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COVID-19: Vaccine and testing procedures Megathread Part 3 - Read OP

Beasty

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Thread 2

No anti-vax stuff in this thread - it's to discuss the various vaccines available and how they are getting rolled out, as well as testing procedures

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DaSilva

is_that_so wrote: »

I admire your efforts in decoding it! There was survey of academics I recall about reading research papers. The word impenetrable emerged as a comment on a lot of them. Concise and precise are great qualities in writing but the key factor is comprehensibility. That tweet has words has no meaning to anyone except a very select few.

Let me be real clear here, I have no expertise in this field, that is just my best understanding of the information in these two documents, most important bits (to me) quoted below:

Novavax early results news release
https://ir.novavax.com/news-releases/news-release-details/novavax-covid-19-vaccine-demonstrates-893-efficacy-uk-phase-3

... in this trial, approximately 1/3 of the patients enrolled ... were seropositive, demonstrating prior COVID-19 infection ... the pre-trial infections are thought to have been caused by the original COVID-19 strain (i.e., non-variant), while the subsequent infections during the study were largely variant virus. These data suggest that prior infection with COVID-19 may not completely protect against subsequent infection by the South Africa escape variant

Paper quoted in tweet
https://onlinelibrary.wiley.com/doi/10.1111/tmi.13569

15 of 600 African sera were ... positive in ... spike/S1‐based Euroimmun ELISA, but did not inhibit spike/ACE2 binding in a surrogate virus neutralization test.

... SARS‐CoV‐2 IgG ELISA specificity may be significantly reduced in certain populations

is_that_so

Hardyn wrote: »

Okay. I'll try again. The trial showed that people who previously had Covid and those who didn't were infected with the South African variant at the same rate. This new study suggests that the tests Novavax used to check for antibodies from past infection are significantly less accurate in African samples. It means they possibly overestimated the number of participants who previously had Covid. This means their findings may be inaccurate and that prior infection does offer some protection.

That's English- the tweet is utter rubbish!

[Deleted User]

jackryan34 wrote: »

Give me a bit room here, it wasn't intelligence that got me this far.

Antibody tests don't work well on Africans?

They work well on Europeans and Americans, yeah ok, hmmm

Because of that the Novavax vaccine is now a very good vaccine and works well against SA variant

Okay. I'll try again. The trial showed that people who previously had Covid and those who didn't were infected with the South African variant at the same rate. This suggested that prior infection offered no protection from the reinfection with the variant. This new study suggests that the tests Novavax used to check for antibodies from past infection are significantly less accurate in African samples. It means they possibly overestimated the number of participants who previously had Covid. This means their findings may be inaccurate and that prior infection does offer some protection.

jackryan34

is_that_so wrote: »

I admire your efforts in decoding it! There was survey of academics I recall about reading research papers. The word impenetrable emerged as a comment on a lot of them. Concise and precise are great qualities in writing but the key factor is comprehensibility. That tweet has words has no meaning to anyone except a very select few.

It's kind of why peer review stuff is very flawed, I have been on peer review projects and most wouldn't have a clue what they are reading :pac:

is_that_so

DaSilva wrote: »

No I don't think it really changes the efficacy results of the vaccine trial, it just effects the observation they made where they seemed to notice that people were getting infected with the new variant regardless of their previous infection status, now it seems like that observation might have been muddied by those tests not being very accurate in some groups of people. In fact what it might be saying is that natural immunity is better than the trial suggested.

I admire your efforts in decoding it! There was survey of academics I recall about reading research papers. The word impenetrable emerged as a comment on a lot of them. Concise and precise are great qualities in writing but the key factor is comprehensibility. That tweet has words but has no meaning to anyone except a very select few.

jackryan34

DaSilva wrote: »

In fact what it might be saying is that natural immunity is better than the trial suggested.

That is very good news then

We are 15 months into this mess and re-infections are still very rare, the variants are so dangerous then?

DaSilva

jackryan34 wrote: »

Give me a bit room here, it wasn't intelligence that got me this far.

Antibody tests don't work well on Africans?

They work well on Europeans and Americans, yeah ok, hmmm

Because of that the Novavax vaccine is now a very good vaccine and works well against SA variant

No I don't think it really changes the efficacy results of the vaccine trial, it just effects the observation they made where they seemed to notice that people were getting infected with the new variant regardless of their previous infection status, now it seems like that observation might have been muddied by those tests not being very accurate in some groups of people. In fact what it might be saying is that natural immunity is better than the trial suggested.

degsie

MM be like.....

Pathetic really....

jackryan34

Hardyn wrote: »

One of the findings of the South African Novavax trial was a similar attack rate between participants who previously had Covid and those who didn't. Novavax used their own in-house ELISA test to check for antibodies in the participants. This study suggests that ELISAs used in samples from Africa show markedly reduced specificity, possibly due to interference from local endemic pathogens. There's a possibility that the 30% seropositivity rate from the trial may have been an overestimate.

Give me a bit room here, it wasn't intelligence that got me this far.

Antibody tests don't work well on Africans?

They work well on Europeans and Americans, yeah ok, hmmm

Because of that the Novavax vaccine is now a very good vaccine and works well against SA variant

DaSilva

jackryan34 wrote: »

It means?

My best understanding, serology tests used to determine if you were previously infected with sars-cov-2 are not as precise in African populations as they are in other groups.

In some tests they did, these tests produced false positives, which means these people were not previously infected, but the tests suggested they were.

What does this have to do with Novavax? When Novavax released preliminary results earlier this year they suggested that 1/3 of people in their trial were seropositive (i.e. had already been infected with sars-cov-2), and they noticed that despite this people were becoming infected again. They assumed this meant people were being reinfected because of the new variant, now those results are being questioned because some of those people may have been falsely flagged as seropositive and in fact the reinfections in some might have really been first infections.

I think.

[Deleted User]

titan18 wrote: »

https://www.nytimes.com/2021/03/10/world/europe/eu-exports-vaccines.html

EU are being too nice imo when we're not getting supplies promised. Particularly shipping to US who refuse to ship to anyone else atm

We're not dicks. Everyone needs a vaccine. We still have given over double our fair share compared to the average

Hurrache

brickster69 wrote: »

So in other words just political bollox

https://twitter.com/nickgutteridge/status/1369643211837300740

Not really, the figures say otherwise
https://twitter.com/DaveKeating/status/1369600881742778371
https://twitter.com/DaveKeating/status/1369638267700846595

(cross posting from the Brexit thread)

josip

jackryan34 wrote: »

It means?

Patience Jack.
Wait for them to dumb it down for the rest of us.

In order to speed up the translation from those with the expertise, and in the best traditions of the Internet, I will post something completely incorrect.
It means that the Covid vaccines don't work as well on people in Africa.

...revealed markedly reduced #specificity when applied to human sera from Africa...

jackryan34

Hardyn wrote: »

Well now. This is interesting.

https://twitter.com/florian_krammer/status/1369668488500019209?s=20

It means?

[Deleted User]

Well now. This is interesting.

https://twitter.com/florian_krammer/status/1369668488500019209?s=20

titan18

Melanchthon wrote: »

Whats the UK done apart from making sure that they have ring fenced their contracts?

Also there is a massive difference between being open about what your going to do RE the USA, and changing the situation this late after condemning similar last year.

UK is an export ban in everything but name really. It might not be as harsh as the US one but they're not exporting vaccines like the EU (we exported 8m to them). My opinion is unless they're going to play fair we shouldn't with them or the US.

Melanchthon

seamus wrote: »

UK would have no basis to complain about the EU engaging in a little bit of vaccine nationalism at this stage .

Whats the UK done apart from making sure that they have ring fenced their contracts?

Also there is a massive difference between being open about what your going to do RE the USA, and changing the situation this late after condemning similar last year.

seamus

It's a good opportunity for the E.U. to tighten up on exports. The evidence is right there that the EU has not engaged in vaccine nationalism despite manufacturers continuously letting us down even while exporting doses out of the EU.

The US or UK would have no basis to complain about the EU engaging in a little bit of vaccine nationalism at this stage.

Warn manufacturers that if there are any further shortfalls in delivery, their products will not leave the EU until the shortfall has been rectified.

titan18

https://www.nytimes.com/2021/03/10/world/europe/eu-exports-vaccines.html

EU are being too nice imo when we're not getting supplies promised. Particularly shipping to US who refuse to ship to anyone else atm

trellheim

ACitizenErased wrote: »

So the Irish Times article pushed by a specific person on here yesterday is complete BS, as proven at the time

It was me and we agreed to wait and see who was right at the end of the month. Not complete BS. The IT article was in relation to the Taoiseach's comments.

The article quotes the Tanaiste.

As is well known now looking at Jan and Feb , until its the end of march we really won't know will we ?

I think the difference between it is 150,000 vaccines.

Slightly and welcomingly muddled by the extra 46500 Pfizer announced today,

josip

marno21 wrote: »

3.85m expected in Q2 atm so. Plus 1.1m from Q1 leaves us at 4.95m by end of Q2.

Some of these will be J&J and some will be AstraZeneca who will be administering little 2nd doses in Q2 (just the March second doses in June).

Should leave us with >80% of the adult population with one dose by Q2 end.

I would sincerely hope we end up getting more than 3.85m doses in Q2.

Which would be 100% or very close to all adults who want to/can get vaccinated.
15% have said they don't want an approved vaccine.

[Source] Boards.ie peer reviewed study.

ShyMets

astrofool wrote: »

The horse will likely have long bolted at that stage, now is the time for them to help, not in 2-3 months time.

Depends on what happens with AZ, who have said they'll meet their quotas in Q2, despite governments using the decreased estimates in planning.

EU also working with J&J to speed up their manufacturing, and more Pfizer capacity coming online all the time.

Hopefully this time it is a conservative amount that increases rather than decreases, however, if we get to 80% by June, that'll be great for the country.

It would be political suicide for Johnson to start giving away vaccines right now. They need to vaccinate more of their population before he can do so

Wolf359f

[Deleted User] wrote: »

Per the 14 day epidemiological reports in the past 14 days 3.75% of 7,683 cases were healthcare setting acquired. In the 14 days to the 29th of January, this was 13% of 27,348 cases

Ah I was going by the HCW reports.
Going by the 14 day epi reports you can see the week on week reductions in HCW's as a % of total new confirmed cases.

stephenjmcd

KrustyUCC wrote: »

That makes for disappointing reading

Looks likely we will be missing out targets for Q2 as well

How ? 3.8m is listed as the Q2 target. No change there

[Deleted User]

Wolf359f wrote: »

I think they need to show a more clearer picture.
Last year week 32-46: 6.8% of all cases were in HCW (2.3% of which where hospitalized)
Week 48-8: 10.2% of all cases were in HCW (2.8% of which were hospitalized)

Filtering out week 7-8 this year, it looks to be 9.2% of all cases are in HCW's.
I could be completely wrong and reading reports wrong, all evidence worldwide points to the vaccine having a massive impact. I would just have thought we'd see a bigger drop in HCW's as a % of the general population.

Per the 14 day epidemiological reports in the past 14 days 3.75% of 7,683 cases were healthcare setting acquired. In the 14 days to the 29th of January, this was 13% of 27,348 cases

Sanjuro

ACitizenErased wrote: »

So the Irish Times article pushed by a specific person on here yesterday is complete BS, as proven at the time

What did the article say?

astrofool

JTMan wrote: »

Gavin Reilly reported ... Taoiseach says Boris Johnson "doesn't have surplus vaccines to give to Ireland right now".

That does not sound like a no to me. Sounds like no for now but maybe the UK will give supplies to us at a later stage.

The horse will likely have long bolted at that stage, now is the time for them to help, not in 2-3 months time.

BigMo1 wrote: »

Is there anything to point to us getting more Q2 supply though? Everything I've read up to now seems to point to less. I'm just scrapping for some hope, I'm to be married at the end of July so trying to cling onto any good news I can get.

Depends on what happens with AZ, who have said they'll meet their quotas in Q2, despite governments using the decreased estimates in planning.

EU also working with J&J to speed up their manufacturing, and more Pfizer capacity coming online all the time.

Hopefully this time it is a conservative amount that increases rather than decreases, however, if we get to 80% by June, that'll be great for the country.

marno21

JTMan wrote: »

Gavin Reilly reported ... Taoiseach says Boris Johnson "doesn't have surplus vaccines to give to Ireland right now".

That does not sound like a no to me. Sounds like no for now but maybe the UK will give supplies to us at a later stage.

He's right there in fairness. They don't have surplus at the minute.

But in the summer when they do have excess vaccinations, and when they are struggling to get vaccinators to work shifts because they have better things to be at like going to the pub or a festival, maybe they can send a few over.

JTMan

Gavin Reilly reported ... Taoiseach says Boris Johnson "doesn't have surplus vaccines to give to Ireland right now".

That does not sound like a no to me. Sounds like no for now but maybe the UK will give supplies to us at a later stage.

Hmmzis

Some interesting reading during lunchtime.

https://assets.researchsquare.com/files/rs-310773/v1_stamped.pdf

It describes how the current mRNA vaccines are working within vaccinated humans with a very close look at the lymph nodes and germinal center B cells. GC B cells are important in terms of antibody maturation, longevity of the response and the affinity of antibodies (countering variations in the virus). There is some very interesting data there for those interested. For the TL;DR synopsis, here are a few of the important bits:

In the draining lymph nodes, we detected robust SARS-CoV-2 S-binding GC and PB responses in aspirates from 12 of 12 participants. These responses were detectable after the first immunization and increased after the second.
...
These results with mRNA vaccines are superior to those seen after seasonal influenza virus vaccination in humans, where hemagglutinin-binding GC B cells were detected in only three of eight participants

S-specific PB pool that persists in the draining lymph nodes contained a substantial fraction of IgA+ cells. This observation is intriguing because it occurred after intramuscular rather than mucosal vaccination.

IgA class of antibodies is very important in protecting mucosal membranes as there is very little IgG type antibodies residing in our snot.

Too long for a quote, but previously infected and then vaccinated individuals had a significantly broader response to all circulating variants (good thing).

Note: it's a preprint but their methods look good and the names on the paper look solid (Florian Krammer among them).