Developing the Covid-19 vaccine

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Millennie Al
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Re: Developing the Covid-19 vaccine

Post by Millennie Al » Thu Mar 25, 2021 5:22 am

shpalman wrote:
Wed Mar 24, 2021 11:43 am
Since we don't really know anything I'm going to have to keep making stuff up.

What we do know, from the press release, is that there were 32449 participants of which 21583 received "at least one dose of the vaccine" and that there were 141 symptomatic cases of covid in total.

Something like 41-42 cases in the vaccine group and 99-100 cases in the control group would, according to wot I reckon, give something which rounds to 79% efficacy if I've calculated it right.

To get down from there to 72% (in the middle of the 69-74% range the DSMB gets when looking at the full data) you'd need about 12 extra cases in the vaccine group assuming no new cases in the control group.

So we don't really seem to be talking about 1-2 more cases...

Of course, I'll stop wot I reckoning once they publish the f.cking data instead of bullshitting about it.
From https://www.niaid.nih.gov/news-events/s ... s-covid-19 it seems the 79% is 78.9%, which suggests 42 of 21583 and 99 of 10866, though that's 78.6% when rounded. To round to 72% it would be 50 vs 91, so 8 cases in the wrong bin, but I wonder if it's actually not 141 for both estimates, if the complaint is about outdated information. Presumably the number of participants is constant.

Then we have https://www.niaid.nih.gov/news-events/n ... ca-vaccine which says:
Late Monday, the Data and Safety Monitoring Board (DSMB) notified NIAID, BARDA, and AstraZeneca that it was concerned by information released by AstraZeneca on initial data from its COVID-19 vaccine clinical trial. The DSMB expressed concern that AstraZeneca may have included outdated information from that trial, which may have provided an incomplete view of the efficacy data. We urge the company to work with the DSMB to review the efficacy data and ensure the most accurate, up-to-date efficacy data be made public as quickly as possible.
While I very much agree with a desire for the data to be made public, I'm not clear on what this is saying. Surely it is not indicating that the US regulator is evaluating the vaccine based on press releases! So does it mean that AZ have submitted incorrect data as part of regulatory approval, or it is just complaining about data in press releases??
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Re: Developing the Covid-19 vaccine

Post by Grumble » Thu Mar 25, 2021 6:50 am

The DSMB aren’t a main part of the regulator though. They’re a side committee, who also should be looking at trial data not press releases.
I know this is vitriol, no solution, spleen venting, but I feel better having screamed, don’t you?

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Re: Developing the Covid-19 vaccine

Post by shpalman » Thu Mar 25, 2021 8:41 am

AstraZeneca's random number generator has today come out with 76% and that's our final offer.

Sorry, I mean that they've "released" some "data" somewhere where we can't see.
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Re: Developing the Covid-19 vaccine

Post by bob sterman » Thu Mar 25, 2021 8:45 am

shpalman wrote:
Thu Mar 25, 2021 8:41 am
AstraZeneca's random number generator has today come out with 76% and that's our final offer.
Maybe we should get Noel Edmonds in to broker the vaccine deal with the EU?

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Re: Developing the Covid-19 vaccine

Post by shpalman » Thu Mar 25, 2021 8:47 am

Millennie Al wrote:
Thu Mar 25, 2021 5:22 am
shpalman wrote:
Wed Mar 24, 2021 11:43 am
Since we don't really know anything I'm going to have to keep making stuff up.

What we do know, from the press release, is that there were 32449 participants of which 21583 received "at least one dose of the vaccine" and that there were 141 symptomatic cases of covid in total.

Something like 41-42 cases in the vaccine group and 99-100 cases in the control group would, according to wot I reckon, give something which rounds to 79% efficacy if I've calculated it right.

To get down from there to 72% (in the middle of the 69-74% range the DSMB gets when looking at the full data) you'd need about 12 extra cases in the vaccine group assuming no new cases in the control group.

So we don't really seem to be talking about 1-2 more cases...

Of course, I'll stop wot I reckoning once they publish the f.cking data instead of bullshitting about it.
From https://www.niaid.nih.gov/news-events/s ... s-covid-19 it seems the 79% is 78.9%, which suggests 42 of 21583 and 99 of 10866, though that's 78.6% when rounded. To round to 72% it would be 50 vs 91, so 8 cases in the wrong bin, but I wonder if it's actually not 141 for both estimates, if the complaint is about outdated information. Presumably the number of participants is constant.
The number of participants is constant, but I'm sure we're not talking about the same number of cases but put in the wrong bin, I reckon we're talking about a whole load of extra cases, more of which were in the "vaccine" group.

In fact, the locked filing cabinet with a sign on the door saying "beware of the leopard" says "An additional 49 cases were added to the previously announced results."

So instead of 42:99, it would be (to get 76%) something like 61:129.
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Re: Developing the Covid-19 vaccine

Post by shpalman » Thu Mar 25, 2021 8:51 am

Grumble wrote:
Thu Mar 25, 2021 6:50 am
The DSMB aren’t a main part of the regulator though. They’re a side committee, who also should be looking at trial data not press releases.
Well yes, they looked at the trial data, and pulled AstraZeneca up on the b.llsh.t number they were quoting in their press release.
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Re: Developing the Covid-19 vaccine

Post by shpalman » Thu Mar 25, 2021 1:56 pm

baffled by AstraZeneca’s communication ineptitude

(SUPPORT Science Mag's non-profit journalism... by paying a couple of thousand dollars to publish a scientific article with them.)
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Re: Developing the Covid-19 vaccine

Post by Millennie Al » Fri Mar 26, 2021 4:00 am

So the whole fuss could have been avoided by AZ including the words "as of 17 February" in their press release. I don't think it's unreasonable for a company to get the latest data to a regulator with greater urgency than to keep their press office up to date. How long before the press release was the new data known???
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Re: Developing the Covid-19 vaccine

Post by Grumble » Fri Mar 26, 2021 8:42 am

shpalman wrote:
Thu Mar 25, 2021 8:51 am
Grumble wrote:
Thu Mar 25, 2021 6:50 am
The DSMB aren’t a main part of the regulator though. They’re a side committee, who also should be looking at trial data not press releases.
Well yes, they looked at the trial data, and pulled AstraZeneca up on the b.llsh.t number they were quoting in their press release.
Why are they bothered about a press release though?
I know this is vitriol, no solution, spleen venting, but I feel better having screamed, don’t you?

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Re: Developing the Covid-19 vaccine

Post by shpalman » Fri Mar 26, 2021 9:10 am

They're bothered about a drug company making data public which they already know to be false.
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Re: Developing the Covid-19 vaccine

Post by Bird on a Fire » Fri Mar 26, 2021 10:12 am

Something which, when the press release first appeared, I pointed out that AstraZeneca have been fined astrazillions of dollars for doing in the past.
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Re: Developing the Covid-19 vaccine

Post by Grumble » Fri Mar 26, 2021 10:47 am

shpalman wrote:
Fri Mar 26, 2021 9:10 am
They're bothered about a drug company making data public which they already know to be false.
Not false so much as outdated, to be fair.
I know this is vitriol, no solution, spleen venting, but I feel better having screamed, don’t you?

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Re: Developing the Covid-19 vaccine

Post by jimbob » Fri Mar 26, 2021 1:52 pm

tom p wrote:
Tue Mar 23, 2021 4:44 pm
tom p wrote:
Fri Mar 19, 2021 11:08 am
shpalman wrote:
Fri Mar 19, 2021 9:40 am


I wouldn't have expected that. I expected something more like the link you give below, except with some graphs or tables of data or something.

The past year has seen a lot of opening up of access, both in terms of real-time statistics on government websites, and in terms of preprints of scientific publications. Within the limits of industrial intellectual property protection and patient confidentiality I'd like to see the same from medicine regulators.

(The approval process seemed to go like "vaccine submitted to regulator and expected to be approved by [date]" "[date]: yep it's approved" as if the regulator just gives a meaningless rubber stamp to whatever the drug company says, and not a whole load of detailed rules and guidelines about how [and how not] to produce, transport, store, and administer the vaccine. Please explain this to us, because nobody else seems to be doing it.)
That's an interesting question.
Normally the expectedness of approval is far less certain. I will reply later about this, 'cos i want to give a full answer without writing too much.
Normal drug approvals process:
1. academic identifies possible cause of a disease - e.g. a dodgy receptor on a cell surface
2. companies read about this and rush to synthesise the faulty receptor & then run their massive banks of hundreds of thousands of chemicals & proteins against it. In parallel, they look at synthesising things which will mimic what should bind with it & then try those.
3. anything that shows some form of binding with the receptor is then (a) patented & (b) studied to death through many phases of pre-clinical trials (lab & then animals)
4. companies then look at what has been patented by others & copy that, but adding a slight twist & study that too
5. the top 100 or so candidates go into phase 1 trials with healthy volunteers (all youngish blokes: students, unemployed & backpacking aussies who are happy to swap a bit of blood to be paid 2 grand to spend a week playing playstation)
6. the top 10 or so go into phase 2 trials (hopeless cases who all other drugs have failed)
7. the top 1 to 3 go into phase 3 trials.
8. early phase 3 trial results whittle it down to the best 1
8a. if things are looking good, then company starts to focus on manufacturing and storage details. They were obviously caring about it before, but now it ramps up.
9. company sends all their data to the regulators (following the guidance here - summat the RDIF should have read, the dozy twonks) & crosses their fingers
10. bit of back and forth between regulators and company to clarify any questions the regulators have (here's a list of basic validation issues frequently found - the potential issues with the actual data are far greater)
11. committee meeting when the regulators decide whether or not to grant a license and, if so, under what conditions.

Steps 1-9 take 12-15 years and cost $250 to 1,000 million. Steps 10 & 11 take 9-18 months depending on how many questions the regulators have.
A far better & more thorough overview is available here
On top of all this, there are inspections and certification all along the chain: GLP, GCP, GMP &c.

A not insignificant number of applications are rejected each year, or have very strict restrictions placed on their use.

Companies who come to the EMA to use their scientific advice service have a far greater chance of getting approval. Sadly I can't find the figures right now for the % rejected with/without scientific advice.
Thanks
Have you considered stupidity as an explanation

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Re: Developing the Covid-19 vaccine

Post by Herainestold » Mon Mar 29, 2021 8:13 pm

Labour M P argues that UK gov should release the patents of covid vaccines to increase supply and have stocks of vaccine for developing countries.
As we know the AZ vaccine began at Oxford University, which received £65.5 million of public funding. Moderna’s vaccine was largely funded by the National Institute of Health in the US. Billions in public funding has been poured into developing the vaccines. Yet pharmaceutical companies are set to make ludicrous profits off the back of this. For example, Moderna has seen its share price increase by 372% and expects 2021 sales of $18.4bn and AstraZeneca’s ‘no-profit’ promise could expire as early as July this year.
The UK government should back initiatives that would create the space for more manufacturers to enter the market to ensure a sustained supply of vaccines at low prices. This means removing barriers to know-how and stopping the ‘right’ to produce the vaccines being the preserve of a small number of private companies.
Critically, we need to strengthen the ability of all countries to respond to pandemic threats without being dependent on global supply chains. There are qualified vaccine producers all over the world standing ready to produce more vaccines, if only they were allowed to access to the technology and know-how now being held under lock and key by pharmaceutical companies through their monopoly control of the patents.
Practically we need the UK government to support the temporary waiver on patents which is on the table at the WTO, initiated by South Africa and India and now co-sponsored by 57 countries. It should back the WHO’s efforts to strengthen local and regional manufacturing of the vaccine. It should put pressure on industry to share their Intellectual Property and know-how with the Covid-19 Technology Access Pool so we can scale up production, reach global immunity and end this pandemic.

If we treat the pandemic as an opportunity for more greed and to boost capitalism this will come back to bite us. Public disgust over the Prime Minister’s remarks should be a moment to spur the government into supporting efforts to define Covid-19 tools as a global public good.
https://www.politicshome.com/thehouse/a ... 9-pandemic

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Re: Developing the Covid-19 vaccine

Post by Herainestold » Mon Mar 29, 2021 10:38 pm

Study in America shows Pfizer and Moderna vaccines inhibit transmission of virus.
new study suggests the messenger RNA vaccines produced by Moderna and the Pfizer-BioNTech partnership appeared to be 90% effective in preventing Covid-19 infection in a real-world setting.
The study followed nearly 4,000 health care workers, first responders, and other essential workers in eight U.S. locations as the first Covid vaccines were rolled out starting in December. Participants were tested weekly to look for all cases of Covid infection, even asymptomatic ones.

In the period from Dec. 14, 2020, to March 13, 2021, nearly 75% of the workers in the cohort received at least one dose of one of the mRNA vaccines. Both are given in a two-dose schedule.
Related:

There were 161 Covid infections in the unvaccinated workers, compared with 16 in workers who had received only one dose by the time of their infection and only three infections in people who had received both doses and were two weeks out from their second dose. The vaccine effectiveness following two doses was 90% — roughly in line with the 95% and 94% that the Pfizer and Moderna vaccines showed, respectively, in the clinical trials that supported their emergency use authorizations.
https://www.statnews.com/2021/03/29/rea ... effective/

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Re: Developing the Covid-19 vaccine

Post by shpalman » Tue Mar 30, 2021 6:08 am

molto tricky

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Re: Developing the Covid-19 vaccine

Post by Woodchopper » Tue Mar 30, 2021 6:21 am


Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.7 and B.1.351 variants were first identified in the United Kingdom and South Africa, respectively, and have since spread to many countries. These variants harboring diverse mutations in the gene encoding the spike protein raise important concerns about their immune evasion potential. Here, we isolated infectious B.1.1.7 and B.1.351 strains from acutely infected individuals. We examined sensitivity of the two variants to SARS-CoV-2 antibodies present in sera and nasal swabs from individuals infected with previously circulating strains or who were recently vaccinated, in comparison with a D614G reference virus. We utilized a new rapid neutralization assay, based on reporter cells that become positive for GFP after overnight infection. Sera from 58 convalescent individuals collected up to 9 months after symptoms, similarly neutralized B.1.1.7 and D614G. In contrast, after 9 months, convalescent sera had a mean sixfold reduction in neutralizing titers, and 40% of the samples lacked any activity against B.1.351. Sera from 19 individuals vaccinated twice with Pfizer Cominarty, longitudinally tested up to 6 weeks after vaccination, were similarly potent against B.1.1.7 but less efficacious against B.1.351, when compared to D614G. Neutralizing titers increased after the second vaccine dose, but remained 14-fold lower against B.1.351. In contrast, sera from convalescent or vaccinated individuals similarly bound the three spike proteins in a flow cytometry-based serological assay. Neutralizing antibodies were rarely detected in nasal swabs from vaccinees. Thus, faster-spreading SARS-CoV-2 variants acquired a partial resistance to neutralizing antibodies generated by natural infection or vaccination, which was most frequently detected in individuals with low antibody levels. Our results indicate that B1.351, but not B.1.1.7, may increase the risk of infection in immunized individuals.
https://www.nature.com/articles/s41591-021-01318-5

SARS-CoV-2 variants of concern (VOC) have arisen independently at multiple locations [1, 2] and may reduce the efficacy of current vaccines targeting the spike glycoprotein [3]. Here, using a live virus neutralization assay (LVNA), we compared neutralization of a non-VOC variant versus the 501Y.V2 variant using plasma collected from adults hospitalized with COVID-19 from two South African infection waves, with the second wave dominated by 501Y.V2 infections. Sequencing demonstrated that infections in first wave plasma donors were with viruses harbouring none of the 501Y.V2-defining mutations, except for one with the E484K mutation in the receptor binding domain. 501Y.V2 virus was effectively neutralized by plasma from second wave infections and first wave virus was effectively neutralized by first wave plasma. In cross-neutralization, 501Y.V2 virus was poorly neutralized by first wave plasma, with a 15.1-fold drop relative to 501Y.V2 neutralization by second wave plasma across participants. In contrast, second wave plasma cross-neutralization of first wave virus was more effective, showing only a 2.3-fold decline relative to first wave plasma neutralization of first wave virus. While we only tested one plasma elicited by E484K alone, this potently neutralized both variants. The observed effective neutralization of first wave virus by 501Y.V2 infection elicited plasma provides preliminary evidence that vaccines based on VOC sequences could retain activity against other circulating SARS-CoV-2 lineages.
https://www.nature.com/articles/s41586-021-03471-w

Probably posted the preprints earlier.

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Re: Developing the Covid-19 vaccine

Post by shpalman » Tue Mar 30, 2021 8:00 am

Herainestold wrote:
Mon Mar 29, 2021 10:38 pm
Study in America shows Pfizer and Moderna vaccines inhibit transmission of virus.
new study suggests the messenger RNA vaccines produced by Moderna and the Pfizer-BioNTech partnership appeared to be 90% effective in preventing Covid-19 infection in a real-world setting.
The study followed nearly 4,000 health care workers, first responders, and other essential workers in eight U.S. locations as the first Covid vaccines were rolled out starting in December. Participants were tested weekly to look for all cases of Covid infection, even asymptomatic ones.

In the period from Dec. 14, 2020, to March 13, 2021, nearly 75% of the workers in the cohort received at least one dose of one of the mRNA vaccines. Both are given in a two-dose schedule.
Related:

There were 161 Covid infections in the unvaccinated workers, compared with 16 in workers who had received only one dose by the time of their infection and only three infections in people who had received both doses and were two weeks out from their second dose. The vaccine effectiveness following two doses was 90% — roughly in line with the 95% and 94% that the Pfizer and Moderna vaccines showed, respectively, in the clinical trials that supported their emergency use authorizations.
https://www.statnews.com/2021/03/29/rea ... effective/
No, the Pfizer and Moderna vaccines inhibit infections, not transmission.

But don't worry, that AstraZeneca preprint makes the same mistake.

You'd only know if it inhibits transmission if unvaccinated people got infected less when surrounded by lots of vaccinated people.
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Re: Developing the Covid-19 vaccine

Post by headshot » Tue Mar 30, 2021 9:52 am

If vaccinated people don’t get infected, how would they transmit the virus?

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Re: Developing the Covid-19 vaccine

Post by shpalman » Tue Mar 30, 2021 9:58 am

headshot wrote:
Tue Mar 30, 2021 9:52 am
If vaccinated people don’t get infected, how would they transmit the virus?
Don't look at me I'm not the one saying oH BUt It DoeSN't giVe yOU stErilISiNg imMunitY.
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Re: Developing the Covid-19 vaccine

Post by jdc » Tue Mar 30, 2021 4:39 pm

https://www.bbc.com/future/article/2021 ... d-covid-19 on how various vaccines fail to provide sterilising immunity:
Take meningitis as an example. For the kind caused by the bacteria Neisseria meningitidis, there are many vaccines available for the tens of different strains. The three given in the US – MCV4, MPSV4 and MenB – can together prevent 85-90% of disease cases. However, several have been shown to still allow people to "carry" the bacteria involved.

They can hide out in the nose or the back of the throat, from where they are able to infect others via sneezing, coughing, kissing, or sharing cigarettes or utensils. In one study of university students in the United Kingdom, the vaccine had no effect on the proportion of people harbouring the pathogen four weeks later.
And from Woodchopper's quote:
Neutralizing antibodies were rarely detected in nasal swabs from vaccinees.
So maybe it DoeSN't giVe yOU stErilISiNg imMunitY. I guess we'll find out at some point as a bunch of scientists are doing research in (I think) Brazil, Israel and Nottingham into whether unvaccinated people got infected less when surrounded by lots of vaccinated people.

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Re: Developing the Covid-19 vaccine

Post by jdc » Tue Mar 30, 2021 4:42 pm

Here's a bit on those studies: https://www.nature.com/articles/d41586-021-00450-z
To really nail down whether vaccines prevent transmission, researchers are tracking the close contacts of vaccinated people to see whether they are being indirectly protected from infection.

As part of an ongoing study of hundreds of health-care workers in England, known as PANTHER, researchers at the University of Nottingham tested health-care workers and the people they lived with for SARS-CoV-2 antibodies and viral RNA between April and August last year, around the time of the first pandemic wave. They will now retest some of those workers after they receive the Pfizer vaccine, as well as their close contacts who won’t have been vaccinated, to see whether the risk of infection has decreased for the close contacts, says Ana Valdes, a genetic epidemiologist at the University of Nottingham. If the risk decreases, that would mean the vaccines are probably preventing transmission, says Valdes.

Other groups, in Israel, are also planning to study households in which one member has been vaccinated. If these people become infected, researchers can see whether they pass on the virus to other household members.

In Brazil, a trial will randomly distribute doses of the COVID-19 vaccine produced by the Beijing-based drug company Sinovac to the town of Serrana in stages over several months. This approach could show whether drops in COVID-19 in vaccinated regions also contribute to reduced transmission in unvaccinated areas. This would demonstrate the indirect effects of vaccines, says Nicole Basta, an infectious-disease epidemiologist at McGill University in Montreal, Canada.

Studies of individuals and larger populations are needed to see how well vaccines protect against transmission, says Basta. “We really do need evidence that spans the whole spectrum.”

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Re: Developing the Covid-19 vaccine

Post by jdc » Tue Mar 30, 2021 6:13 pm

Speaking of which, just saw this on twitter: https://www.telegraph.co.uk/global-heal ... tand-covid about the Brazilian project.

It also refers to some bits from Scotland and Israel:
Researchers in Scotland found people living with health workers who had received two doses of either the Pfizer-BioNtech or Oxford-AstraZeneca jab were 54 per cent less likely to be infected with Covid-19 than the general population.

Meanwhile in Israel researchers have found the viral load, considered a good proxy for contagiousness, significantly dropped in a small number of people who were infected with Covid-19 two to four weeks after they had the Pfizer jab.


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Re: Developing the Covid-19 vaccine

Post by raven » Thu Apr 01, 2021 10:57 am

I think it's looking more likely that these unusual clotting events are a rare but real side effect of AZ. Which will presumably have an impact on our vaccine roll out here in the UK as we get to younger people. Oh dear.

But at least it's treatable if it's caught in time and we've got Moderna coming...

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