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

[jimbob]

Originally Posted by angrysoba

Generally speaking what can make a virus less virulent is that a very virulent one could simply kill its hosts before transmitting whereas any variant that keeps its hosts alive long enough to transmit above the R1 rate (or perhaps with a large reservoir host population) doesn’t have selective pressure to become less virulent (but still might by chance).

I think Covid has plenty of room for increased virulence without hampering its transmission rate and if it does have the ability to reinfect way above Delta and if it is more transmissible than Delta and presumably if it also allows for greater cryptospread (is that the right term or is occult spread better) through asymptomatic cases then sure it *could* get more virulent as well.

Smallpox was highly infectious and also lethal for at least three millennia

[marting]

Nice log plot of cases in Guateng. It's about as perfect exponential chart as I've seen. I would have expected some lowering of Rt as the population impliments their own NPIs as the press there has been highlighting this big time for the last week+ but nothing yet.

Topol with a retweet from Pagel, two of the best.
https://twitter.com/EricTopol/status...62431003131906

[angrysoba]

Originally Posted by jimbob

Smallpox was highly infectious and also lethal for at least three millennia

Indeed.

[The Atheist]

Further evidence omicron is out and about all over, and has been for an unknown amount of time: https://www.bbc.com/news/uk-59553460

[marting]

Originally Posted by The Atheist

Further evidence omicron is out and about all over, and has been for an unknown amount of time: https://www.bbc.com/news/uk-59553460

Oh yeah. My current estimate is that Omicron will surpass Delta between Dec 31 and Jan 13 in the UK and parts of the EU and about 3 days later in the USA. Good question where the peak will be after that but it will likely be very high with a sharp decline after it does it's thing. Guess is about 2-4 weeks after it overtakes Delta

Just astonishingly consistent growth rates and early UK and EU data looks the same as early data in SA.

Still unclear the degree of Vax escape but likely as high or higher than prior Covid infection escape (85% -> 55%). My expectation is that Vax escape is at least as large as prior infection escape. Both should still help reduce severity.

[The Atheist]

Originally Posted by marting

Still unclear the degree of Vax escape but likely as high or higher than prior Covid infection escape (85% -> 55%). My expectation is that Vax escape is at least as large as prior infection escape. Both should still help reduce severity.

You'd think so, but the little bastard's travelling faster than the research at this stage, so we can but hope. I agree with you that they should help, but we'll know pretty damned soon.

Merry Christmas!

[marting]

Originally Posted by The Atheist

Merry Christmas!

Second verse, same as the first.

But with Gusto!

[The Atheist]

Originally Posted by Planigale

Not unexpected. This is also true with flu or all cause pneumonia. Being ill with one thing in general increases your risk of being ill with something else in the next year. This is a 'being ill' phenomena not a covid phenomena.

Do you have evidence to back that up? I can't find anything, and if an influenza infection doubles the risk of dying within 12 months I'd expect it to be well known.

Originally Posted by Planigale

Vaccines and prior infections are the most likely explanation for differing severity of illness reported than an intrinsic change in the virus.

That's just a stab in the dark at this stage, although the low vaccine rate in SA should show up very quickly if vaccines are protective against severe disease.

Originally Posted by Planigale

Certainly a worry if it can cause even moderate illness in children with prior infection. The last thing I saw suggested in the UK about 90% children had evidence of immunity mostly from previous infections.

It's an interesting one alright. It could be an artifact of very wide spread among kids - all their schools have been full for some time. I hope so, because getting 0-5s vaccinated is going to be hard work.

[The Atheist]

Originally Posted by marting

Second verse, same as the first.

But with Gusto!

My mind boggles that this is the third christmas for SARS-CoV-2, and we're nowhere near being in control. I am not buying it a present.

[marting]

Bugger.

Antibody escape calculator:

https://twitter.com/EricTopol/status...24011196039171

Calculating the effect of Omicron's receptor binding domain mutations impact on antibody escape "These scores... emphasize the ominous antigenic properties of the recently described Omicron variant"

[marting]

On the positive side, cases in Gauteng dropped to 4.5k, about 30% more than 7 days ago. OTOH positivity rate was 26% but 10% 7 days ago. Which means, among other things, that a lot less testing was done today. Weekend effect accounts for some of this but the decline is a bit more than one would anticipate.

Other interesting positive data is that covid deaths still don't show any sign of a ramp.

Along those lines this piece is interesting:
https://www.thesouthafrican.com/news...ne-6-december/

Quote:

A majority of patients profiled in the study were unvaccinated, too. There were no vaccinated patients who required ICU treatment, and only one double-jabbed person needed oxygen to manage their symptoms – and even then, it is reported that they already suffered from Chronic Obstructive Pulmonary Disease (COPD).

‘VACCINATION MAKING A DIFFERENCE’ – SAMRC
However, the most encouraging sign of the lot comes from the data which looks at the length of hospital stays. In the last fortnight, the average inpatient spends just under three days on a ward. This is down almost three-fold, from 8.5 days reported over the last 18 months. This could be a gamechanger for health services and their capacity.

[marting]

Another silicon study indicates moderately reduced antibody activity.

https://www.biorxiv.org/content/10.1...024v1.full.pdf

Quote:

Conclusion and Discussion
While in vitro experiments are needed to validate these predictions, the predicted results here suggest that existing neutralizing antibodies will still bind to the mutated spike protein of the Omicron variant. However, it appears that the affinity of Omicrons’s RBD for neutralizing antibodies is reduced compared to the reference RBD structures. This result suggests that antibodies elicited from vaccines or a previous infection will provide some protection against Omicron

[angrysoba]

Originally Posted by The Atheist

Do you have evidence to back that up? I can't find anything, and if an influenza infection doubles the risk of dying within 12 months I'd expect it to be well known.

Planigale mentioned this way back at the begining of the pandemic explaining that excess deaths reflect how bad a flu year is, largely because although most people get over flu, a lot of people who have the flu get heart attacks or strokes within a year.

This confirms the old adage, "That which doesn't kill you, makes it much easier for something else to finish you off later."

[dann]

Originally Posted by The Atheist

... getting 0-5s vaccinated is going to be hard work.

Why? Cuba already did it with 2-5s.

[Planigale]

Originally Posted by The Atheist

Do you have evidence to back that up? I can't find anything, and if an influenza infection doubles the risk of dying within 12 months I'd expect it to be well known.

It is well known, by those in the know. There is an aphorism in medicine that you are more likely to die of a heart attack after pneumonia than you are to die of the pneumonia. This may not be statistically accurate but it makes the point. For pneumonia in general see references here.

https://pubmed.ncbi.nlm.nih.gov/29325222/

For influenza see examples here

https://pubmed.ncbi.nlm.nih.gov/15709912/

Quote:

Influenza is an important trigger for acute coronary syndromes, and it has been shown that in the US it may cause up to 90,000 deaths per year simply by triggering fatal myocardial infarctions.

https://bmjopen.bmj.com/content/10/11/e042487
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5158013/

Seventy per cent increase in stroke in the year following an influenza like illness.

https://bmcpublichealth.biomedcentra...89-021-10916-4

[The Atheist]

Originally Posted by marting

Weekend effect accounts for some of this but the decline is a bit more than one would anticipate.

No, it's exactly what I'd expect from SA.

Now I've caught up with what ******* day it is, I'm not surprised the numbers dived on Saturday, and dived even further on Sunday.

Tomorrow will be interesting, but we really can only go on averages there. I think we saw good reporting at the start due to the novelty, but nobody's doing overtime for it.

Originally Posted by angrysoba

This confirms the old adage, "That which doesn't kill you, makes it much easier for something else to finish you off later."

Originally Posted by Planigale

It is well known, by those in the know.

I don't doubt that it happens. (and that's a fairly smarmy response, Planigale)

I just wanted to compare the actual numbers. The Covid study is specific and you said other diseases caused the same levels of harm. I'm sure it will be quantified somewhere.

Originally Posted by dann

Why? Cuba already did it with 2-5s.

Jesus mate, where have you been for the past couple of years? Cuba is an exceptional case, and I don't imagine they see the same resistance that we will in the west.

I think it's going to be a very hard sell, and nowhere in the west has even started studies for vaccine for <5 kids yet, so the question is moot, because it'll be over before toddlers get near a needle.
______________________________

Meanwhile, some early results from SA are still encouraging:

Quote:

Eight per cent of Covid-positive hospital patients are being treated in intensive care units, down from 23 per cent throughout the Delta wave. And just 2 per cent are on ventilators, down from 11 per cent.

https://www.ft.com/content/d315be08-...c-811290ad488e

And with SA's vaccine rate of 25% fully vaccinated, it's not vaccines making that size difference.

As noted, it's going to be a problem due to sheer numbers through speed of transmission, so it'll be bloody lucky if it is that much less severe.

[zooterkin]

Very scary projection, based on early data.

Originally Posted by @AlastairGrant4 on Twitter

Numbers of COVID cases likely to be the #OmicronVariant are increasing rapidly in England
SGTF data indicate 994 likely cases, including 2% of swabs from 4th December
This gives a worst case scenario of ~2500 cases so far and an R-value of 3.47 (CI 2.75 - 4.40)
Detail in thread

[The Great Zaganza]

wake me in two weeks, when we know how many omicronians need to be hospitalized.

[Meridian]

This from VOA news (no idea what they are like as a source, sorry) is rather worrying.

Quote:

"Unfortunately, we’re seeing a more than doubling of hospital admissions each day,” said Ian Sanne, an infectious diseases specialist who serves on South Africa’s COVID-19 presidential advisory committee.

Sanne is advising hospitals to prepare for “significant surges” of patients in the coming weeks and months, and to make sure they have plenty of oxygen.

Dr. Fareed Abdullah, who heads the South African Medical Research Council, says the surges are already happening in Johannesburg and Tshwane.

It does not give concrete numbers though.

Here is a post on reddit (sorry for the source) commenting on this in relation to the previous `seems mild so far' report. It contains this passage with numbers on oxygen recently, including links to the source for those (https://www.nicd.ac.za/wp-content/up...t-20211203.pdf for Dec 3rd, for example).

Quote:

10 days from Nov 22 is Dec 2. Compare hospitalization reports in South Africa from Nov 29, Nov 30, Dec 1, Dec 2, and Dec 3. They stopped reporting on Dec 3, which is odd - they've consistently reported daily for the entire duration of the pandemic. The data from Dec 2 & 3 is very worrying though - hospitalizations went 64, 81, 79, 176, 135 over those 5 days. Worse, the number of patients requiring oxygenation (presumably in for pneumonia, not incidental admissions) went 117, 135, 149, 165, 203, 225. If you take hospitalizations as a percent of cases 10 days ago, it's roughly 10%, which is consistent with the original strain of COVID.

NB the numbers for on oxygen (does not mean ventilated) are for Guatend province, not nationally.

[AcesHigh]

Originally Posted by The Atheist

Jesus mate, where have you been for the past couple of years? Cuba is an exceptional case, and I don't imagine they see the same resistance that we will in the west.

Cuba is west of most of Europe. Havana is west of Washington, Boston, NY, etc.


The fact it is a dictatorship... communist or whatever else is their current economic system, shouldn´t be used to tell if a country is western or not.

I mean... most of the countries in the "west" have gone through dictatorships, absolutist monarchies, etc. That includes Franco, Hitler, Mussolini just in the past 100 years.

[Dr.Sid]

Originally Posted by AcesHigh

Cuba is west of most of Europe. Havana is west of Washington, Boston, NY, etc.


The fact it is a dictatorship... communist or whatever else is their current economic system, shouldn´t be used to tell if a country is western or not.

I mean... most of the countries in the "west" have gone through dictatorships, absolutist monarchies, etc. That includes Franco, Hitler, Mussolini just in the past 100 years.

You just have to go around once more. Cuba is east of everyone.

[dann]

Originally Posted by The Atheist

Jesus mate, where have you been for the past couple of years?

I haven't left Denmark during the pandemic. I wouldn't mind going to Cuba soon, but I don't fancy sharing a plane with a lot Omicron carriers.

Quote:

Cuba is an exceptional case, and I don't imagine they see the same resistance that we will in the west.

Of course, it's exceptional! That's why it's worth studying and learning from them. It is insane that vaccine resistance is even a thing, but you're right, it isn't in Cuba. People have confidence in the vaccines and in the people administering them. It is one of the best vaccinated countries in the world, and not just against Covid-19.

Quote:

I think it's going to be a very hard sell, and nowhere in the west has even started studies for vaccine for <5 kids yet, so the question is moot, because it'll be over before toddlers get near a needle.

I am pretty sure that the Cuban vaccine manufacturers can be persuaded to sell their vaccines for dollars. They have already started selling it to countries like Vietnam, Iran and Venezuela, i.e. countries where the vaccine rollout, like in Cuba, has been hampered by U.S. blockades - in the name of humanitarianism.

[The Atheist]

Originally Posted by dann

Of course, it's exceptional! That's why it's worth studying and learning from them.

I don't see them having done anything too extraordinary so far. They look to have kept a lid on Covid for a long time, then had almost 10,000 deaths. Getting reliable data on the their vaccines might be an issue, too.

I agree it's crazy they're ostracised, but I wouldn't necessarily think they have the key to stop Covid.

[The Atheist]

And whether or not vaccines manage to deal with omicron, they sure as hell are not keeping delta at bay - 70/170 people at a christmas party, all vaccinated, all with negative antigen tests.

But at least all of them are asymptomatic, which is more important.

https://www.bbc.com/news/world-europe-59561876

I have to wonder if it's omicron, because that's a helluva high percentage. I think there's a reasonable chance it's been spreading quietly all over, going by the clusters being found.

[Planigale]

Originally Posted by The Atheist

And whether or not vaccines manage to deal with omicron, they sure as hell are not keeping delta at bay - 70/170 people at a christmas party, all vaccinated, all with negative antigen tests.

But at least all of them are asymptomatic, which is more important.

https://www.bbc.com/news/world-europe-59561876

I have to wonder if it's omicron, because that's a helluva high percentage. I think there's a reasonable chance it's been spreading quietly all over, going by the clusters being found.

Roughly 1/3 have been infected. Given they are all vaccinated, clearly someone was spreading a lot of virus around, and the vaccine did not prevent infection so I agree this is likely omicron which seems to be a bit of a party lover, given several other party associated outbreaks. Clearly omicron hit Europe at just the right time to go from Xmas party to new year party, so I guess we'll all be under a lot of stress come mid to late January 2022.

Not clear the date of the party but given a 2 week lag between infection and onset of serious illness it may be too early to assume no one gets seriously ill. Although since it is likely most attendees are going to be relatively young, fit and vaccinated I think it is most likely no one will become seriously ill.

[Roger Ramjets]

Originally Posted by The Atheist

And whether or not vaccines manage to deal with omicron, they sure as hell are not keeping delta at bay - 70/170 people at a christmas party, all vaccinated,

Vaccination is only one tool in the fight against Covid. Going to a Christmas party while vaccinated is like going into a war zone with a flak jacket on. We know it isn't 100% effective, and we suspect current vaccines are less effective against newer variants. Sensible people don't put themselves at more risk than necessary - and a Christmas party is way down the list of 'necessary'.

When will people realize there is no 'going back to normal' with this virus?

[The Atheist]

Originally Posted by Roger Ramjets

When will people realize there is no 'going back to normal' with this virus?

I don't think a party where everyone is vaccinated and has passed a negative test is anything like normal. These were hospital staff taking every possible precaution, not a football crowd.

[The Atheist]

Originally Posted by Planigale

Roughly 1/3 have been infected. Given they are all vaccinated, clearly someone was spreading a lot of virus around, and the vaccine did not prevent infection so I agree this is likely omicron which seems to be a bit of a party lover, given several other party associated outbreaks. Clearly omicron hit Europe at just the right time to go from Xmas party to new year party, so I guess we'll all be under a lot of stress come mid to late January 2022.

Do you know how much genomic testing Spain is doing?

If they've let omicron get this far under their guard, they're in it deep.

[The Atheist]

Here's why omicron might have been spreading for some time: https://www.theguardian.com/world/20...-covid-variant

If countries aren't doing large-scale genomic testing, they won't be finding cases.

[marting]

Some evidence of decreased virulence.

https://twitter.com/jburnmurdoch/sta...10548609744904

Key features: Lower percentage of people needing ventilators and significantly shorter hospital stays. Both are a factor of more than 2.

Initial analysis of Omicron's reduction in neutralization from Pfizer is 40 fold. Note that this doesn't mean 40 fold reduction in efficacy. It's not a linear function. But it is consistent with the spread seen amongst fully vaccinated and 3 fold decreased immunity from prior infection.

https://twitter.com/_b_meyer/status/1468319835012673549

[marting]

Originally Posted by The Atheist

Here's why omicron might have been spreading for some time: https://www.theguardian.com/world/20...-covid-variant

If countries aren't doing large-scale genomic testing, they won't be finding cases.

Given the incredible ramp of Omicron, I'd look to Denmark and the UK for the most current info on distribution of Omicron subvariants and use that to estimate prevalence elsewhere with PCR S-Gene dropout tests. Unlikely the subvariant without the dropout is significantly different from the main clade so the relative ratios can be used with the dropout proxy. Until we know otherwise.

[Puppycow]

Looks like I made it back to Japan just in the nick of time.

https://www.japantimes.co.jp/news/20...-omicron-case/

They are finding cases of omicron here but so far only in people arriving from overseas.

No clear uptick in cases due to community spread yet.

https://toyokeizai.net/sp/visual/tko/covid19/en.html

Personal note, I am currently quarantining at a hotel near the airport. If I test negative, I can go home this afternoon.

[marting]

Twitter thread on 2 early results. One a pseudo-assay which shows a 7 fold neutralization reduction. The other is a live virus one showing a larger reduction.

https://twitter.com/BenjMurrell/stat...41490632077317
https://twitter.com/sigallab

[dann]

Originally Posted by The Atheist

I don't see them having done anything too extraordinary so far.

You were the one who claimed, "Cuba is an exceptional case", and I agreed with you.
Cuba was hit hard by Delta before the vaccine campaign had started, and yet the country managede to get the whole population vaccinated with in six months with Cuban vaccines. They now have fewer cases than NZ. I think that is extraordinarily exceptional:
Daily COVID-19 vaccine doses administered per 100 people: CUB~NZL~USA
Share of people vaccinated against COVID-19: CUB~NZL~USA
Daily new confirmed COVID-19 cases per million people: CUB~NZL~USA

Quote:

They look to have kept a lid on Covid for a long time, then had almost 10,000 deaths.

Yes, in spite of being very dependent on tourism, they managed to keep down Covid - until Delta. Unlike NZ, the population wasn't vaccinated when Delta hit them. And unlike NZ, the vaccine rollout was hampered by a blockade.

Quote:

Getting reliable data on the their vaccines might be an issue, too.

I don't think so. They handed over their data to WHO when they applied for approval a couple of months ago: Cuba seeks WHO approval of COVID-19 vaccines as toddlers next for shot (Reuters, Sep 15, 2021)

Quote:

I agree it's crazy they're ostracised, but I wouldn't necessarily think they have the key to stop Covid.

I seriously doubt that there is one key to stop Covid, and it is ridiculous to dismiss any of the many keys necessary to end it because they are not the one and only.

[The Atheist]

Originally Posted by marting

Twitter thread on 2 early results.

More, and encouraging early results here: https://www.odt.co.nz/news/world/omi...-vaccine-study

Originally Posted by dann

I seriously doubt that there is one key to stop Covid, and it is ridiculous to dismiss any of the many keys necessary to end it because they are not the one and only.

I'm not dismissing anything - we already have vaccines, and unless theirs is significantly better than we have, it's not going to matter.

[Capsid]

Some data on neutralisation sensitivity coming.
https://www.ahri.org/wp-content/uplo...17v1-Sigal.pdf
https://drive.google.com/file/d/1Cux...ntxXwlfXQ/view

There is a large reduction (~40 fold) in neutralisation activity compared to the ancestral strain.

[Lplus]

Originally Posted by Capsid

Some data on neutralisation sensitivity coming.
https://www.ahri.org/wp-content/uplo...17v1-Sigal.pdf
https://drive.google.com/file/d/1Cux...ntxXwlfXQ/view

There is a large reduction (~40 fold) in neutralisation activity compared to the ancestral strain.

How does that compare with the Delta strain?

[Capsid]

Originally Posted by Lplus

How does that compare with the Delta strain?

The second link shows that Omicron is less sensitive to neutralisation than delta but not by much. (Figure 1 left hand panel)

[The Atheist]

Originally Posted by Capsid

Some data on neutralisation sensitivity coming.
https://www.ahri.org/wp-content/uplo...17v1-Sigal.pdf
https://drive.google.com/file/d/1Cux...ntxXwlfXQ/view

There is a large reduction (~40 fold) in neutralisation activity compared to the ancestral strain.

Thanks for yet again presenting us with real-time science!

[dann]

Originally Posted by The Atheist

I'm not dismissing anything - we already have vaccines, and unless theirs is significantly better than we have, it's not going to matter.

Saying that a measure against Covid-19 is not the key has been Swedish state epidemiologist Anders Tegnell's favourite way of dismissing all other measures than the ineffective ones he proposed - while waiting for herd immunity by infection.

It is going to matter to countries that don't have the cooling capacities to prevent the Pfizer-BioNTech, Moderna and AZ/Covishield vaccines from deteriorating fast.
It remains to be seen if the Cuban vaccines have other advantages in comparison to those.

Quote:

He said he was in touch with the leaders of countries which needed more vaccines, but many of them would "sadly" not be able to lift from India unless they improved their logistics and cold storage facilities.
Covishield: India vaccine maker halves production (BBC News, Dec 8, 2021)

Quote:

Both vaccines are “low” tech, meaning they use a traditional approach deploying a part of the virus’s spike protein which helps the virus enter and infect cells, to build up the immune system.
These vaccines are generally less expensive to develop and easier to store and transport as they do not require extremely low temperatures.
Cuba says second COVID-19 vaccine Soberana 2 boasts 91.2% efficacy (Reuters, July 9, 2021)