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

[The Don]

Originally Posted by Airfix

Why aren't flu infection rates rising at the same rate as Covid ? Is flu a lot less infectious ?

What makes you think that 'flu infection rates should rise at the same rate as Covid ?

[zooterkin]

Originally Posted by Airfix

Why aren't flu infection rates rising at the same rate as Covid ?

Why would they?

Quote:

Is flu a lot less infectious ?

Yes. R0 for flu is around 1.3. Covid-19 is much higher, even without the latest strain. And many people have been vaccinated against flu.

[JoeMorgue]

Originally Posted by Airfix

Why aren't flu infection rates rising at the same rate as Covid ? Is flu a lot less infectious ?

What?

[Darat]

Originally Posted by JoeMorgue

What?

Sadly it will be the typical CT nonsense.

[Chris_Halkides]

The active form of vitamin K is a cofactor necessary in the post-translational modification of particular glutamyl* residues to become gamma-carboxyglutamyl residues for some of the proteins within the coagulation cascade, including thrombin. IIRC this modification is needed to chelate calcium ions. In this context chelation basically means to grab onto something (often a metal ion) with at least two points of attachment. In this case, there is electrostatic attraction. What I am not immediately seeing is how this might relate to Covid-19. That calcium ions are part of the coagulation story is interesting.
*Notes: Glutamate is one of the twenty amino acids routinely specified in the genetic code. Once it is incorporated into a protein, it is common to refer to it as a glutamyl residue, but among friends calling it a glutamate residue is fine.

[Rolfe]

Thrombin (as well as platelets) is necessary to maintain the integrity of the endothelium. It's mainly platelet disorders that lead to spontaneous petechiation (cascade disporders more commonly lead to uncontrolled bleeding), but the role in continuous running maintenance of the endothelium is important. It appears that the fundamental issue (or one of the fundamental issues) in covid is the function of the endothelium, so I can see the connection.

[lionking]

Interesting table on covid sequencing rates by country:

https://twitter.com/DrEricDing/statu...447808/photo/1



With sequencing rates so low in the US they barely know what variant is rampaging through the nation.

[Meadmaker]

Originally Posted by lionking

Interesting table on covid sequencing rates by country:

https://twitter.com/DrEricDing/statu...447808/photo/1

http://www.internationalskeptics.com...37ed784733.jpg

With sequencing rates so low in the US they barely know what variant is rampaging through the nation.

I used to be just a tiny bit smug about being an American. Those were the days.

[The Atheist]

Originally Posted by lionking

Interesting table on covid sequencing rates by country:

Just to note on that - the rate in NZ since the end of the first outbreak is 100%. Every case, whether found in quarantine or not, is sequenced within 24 hours.

[The Atheist]

And I'm not sure whether I should post this in the Covid Anger thread, but we're less than a month away from hitting the double of 100 million cases and 2 million deaths worldwide.

The true numbers are obviously much higher, and it makes me very angry that all those lives have been affected when it need not have happened. We could have stopped it at under 10,000 deaths with concerted action.

[marting]

Originally Posted by Meadmaker

I used to be just a tiny bit smug about being an American. Those were the days.

What? The 2019 report on the pandemic preparedness of countries that put the USA and UK as number 1 and 2 respectively is, well, a bit flawed?

The initial rollout of contaminated tests by the vaunted CDC and slowness to fix it allowed the virus to take root largely unnoticed. And it turns out the USA is pretty far behind in sequencing. And I thought just muddling through was a British thing.

But hey, we're number one. In all the ways a country doesn't aspire to.

As an American, hopefully we will have a bit less hubris in the future. I sure hope we take a long hard look at our approach and implement improvements for there will be a next time and it might be a more virulent bug.

[Planigale]

Originally Posted by Rolfe

Thrombin (as well as platelets) is necessary to maintain the integrity of the endothelium. It's mainly platelet disorders that lead to spontaneous petechiation (cascade disporders more commonly lead to uncontrolled bleeding), but the role in continuous running maintenance of the endothelium is important. It appears that the fundamental issue (or one of the fundamental issues) in covid is the function of the endothelium, so I can see the connection.

To expand a bit on this. Vitamin K is essential in synthesis in the liver of factors that control clotting. Although classically vitamin K deficiency results in bleeding more easily, it is also important in pro-coagulant factors that reduce bleeding so predicting whether some one is in a pro-coagulant or anti-coagulant state is difficult, and both may co exist. However, as Rolfe says a key trigger to clotting is injury to the endothelium (this is the lining of blood vessels), this can provoke the onset of clotting in the blood. A third factor is platelets, cell like structures in blood that get caught up in the clot and bulk it out. They are important in physically blocking a hole in blood vessels. However, there has to be a balance, what you don't want is one hole in a blood vessel to provoke clotting that spreads uncontrollably round the body turning all the blood solid. So at the same time as clotting is started, anti clotting also starts. But the kinetics have to be such that a clot can form but is inhibited from causing a chain reaction.

Inflammation and coagulation are closely related. Inflammation can cause damage to the endothelium causing intra-vascular (within blood vessel) clotting - this seems a cause of severe illness in covid. Bradykinin has been identified as a key chemical in covid it links inflammation and coagulation. Its levels are affected by circulating serum ACE and the ACE receptor is where covid virus binds to cells to infect them.

So whilst normally low vitamin K is thought to cause bleeding in covid it might also make blood more prone to be sticky and clots to form on endothelium (on the walls of blood vessels). Bleeding and clotting problems can occur at the same time in covid.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5025506/
https://ashpublications.org/blood/ar...and-thrombotic
https://www.the-scientist.com/news-o...ovid-19--67876

[Planigale]

Originally Posted by marting

What? The 2019 report on the pandemic preparedness of countries that put the USA and UK as number 1 and 2 respectively is, well, a bit flawed?

The initial rollout of contaminated tests by the vaunted CDC and slowness to fix it allowed the virus to take root largely unnoticed. And it turns out the USA is pretty far behind in sequencing. And I thought just muddling through was a British thing.

But hey, we're number one. In all the ways a country doesn't aspire to.

As an American, hopefully we will have a bit less hubris in the future. I sure hope we take a long hard look at our approach and implement improvements for there will be a next time and it might be a more virulent bug.

This is a really important point. There are worse viruses out there. I really worry that people in positions of power will think now we have got through this we do not need to worry about another pandemic for decades. Another and worse virus could come next year.

Prior to the 2009 flu pandemic the UK's pandemic preparedness plan could have coped with covid. 2009 was a mild pandemic, the post pandemic reviews suggested that the UK had over-reacted, the plan was scaled back. One of the crucial failings in the UK was complacency, we had a good plan in 2009 it over managed a mild pandemic, the mistake was to think that the next pandemic would be equally mild. A classic case of fighting the last war. The UK did have excellent pandemic preparedness but just for the wrong pandemic. Having an excellent plan was a problem, people stuck to the plan for too long and did not look up to see covid was not following the plan.

[lionking]

Originally Posted by The Atheist

Just to note on that - the rate in NZ since the end of the first outbreak is 100%. Every case, whether found in quarantine or not, is sequenced within 24 hours.

And so too are ours since August. It’s why we can say with confidence that “this virus originated in Avalon” etc.

Ironically the sequencing technology we use came from the US.

[lionking]

Originally Posted by marting

What? The 2019 report on the pandemic preparedness of countries that put the USA and UK as number 1 and 2 respectively is, well, a bit flawed?

The initial rollout of contaminated tests by the vaunted CDC and slowness to fix it allowed the virus to take root largely unnoticed. And it turns out the USA is pretty far behind in sequencing. And I thought just muddling through was a British thing.

But hey, we're number one. In all the ways a country doesn't aspire to.

As an American, hopefully we will have a bit less hubris in the future. I sure hope we take a long hard look at our approach and implement improvements for there will be a next time and it might be a more virulent bug.

This is precisely the position of the WHO. This is just a dress rehearsal and we better get it right so we can fight off the “real” pandemic.

[Planigale]

Originally Posted by The Atheist

Just to note on that - the rate in NZ since the end of the first outbreak is 100%. Every case, whether found in quarantine or not, is sequenced within 24 hours.

I think you slightly overstate the case, although I accept NZ is doing excellently.

From this paper on sequencing in NZ

Quote:

only 42% of cases in those quarantine facilities had adequate viral RNA for successful genomic sequencing

So not a 100% according to those doing the sequencing.

https://www.medrxiv.org/content/10.1...853v1.full.pdf

[Rolfe]

It has been suggested that this virus was the perfect storm, and that if it had been more deadly then paradoxically it might have been stopped. If the mortality rate had been 20% and young people were at least as likely to die as the elderly, politicians might have taken it seriously from the start and stamped it out like the eastern counries did.

It's a bit too easy to headline "only" 1% of infected people dying and nearly all of these are elderly or with "underlying health problems" (like asthma or well-managed diabetes or a stable heart condition) and sucker politicians into a false sense of security, and people in general not being frightened enough to obey the restrictions.

[Roger Ramjets]

Originally Posted by The Atheist

Every case, whether found in quarantine or not, is sequenced within 24 hours.

Originally Posted by Planigale

I think you slightly overstate the case...

Quote:

only 42% of cases in those quarantine facilities had adequate viral RNA for successful genomic sequencing

But you may be understating it.

Quote:

The re-emergence of COVID-19 into New Zealand in August 2020 exemplified one of the most complete genomic data sets for a specific outbreak compiled to date, comprising 81% of positive cases (145 of 179 total PCR positive cases)

[TellyKNeasuss]

I found this old article (Nov. 19) about a covid breathalyzer test developed by Texas A&M University and a software company. The system returns results in about 10 seconds. They claim that preliminary tests (~800 people) showed that it was as accurate as PCR tests.

https://today.tamu.edu/2020/11/19/te...-breathalyzer/

[Roger Ramjets]

Originally Posted by Rolfe

It has been suggested that this virus was the perfect storm, and that if it had been more deadly then paradoxically it might have been stopped. If the mortality rate had been 20% and young people were at least as likely to die as the elderly, politicians might have taken it seriously from the start and stamped it out like the eastern countries did.

Not just eastern countries. But what do those countries that 'stamped it out' have in common?

Quote:

It's a bit too easy to headline "only" 1% of infected people dying and nearly all of these are elderly or with "underlying health problems" (like asthma or well-managed diabetes or a stable heart condition) and sucker politicians into a false sense of security, and people in general not being frightened enough to obey the restrictions.

One factor you haven't included in that 'perfect storm' - political ideals that favor 'the economy', 'personal freedom', and 'small government' over empathy, cooperation, and strong action when needed. It's no coincidence that Trump and Brexit happened to two countries that then did a remarkably poor job of dealing to the virus.

The most intelligent species on the planet just got 'suckered' by a virus that doesn't think at all? No, it was our own hubris that 'suckered' us.

[Rolfe]

Well, what I mean is that a virus with a higher mortality rate might have been taken seriously by the idiot politicians. The existence of the idiot politicians is sort of factored in.

[Planigale]

Originally Posted by Roger Ramjets

But you may be understating it.

I was only quoting from a paper that stated in a sub group only 42% were sequenced, not making a statement about the rate in the whole population. Your reference is still below the 100% suggested. In fairness I wonder whether what was meant was 100% are sent for sequencing, this would not be incompatible with e.g. only 42% were able to be sequenced. i suspect this is just a slight confusion in terminology.

ETA could you link your quote so it can be verified?

[Planigale]

Originally Posted by TellyKNeasuss

I found this old article (Nov. 19) about a covid breathalyzer test developed by Texas A&M University and a software company. The system returns results in about 10 seconds. They claim that preliminary tests (~800 people) showed that it was as accurate as PCR tests.

https://today.tamu.edu/2020/11/19/te...-breathalyzer/

Lots of these types of tests have been announced none seem to have gone very far. The concept of a test that detects airways inflammation is sound. What is less clear is can it differentiate between, asthma, bronchitis, flu, a common cold and covid-19? If all it tells you is 'you have a cough' there are simpler ways of knowing that. They are detecting the body's response to infection, this is not likely to be very different between infections. perhaps as a pre screen test it might work blow into the tube, if it comes up red get a specific swab test, if green proceed.

[Chris_Halkides]

Originally Posted by dann

Forskere på sporet af spændende corona-hypotese: Hårdt ramte patienter mangler K-vitamin (Videnskab.dk, Jan. 4, 2021)
Researchers on the trail of intriguing corona hypothesis: Severely impacted patients lack vitamin K.
Broccoli, anyone?!

ETA: Low vitamin K status predicts mortality in a cohort of 138 hospitalized patients with COVID-19 (preprint!)

"Second, we did not have data on Vitamin D status such as blood levels of 25-OH Vitamin D. This is a limitation because it has been hypothesized that Vitamin D and K could interact in COVID-19 disease.⁹"
⁹Janssen R, Visser MPJ, Dofferhoff ASM, Vermeer C, Janssens W, Walk J. Vitamin K metabolism as the potential missing link between lung damage and thromboembolism in Covid-19. Br J Nutr. Published online 2020:1-25. doi:10.1017/S0007114520003979.

I don't have an opinion on this myself, but the idea is intriguing.

[marting]

Comparative efficacy and safety of pharmacological interventions for the treatment of COVID-19: A systematic review and network meta-analysis

https://journals.plos.org/plosmedici...l.pmed.1003501

Numerous clinical trials and observational studies have investigated various pharmacological agents as potential treatment for Coronavirus Disease 2019 (COVID-19), but the results are heterogeneous and sometimes even contradictory to one another, making it difficult for clinicians to determine which treatments are truly effective.

They reviewed a large collection of studies but only where patients required hospitalization so no info on prophylactic or symptomatic but not yet seriously ill.

It's a pretty large study with many charts. RCT as well as Observational. Worth a look.

Conclusions
In this NMA, we found that anti-inflammatory agents (corticosteroids, tocilizumab, anakinra, and IVIG), convalescent plasma, and remdesivir were associated with improved outcomes of hospitalized COVID-19 patients. Hydroxychloroquine did not provide clinical benefits while posing cardiac safety risks when combined with azithromycin, especially in the vulnerable population. Only 29% of current evidence on pharmacological management of COVID-19 is supported by moderate or high certainty and can be translated to practice and policy; the remaining 71% are of low or very low certainty and warrant further studies to establish firm conclusions.

[dann]

Originally Posted by lionking

Interesting table on covid sequencing rates by country:

https://twitter.com/DrEricDing/statu...447808/photo/1

http://www.internationalskeptics.com...37ed784733.jpg

With sequencing rates so low in the US they barely know what variant is rampaging through the nation.

Does anybody know where the original table can be found? I keep finding only the same one from WP: top ten + the USA

[Aridas]

Originally Posted by marting

What? The 2019 report on the pandemic preparedness of countries that put the USA and UK as number 1 and 2 respectively is, well, a bit flawed?

They probably weren't wrong, honestly, given the factors that they were looking at. However, they didn't take into account leadership, though, as was stated later... and that the leadership was actively sabotaging pretty much every aspect of the US' pandemic preparedness definitely mattered and was completely outside their calculations.

[EHocking]

Originally Posted by dann

Does anybody know where the original table can be found? I keep finding only the same one from WP: top ten + the USA

GSAID seems to be the data source for the article
https://bioinfo.lau.edu.lb/gkhazen/c.../genomics.html

[marting]

Originally Posted by Aridas

They probably weren't wrong, honestly, given the factors that they were looking at. However, they didn't take into account leadership, though, as was stated later... and that the leadership was actively sabotaging pretty much every aspect of the US' pandemic preparedness definitely mattered and was completely outside their calculations.

I don't think different leadership would have made a big difference in the initial CDC screwup. And that delay also delayed getting EUA for private sector testing. And there were also territorial issues since many research groups had the equipment and knowledge to PCR test based on China's published genome but were prohibited from doing so. But no doubt leadership, or the effective absence of it, didn't exactly facilitate greasing the bureaucracy. Also, the deprecation of pandemic preparedness and focus at the NSC had already happened before the study came out. And it was supposed to reflect the country's preparedness and that certainly includes leadership.

None of which excuses the abysmal subsequent decisions leadership made. But it got off to a really bad start with more warning than most countries had.

[Skeptic Ginger]

Originally Posted by marting

I don't think different leadership would have made a big difference in the initial CDC screwup. And that delay also delayed getting EUA for private sector testing. And there were also territorial issues since many research groups had the equipment and knowledge to PCR test based on China's published genome but were prohibited from doing so. But no doubt leadership, or the effective absence of it, didn't exactly facilitate greasing the bureaucracy. Also, the deprecation of pandemic preparedness and focus at the NSC had already happened before the study came out. And it was supposed to reflect the country's preparedness and that certainly includes leadership.

None of which excuses the abysmal subsequent decisions leadership made. But it got off to a really bad start with more warning than most countries had.

The CDC leadership most certainly made a difference early on in the pandemic. Early CDC Interim guidelines tied providers' hands.

More than that goes in the politics thread.

[Aridas]

Originally Posted by Skeptic Ginger

The CDC leadership most certainly made a difference early on in the pandemic. Early CDC Interim guidelines tied providers' hands.

More than that goes in the politics thread.

Yeah, I'll agree with that, including the better delved into in the politics thread. There's fairly certainly a few aspects there that can be delved into, either way.

[dann]

Originally Posted by EHocking

GSAID seems to be the data source for the article
https://bioinfo.lau.edu.lb/gkhazen/c.../genomics.html

Great! Thanks!

[Segnosaur]

Some more concerns about virus mutations (in addition to the British Covid variant)...

From: CBC
Both Britain and South Africa have detected new, more transmissible variants of the COVID-19-causing virus in recent weeks that have driven a surge in cases. British Health Secretary Matt Hancock said on Monday he was now very worried about the variant identified in South Africa....Simon Clarke, an associate professor in cellular microbiology at the University of Reading, said that while both variants had some new features in common, the one found in South Africa "has a number additional mutations … which are concerning." He said these included more extensive alterations to a key part of the virus known as the spike protein — which the virus uses to infect human cells — and "may make the virus less susceptible to the immune response triggered by the vaccines."

Not sure if its a need to be concerned. Hopefully they'll be able to tell fairly quickly if the new variant is affected by the vaccines currently in use.

[The Atheist]

Originally Posted by Segnosaur

He said these included more extensive alterations to a key part of the virus known as the spike protein — which the virus uses to infect human cells — and "may make the virus less susceptible to the immune response triggered by the vaccines."

"May".

I'm starting to get really bloody annoyed at these scientists determined to have their 15 minutes of fame by coming out with scenarios that "may" occur.

In lack of evidence, a "don't know" makes a lot more sense.

But creates smaller headlines...

_____________________________


Meanwhile, Johnson & Johnson are nearing completion of Stage III trials and expect to seen emergency authorisation for their vaccine shortly: https://www.king5.com/article/news/h...e-0f5da893035c

Being single shot and requiring no ultra-cold storage sounds handy.

[marting]

Originally Posted by The Atheist

"May".

I'm starting to get really bloody annoyed at these scientists determined to have their 15 minutes of fame by coming out with scenarios that "may" occur.

In lack of evidence, a "don't know" makes a lot more sense.

I read "may" and "don't know" as having the same meaning. That is I would take the following to mean the same thing:

The alterations may allow the virus to escape vaccine immunity.

or

We don't know if the alterations will allow the virus to escape vaccine immunity.


But neither is very productive. A more useful piece would describe when and how we will know.

[RecoveringYuppy]

Originally Posted by The Atheist

"May".

I'm starting to get really bloody annoyed at these scientists determined to have their 15 minutes of fame by coming out with scenarios that "may" occur.

In lack of evidence, a "don't know" makes a lot more sense.

But creates smaller headlines...

It's warranted to call this out as a close call. It is a mutation that is changing the part of the vaccine that at least some vaccines are targeting.

[The Atheist]

Originally Posted by RecoveringYuppy

It's warranted to call this out as a close call. It is a mutation that is changing the part of the vaccine that at least some vaccines are targeting.

There are now 9 or 10 "major" mutations to Covid. With current infection numbers, I figure we'll see one a month until the vaccine starts to reduce numbers. Every one of them could mutate in several ways, some positive, some negative, and a couple downright disastrous.

Until we actually know, all the media is doing is speculating, and it's sad that some doctors/scientists see it as an opportunity to get their name in the papers. It doesn't do any good, and may increase anxiety; it's not science's backside, and it's counter-productive at a time when we want people to trust scientists.

The article is crying wolf.
____________________________

Meanwhile, an interesting day in prospect for NZ - awaiting testing of a quarantine worker with symptoms not following the ******* rules and going to a very public indoor situation. https://www.stuff.co.nz/waikato-time...-into-lockdown

Whatever the result, I trust she gets the sack, because she's putting billions of dollars of hard work at risk for what will be a selfish reason.

Queensland will be watching, too.

[The Atheist]

Originally Posted by The Atheist

Meanwhile, an interesting day in prospect for NZ - awaiting testing of a quarantine worker with symptoms not following the ******* rules and going to a very public indoor situation. https://www.stuff.co.nz/waikato-time...-into-lockdown

Whatever the result, I trust she gets the sack, because she's putting billions of dollars of hard work at risk for what will be a selfish reason.

Tested negative, so no problemo.

The law of averages says it will be a positive one of these days. Someone will slip up.

[Roger Ramjets]

Originally Posted by Planigale

ETA could you link your quote so it can be verified?

It's the same link as yours.

[zooterkin]

Has there been any analysis of what the risks of catching Covid-19 in various situations actually are? How risky is shopping at the supermarket, for example?