Continuation The One Covid-19 Science and Medicine Thread Part 4

[marting]

Excellent Overview of O

Patience is crucial': Why we won't know for weeks how dangerous Omicron is
https://www.science.org/content/arti...gerous-omicron

Quote:

Now, once again, the world is watching as researchers work nights and weekends to learn what a new variant has in store for humanity. Is Omicron more infectious? More deadly? Is it better at re-infecting recovered people? How well does it evade vaccine-induced immunity? And where did it come from? Finding out will take time, warns Jeremy Farrar, the head of the Wellcome Trust: “I'm afraid patience is crucial.”

[Dr.Sid]

Originally Posted by The Atheist

Sorry mate, I thought it was so obvious I was being sarcastic that I didn't think anyone would respond.

I actually mentioned it a month or so back when I was looking at the upcoming letters of the Greek alphabet.

It might already be in Australia: https://www.stuff.co.nz/world/austra...-test-positive

This being mostly American audience nobody ever uses sarcasms. Especially not without 10 blinking smileys.

[Michel H]

Originally Posted by Pixel42

South African medical association says Omicron variant causes 'mild disease'

The hospitalisation rates seems to remain low in South Africa: https://covid-19dashboard.news24.com/ (you may have to wait for a while to see this page), and this seems to confirm this report.

There is a sharp increase in the number of cases and in positivity rates, but it seems that many infected people are young (and probably with mild diseases):

Quote:

The arrival of the variant, accompanied by a rapid rise in infections, especially in younger people, fuelled fresh calls for compulsory vaccinations as the daily average rate of jabs slumped to below 100,000 in the last week.

(https://www.timeslive.co.za/sunday-t...-over-omicron/)

[dann]

Maybe not

Quote:

A widely-shared quote from a South African doctor, saying Omicron causes only mild symptoms, is being taken out of context. She was referring to a small group of young, healthy people and warned of severe disease in other groups
South African doctor who raised alarm about omicron variant says symptoms are ‘unusual but mild’ (Telegraph, Nov 27, 2021)
BNO Desk on Twitter (Nov 28, 2021)

[The Atheist]

Israel has banned all foreign nationals, and there are cases now confirmed in Australia.

I see they reckon it started in September, so there should be some sign of it in hospitalisations if it's more virulent, I'd have thought.

I've sent a PM to Capsid for his thoughts on the mutations.

[Oystein]

Originally Posted by The Atheist

...
I hope the Krauts are checking what's driving their enormous wave right now.

I am reading up on a few days back, and you posted this 3 days ago.

The "Krauts" (Germans) have the same "enormous" wave that pretty much all countries in Europe have: There are lots more social contacts than a year ago, now that a majority (though still under 70%, and some a long time ago) is fully vaccinated, and we have the Delta variant - therefore rising case numbers come late fall.
Fewer deaths than a year ago, but too many unvaccinated, so death rate and hospitalizations are become a real problem. ICUs reach capacity in part because there are fewer ICU beds than a year ago, as many nurses and other personnel quit amid the constant work strain!

However.

The Krauts are not doing worse (nor better) than the rest of the continent: Before the wave, Germany's case and death rates ranked around 11th or 12th best among the 27 EU member states; currently, Germany ranks 14th, so not much of a change in rank.

And: Just yesterday, I took death numbers from Worldometers for the most recent week and plotted them against most current "fully vaccinated" rate as per Bloomberg, and, of course, found a very convincing negative correlation: The EU 15 countries with the highest vaccination rates are also the 15 countries with the lowest death rate.

Germany of course has not quite reached its goals for full (2-dose) vaccination, and has so far not managed to roll out boosters with great speed. Vaccination centers have been closed in most places, as it was thought that resident doctors would be able to vaccinate as fast as anyone could wish, but it seems this is not actually working well enough.

[Oystein]

Originally Posted by Michel H

The hospitalisation rates seems to remain low in South Africa ...

As it is throughout Africa, and among a host of reasons are the low median age of Africans in most countries, and the lower prevalence of obesity and related co-morbidities.
As well, of course, as the low number of available hospital beds in many parts of the continent.
And perhaps reporting gaps of various origin.

In fact, it may well be that such high proportions of the overall African populations are young and healthy enough to generally suffer no or very mild symptoms, that some regions might approach something akin to herd immunity without ever going through a mayhem wave even without vaccines - or with few vaccines targeted to just the right groups (medical staff, the old and obese).

[marting]

13 of the 61 covid+ passengers have now been sequenced and have Omicron. This is a somewhat time consuming process and requires a low CT to even succeed. However, there is a proxy, the S-gene dropout that Omicron shares with Alpha and since Alpha is nearly extinct in SA the data on the S-gene dropout is what is needed. This will give a good idea of how prevalent Omicron is faster than full sequencing.

I have been unable to find S-gene data on the 61 passengers which should have been known yesterday.

[The Atheist]

Originally Posted by Oystein

And: Just yesterday, I took death numbers from Worldometers for the most recent week and plotted them against most current "fully vaccinated" rate as per Bloomberg, and, of course, found a very convincing negative correlation: The EU 15 countries with the highest vaccination rates are also the 15 countries with the lowest death rate.

Yeah, I've been using UK as a proxy - their fatality rate has fallen by 90% even as case numbers are higher than last year and winter.

The only question is how omicron behaves among the vaccinated, and it's going to be a couple of weeks or so before we have any idea on that.

[The Atheist]

Since we don't have scientific data on omicron so far, I'm going to indulge in some speculation.

Omicron will be more contagious and less harmful, based on the following:

1 - the fact that it's spread so far already, starting September, without increasing hospitalisations.
2 - while the SA Dr has a potential political agenda, the mildness of infections is encouraging.
3 - evolutionary pressure is towards transmission, not severity.
4 - the only variant that appears more severe is mu, which died out quickly.
5 - we already have evidence that variants may escape the vaccine, but people still retain protection against severe disease.

[Dr.Sid]

Nah, speculation is pointless. Let's just wait.

[marting]

For those interested, you can see data on SA provinces each day here:

https://www.nicd.ac.za/latest-confir...november-2021/

Change the "28" to see results earlier in the month. There's about a 4x increase every 7 days. The very rapid increase in positivity rate from 1% to 9% in 2 weeks is remarkable. Never seen an increase ramp that fast before.

Gauteng: Cases PositivityRate
Nov 14: 126 1%
Nov 21: 545 3%
Nov 28: 2,308 9%

Other provinces were much lower but are now increasing at similar rates. Not a statistical fluke. Elsewhere reported that >90% have the S-gene dropout, a marker for Omicron.

[The Atheist]

Originally Posted by marting

Other provinces were much lower but are now increasing at similar rates. Not a statistical fluke. Elsewhere reported that >90% have the S-gene dropout, a marker for Omicron.

Yeah, I don't think there's any doubt on the infectiousness, but that's been aided by absolutely no masks or restrictions, from what I hear Gauteng/Jo'burg has been like for the past couple of months.

This virus is becoming a real pest. I recall posting about 18 months ago that some scientist reckoned we'd have 80 major variants arise. I think we're up to about 20, so there's lots of life in the pandemic yet.

[The Atheist]

Still early days, but encouraging signs, maybe:

Quote:

Deputy First Minister of Scotland, John Swinney, has been on the BBC’s Good Morning Scotland just now. Of the six people identified as having contracted the Omicron strain, he said:

The individuals concerned are being supported but there is no evidence of serious illness. Obviously we know that Covid can develop into serious illness.

https://www.theguardian.com/world/li...08de86f451e8bb

The question will be - if omicron is less likely to cause severe disease, should we just let it go?

I say yes. At the infection rate, everyone will have it in no time, and with cases now seeded across the planet, I think it's likely to happen anyway.

[dann]

Twitter thread:

Quote:

1/ With the greatest inter-professional courtesy and respect, this is a load of ******* ******** that puts the country at risk at a time when we have no definite information beyond hugely increased transmissibility.
2/ Why is the guy who told us it definitely isn't airborne, who libeled those of us treating legit concerns about AZ as anti-vaxers, who is against vax of kids, and who wanted to open at 50%, given endless air time to spout whatever crap he happens to want to spout that day?
'If it's mild, you actually want it to spread': Coatsworth calls for calm over Omicron transmission (9News.com.au, Nov 29, 2021)

Dr David Berger, Absurdist Chronicler on Twitter (Nov 29, 2021)

[Dr.Sid]

Originally Posted by The Atheist

Still early days, but encouraging signs, maybe:



https://www.theguardian.com/world/li...08de86f451e8bb

The question will be - if omicron is less likely to cause severe disease, should we just let it go?

I say yes. At the infection rate, everyone will have it in no time, and with cases now seeded across the planet, I think it's likely to happen anyway.

What really depends is how fast it can generate cases who needs hospitalization. If it generate twice less hospital cases, but at 4 times the rate, it's still a problem.

[Chris_Halkides]

"But the final study results Merck announced Friday, from all 1,433 volunteers enrolled in the study, raise questions about the drug's benefit. Overall, treatment reduced the relative risk of hospitalization and death in the trial by 30% versus placebo. Roughly 10% of the 699 people who received a placebo were hospitalized or died, compared to about 7% of the 709 patients treated with molnupiravir, Merck said.

Nine people given a placebo died, according to Merck, versus only one who was treated with molnupiravir. The drug's side effect profile was consistent with what the company previously reported." link. The NYT and WaPo also have stories.

[alfaniner]

Oh, I do hope someone tells The President that it's "Omicron", not "Omnicron". It's about as cringeworthy hearing that as "nucular" is.

[marting]

One less unknown and not a good one.

The 13 genomes from the Netherland's planes indicates that the Omicron cases were from multiple sources rather than a single outbreak. This is evidence of a diversity in community spread hence not an anomoly due to a large cluster.

https://twitter.com/CorneliusRoemer/...01876707434496

The observed diversity indicates this was not just one single group but that travellers had picked up Omicron a number of times independently from the community, presumably in South Africa.

[The Atheist]

Originally Posted by marting

One less unknown and not a good one.

I disagree, I think that's great news, because it shows the infection was both widespread and with lots of people infected, and it hasn't shown up in hospitals yet.

I'm interested to see the good doctors in Aussie have been reading my posts with this piece out of a couple of Aussie universities:

Quote:

“We don’t know yet, but there are a few clues coming out that it may be less virulent,” says University of Melbourne epidemiologist Tony Blakely.

“Whilst it is all a bit nerve-racking at the moment, it might work out to our advantage.”

Deakin University epidemiologist Catherine Bennett, while similarly circumspect, says the evidence so far gives cause for optimism.

That would be the most amazing news if it's how it goes down.

(A smart buyer will buy a couple of Dow contracts right now, because if that's what happens, it will go berserk.)
___________________________

I messaged Capsid for his take on omicron, and this is his response:

Quote:

There is a huge interest globally and resources will be thrown at what this all means. It's too early to say really; we'll know more in a few weeks when we have cultured the virus stocks and run assays. We need to look at 1) neutralisation titres of vaccinated people against omicron to measure cross-reactivity, 2) clinical symptoms of infected people and 3) animal modelling to see if it's more pathogenic. All of this is underway.

[angrysoba]

Originally Posted by The Atheist

I disagree, I think that's great news, because it shows the infection was both widespread and with lots of people infected, and it hasn't shown up in hospitals yet.

I'm interested to see the good doctors in Aussie have been reading my posts with this piece out of a couple of Aussie universities:



That would be the most amazing news if it's how it goes down.

(A smart buyer will buy a couple of Dow contracts right now, because if that's what happens, it will go berserk.)
___________________________

I messaged Capsid for his take on omicron, and this is his response:

Capsid’s take is very useful. Specifically “It’s too early to say really.”

[marting]

Originally Posted by The Atheist

I disagree, I think that's great news, because it shows the infection was both widespread and with lots of people infected, and it hasn't shown up in hospitals yet.

My take was that the growth in cases was not from a single superspreader event but general growth in prevalence. Had it been the former then the transmission increase seen there would likely be overestimated. I had a small hope that was the case.

As for the virulence, it's too early to say. Today's number was 25 dead up from yesterday. Overall, that's still slightly lower than what was seen when Delta ramped up at the same point in time integrating in the cases in the prior month as there is a delay betwen cases and deaths. OTOH, the Delta ramp up started with a higher baseline. Cases were exceptionally low when Omicron came along a couple weeks ago. Will know more in a few weeks. Could be anwhere between 1/3 as virulent and just over 1 from what I see now.

I concur with Capsid's comment. Vaccine and prior infection escape is a big unknown.

One thing I find quite odd is how low Delta's prevalence was 3 weeks ago. No signs of growth yet SA's population was pretty much done with NPIs. Delta had previously hit them pretty hard and given their low age demographic it may well have been that well over 50% of the population had already had covid.

If so, that could account for the high growth of Omicron if it has an increased ability to breakthrough prior infections. That could also account for lower hospitalization/deaths as they would likely have milder disease.
This also means the transmissivity isn't as high as one might presume based on the current R (a bit <1) of Delta in SA.

This would result in an apparent lower virulance even if the virulance against a totally naive population would be the same as covid at the start. This, of course, also applies more generally in populations hard hit and/or with high vax rates. This really could be just part of the transition to covid becoming endemic.

[alfaniner]

Originally Posted by alfaniner

Oh, I do hope someone tells The President that it's "Omicron", not "Omnicron". It's about as cringeworthy hearing that as "nucular" is.

Hehe, Jake Tapper opened his show today with the teaser -- "OK, looks like now everyone is going to have to learn how to pronounce 'Omicron'." Watching Don Lemon right now, I'd swear he's saying "Omnicon" as well. It may even be "omnicron".

[marting]

Interesting twitter thread on the interaction of R0 and immune escape. Suggestion that omicron has an R0 less than Delta but omicron Rt is greater due to immune escape.

This is along the lines of my previous observation:

Quote:

This also means the transmissivity isn't as high as one might presume based on the current R (a bit <1) of Delta in SA.

https://twitter.com/trvrb/status/1465364300936085506

Also found a video called #COVIDisairborne out of UCSD. It covers a really astonishing amount of computational work modeling covid at the atomic level in aerosol particles having 300,000,000 atoms.

https://youtu.be/ZfmmJnG7le8

Associated paper:
https://pubmed.ncbi.nlm.nih.gov/34816263/

[Roger Ramjets]

Originally Posted by Oystein

I took death numbers from Worldometers for the most recent week and plotted them against most current "fully vaccinated" rate as per Bloomberg, and, of course, found a very convincing negative correlation: The EU 15 countries with the highest vaccination rates are also the 15 countries with the lowest death rate.

[antivax]But did you include all the people who were killed by the vaccine? I bet you didn't![/antivax]

You say their deaths were the 'lowest', but how much lower were they? Can you post us a graph showing the correlation? Not that I don't believe there is one, but I hate it when people make claims that give no clue as to the magnitude and significance (if any) of the effect.

[macdoc]

healthy, fit ...and dead.

https://www.theguardian.com/society/...-covid-vaccine

[dann]

Originally Posted by Roger Ramjets

[antivax]But did you include all the people who were killed by the vaccine? I bet you didn't![/antivax]

You say their deaths were the 'lowest', but how much lower were they? Can you post us a graph showing the correlation? Not that I don't believe there is one, but I hate it when people make claims that give no clue as to the magnitude and significance (if any) of the effect.

Data shows us that the higher the vaccination rate, the lower the death rate. (European Commission on Twitter) See graph in tweet.

[dann]

Congratulations to Australians, New Zealanders and East Asians.
You are not only relatively unscathed by the pandemic, science literacy is probably increasing, too!

Quote:

People in Australia and New Zealand trusted scientists ‘a lot’ the most (62%) and Sub-Saharan Africa, the least (19%). In East Asia trust rose by the largest margin from 2018 (33%) to 2020 (49%).
Public trust in scientists rose during the Covid-19 pandemic (Wellcome Global Monitor, Nov 29, 2021)

Quote:

As the Covid-19 pandemic raged, New Zealanders and Australians developed the world's highest levels of trust in scientists, newly released survey data has found - and those trust levels soared as the global crisis evolved.
(...)
They were by far the most likely to believe that their governments were making their decisions based on scientific advice.
(...)
Greaves said that while attitudes often return to baseline after a crisis, trust in scientists could endure at a higher level, as the pandemic had increased scientific literacy in media and the population.
Trust in scientists soared in Australia and New Zealand during Covid pandemic, poll finds (The Guardian, Nov 30, 2021)

I am not a big fan of trust in science: Understanding science, science literacy, is important. If people don't acquire the skills that are necessary to distinguish between real science and pseudo-science, appeals to the authority of science may end up being appeals to false authority. We have seen many examples of this during the pandemic.
So it's great to see that in the case of Australia and New Zealand trust in scientists goes hand in hand with increased scientific literacy.

[The Atheist]

Originally Posted by dann

Congratulations to Australians, New Zealanders and East Asians.
You are not only relatively unscathed by the pandemic, science literacy is probably increasing, too!

Dunno about Aussies and Asians, but I don't believe a bar of the idea that scientific literacy has increased here.

Scientists have been very visible and accessible, and lots of people trust their views, but I don't see them gaining actual scientific knowledge as a result.

[dann]

Originally Posted by The Atheist

Dunno about Aussies and Asians, but I don't believe a bar of the idea that scientific literacy has increased here.

Scientists have been very visible and accessible, and lots of people trust their views, but I don't see them gaining actual scientific knowledge as a result.

They obviously weren't told that SARS-CoV-2 is no worse than the flu, that it isn't airborne, that face masks not only don't work but are actually dangerous, that children are immune and don't spread the virus, that lockdowns kill more people than they save etc.
And I assume that people in Australia, New Zealand and East Asia were also provided with information about why and how SARS-CoV-2 is worse than the flu, what exactly airborne means in the case of this virus, how face masks and lockdowns work, and how we know that children get infected and spread the virus.
In many other countries, people received almost no actual information and an awful lot of misinformation to make up for it.

[The Atheist]

Originally Posted by dann

They obviously weren't told that SARS-CoV-2 is no worse than the flu, that it isn't airborne, that face masks not only don't work but are actually dangerous, that children are immune and don't spread the virus, that lockdowns kill more people than they save etc.

No, they had a very clear run at explaining things and got massive amounts of air time. Scientists people would never have heard of became household names.

[The Great Zaganza]

with so many mutations from the variant on which the vaccines are based on, I expect that the number of infections of the vaccinated will rise sharply; this will probably not change hospitalization numbers much, as the vaccines will still provide some protection, and the most at risk people will have already succumbed.

[Chris_Halkides]

"The resistance of SARS-CoV-2 to antivirals, especially nucleoside analogs (NAs), shows the need to identify new CoV inhibition targets. Therefore, this review highlights the importance of nsp14-ExoN as a target for inhibition. Also, nucleoside analogs could be used in combination with existing anti-CoV therapeutics to target the proofreading mechanism."

"There is evidence that Remdesivir has 4.5 times more efficacy in the ExoN mutant background, and Ribavirin has 200 times higher efficacy relative to the wild‐type ExoN viral genome.^4,38 This provides a clear justification for a mixture of Favirpiravir/Remdesivir/Ribavirin/Galidesivir and SARS‐CoV‐2 ExoN inhibitor combinations to be used. abstract. The complete article is also available at this location.

The proofreading enzyme surely removes non-standard nucleotides some of the time, but how much is probably dependent on which nucleotide analog is used. Someone needs to design and synthesize an inhibitor to the proofreading enzyme ExoN, coded by nsp14. A cocktail of this inhibitor with molnupiravir, remdesivir, etc. might be successful.

[alfaniner]

Originally Posted by oddball

"Omicron" is an anagram of "moronic".

My sister just mentioned the anagram this morning, but didn't tell me what it was. Thanks for that.

[The Atheist]

Cases popping up all over the place, several pre-dating the announcement of omicron's discovery.

As Moderna says openly its vaccines may be worthless...

[Chris_Halkides]

"Another advantage is that the production of RNA-based vaccines is more rapid compared to production of traditional vaccines. This rapid production could be a major advantage in face of sudden pandemics. Moreover, RNA-based vaccines may be effective against pandemics because they also provide more flexibility to prevent or treat pathogens that are rapidly evolving [8,9]". 2015 blog entry. Reference 9 is Petsch et al. Nat Biotech (2012) 30(12):1210-1216.

I realize that many commenters here are quite aware of this flexibility already, but this link may be helpful in kitchen table discussions.
EDT
"He [Moderna Chief Executive Stephane Bancel] had earlier said on CNBC that it could take months to begin shipping a vaccine that does work against Omicron." Reuters

[The Atheist]

If omicron escapes the vaccine strongly, I think you can throw all the vaccines in the bin, because it will just evolve further, and with a conservative 6-month lag to get vast numbers of vaccines out, we will be doing no more than chasing Covid's tail forever.

Seems to me that a much more important tool will be Paxlovid. As a protease inhibitor targeting the spikes, it should work against any form of Covid, and it might well end up that we fight the virus more with drugs than vaccines.

[Chris_Halkides]

Originally Posted by The Atheist

Seems to me that a much more important tool will be Paxlovid. As a protease inhibitor targeting the spikes, it should work against any form of Covid, and it might well end up that we fight the virus more with drugs than vaccines.

Or a cocktail of an inhibitor of the proofreading exonuclease and one of the nucleoside analogs. I need to get cracking on this...

[The Atheist]

Originally Posted by Chris_Halkides

Or a cocktail of an inhibitor of the proofreading exonuclease and one of the nucleoside analogs. I need to get cracking on this...

Yeah, go mate! Get that lab coat on.

Meanwhile, BioNTech isn't seeing a need for new vaccines, or over-concern around vaccine escape, particularly after the 3rd shot booster:

Quote:

Our belief [that the vaccines work against Omicron] is rooted in science: If a virus achieves immune escape, it achieves it against antibodies, but there is the second level of immune response that protects from severe disease—the T-cells.

[Samson]

Originally Posted by The Atheist

Dunno about Aussies and Asians, but I don't believe a bar of the idea that scientific literacy has increased here.

Scientists have been very visible and accessible, and lots of people trust their views, but I don't see them gaining actual scientific knowledge as a result.

People trust science when boarding aeroplanes and dying of covid. Give me that vax now!