In the Pfizee trial there was something like 20000 given the vaccine / 9 went on the contract Covid. And 20000 were given a placebo / 83 went on to contract Covid.

This is taken to mean the vaccine prevented people in the vaccinated group from contracting Covid.

However, if you had two placebo groups heck, lets make it 100 placebo groups of 20,000 people, you wouldn't get 83 people in each of the 100 groups going on to contract Covid. You'd get a variation.

How much would that variation be? What would be the total range (highest amount contracting to lowest amount contracting) over the 100 placebo groups of 20,000.

If, for example, the range was 5-300 over the 100 placebo groups, how is there anything of significance to be extracted from the 9-83 trial result? That is, if natural variation is greater than what was observed in the trial, then.the trial doesn't demonstrate very.much

Just wondering what the thinking is around accommodating and taking account of natural variations in placebo groups.

-

Raind replied thus to this question in the last thread but I don't see how it addresses the question asked (which I might not have framed well)

raind wrote:

In your example, the chance of 83 heads and 9 harps occurring in a fair toss is 1 in 5.7quadrillion.

This is kind of how efficacy is calculated. In a trial for example where 100 patients in a trial get covid , 5 of whom had the vaccine, the odds of this occurring by chance are about 1 in 10 to the power of 22.

What a 5 in 100 result tells you is that the proportion of cases in the vaccine population is that its 5%, with a 95% Confidence Interval that the true rate is between 1.6% and 11.3%

stephenjmcd · 19-12-2020 11:09am

markodaly wrote: »

"General Population in Ireland will not get Vaccine till August, says MM" as per the Irish Examiner

Goodbye summer 2021 so, if that is the case.

Its always been late summer for general population thats nothing new.

But there's so many categories ahead of general population that you could have half the country if not more already vaccinated before it gets to general which is the 2nd last category.

When vulnerable groupings get vaccinated the pressure on health services reduces, therefore restrictions can be eased as we go.

Not sure why August is such a shock, personally I didnt expect to be offered it until Q4 and I'm in the second last group.

MM also said last week he expects to be fully open by June/July and even yesterday said a vaccine will have huge benefits for aviation and tourism for summer 2021

Marhay70 · 19-12-2020 11:19am

Listening to LBC Radio this morning they quoted the Telegraph (paywall) as saying football stadia will be opened in early January and a mass vaccination campaign using Oxford vaccine will begin.
Now I know that the Telegraph and Johnson sing from the same hymnsheet most of the time and the sceptic in me thinks propaganda, but it's uplifting to hear all the same rather than the gloom and doom emanating from the press here.

antiskeptic · 19-12-2020 11:26am

stephenjmcd wrote: »

Its always been late summer for general population thats nothing new.

But there's so many categories ahead of general population that you could have half the country if not more already vaccinated before it gets to general which is the 2nd last category.

When vulnerable groupings get vaccinated the pressure on health services reduces, therefore restrictions can be eased as we go.

Not sure why August is such a shock, personally I didnt expect to be offered it until Q4 and I'm in the second last group.

MM also said last week he expects to be fully open by June/July and even yesterday said a vaccine will have huge benefits for aviation and tourism for summer 2021

Wonder will they implement vaccine passports. If they do and you relatively small quantities of people managing to be vaccinated by summer, then the huge boost for aviation and tourism will have something of a hole pricked in it.

stephenjmcd · 19-12-2020 11:48am

Marhay70 wrote: »

Listening to LBC Radio this morning they quoted the Telegraph (paywall) as saying football stadia will be opened in early January and a mass vaccination campaign using Oxford vaccine will begin.
Now I know that the Telegraph and Johnson sing from the same hymnsheet most of the time and the sceptic in me thinks propaganda, but it's uplifting to hear all the same rather than the gloom and doom emanating from the press here.

Things change when Pfizer & BioNTech come on stream in decent numbers, even more so with Moderna as it now doesn't need to be stored at low temperatures but they don't have the manufacturing capacity of Pfizer for example. However then you've Oxford & AstraZeneca, normal storage temps and low cost along with massive production capacity. That changes things again.

Would also in my opinion allow Pfizer & Moderna to be assigned to vulnerable groups while Oxford could go to those less vulnerable & general population, would greatly speed things up.

Sconsey · 19-12-2020 11:51am

markodaly wrote: »

"General Population in Ireland will not get Vaccine till August, says MM" as per the Irish Examiner

Goodbye summer 2021 so, if that is the case.

I did a rough calculation a while back...it was something like 650,000 people over the age of 65. Around 250,000 health care workers and who knows how many key workers...lets say 50,000.

So that is 950,000 to cover the first 6 groups, then comes the medically vulnerable under the age of 65. No idea how many that is but it is hardly more than 500,000 (pure guess!). That is the 7 groups covered before the general population.

Somewhere in the region of 1.5 million is their target between now and August.

scouserstation · 19-12-2020 11:52am

antiskeptic wrote: »

Wonder will they implement vaccine passports. If they do and you relatively small quantities of people managing to be vaccinated by summer, then the huge boost for aviation and tourism will have something of a hole pricked in it.

Countries that rely heavily on tourism will likely not require proof of vaccination this summer, to do this you would need significant investment in the infrastructure required at airports, train stations, ports, roads etc and then you would also be reducing the amount of tourists the visit by 30 - 40% potentially

Water John · 19-12-2020 12:12pm

Marhay70 wrote: »

Listening to LBC Radio this morning they quoted the Telegraph (paywall) as saying football stadia will be opened in early January and a mass vaccination campaign using Oxford vaccine will begin.
Now I know that the Telegraph and Johnson sing from the same hymnsheet most of the time and the sceptic in me thinks propaganda, but it's uplifting to hear all the same rather than the gloom and doom emanating from the press here.

That's simply deflection from his Brexit cave in.

COVID-19: Vaccine and testing procedures Megathread Part 2 [Mod Warning - Post #1]

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