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

[The Atheist]

Ah, an interesting piece of news, which could explain a less-harmful virus - it looks like omicron has picked up a snippet of a common cold coronavirus, or a piece of human DNA:

https://osf.io/f7txy/

[GraculusTheGreenBird]

Originally Posted by The Atheist

Sorry, I meant to address that the other day.

Their plan of staying Covid-free just got blown out of the water, alright. No way is anyone stopping this sucker.

Why exactly?

Much as I hate the unnecessarily long 21 day hotel quarantine for everyone that HK and China has, it does effectively stop community infection. If anyone has a strong chance of remaining Omicron free, its these countries.

We all thought that Delta would get into HK despite the quarantine and wreak havoc, and it didn't. Months since we had a single community infection here.

Greater China has had a few sporadic Delta outbreaks, e.g. a few 10s of cases per day but is now under control, (assuming you believe their figures, which I of course take with a pinch of salt).

[The Atheist]

Originally Posted by GraculusTheGreenBird

Much as I hate the unnecessarily long 21 day hotel quarantine for everyone that HK and China has, it does effectively stop community infection. If anyone has a strong chance of remaining Omicron free, its these countries.

Staff at the quarantine facilities, and more importantly, at the border - pilots, dockyard workers etc - will bring it in.

Omicron is a whole order of magnitude more infectious and nobody's going to be able to keep it out.

[The Atheist]

Australia's already seeing a spread of omicron, of unknown origin.

https://www.abc.net.au/news/2021-12-...rows/100671290

Seems to me, with omicron evading some PCR tests, it's going to be cropping up everywhere very quickly. By my count, we've gone from 1 to 40 countries with omicron in the space of 8 days.

[The Great Zaganza]

Originally Posted by The Atheist

Ah, an interesting piece of news, which could explain a less-harmful virus - it looks like omicron has picked up a snippet of a common cold coronavirus, or a piece of human DNA:

https://osf.io/f7txy/

GENE THERAPY !!!

[Planigale]

Originally Posted by The Atheist

Ah, an interesting piece of news, which could explain a less-harmful virus - it looks like omicron has picked up a snippet of a common cold coronavirus, or a piece of human DNA:

https://osf.io/f7txy/

Why should this explain a less-harmful virus? The insertion is at a T-cell epitope, so may make omicron less susceptible to T-cell mediated immunity. Common colds are notorious for not producing prolonged immunity.

As an RNA virus it cannot pick up any human (or viral) DNA.

[dann]

Originally Posted by The Atheist

Australia's already seeing a spread of omicron, of unknown origin.

https://www.abc.net.au/news/2021-12-...rows/100671290

Seems to me, with omicron evading some PCR tests, it's going to be cropping up everywhere very quickly. By my count, we've gone from 1 to 40 countries with omicron in the space of 8 days.

Some countries don't do gene-sequencing analysis at all, others do it of very few of their positive cases. Some countries didn't know what to look for. Now they do.
It's probably everywhere already.

[The Atheist]

Originally Posted by Planigale

Why should this explain a less-harmful virus? The insertion is at a T-cell epitope, so may make omicron less susceptible to T-cell mediated immunity. Common colds are notorious for not producing prolonged immunity.

Which would explain why it's evading previous infections and vaccines. Why it might be less harmful is that if the new code is stolen from a less-harmful virus, it might well translate to making this one less harmful. Early indication are that it might be.

Originally Posted by Planigale

As an RNA virus it cannot pick up any human (or viral) DNA.

RNA then.

Originally Posted by dann

Some countries don't do gene-sequencing analysis at all, others do it of very few of their positive cases. Some countries didn't know what to look for. Now they do.
It's probably everywhere already.

I have no doubt of that.

Aussie still has a pretty hard border and it's already through that and into the community. Given it being in schoolkids, it's obviously a lot more widespread than the known cases.

Shows how pathetic we are at dealing with viruses - this little sucker evolved into an unknown one behind our back. Sneaky. Should have named it Baldrick.

[jt512]

A preprint of a preliminary surveillance study in South Africa indicates that Omicron is 2- to 3-times as likely to escape immunity from prior infection as previous strains of the virus; that is, the probability of reinfection from Omicron is 2- to 3-times as high as from other variants (see last paragraph on p.19 and Figure 5). The study has a lot of limitations, but it is the first quantitative estimate of reinfection from Omicron that I have seen.

The authors comment that escape from immunity from prior infection predicts escape from immunity from vaccination.

[Planigale]

Originally Posted by The Atheist

Which would explain why it's evading previous infections and vaccines. Why it might be less harmful is that if the new code is stolen from a less-harmful virus, it might well translate to making this one less harmful. Early indication are that it might be.
.

Equally it might make it more harmful.

The insertion sequence is 'GAGCCAGAA' it codes for three amino acids and has been inserted into the spike protein. The most likely origin is primate RNA (the most likely primate being H. sapiens). But with such a short sequence I am sure that other similar sequences can be found in other RNA viruses or putative hosts. This is not going to carry some 'common cold' features into SARS-CoV-2 any more than a human origin means it is developing intelligence. If it significantly impeded replication ability it would not be persisting.

To throw a little conspiracy in, a very similar insertion sequence is found in a bat corona virus genome from China; ins214 with four amino acids (ins214GATP) in bat SC2r-CoV from China (RmYN02). So anytime soon we may start seeing posts that omicron is another escapee from China!

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7211627/

[Planigale]

For a bit of background on virulence and why we should not expect SARS-CoV-2 to become less virulent these articles are not too bad. Suffice to say, we do not fully understand why SARS-CoV-2 is a killer nor why it is especially so for old fat men. Transmission and virulence are different and selective pressure is to increase transmission not to decrease virulence.

https://onlinelibrary.wiley.com/doi/10.1111/jeb.13896
https://onlinelibrary.wiley.com/doi/10.1002/jmv.26615

[angrysoba]

Originally Posted by Planigale

Equally it might make it more harmful.

The insertion sequence is 'GAGCCAGAA' it codes for three amino acids and has been inserted into the spike protein. The most likely origin is primate RNA (the most likely primate being H. sapiens). But with such a short sequence I am sure that other similar sequences can be found in other RNA viruses or putative hosts. This is not going to carry some 'common cold' features into SARS-CoV-2 any more than a human origin means it is developing intelligence. If it significantly impeded replication ability it would not be persisting.

To throw a little conspiracy in, a very similar insertion sequence is found in a bat corona virus genome from China; ins214 with four amino acids (ins214GATP) in bat SC2r-CoV from China (RmYN02). So anytime soon we may start seeing posts that omicron is another escapee from China!

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7211627/

Oh, you are late to the party on that one. There were claims of this being a lab leak since ... when was Omicon announced? Well, it was then anyway.

[marting]

Originally Posted by Planigale

For a bit of background on virulence and why we should not expect SARS-CoV-2 to become less virulent these articles are not too bad. Suffice to say, we do not fully understand why SARS-CoV-2 is a killer nor why it is especially so for old fat men. Transmission and virulence are different and selective pressure is to increase transmission not to decrease virulence.

https://onlinelibrary.wiley.com/doi/10.1111/jeb.13896
https://onlinelibrary.wiley.com/doi/10.1002/jmv.26615

Everyone needs to keep this point in mind. If a virus evolves to be less virulent it's a happy accident but it is not from evolutionary pressure.

SA's hospitalization numbers are not current. They backfill as data comes in. Somewhat similar to Florida's death numbers which don't come in for weeks and, back during Florida's summer Delta wave resulted in significant understating daily deaths.

[marting]

Meanwhile now over 100 of the 120 fully vaccinated (two dose) attendees at the Norwegian restaurant have tested positive.

Computational study of Omicron indicates higher spike binding as well as greater structural stability.

Omicron and Delta Variant of SARS-CoV-2: A Comparative Computational Study of Spike protein

https://www.biorxiv.org/content/10.1...12.02.470946v1

Quote:

Based on docking studies, the Q493R, N501Y, S371L, S373P, S375F, Q498R, and T478K mutations contribute significantly to high binding affinity with human ACE2. In comparison to the Delta variant, both the entire spike protein and the RBD in Omicron include a high proportion of hydrophobic amino acids such as leucine and phenylalanine. These amino acids are located within the protein's core and are required for structural stability. Omicron has a higher percentage of alpha-helix structure than the Delta variant in both whole spike protein and RBD, indicating that it has a more stable structure

[marting]

Some signs that Omicron may be less virulent. Early days yet but among the new hospitalizations there is a much lower percentage with low Ox.

https://www.samrc.ac.za/news/tshwane...early-features

Quote:

A snapshot of 42 patients in the ward on 2 December 2021 reveals that 29 (70%) are not oxygen dependent. These patients are saturating well on room air and do not present with any respiratory symptoms. These are the patients that we would call ‘incidental COVID admissions’, having had another medical or surgical reason for admission. Thirteen (13) patients are dependent on supplemental oxygen of which nine (21%) have a diagnosis of COVID-19 pneumonia based on a combination of symptoms, clinical signs, CXR and inflammatory markers. All are being prescribed steroids as the mainstay of therapy. The remaining 4 patients are on oxygen for other medical reasons (2 previously on home oxygen, 1 in heart failure and 1 with a confirmed diagnosis of Pneumocystis Pneumonia)

We might just get lucky.

[Meridian]

From the same link:

Quote:

The main observation that we have made over the last two weeks is that the majority of patients in the COVID wards have not been oxygen dependent. SARS-CoV-2 has been an incidental finding in patients that were admitted to the hospital for another medical, surgical or obstetric reason.

As the source says, it's still very early days, but it's something to be born in mind: that figures for people admitted to hospital with covid are not necessarily people admitted to hospital because of covid.

(Of course, it is still very worrying to have a variant spread this fast even if it does turn out to be much milder, in case that changes later/is different in different populations.)

[Dr.Sid]

Originally Posted by marting

We might just get lucky.

It spreads 3 times faster than delta. It has to generate 3 times less hospitalizations, otherwise it will be worse. And Europe is near limits.
I only expect the worst.

[marting]

Originally Posted by Dr.Sid

It spreads 3 times faster than delta. It has to generate 3 times less hospitalizations, otherwise it will be worse. And Europe is near limits.
I only expect the worst.

Oh, it's going to bad. But maybe it won't be catastrophic. But it's early. I don't have a specific expectation (as opposed to concern) yet except that it's going to run though the World like a hot knife through butter. Wake damage will be anywhere between bad and horrible but it will be relatively fast. Likely to speed up endemicity.

[The Atheist]

Originally Posted by marting

Everyone needs to keep this point in mind. If a virus evolves to be less virulent it's a happy accident but it is not from evolutionary pressure.

Maybe not evolutionary pressure, but there's a definite advantage in being less virulent. The more virulent it is, the more careful people will be, masking and so on, while we don't do that for winter colds.

Either way, if it is less virulent I'm just as happy with a happy accident.

Originally Posted by marting

Oh, it's going to bad. But maybe it won't be catastrophic. But it's early. I don't have a specific expectation (as opposed to concern) yet except that it's going to run though the World like a hot knife through butter. Wake damage will be anywhere between bad and horrible but it will be relatively fast. Likely to speed up endemicity.

The speed is out of this universe - I'm beginning to warm to the "came from outer space" idea.

I was looking at previous waves in SA and they look like this:

1st wave - it took from 23 May to 11 July to get from 1000 cases/day to the peak of 11,000. 49 days

2nd wave - took from 11 November to 8 Jan to go from 2000 cases/day to the peak of 22,000. 57 days

3rd wave - 6 May to 30 June to get to 16,000 cases/day and until 3 July to get to the peak of 26,000. 55 and 59 days respectively.

Now - they hit 1000 cases on 24 November, and 9 days later they hit 16,000.

I think 3 times faster might be an understatement.

[marting]

Originally Posted by The Atheist

I think 3 times faster might be an understatement.

i think you were the first to link to a piece on the beast which i read and have also been following closely. And here we are not even 2 weeks later. Sheesh.

Much of the unreal rate of growth is from vaccine and prior infection escape which Delta didn't have as both materially suppressed Delta. Not any more. This bugger escapes both vaccine and prior immunity, at least as regards infections.

But it's clearly more than just escape. Growth rate is just too damned fast. I think it's well more than Delta with a totally naive population and that's what we have now. Effectively a naive, fresh set of places for Omicron to attack.

[angrysoba]

Originally Posted by The Atheist

Maybe not evolutionary pressure, but there's a definite advantage in being less virulent. The more virulent it is, the more careful people will be, masking and so on, while we don't do that for winter colds.

Either way, if it is less virulent I'm just as happy with a happy accident.




.

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.

[marting]

Cruise ship 6 days after start with everyone vaccinated now has 10 Covid cases. Presumably a single index patient at the start but we'll see. Could be a good lab for CDC to track transmission dynamics.

https://www.msn.com/en-us/news/us/co...ans/ar-AARtpXu
Ten people aboard the cruise ship, approaching New Orleans, have tested positive for COVID-19, officials said Saturday night, Dec. 4, 2021. The Norwegian Breakaway had departed New Orleans on Nov. 28 and is due to return this weekend, the Louisiana Department of Health said in a news release. Over the past week, the ship made stops in Belize, Honduras and Mexico

Note that they are still in the process of testing passengers to disembark tomorrow. It's not stated how many of the 3200 have been tested so far.

[The Atheist]

Originally Posted by marting

But it's clearly more than just escape. Growth rate is just too damned fast. I think it's well more than Delta with a totally naive population and that's what we have now. Effectively a naive, fresh set of places for Omicron to attack.

It's basically a whole new pandemic, with unknown protection through vaccines.

I think we can officially say Covid is the biggest thing since WWII. Amazing time to be alive. Just two years ago, the very first cases were appearing, unknown to anyone.

Originally Posted by angrysoba

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.

The really disturbing thing is we're at this point after five major mutations. Those mutations have arisen from a tested 270 million cases, and probably an actual case load of 2 billion. It could get a lot more virulent. I certainly haven't dismissed Captain Trips yet.

And what's the next mutation going to be?

[Planigale]

Originally Posted by marting

Some signs that Omicron may be less virulent. Early days yet but among the new hospitalizations there is a much lower percentage with low Ox.

https://www.samrc.ac.za/news/tshwane...early-features



We might just get lucky.

The age profile of admissions is quite young. So one would expect milder disease.
Whether this may reflect higher vaccine coverage in the older population I do not know. It is somewhat similar to the recent UK experience where most cases have been occurring in young people so the number of hospitalisations and deaths versus number of cases has fallen. That does not mean delta is less virulent (actually there is some evidence current delta strains are more virulent).

One can argue since being sick makes people look after you, and hospitals seem a good place to transmit infections, being virulent might aid transmission!

[The Atheist]

Someone's telling porkies.

You can't tell me SA has gone from 0-16,000 cases of omicron is a week, then dropping to 11,000 by Wednesday.

https://www.worldometers.info/corona.../south-africa/

Meanwhile, we should now be really concerned - Fauci is talking it down, as he did with masks, as he with aerosol spread. https://www.stuff.co.nz/world/us-can...-the-us--fauci

[Aridas]

Originally Posted by The Atheist

Meanwhile, we should now be really concerned - Fauci is talking it down, as he did with masks, as he with aerosol spread. https://www.stuff.co.nz/world/us-can...-the-us--fauci

Talking it down? You're talking about -

Quote:

“Thus far, it does not look like there’s a great degree of severity to it,” Fauci said. “But we have really got to be careful before we make any determinations that it is less severe or it really doesn’t cause any severe illness, comparable to Delta.”

That's largely just acknowledging the current data and offering up standard, appropriate caveats that the current data may be a bit deceptive, is it not?

ETA:

Originally Posted by The Atheist

Someone's telling porkies.

You can't tell me SA has gone from 0-16,000 cases of omicron is a week, then dropping to 11,000 by Wednesday.

https://www.worldometers.info/corona.../south-africa/

Looking at the daily numbers there, I'd say that there's no actually good reason to claim that lying happened, just based on the numbers. There are a bunch of potential reasons for significant variation in officially tested and reported numbers from day to day. It's reasonable to think that the numbers going down to 11K from 16K the day before is not an accurate representation of what's actually happened, but too soon and too little evidence to assume lying. Now, if lowered numbers continue while damage is clearly being done, that would certainly be reason.

[Dr.Sid]

Denmark tripled omicron case count in 48 hours. Sure, it's just small number, great statistical errors. But it seems SA boom was no fluke.
Christmas will be after. Expect armagedon soon after though.

[marting]

Originally Posted by The Atheist

Someone's telling porkies.

You can't tell me SA has gone from 0-16,000 cases of omicron is a week, then dropping to 11,000 by Wednesday.
[/url]

You mean today, Sunday?

SA, like virtually every other country, has a weekday/weekend effect. Use 7 day moving average or compare days against growth from 7 days earlier.

[zooterkin]

Originally Posted by marting

You mean today, Sunday?

SA, like virtually every other country, has a weekday/weekend effect. Use 7 day moving average or compare days against growth from 7 days earlier.

Indeed. I'd have thought anyone watching the numbers over the last 18 months would be aware of that by now.

[The Atheist]

Originally Posted by marting

You mean today, Sunday?

Mea culpa.

I was looking at the wrong month - yeah, it was Sunday and the weekend factor will explain it.

I'll go an give myself a good beating. Idiot! Shows you what three months of lockdown does.

[The Atheist]

Meanwhile, more on kids and omicron, and it's not good news, although the anecdote of none of the hospitalised kids being vaccinated is potentially positive.

https://www.nzherald.co.nz/world/cov...N3UOJU5PEZXYM/

[The Atheist]

Originally Posted by Aridas

Talking it down? You're talking about -

That's largely just acknowledging the current data and offering up standard, appropriate caveats that the current data may be a bit deceptive, is it not?

Then why on earth did he start with the statement "there doesn't look to be a great degree of severity"?

The guy's a scientist, and statements like that aren't science, especially when your next statement is a big "we don't know".

Fauci already **** all over his shoes with masks and aerosols, and he's not aiding his credibility by offering opinions without evidence. When you need people to trust the science, it's smart to stick to the actual science.

[marting]

The USA took it's time to acknowledge aerosols as a significant vector but it's been clear for a while that it's a primary vector. On April 1, 2020 the National Academy put out a paper saying "Consider Aerosols" and that started a shift here. Pretty sure I posted a link to it at the time. I suspect much of the delay was fear hospitals wouldn't be able to get enough PPEs.

OTOH, the WHO really dragged it's heels. Even after hundreds of scientists chimed in during the Summer of 2020.

Still early to get a good handle on the virulence of Omicron. Key will be the relative protection of prior infection, vaccination v. naive impact. And it may well change with age.

I do suspect there will be differences. The lower Ox requirements and different symptoms suggests it isn't going to be the same as the original Wuhan bug or its other variants which have been similar except for transmission. But it's very early and will be a lot clearer in a few weeks and possibly sooner.

[Bob001]

Another long covid worry:

Quote:

A new study of long Covid patients is shedding light on a combination of underreported symptoms, including Parkinson's-like tremors and internal vibrations, that are severely impacting the lives of those affected.
....
"Now here at almost 8 months post covid, I have dealt with these horrible tremors daily," one participant in the study stated. "They are constant, they don't come and go. They are 24/7. I feel them more when I am still and resting or at night and early morning, or during naps."

https://www.salon.com/2021/12/03/tre...like-symptoms/

[The Atheist]

There's so much happening I'm not sure if posted this before - regarding severe Covid. People who have been through it have double the chance of dying in the next year.

Nobody's counting those, but they probably should be. Small study, bad numbers.

https://www.businessinsider.com.au/s...1-12?r=US&IR=T

[Planigale]

Originally Posted by Bob001

Another long covid worry:
https://www.salon.com/2021/12/03/tre...like-symptoms/

The article misinterprets the actual research. The authors say the tremors are "Parkinson's like", but that is not from the research. The tremors are not Parkinson's like. I think the journalists just made the assumption that because you get tremors in parkinson's all tremors are Parkinson's like.

The problem with this research and many long covid papers is there is no control group, are these symptoms to due to covid, or are these symptoms occurring in people who have had covid? Do these symptoms occur in non-covid people?

Some symptoms sound like small fibre neuropathy +/- autonomic neuropathy, which is not uncommon after serious illness of any cause. Others sound like 'medically unexplained' symptoms. These are challenging when patients want a physical explanation for the symptoms and a physical treatment and doctors do not have that, but experience suggests that talking therapies help patients deal with and cope with life better and learn to live with their medically unexplained symptoms. Experience also suggests that in the vast majority these symptoms will improve in time with no specific treatment. One important issue is to prevent potentially harmful self treating like excessive vitamin dosing or unduly restrictive diets or even more extreme things like courses of highly expensive 'stem cell' infusions. Although evidence suggests talking therapies are helpful patients are often resistant as they think that it means that the symptoms are 'all in the mind' or being put on.

[Planigale]

Originally Posted by The Atheist

There's so much happening I'm not sure if posted this before - regarding severe Covid. People who have been through it have double the chance of dying in the next year.

Nobody's counting those, but they probably should be. Small study, bad numbers.

https://www.businessinsider.com.au/s...1-12?r=US&IR=T

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.

[Planigale]

Originally Posted by The Atheist

Meanwhile, more on kids and omicron, and it's not good news, although the anecdote of none of the hospitalised kids being vaccinated is potentially positive.

https://www.nzherald.co.nz/world/cov...N3UOJU5PEZXYM/

There is nothing obvious in the mutations to explain why omicron should be significantly more or les virulent than delta or alpha. Vaccines and prior infections are the most likely explanation for differing severity of illness reported than an intrinsic change in the virus.

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.

[Pixel42]

Originally Posted by The Atheist

There's so much happening I'm not sure if posted this before - regarding severe Covid. People who have been through it have double the chance of dying in the next year.

Nobody's counting those, but they probably should be. Small study, bad numbers.

https://www.businessinsider.com.au/s...1-12?r=US&IR=T

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.

My sister in law had severe Covid in June 2020, but recovered. She died a couple of days before Christmas after being rushed to hospital with breathing difficulties. She had a genetic muscular wasting disease, but no other underlying health problems. She was 65.

[jimbob]

Originally Posted by Dr.Sid

It spreads 3 times faster than delta. It has to generate 3 times less hospitalizations, otherwise it will be worse. And Europe is near limits.
I only expect the worst.

That's an optimistic assessment.

If Delta R was 0.8 and Omicron was 2.4, what is the ratio of cases after 2 generations?

0.64 vs 5.76