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

ACitizenErased

Redordeadqwwer wrote: »

Jesus Christ. Is this strain everywhere?

Edit: This is 8 hours old and is all I can where he talks about new variant and vaccines. He says they will still work here? Unless I’m reading it wrong.

https://www.medpagetoday.com/infectiousdisease/covid19/90833

He says they'll work yup. I'd trust Fauci to be honest.

Leftwaffe

ACitizenErased wrote: »

He says they'll work yup. I'd trust Fauci to be honest.

I actually misread the poster. I thought it said it would fall ‘by’ 80%. Not ‘to’ 80%. Panic over. An 80% effective vaccine is incredible as it is.

Irish Stones

One of Italian regions' administration asked Pfizer to be granted the license to produce their vaccine in local pharmaceutical plants in order to ramp up the production and by-pass further possible issue with the European plants in Belgium.
It wouldn't be bad if more countries asked Pfizer the same thing.
Pfizer wouldn't lose their money, they would paid the same amount for all doses produced elsewhere under their license.
Could such a thing be done, in your opinion?

NeuralNetwork

The vaccines to date are all quite narrowly focused on creating a replica of a spike protein for your immune system to train to attack.

The mRNA and viral vector vaccines take different approaches to delivering the code, but effectively they're doing the same thing, just with a different methodology.

They both use your cells to build replica spike proteins.

That's quite different to what's done with more traditional vaccines like those used for the flu, which typically uses an inactivated split virion. That's quite a complex protein and your immune system will probably develop immunity to various aspects of it.

With the spike protein focused vaccines, it's quite specific, your immune system's attention is all on that one feature and it's quite a generic feature of this type of virus, so the hope is that it will be fairly robust immunity if the strains change.

That's the hope anyway from what I've read.

landofthetree

Cork2021 wrote: »

Its covering up their fûck ups!

They told business groups in a web seminar if vaccines wont work on new strains we are back to square one. Daily Mail/Sky news got hold of it and thats why they had to admit it today.

The coronavirus variant first identified in South Africa could reduce the efficacy of vaccines by half, the health secretary has said.

Matt Hancock made the remark during a webinar with business leaders and travel agents on Tuesday.

"Nevertheless, if we vaccinated the population, and then you got in a new variant that evaded the vaccine, then we'd be back to square one."

https://news.sky.com/story/covid-19-matt-hancock-says-south-african-variant-could-reduce-vaccine-efficacy-by-half-12195907

Itsaduck1

NeuralNetwork wrote: »

The vaccines to date are all quite narrowly focused on creating a replica of a spike protein for your immune system to train to attack.

The mRNA and viral vector vaccines take different approaches to delivering the code, but effectively they're doing the same thing, just with a different methodology.

They both use your cells to build replica spike proteins.

That's quite different to what's done with more traditional vaccines like those used for the flu, which typically uses an inactivated split virion. That's quite a complex protein and your immune system will probably develop immunity to various aspects of it.

With the spike protein focused vaccines, it's quite specific, your immune system's attention is all on that one feature and it's quite a generic feature of this type of virus, so the hope is that it will be fairly robust immunity if the strains change.

That's the hope anyway from what I've read.

Good read, well explained

From your research what changes would need to take place for Covid to evade vaccines entirely?

What are they worried about?

plodder

Irish Stones wrote: »

One of Italian regions' administration asked Pfizer to be granted the license to produce their vaccine in local pharmaceutical plants in order to ramp up the production and by-pass further possible issue with the European plants in Belgium.
It wouldn't be bad if more countries asked Pfizer the same thing.
Pfizer wouldn't lose their money, they would paid the same amount for all doses produced elsewhere under their license.
Could such a thing be done, in your opinion?

It's always possible in principle. But I wouldn't just assume that any pharmaceutical plant could produce this vaccine.

NeuralNetwork

Itsaduck1 wrote: »

Good read, well explained

From your research what changes would need to take place for Covid to evade vaccines entirely?

What are they worried about?

They're worried in case a mutation that changes the spike protein might render it undetected to our immune systems as it would differ sufficiently from the vaccine.

However, and this is just based on listening to and reading technical discussions, I do not claim to be any kind of expert, the spike protein itself is quite specialised. It's adapted to be able to plug into our ACE2 receptors, much like a key into a lock. That's quite a specialised adaptation.

The theory that was being discussed was that if the mutation was significant enough to make the spike proteins undetectable to the vaccinated person's immune system, then it would also likely be a radical enough change to the spike protein to make it useless anyway, a bit like if you altered the shape of a key.It would probably stop fitting the lock.

Now, that doesn't mean to say that there is still some possibility that a mutation happens and makes that possible, but it just seems somewhat less likely.

Nothing's beyond the realms of possibility, but it just seems because of the very specific mechanisms involved we might be relatively less at risk of that happening.

Again though this is all just theorising and biology can throw up some remarkable solutions to stuff and by solutions in this case, I mean the virus finding solutions to ensure it can continue to infect cells.

There are plenty of other adaptations that a virus can use to evade detection in other ways too. Just keep your fingers crossed that it doesn't find any of those solutions!

Itsaduck1

landofthetree wrote: »

They told business groups in a web seminar if vaccines wont work on new strains we are back to square one. Daily Mail/Sky news got hold of it and thats why they had to admit it today.

How wouldnt they work though?

The Biontech CEO said recently that while the new strains have many mutations, only 1% of the relevant protein has changed.

Can the new strains infect differently or something?

astrofool

Itsaduck1 wrote: »

Good read, well explained

From your research what changes would need to take place for Covid to evade vaccines entirely?

What are they worried about?

I think essentially for the spike protein to change in such a way that current vaccines no longer work, however, we think that the spike protein is one of the major features of the virus that allows it to spread and cause sickness effectively, such that if it changed much, it's effectiveness also drops significantly.

ax530

Any update on how vaccine roll out is going here in Ireland? Have all hospital staff now for first vaccine?
Is Moderna still in use or was supply used up last week for GP clinics?

Itsaduck1

NeuralNetwork wrote: »

They're worried in case a mutation that changes the spike protein might render it undetected to our immune systems as it would differ sufficiently from the vaccine.

However, and this is just based on listening to and reading technical discussions, I do not claim to be any kind of expert, the spike protein itself is quite specialised. It's adapted to be able to plug into our ACE2 receptors, much like a key into a lock. That's quite a specialised adaptation.

The theory that was being discussed was that if the mutation was significant enough to make the spike proteins undetectable to the vaccinated person's immune system, then it would also likely be a radical enough change to the spike protein to make it useless anyway, a bit like if you altered the shape of a key.It would probably stop fitting the lock.

Now, that doesn't mean to say that there is still some possibility that a mutation happens and makes that possible, but it just seems somewhat less likely.

Nothing's beyond the realms of possibility, but it just seems because of the very specific mechanisms involved we might be relatively less at risk of that happening.

Again though this is all just theorising and biology can throw up some remarkable solutions to stuff and by solutions in this case, I mean the virus finding solutions to ensure it can continue to infect cells.

Thanks man, alot of that is way over my head, but you did a good job of explaining it in simple terms for me

Key and lock is enough for me ;-)

NeuralNetwork

Itsaduck1 wrote: »

Thanks man, alot of that is way over my head, but you did a good job of explaining it in simple terms for me

All I'd say is that you're looking at a virus that is adapting to its environment and reproducing at an enormous rate, with each generation making random errors, some of which are useful and some of which aren't. The successful 'errors' are the adaptions that it uses to improve its ability to infect cells and reproduce.

Biology and evolution produces some absolutely amazing solutions to difficulties that it's presented with so, I wouldn't county my chickens !

Reducing the infection rates is of huge importance as it reduces the sheer volume of opportunities it has to continue to evolve.

With millions upon millions of live COVID cases, you've probably hundreds of trillions of viruses doing their thing and each one is playing the lotto with those mutations. The more live infections, the better the odds for the virus to find adaptations.

So getting the R0 rate down is still absolutely vital in any case and will give the vaccines more hope of being long-term effective too.

Itsaduck1

astrofool wrote: »

I think essentially for the spike protein to change in such a way that current vaccines no longer work, however, we think that the spike protein is one of the major features of the virus that allows it to spread and cause sickness effectively, such that if it changed much, it's effectiveness also drops significantly.

Thanks Astro

When the Biontech CEO is talking about 6 weeks for a new modified vaccine to combat those strains, whats he modifying if these vaccines we have now already target the spike protein?

Will they target something else? Not the spike proteins?

On your last point the SA variant is supposed to be more transmissable and deadly, while also having changes to the spike protein

Shouldn't that be impossible as its spike protein has changed?

HalfAndHalf

https://www.rte.ie/news/coronavirus/2021/0122/1191541-astrazeneca-vaccine/

Reads to me like it’s just another EU procrastination that led to delays on the other vaccines.

AZ are a business, while other countries approved the vaccine ready to take delivery the EU have only this week brought forward their approval decision to the 29th!

What if the EU don’t approve the vaccine, will they still pay for the original order, of course they wouldn’t, so how can they expect a business to hold on to 400 million doses that every other country in the world would want!

Smacks of self importance and yet another example of not being able to react fast enough.

NeuralNetwork

Those vaccines are almost 'programmable' in a way. You can just take the new spike protein code and insert it into the vaccine (a few more steps than that but basically that's the gist of it).

In the case of the mRNA vaccines, it's just a a little microcapsule of mRNA which instructs your cells to temporarily make spike proteins.

In the AstraZeneca it's DNA carried in a harmless adenovirus that's incapable of reproduction itself. In that case there's an extra intermediary step but the end result is similar

Both types can be tweaked, but AFAIK the mRNA vaccines are easier to do this with as they're far simpler in a lot of ways as a product, but more complex to store and manufacture.

NeuralNetwork

HalfAndHalf wrote: »

Reads to me like it’s just another EU procrastination that led to delays on the other vaccines.

AZ are a business, while other countries approved the vaccine ready to take delivery the EU have only this week brought forward their approval decision to the 29th!

What if the EU don’t approve the vaccine, will they still pay for the original order, of course they wouldn’t, so how can they expect a business to hold on to 400 million doses that every other country in the world would want!

Smacks of self importance and yet another example of not being able to react fast enough.

It's rumored to have been brought further forward to Wednesday, 27th.

The EU took a spread bet on a whole range of vaccines which were in development a few months ago. They also invested considerable money in their development. So, it's a bit more complex than just being a customer.

The member states basically buy them as per a negotiated preorder by the European Commission.

Some of those bets aren't going to lead to much. For example they bet on Sanofi and GSK, which was a logical bet as they are the world's two largest vaccine makers, but it's not where the vaccine has come from. Instead, it was from some of their smaller bets with more innovative technology platforms.

Of course some money will be written off in this, but that was the plan.

The aim of the programme was to get access to an array of different candidate vaccines with a spread of technologies and companies. What's happening now is they're refocusing on the most successful candidates.

I'd agree the programme should have been bigger, and has had to be ramped up in recent weeks to scale it but they couldn't have predicted which candidates would have come up with the goods that early on.

The UK to a degree got very lucky with AstraZeneca. It was also very possible that it could have been a dud and the data on it was quite inconsistent which is why the regulatory approval has taken longer than it did in the UK.

The delays at the moment are both manufacturing speed bumps, so I don't really know what anyone could do about that. Stuff like that is inevitable with a new product and production system.

The regulatory red tape is for safety but they need to ensure they are being as fast as they can be, with that safety margin.

berocca2016

ax530 wrote: »

Any update on how vaccine roll out is going here in Ireland? Have all hospital staff now for first vaccine?
Is Moderna still in use or was supply used up last week for GP clinics?

Still waiting on full rollout to the non-acute hospitals.....

Itsaduck1

NeuralNetwork wrote: »

Those vaccines are almost 'programmable' in a way. You can just take the new spike protein code and insert it into the vaccine (a few more steps than that but basically that's the gist of it).

In the case of the mRNA vaccines, it's just a a little microcapsule of mRNA which instructs your cells to temporarily make spike proteins.

In the AstraZeneca it's DNA carried in a harmless adenovirus that's incapable of reproduction itself. In that case there's an extra intermediary step but the end result is similar

Both types can be tweaked, but AFAIK the mRNA vaccines are easier to do this with as they're far simpler in a lot of ways as a product, but more complex to store and manufacture.

Another great answer, thanks

Say it is true on the variants, efficacy has dropped, like on the news today,
with the top medical people Dr Fauci USA and Hancock health secretary UK saying it will go down to 80% efficacy or 45% Hancock eluded to in his off the record chat with investors.

How can they prove that?

Do they get the blood of 100 people that had both shots of the vaccine at correct intervals for. maximum protection and expose it to that strain and 20 and 55 peoples blood respectively dont beat the virus?

Are they doing testing like that?

NeuralNetwork

As far as I am aware, you can do lab based testing using plasma donated from people who were vaccinated to see if those new strains are killed by their antibodies.

You can do similar tests for people who've recovered from COVID-19 and have natural antibodies and likewise for monoclonal antibodies used in treatments that are infused.

The UK strain was raising relatively little concern in that regard, the South African one was of much more concern as it's getting around some of those antibodies certainly in the tests they did in South Africa itself with plasma donated by people who'd had COVID.

Obviously they'll also have observed data from real life medical situations too coming in as those variants start turning up.

If we do end up with a serious vaccine resistant form, the vaccines can be reworked, but it would mean a second round of shots for all those vaccinated already.

So we are absolutely going to need to speed up these delivery systems.

It's also why anti-viral and other treatments will likely play a huge role in managing this too if they can make it less deadly, nip it in the bud at an early stage.

Wolf359f

HalfAndHalf wrote: »

https://www.rte.ie/news/coronavirus/2021/0122/1191541-astrazeneca-vaccine/

Reads to me like it’s just another EU procrastination that led to delays on the other vaccines.

AZ are a business, while other countries approved the vaccine ready to take delivery the EU have only this week brought forward their approval decision to the 29th!

What if the EU don’t approve the vaccine, will they still pay for the original order, of course they wouldn’t, so how can they expect a business to hold on to 400 million doses that every other country in the world would want!

Smacks of self importance and yet another example of not being able to react fast enough.

Don't lie, they didn't decide this week to bring forward the date for approval to the 29th, that was decided on the 12th, the week before that.
https://www.ema.europa.eu/en/news/ema-receives-application-conditional-marketing-authorisation-covid-19-vaccine-astrazeneca
Which looks to be the same day they received an application for approval from Astrazenca. The EMA cannot approve a vaccine before the manufacturer applies for it FFS!

And yes other countries have approved AZ, the list is:
UK, Argentina, El Salvador, Dominican Republic, India, Bangladesh, Mexico, Nepal, Pakistan, Brazil, Saudi Arabia, Iraq, Hungary, Thailand
Do go making out like the EU will be the last to approve it.
That's 13 countries, 12 countries have also approved the Russian Sputnik Vaccine, shall we just go ahead and approve that without any checks?

AdamD

So, having myself given out about the EU/EMA potentially stopping Ireland from getting early deliveries from Astrazenica as the vaccine isn't yet approved, is it actually completely irrelevant as it appears Astrazenica haven't anything close to the supplies they had agreed to?

Wolf359f

AdamD wrote: »

So, having myself given out about the EU/EMA potentially stopping Ireland from getting early deliveries from Astrazenica as the vaccine isn't yet approved, is it actually completely irrelevant as it appears Astrazenica haven't anything close to the supplies they had agreed to?

My understanding and I'm totally open to correction, most vaccine manufacturers sign a contract to deliver a certain number of doses per quarter.
AZ said they hoped to deliver a certain amount in the first shipment in Feb, but that has been scaled back. My understanding it by the end of the first quarter they will have delivered all that had been agreed to. It's a delay not a reneging on the contract.

NeuralNetwork

Bear in mind the AstraZeneca vaccine is made in multiple locations, some of which wouldn't necessarily be approved for use in Europe if they hadn't applied for EMA approval of the facility.

The supply for say India for example is made in India.

The facility that's had a yield issue in Europe is a production partner. They are using companies like Novasep in Belgium, Halix BV in the Netherlands and there are production facilities in the US doing it and so on.

It isn't a case of other countries buying up European supplies, rather it's just a glitch in the supply chain in Europe.

It's not just doable by any pharma plant either, it's a biologics type product and needs fairly specific facilities.

amandstu

Can I ask if anyone here with epidemiology/math skills can explain the impact of low levels of population vaccination has on ongoing levels of infection in a typical setting?

Do we only see any appreciable effects once we approach the 70% herd immunity levels or is some benefit noticeable as we approach for example 10%?

I note that Israel is approaching 40% now and the UK is around 8%

Are there any graphs that map these two aspects to each other?( vaccination levels and damping effects)

markodaly

The shortfall of the Oxford Vaccine is a bit of a disaster tbh. I don't know how one can say otherwise. That was the one that was going to do the heavy lifting, in all this, now the EU and by extension Ireland are going to have their allocations cut by 60%?

Impossible to get everyone done by September now.
We will get there but 2021 is going to be a long hard slog for everyone. We are very much still in the thick of this. Nothing is really certain yet.

JacksonHeightsOwn

markodaly wrote: »

The shortfall of the Oxford Vaccine is a bit of a disaster tbh. I don't know how one can say otherwise. That was the one that was going to do the heavy lifting, in all this, now the EU and by extension Ireland are going to have their allocations cut by 60%?

Impossible to get everyone done by September now.
We will get there but 2021 is going to be a long hard slog for everyone. We are very much still in the thick of this. Nothing is really certain yet.

Who said our allocation is getting reduced by 60%?

tippilot

Wolf359f wrote: »

My understanding and I'm totally open to correction, most vaccine manufacturers sign a contract to deliver a certain number of doses per quarter.
AZ said they hoped to deliver a certain amount in the first shipment in Feb, but that has been scaled back. My understanding it by the end of the first quarter they will have delivered all that had been agreed to. It's a delay not a reneging on the contract.

The Q1 allocation is reduced by 60%. 31 million doses will be delivered instead of 80 million. The 31 million will be delivered over roughly 6 weeks from mid Feb. Production will ramp up in Feb/March for increased deliveries in Q2. However, AZ's credibility to deliver is now in question and the EU has requested a concrete delivery schedule.

In practical terms for Ireland, based on 1.1% of the EU allocation, it would mean a reduction in doses from an expected 800,000+ to 340,000. It pretty much kills any chance of vaccinating 700,000 people by end of March. MM last night estimated roughly 1 million vaccinated by June, which is disastrous if true. Hopefully a vast underestimation.

JacksonHeightsOwn

tippilot wrote: »

The Q1 allocation is reduced by 60%. 31 million doses will be delivered instead of 80 million. The 31 million will be delivered over roughly 6 weeks from mid Feb. Production will ramp up in Feb/March for increased deliveries in Q2. However, AZ's credibility to deliver is now in question and the EU has requested a concrete delivery schedule.

In practical terms for Ireland, based on 1.1% of the EU allocation, it would mean a reduction in doses from an expected 800,000+ to 340,000. It pretty much kills any chance of vaccinating 700,000 people by end of March. MM last night estimated roughly 1 million vaccinated by June, which is disastrous if true. Hopefully a vast underestimation.

Is that confirmed?

The cynic in me says Oxford has been keeping as many doses as they possibly could for the UK, and that's another reason they didn't bother their arse trying to get European approval quicker.

Gael23

tippilot wrote: »

The Q1 allocation is reduced by 60%. 31 million doses will be delivered instead of 80 million. The 31 million will be delivered over roughly 6 weeks from mid Feb. Production will ramp up in Feb/March for increased deliveries in Q2. However, AZ's credibility to deliver is now in question and the EU has requested a concrete delivery schedule.

In practical terms for Ireland, based on 1.1% of the EU allocation, it would mean a reduction in doses from an expected 800,000+ to 340,000. It pretty much kills any chance of vaccinating 700,000 people by end of March. MM last night estimated roughly 1 million vaccinated by June, which is disastrous if true. Hopefully a vast underestimation.

1 million by June is not unreasonable given what’s happened with AstraZeneca. They can’t keep level 5 for that long though