Continuation The One Covid-19 Science and Medicine Thread Part 3

[Skeptic Ginger]

Originally Posted by marting

Take an example where among the 10's of thousands that were "vaccinated," half with a placebo, half with actual. Let's say over the course of 3 months 4 people in the vaccinated group test positive but 200 people in the placebo group test positive giving the 95% efficacy rate, that strongly implies that false positives are below 5% of all positives else the vaccinated group would have shown higher case counts. And were the 4 people that tested positive in the vaccinated group false positives, that would require the vaccine be essentially 100% effective. Neither the docs, testers, nor the people in the study knew whether the vaccination was placebo.

When doing thorough research that this would require, you follow up on the positives and confirm them. There would be zero false positives in the final report.

[The Atheist]

Originally Posted by Meridian

I wonder whether something similar might be happening elsewhere, in particular in Germany: the overall numbers were pretty static for November, and then started growing for no (to me, but what do I know?) obvious reason around the start of December. I don't believe any restrictions were loosened.

Any pointers to good information on this welcome!

There isn't a lot of good information so far, and the "70%" is a wild-arse guess. Guardian states:

Quote:

“the New and Emerging Respiratory Virus Threats Advisory Group (Nervtag) now considers that the new strain can spread more quickly.

Along with a little humour:

Quote:

Exactly where the variant first appeared is not known. It may simply be that Britain’s extremely robust virus surveillance system spotted it before other nations did.

I'd think Germany's systems are every bit as good as Britain's at the absolute minimum, so I'd be surprised if it was the same variant.

It's certainly possible that it results from evolutionary pressure, but seems more likely to be just the 9th major mutation the virus has undergone. If it's more infectious, there's probably not much more can be done than already is.

[marting]

Originally Posted by Skeptic Ginger

When doing thorough research that this would require, you follow up on the positives and confirm them. There would be zero false positives in the final report.

Good point. While they wouldn't know which people had the vaccine or placebo, they would know they were in a study. Which brings up another question. Before they hospitalize any patient for Covid-19 do they do multiple tests. Perhaps a different PCR test that uses a different RNA sequence? You wouldn't want a patient in a Covid-19 ward that didn't have Covid-19. I would think there would be more care back when the positive test rate was 2%. Less of an issue now that it's running 8% or more in lots of places.

[Skeptic Ginger]

Originally Posted by marting

... Before they hospitalize any patient for Covid-19 do they do multiple tests. Perhaps a different PCR test that uses a different RNA sequence? You wouldn't want a patient in a Covid-19 ward that didn't have Covid-19. I would think there would be more care back when the positive test rate was 2%. Less of an issue now that it's running 8% or more in lots of places.

You don't put a person in the hospital per se for COVID. You put them in the hospital because they need to be there.

Once you are sick enough to be in the hospital, the work-up would include ruling COVID in or out if that wasn't already done.

[marting]

The recent publication of the Great Barrington Declaration (GBD), which calls for relaxing all public health interventions on young, healthy individuals, has brought the question of herd immunity to the forefront of COVID-19 policy discussions, and is partially based on unpublished research that suggests low herd immunity thresholds (HITs) of 10-20%. [We re-evaluate these findings and correct a flawed assumption leading to COVID-19 HIT estimates of 60-80%.

https://icite.od.nih.gov/covid19/sea...12.01.20242289

[Skeptic Ginger]

Originally Posted by marting

The recent publication of the Great Barrington Declaration (GBD), which calls for relaxing all public health interventions on young, healthy individuals, has brought the question of herd immunity to the forefront of COVID-19 policy discussions, and is partially based on unpublished research that suggests low herd immunity thresholds (HITs) of 10-20%. [We re-evaluate these findings and correct a flawed assumption leading to COVID-19 HIT estimates of 60-80%.

https://icite.od.nih.gov/covid19/sea...12.01.20242289

From the link:

Quote:

If policymakers were to adopt a herd immunity strategy, in which the virus is allowed to spread relatively unimpeded, we project that cumulative COVID-19 deaths would be five times higher than the initial estimates suggest. Our re-estimates of the COVID-19 HIT corroborate strong signals in the data and compelling arguments that most of the globe remains far from herd immunity, and suggest that abandoning community mitigation efforts would jeopardize the welfare of communities and integrity of healthcare systems.

And yet people who want to wish this pandemic away keep pushing.

[Planigale]

Originally Posted by marting

Take an example where among the 10's of thousands that were "vaccinated," half with a placebo, half with actual. Let's say over the course of 3 months 4 people in the vaccinated group test positive but 200 people in the placebo group test positive giving the 95% efficacy rate, that strongly implies that false positives are below 5% of all positives else the vaccinated group would have shown higher case counts. And were the 4 people that tested positive in the vaccinated group false positives, that would require the vaccine be essentially 100% effective. Neither the docs, testers, nor the people in the study knew whether the vaccination was placebo.

The problem is that in most of the vaccine trials (with the exception of the Oxford vaccine), only symptomatic people were tested for infection. Since the false positive rate depends on your a priori risk, you will have a lower false positive risk when testing symptomatic people than when testing / screening asymptomatic people. The UK trial of the Oxford vaccine involved weekly swabbing of participants. This data has not been published yet. It will give the answer whether this vaccine reduces transmission or just reduces severity of disease.

[Planigale]

Originally Posted by marting

Hard to say what "70%" faster means. Are they saying the R is 70% higher? Or is it spreading such that in two weeks the number of new variant case increases was 70% more than the old? Without specifics it's pretty hard to tell anything other than it seems more infectious.

To some degree this is normal. Bugs want to evolve to be more "fit" and that means spreads more easily. "Fitness" for the bug is not positively correlated to how serious/fatal it is. That doesn't help it spread through evolutionary pressure. We've already seen one variant that took over back in the Spring pretty much everywhere.

This is the briefing document on the new strain. It appears to reproduce more efficiently so viral loads are higher which is probably why transmission is higher more virus is shed. Severity of disease seems unchanged, probably because this is more host determined than virus. Worryingly about 0.5% of cases appear to be reinfections (in the southeast where this new strain is most common around 15% of the population has probably had covid so this means the reinfection risk might be around 3%, so there is some concern that this strain ids different enough that repeat infections are more likely.) Currently it does not appear repeat infections are more severe.

https://khub.net/documents/135939561...=1608470511452

[Roger Ramjets]

Originally Posted by marting

Hard to say what "70%" faster means. Are they saying the R is 70% higher? Or is it spreading such that in two weeks the number of new variant case increases was 70% more than the old? Without specifics it's pretty hard to tell anything other than it seems more infectious.

Apparently it has a shorter incubation period. So the 'spreads 70% faster' means just what it says.

Quote:

To some degree this is normal. Bugs want to evolve to be more "fit" and that means spreads more easily. "Fitness" for the bug is not positively correlated to how serious/fatal it is.

Bugs don't 'want' to evolve, they just do. Natural selection weeds out those that aren't viable, and promotes those that are more virulent. But it also selects against those that are too fatal or too obvious.

A virus with a long 'asymptomatic' incubation period has the potential to infect more unaware victims and so spread further, but slower than one that activates sooner. The faster the virus replicates the quicker it can become infectious so the faster it can spread. The more virulent it is the more payload it can spread, making infections easier - but being too virulent may kill the host before it has a chance to infect many others, and nasty symptoms cause people to isolate more.

The virus isn't changing because it wants to, it's doing it anyway - and we are promoting the versions we haven't stomped on. If the average test takes 3-5 days then a version that becomes infectious within that time frame will thrive, which is exactly what we are seeing. If everybody isolated to stop any spread then none would survive. That means no new mutations and no chance for them to find a niche. But we won't do that because we are stupid.

[The Atheist]

Originally Posted by Planigale

Worryingly about 0.5% of cases appear to be reinfections (in the southeast where this new strain is most common around 15% of the population has probably had covid so this means the reinfection risk might be around 3%, so there is some concern that this strain ids different enough that repeat infections are more likely.)

That's going to be worth keeping a close watch on.

Originally Posted by Roger Ramjets

If everybody isolated to stop any spread then none would survive. That means no new mutations and no chance for them to find a niche. But we won't do that because we are stupid.

I've just been talking to a few of those non-compliant types and I reckon the split is about 50/50 between stupid and bloody-minded.

[marting]

Originally Posted by Planigale

This is the briefing document on the new strain. It appears to reproduce more efficiently so viral loads are higher which is probably why transmission is higher more virus is shed. Severity of disease seems unchanged, probably because this is more host determined than virus. Worryingly about 0.5% of cases appear to be reinfections (in the southeast where this new strain is most common around 15% of the population has probably had covid so this means the reinfection risk might be around 3%, so there is some concern that this strain ids different enough that repeat infections are more likely.) Currently it does not appear repeat infections are more severe.

https://khub.net/documents/135939561...=1608470511452

Holy crap!

Growth rate from genomic data: which suggest a growth rate of VUI-202012/01 that
that is 71% (95%CI: 67%-75%) higher than other variants.
o Studies of correlation between R-values and detection of the variant: which
suggest an absolute increase in the R-value of between 0.39 to 0.93

So it's a combo of higher R value (raises herd immunity threshold) and shorter time between infection and being infectious.

And an indication the variant is slightly more capable of re-infection of people recovered from the earlier variant.

Yikes. If, or more likely when, this puppy gets loose it's going to raise hell. Hope the vaccines under development work at high percentages.

[Aridas]

To poke at the vaccine concerns for the variant...

Scientists aren't concerned about new coronavirus variant eluding current vaccines

[Planigale]

Originally Posted by marting

Holy crap!

Growth rate from genomic data: which suggest a growth rate of VUI-202012/01 that
that is 71% (95%CI: 67%-75%) higher than other variants.
o Studies of correlation between R-values and detection of the variant: which
suggest an absolute increase in the R-value of between 0.39 to 0.93

So it's a combo of higher R value (raises herd immunity threshold) and shorter time between infection and being infectious.

And an indication the variant is slightly more capable of re-infection of people recovered from the earlier variant.

Yikes. If, or more likely when, this puppy gets loose it's going to raise hell. Hope the vaccines under development work at high percentages.

No this is incorrect. Although in vitro viral replication is faster, this does not mean the disease progresses any faster; there is no evidence that this mutation has any difference in the disease it produces. It probably just causes the infected people to shed more viable virus.

[Planigale]

Originally Posted by The Atheist

There isn't a lot of good information so far, and the "70%" is a wild-arse guess. Guardian states:



Along with a little humour:



I'd think Germany's systems are every bit as good as Britain's at the absolute minimum, so I'd be surprised if it was the same variant.

It's certainly possible that it results from evolutionary pressure, but seems more likely to be just the 9th major mutation the virus has undergone. If it's more infectious, there's probably not much more can be done than already is.

Just to be clear the UK has vastly greater ability to sequence the virus than any other country (except perhaps the US), the intent is that every isolate in the UK is sequenced. Roughly half of the sequenced viruses worldwide are done by UK laboratories. The UK had invested in significant sequencing resources (primarily to sequence human genomes), this has been repurposed to sequencing Sars-CoV-2. So in this particular aspect Germany does not match the UK. Germany despite fewer cases does not have universal isolate sequencing capability. So not humour.

[Planigale]

Originally Posted by Aridas

To poke at the vaccine concerns for the variant...

Scientists aren't concerned about new coronavirus variant eluding current vaccines

The worry is that as vaccination roles out that the virus strains selected will be those that evade the vaccine. The hope is that replication critical domains have been chosen for the vaccine and a viable mutant can not arise that evades the vaccine.

An interesting observation was that the strain was picked up because it gave a false negative on the PCR test. The standard UK PCR test uses three primers looking at different parts of the viral genome (in general targeting sites with low variation). One of the primers poorly detects this new strain as this is a site of mutation.

These two documents list the mutations and probable impact of mutations.
https://www.gisaid.org/references/gi...-vui-20201201/
https://www.cogconsortium.uk/wp-cont...-Mutations.pdf

[Meridian]

Originally Posted by Planigale

Just to be clear the UK has vastly greater ability to sequence the virus than any other country (except perhaps the US), the intent is that every isolate in the UK is sequenced. Roughly half of the sequenced viruses worldwide are done by UK laboratories. The UK had invested in significant sequencing resources (primarily to sequence human genomes), this has been repurposed to sequencing Sars-CoV-2. So in this particular aspect Germany does not match the UK. Germany despite fewer cases does not have universal isolate sequencing capability. So not humour.

Thanks! From the reporting in Germany that I've seen it's not been clear to me whether the new variant has been tested for (by sequencing). Presumably if not, they'll start checking now!

[Skeptic Ginger]

Originally Posted by Meridian

Thanks! From the reporting in Germany that I've seen it's not been clear to me whether the new variant has been tested for (by sequencing). Presumably if not, they'll start checking now!

They wouldn't know it was a new variant without genetic sequencing.

[marting]

Early use of steroids associated with increased mortality

preprint:

https://icite.od.nih.gov/covid19/sea...a0177f48f57ccb

Quote:

Early initiation of corticosteroid use (≤ 3 days after ICU admission) was associated with an increased 90-day mortality. Early use of methylprednisolone in the ICU is therefore not recommended in patients with severe COVID-19.

[The Atheist]

error

[Roger Ramjets]

Originally Posted by Planigale

The worry is that as vaccination roles out that the virus strains selected will be those that evade the vaccine. The hope is that replication critical domains have been chosen for the vaccine and a viable mutant can not arise that evades the vaccine.

We can't afford to rely on hope. But we will anyway.

First we hoped it would stay in China. It didn't.

Then we hoped that 'flattening the curve' would be sufficient, because locking down for long enough to make it die out would (purportedly) destroy our economies. It wasn't.

So we pinned our hopes on masks and sensible behavior getting us through. They didn't.

Now the situation is desperate. All our hopes were dashed as our half-hearted measures let the virus mutate into a form which is spreading much faster. The economies we were so afraid of hurting are hurting worse than if we had taken strong action from the start.

but no worries, now we have vaccines which we hope will put an end to it.

If we are lucky, vaccines will squash the virus faster than it can mutate. Some scientists tell us that it generally takes years for a virus to mutate sufficiently to evade vaccines. But what they don't tell us is that it's a matter of luck. Do you feel lucky?

We had a plan that would have virtually eliminated the luck element, but we didn't take it because we hoped we wouldn't have to. And we are still hoping. Because we are stupid.

[Samson]

Needed:
A scientific study of mortality amongst those who always wear masks.
1. Mask wearing reduces quantity of virus received.
2. Mortality is proportional to quantity.

Thoughts anyone?

[rjh01]

Originally Posted by Samson

Needed:
A scientific study of mortality amongst those who always wear masks.
1. Mask wearing reduces quantity of virus received.
2. Mortality is proportional to quantity.

Thoughts anyone?

It would be difficult to measure mask-wearing. The person may say "I always wear a mask." But in fact they do not.
Also a mask protects others when the wearer is sick.

Otherwise a good idea.

[Skeptic Ginger]

Originally Posted by Samson

Needed:
A scientific study of mortality amongst those who always wear masks.
1. Mask wearing reduces quantity of virus received.
2. Mortality is proportional to quantity.

Thoughts anyone?

That's not the point of wearing masks, or did you miss all the research? The masks protect other people from you.

If you want to know how well masks will protect you, just look at how many health care workers have become infected taking care of COVID patients.

[Puppycow]

Originally Posted by Samson

Needed:
A scientific study of mortality amongst those who always wear masks.
1. Mask wearing reduces quantity of virus received.
2. Mortality is proportional to quantity.

Thoughts anyone?

Purely anecdotal I'm sure, but in Japan, the mortality seems to be rather low. Also, going by the Worldometer data, the CFR in Japan is 1.7% compared to 2.9% in the United States.

I live in Japan, and I think that mask wearing is much more prevalent here. No law compels it, it's just a social norm.

Overall mortality is 43 times lower, because there are also fewer infections (as well as a lower CFR).

Of course, I can't say for sure that masks are the reason for the difference, but I believe that they make a big difference.

Obviously, it isn't a scientific study, but I think it's a kind of natural experiment.

[arthwollipot]

Antarctica.

[Puppycow]

Originally Posted by Skeptic Ginger

That's not the point of wearing masks, or did you miss all the research? The masks protect other people from you.

If you want to know how well masks will protect you, just look at how many health care workers have become infected taking care of COVID patients.

Wear Masks To Protect Yourself From The Coronavirus, Not Only Others, CDC Stresses

Quote:

Wearing a mask protects the wearer, and not just other people, from the coronavirus, the Centers for Disease Control and Prevention emphasized in an updated scientific brief issued Tuesday. And the protective benefits of masks are stronger the more people wear masks consistently and correctly, the agency says.

When the CDC first recommended that Americans wear cloth face coverings back in April, it cited evidence that the coronavirus could be transmitted by asymptomatic people who might not be aware of their infectiousness – a group estimated to account for more than 50% of transmissions. The agency said masks were intended to block virus-laden particles that might be emitted by an infected person.

In a report updated Tuesday, the CDC says that is still the primary intention of wearing masks. But it also cites growing evidence that even cloth masks can also reduce the amount of infectious droplets inhaled by the wearer.
. . .

Ghandi argued in a recently published paper that wearing masks can reduce the severity of illness with COVID-19, even if the wearer does become infected.

Not only does it protect others, it also protects the mask-wearer. It can reduce the severity of illness.

[Samson]

Originally Posted by Puppycow

Wear Masks To Protect Yourself From The Coronavirus, Not Only Others, CDC Stresses



Not only does it protect others, it also protects the mask-wearer. It can reduce the severity of illness.

Which is the precise point of my question.
I always wear a mask then if I get infected my symptoms are mild then I am immune.
No study could sensibly include who else was wearing a mask.

[Puppycow]

One other link from NPR about the effectiveness of masks on airplanes:

https://www.npr.org/sections/goatsan...-plane-flights

They seem to work quite well, even if others on the flight are infected. Assuming everyone on the flight wears them (however, I imagine that on long flights, people remove them to eat and drink).

[Skeptic Ginger]

Originally Posted by Puppycow

Wear Masks To Protect Yourself From The Coronavirus, Not Only Others, CDC Stresses

Not only does it protect others, it also protects the mask-wearer. It can reduce the severity of illness.

I will review the literature and get back to the thread, but do keep in mind how screwed up the CDC mask messaging has been with Trump screwing with everything and Fauci ignoring early research supposedly on purpose to conserve PPE for health care workers.

[The Atheist]

Originally Posted by Planigale

Just to be clear the UK has vastly greater ability to sequence the virus than any other country (except perhaps the US), the intent is that every isolate in the UK is sequenced.

I've just been watching a highly informative piece on Al Jazeera about the mutation.

The first surprise was that it was actually first identified in September, so I'm struggling to see why it's such a big deal in December.

It seems to me it's just another dominant strain, as happened at the start where the Chinese original virus got supplanted by the Italian variant.

Interestingly, nearly identical mutations have been found in South Africa & Brazil that aren't related to the UK one, so it might be some kind of natural process de-selecting less hardy strains.

The big point made was the one I've been on for some time - the mutations are speeding up now so many people have the virus and if we don't act in concert to stop it, it will mutate out of the vaccine's scope.

Originally Posted by arthwollipot

Antarctica.

That's so incredibly stupid I can't even think up words to describe it. They should have been quarantined prior to travel, as our and US staff have been. Just as well Chile doesn't have a space program or it'd be in space as well.

[The Atheist]

Oh, and Taiwan has its first community case in 250 days.

Thanks, New Zealand!

https://www.theguardian.com/world/20...-than-250-days

[Skeptic Ginger]

Originally Posted by The Atheist

I've just been watching a highly informative piece on Al Jazeera about the mutation.

The first surprise was that it was actually first identified in September, so I'm struggling to see why it's such a big deal in December.

It seems to me it's just another dominant strain, as happened at the start where the Chinese original virus got supplanted by the Italian variant.

Interestingly, nearly identical mutations have been found in South Africa & Brazil that aren't related to the UK one, so it might be some kind of natural process de-selecting less hardy strains.

The big point made was the one I've been on for some time - the mutations are speeding up now so many people have the virus and if we don't act in concert to stop it, it will mutate out of the vaccine's scope.

That's so incredibly stupid I can't even think up words to describe it. They should have been quarantined prior to travel, as our and US staff have been. Just as well Chile doesn't have a space program or it'd be in space as well.

You sample virus from multiple people and places. You can do a lot with that information.

Sequencing the virus in Seattle (Fred Hutch) the scientists were able to see that the virus from the original patient who had come from Wuhan and was hospitalized in Everett, (the next city north of Seattle) was the same virus strain that had broken out in the Life Care Center miles away in Kirkland (east of Seattle). And there was another person in Seattle who was part of an influenza study who had COVID, not flu. By demonstrating the three were all related one could conclude the virus was circulating in the Seattle area undetected for a number of months. We didn't have the connecting dots, only the 3 disconnected points.

Fast forward to the recent detection of the new variant. You detect it in Sept. But it's not until Dec when you find it is replacing the existing strains. Now it becomes clear this strain has a particular quality that gives it an advantage over the other circulating strains. It is more contagious.

The point being you don't know the significance just from the genetic sequence. You have to see what it does.

As for developing vaccine resistance, that will only come with evolutionary pressure that selects for vaccine resistance. We're not there yet and there's no way to prevent it. We haven't been able to contain this virus at all. I can't imagine we could suddenly nip a more contagious form of it now.


On the more positive side, the vaccine manufacturers have said they can easily tweak the mRNA vaccine.

[jimbob]

Good thread on the spike mutation, which has arisen independently in both the UK and South Africa and become the dominant strain in both countries.

So it almost certainly does have a selective advantage.

https://twitter.com/firefoxx66/statu...395861506?s=21

[The Atheist]

More on the variant:

It may be more effective at infecting children. That would explain the sharp increase in cases.

As per my previous post, it could be nothing to be to worried about, or as MIT puts it: The situation could prove to be a false alarm.

[The Atheist]

And we may have discovered why disabled rank #1 in likelihood of dying from Covid.

They're not worth saving.

https://www.kenw.org/post/oregon-hos...le-denied-care

[The Atheist]

I may have missed this being posted, but I've only just seen it myself

https://vitamindforall.org/letter.html

Must dash - off to prepare my acceptance speech.

[rjh01]

Originally Posted by The Atheist

I may have missed this being posted, but I've only just seen it myself

https://vitamindforall.org/letter.html

Must dash - off to prepare my acceptance speech.

Did you do any primary research? If so please give links to the published papers. Otherwise no prize.

[The Atheist]

Originally Posted by rjh01

Did you do any primary research? If so please give links to the published papers. Otherwise no prize.

Can you show me where they are requirements?

https://www.nobelprize.org/nomination/medicine/

[marting]

https://github.com/mbevand/covid19-age-stratified-ifr

Interesting data set and chart comparing various published estimates of influenza and Covid-19 IFR rates v age.

Basically Flu v C19 converges around age 5 and diverges to 2.9 at age 30, 8.5 at age 50 and 13.5 at age 70.

C19 includes 13 data sets around the world. Flu is USA CDC sets from the last 7 flu seasons.

[rjh01]

Originally Posted by The Atheist

Can you show me where they are requirements?

https://www.nobelprize.org/nomination/medicine/

Quote:

The Nobel Prize for Physiology or Medicine is awarded for discovery of major importance in life science or medicine. Discoveries that have changed the scientific paradigm and are of great benefit for humankind are awarded the prize,

Let me rephrase my question.
Have you made a discovery yourself? Have what you have discovered been of great benefit for humankind?

How can you say yes to the above questions without having published papers?

Edit. If I am wrong and you are awarded the Nobel prize, then there is no rush. It will not be announced until October and awarded in December.