Covid - Plan B & Omicron

[Northern_Brewer]

Tell you what NB you are on the ball with everything, i would like to sit down with you over a pint or two, i am not very good with written answers, don't take this post the wrong way

No worries - I just try to call it as I see it, based on reading actual virologists etc rather than people who may have medical qualifications but use them to push an agenda. Usually that means I'm a bit more cautious than average, but in the case of B.1.640.2 it seems to be getting hyped the other way.

The real lesson from B.1.640.2 is not the variant itself, but it emphasises how Africa has been rather forgotten during the pandemic. They've suffered less than many places because their population is so young, but they have relatively little vaccine coverage and so are getting hammered during the "mild" omicron wave. Couple that with the fact that both omicron and B.1.640.2 have "appeared" with lots of mutations, which implies they've been quietly mutating away without being spotted - you normally reckon on 2-3 mutations per month. That could mean a chronic infection in an individual with a weak immune system (eg from HIV), a series of infections in a human population that's not well monitored, or an animal reservoir.

Aside from getting more vaccines to Covax (the scheme to distribute to poor countries), one of the best things we could do is get a couple of young scientists over from places like Kenya and Nigeria, train them at our (absolutely world-class) sequencing labs, then send them home with a couple of sequencing machines and a freezer full of reagents. Would cost peanuts in the scheme of things and wouldn't just help the world keep tabs on new SARS2 variants, but HIV, Ebola and all sorts of other things.

do rabies, measels and smallpox viruses mutate enough to evade vaccination/effective treatment? Because smallpox has been vaccinated out of existence

I don't want to get too hung up on other diseases as they're all different in detail to SARS2, I just wanted to make the point that this "rule" of declining virulence is BS. It all depends on the detailed lifecycle of the virus. Immune evasion is a separate issue to inherent virulence. I don't know much about the genetics of measles or rabies but I would note that there is a small zoo of different strains that cause both rabies and measles which I assume is partly in response to vaccines, although AIUI neither has particularly good treatments other than vaccination.

Smallpox is the only human disease that we've managed to eradicate, and that took a really effective vaccine, great vaccine uptake and some favourable characteristics, like no animal reservoirs in the wild. The SARS2 vaccines are good but not that good, and what now look like multiple animal reservoirs means that we're probably never going to eradicate it.

If a virus is causing more serious disease and therefore introducing greater mortality won't severe government restrictions hamper its ability to spread in favour of a milder less serious variant that we are not so concerned about?

I know what you're getting at and in theory you have a point but in reality the world doesn't work like that, government restrictions aren't applied uniformly or consistently, in every country around the world and to the animal populations within them, not just humans.

I have read that mutations usually are a trade off of one ability against another, so its unlikely that a virus can spread much easier, evade vaccinations and become more lethal. Has vaccination and restrictions led to some evolutionary pressure?

The tradeoff thing applies more to "established" pathogens, but when a pathogen is new it still has quite a lot of freedom to improve without tradeoffs. SARS2 is still at the Model T stage where it has lots of room for improvement and is inferior in every way to eg a modern pickup truck. In time it will become "better" and more specialised, like a modern Transit van or Ferrari, which have to tradeoff between eg cargo capacity and speed/handling.

You've seen this with delta, which is much more transmissible but was still about as nasty as "classic" Wuhan virus. As I keep saying - SARS2 doesn't really "care" if it's more lethal or not, because it's spreading before the host gets sick.

 

[Northern_Brewer]

Getting hold of LFT's are the bugger. It seems they were scarce in Wales so they sent what they had to England, not the best move.

Someone's built a bot that watches for when they're available or not :
https://twitter.com/LFT_alert
It suggests that the Celts are mostly OK, it's mainly England that has a problem. They seem to be available at 07.15, 12.15 and 4.15 for an hour or two each time.

 

[VW911]

Phew!
Son, daughter-in-law and grandson (only 5 and seriously disabled) all tested positive over Christmas.
Just had the news that they are all ok now, and all testing negative.

 

[Chippy_Tea]

Roger Johnson
@RogerJ_01

BREAKING: Hospitals across Greater Manchester pause some non-urgent surgery and appointments due to impact of Covid.

Statement and list of affected hospitals below.

 

[dad_of_jon]

No worries - I just try to call it as I see it, based on reading actual virologists etc rather than people who may have medical qualifications but use them to push an agenda. Usually that means I'm a bit more cautious than average, but in the case of B.1.640.2 it seems to be getting hyped the other way.

The real lesson from B.1.640.2 is not the variant itself, but it emphasises how Africa has been rather forgotten during the pandemic. They've suffered less than many places because their population is so young, but they have relatively little vaccine coverage and so are getting hammered during the "mild" omicron wave. Couple that with the fact that both omicron and B.1.640.2 have "appeared" with lots of mutations, which implies they've been quietly mutating away without being spotted - you normally reckon on 2-3 mutations per month. That could mean a chronic infection in an individual with a weak immune system (eg from HIV), a series of infections in a human population that's not well monitored, or an animal reservoir.

Aside from getting more vaccines to Covax (the scheme to distribute to poor countries), one of the best things we could do is get a couple of young scientists over from places like Kenya and Nigeria, train them at our (absolutely world-class) sequencing labs, then send them home with a couple of sequencing machines and a freezer full of reagents. Would cost peanuts in the scheme of things and wouldn't just help the world keep tabs on new SARS2 variants, but HIV, Ebola and all sorts of other things.



I don't want to get too hung up on other diseases as they're all different in detail to SARS2, I just wanted to make the point that this "rule" of declining virulence is BS. It all depends on the detailed lifecycle of the virus. Immune evasion is a separate issue to inherent virulence. I don't know much about the genetics of measles or rabies but I would note that there is a small zoo of different strains that cause both rabies and measles which I assume is partly in response to vaccines, although AIUI neither has particularly good treatments other than vaccination.

Smallpox is the only human disease that we've managed to eradicate, and that took a really effective vaccine, great vaccine uptake and some favourable characteristics, like no animal reservoirs in the wild. The SARS2 vaccines are good but not that good, and what now look like multiple animal reservoirs means that we're probably never going to eradicate it.



I know what you're getting at and in theory you have a point but in reality the world doesn't work like that, government restrictions aren't applied uniformly or consistently, in every country around the world and to the animal populations within them, not just humans.



The tradeoff thing applies more to "established" pathogens, but when a pathogen is new it still has quite a lot of freedom to improve without tradeoffs. SARS2 is still at the Model T stage where it has lots of room for improvement and is inferior in every way to eg a modern pickup truck. In time it will become "better" and more specialised, like a modern Transit van or Ferrari, which have to tradeoff between eg cargo capacity and speed/handling.

You've seen this with delta, which is much more transmissible but was still about as nasty as "classic" Wuhan virus. As I keep saying - SARS2 doesn't really "care" if it's more lethal or not, because it's spreading before the host gets sick.

ah yes animal reservoirs I forgot about that - DOH! - There was a cull of wildlife in the UK when there was a rabies outbreak and the uk is considered rabies free now.

What's your view on the claim that the USA financed gain-of-function research being done in china in relation to coronavirus?

 

[Northern_Brewer]

ah yes animal reservoirs I forgot about that - DOH! - There was a cull of wildlife in the UK when there was a rabies outbreak and the uk is considered rabies free now.

TB is another one with animal reservoirs, hence the badger cull, although that's more about preventing TB in cows.

What's your view on the claim that the USA financed gain-of-function research being done in china in relation to coronavirus?

To be honest I keep away from that stuff for my own sanity - it seems to be a swamp of people with agendas going "he said...she said" with no realistic chance of anything tangible coming out of it. Sometimes you just need to know when to block things out.

But if you look at the biology and epidemidiology of the original outbreaks, the balance of evidence seems to point to a "natural" rather than a lab origin, see eg :
https://www.technologyreview.com/20...an-natural-spillover-wuhan-wet-market-huanan/
At the very least, we know that these things emerge from nature all the time, so a lab origin should be regarded as an extraordinary claim that needs extraordinary evidence to support it, and we're a long way away from having that kind of evidence and in all likelihood never will, even if it was made in a lab. So I don't think it's something for the ordinary person to worry about it. Covid exists, and regardless of how it really originated we're unlikely to have sufficient "proof" of a lab origin to do anything about it. Wwhat would we do - invade China? So why waste mental energy on something that will go nowhere even if there was "proof". But just to be clear - the balance of evidence seems to me to point to a natural origin. But the nature of these things means that it's hard to prove the negative, that it wasn't natural, and that will be enough to keep the conspiracy nuts going for years to come.

 

[dad_of_jon]

@Northern_Brewer - Ty for the reply. There are 2 hypothesis on its origin and if it escaped from the lab and USA had been funding research maybe pressure could be brought to curb the risks in future. If it came from a low tech origin there'd be more chance of a repeat as it would be difficult to stop that avenue.

I don't think anyone would think of invading China. It seems to me we have farmed most of our production to China, I'd not be surprised if that included gain of function research even if that seems to me as a layman a dangerous thing to do.

 

[Chippy_Tea]

It's being reported 90% of all people in ICU haven't had a vaccination, I wonder what percentage of them didn't have it because of health issues.

 

[Shirley Bassett]

I thought Johnson said yesterday that 60% of people in ICU in England weren’t vaccinated.

The 90% figure referred to people who hadn’t had a booster jab.

There was also a report the other day in the Daily Record that only one person in Scotland‘s ICU has the Omicron variant of COVID.

https://www.dailyrecord.co.uk/news/scottish-news/only-one-scots-omicron-patient-25836361

 

[Scrattajack]

According to this, the unvaccinated figure from the latest available data (the four weeks up until 19 December) is 46%.

 

[DavidDetroit]

Statistics only paint a useable picture when all relevant information is included. Right off, if the UK is 90% vaccinated, that's 10% that isn't. That 10% therefore makes up almost half of the total ICU cases (just going by this thread). I would see this deceitful practice a lot when I followed the news. Our RWers are world-renowned masters at cherry picking data. Exposing it is not a skill I ever wanted to have.
It's the "I haven't had a beer all year" misleading statement. It's 5 January. Not so impressive now.

 

[Chippy_Tea]

Intensive care units in the UK are filling up with patients with covid-19 who have not been fully vaccinated, a number of media reports have claimed over the past week.

It led to the prime minister, Boris Johnson, urging people to get vaccinated to reduce the pressure on hospitals. He said that he had been told by doctors that as many as 90% of patients with covid-19 in intensive care had not received a booster vaccination.1 Other media reports have suggested that 80-90% of patients in intensive care are unvaccinated.2

Are these reports accurate?
The Intensive Care National Audit and Research Centre (ICNARC), which has been monitoring activity throughout the pandemic, provides information on admissions to intensive care.3 Its latest report, published on 31 December, showed that the proportion of patients admitted to critical care in December 2021 with confirmed covid-19 who were unvaccinated was 61%. This proportion had previously fallen from 75% in May 2021 to 47% in October 2021—consistent with the decreasing proportion of the general population who were unvaccinated—before rising again in December 2021.
The proportion of unvaccinated patients in intensive care varied by English region, with the highest rates recorded in London (66%), the south west, and the north west. Being unvaccinated was classed as a person having no record of receiving any vaccination or having had a first dose administered within 14 days of receiving a positive covid test, and only 1.9% of the “unvaccinated” group had received a first dose within that period.
The 61% figure is lower than the 80-90% reported at some hospitals. But the latest ICNARC data span only to 15 December, and the proportion of patients in intensive care who are unvaccinated may have increased as the omicron variant spread in December. Some hospitals will also have been more badly affected than others.
https://www.bmj.com/content/376/bmj.o5

 

[Chippy_Tea]

A father-of-three says he has been given a "second chance" after spending Christmas in an intensive care unit with coronavirus.

Andy Pugh, from Worcester, had declined to have a Covid vaccine before he became ill on 4 December.
He was taken to hospital where he spent three weeks in intensive care and was told he had a 50% chance of surviving.
Now in recovery, he said his experience had changed his perspective and urged others like him to get a jab.
Mr Pugh, a refuse worker, remains at the Worcestershire Royal Hospital and said he was feeling slightly better but was still reliant on oxygen.
In intensive care he was "really scared", he said. "I was hallucinating, thinking the doctors were trying to kill me, when really they were trying to help me.
"They phoned up my Mrs and said 'you've got to prepare for the worst'."

'Changed my morals'
Mr Pugh said his wife was a carer and so had had the vaccine and been urging him to do the same.
However, he said he had been "really put off" by the speed of the rollout.
"Now I've had this, it's changed my morals altogether," he said. "I've been given a second chance."

https://www.bbc.co.uk/news/uk-england-hereford-worcester-59880788

 

[Shirley Bassett]

Speaking of statistics.

When I was at sixth form and was in my first A level maths with statistics lesson. The tutor asked, “does anyone know anything about statistics”.

The young lady on my left instantly replied, “92.41765% of them are made up on the spot Sir”.

 

[Leon103]

So no need to take a pcr if you have a positive lft but no symptoms. I guess it will be harder to detect new variants like the new French version.

https://www.independent.co.uk/news/world/europe/ihu-covid-variant-france-mutations-b1986953.html?amp

 

[Northern_Brewer]

@Northern_Brewer - Ty for the reply. There are 2 hypothesis on its origin and if it escaped from the lab and USA had been funding research maybe pressure could be brought to curb the risks in future. If it came from a low tech origin there'd be more chance of a repeat as it would be difficult to stop that avenue.

There's two ifs there - and the lab leak one needs to be true before you even start to begin on the issue of what the US had been funding. And there's no good evidence for it being a lab leak.

I don't think anyone would think of invading China.

Oh, there's a definite correlation between the people making most noise about lab leaks and gain of function and people who would quite like the US to go to war with China, or at the very least want to ramp up tensions between the West and China. And that's why I steer clear of that particular "debate", it seems to be mostly about US-China relations and not very much about the science, 95+% of the people involved seem to have a political agenda.

The sad thing is that there is a real scientific debate to be had here, but between the <5% of people who aren't trying to push an agenda, and at the moment they're just getting swamped by idiots.

It seems to me we have farmed most of our production to China, I'd not be surprised if that included gain of function research even if that seems to me as a layman a dangerous thing to do.

Well you should be surprised. IF you're talking about the EcoHealth Alliance stuff, a)the kind of research involved wasn't going to lead to "a supervirus" b)the dangers led to the US not funding some of the most risky bits c) the constructing things bit that did happen was in North Carolina, thousands of miles from Wuhan d) the proposal was to try and "vaccinate" bats using either non-specific immune stimulants, or bits of spike protein without live virus, similar to the Pfizer and Moderna vaccines.

It's not really my field, but I suggest you read people who are active in this area, such as Stuart Neil of KCL :

 

[Hop_it]

Woke up this morning feeling rough (thick head, runny nose and aching limbs). Thought it wise to take an LFT. . . . . . Result: +ve
So, I set about trying to book a PCR test. There were no appointments available anywhere in the country when I went on-line. I had no other choice than to request a home delivery. It will be interesting to see how long that takes to arrive ?????
My wife took a test when mine showed up +ve. Fortunately her result was -ve. Hopefully that will remain the case

I've not been on for a few days because I was feeling really rough. But fortunately I'm a bit less rough today, so perhaps I'm over the worst.

The PCR test kit arrived the following day (i.e. Tuesday), so I got that done immediately, and my wife took it straight away to the nearest 'priority' post box as instructed. However, it's now Friday and I still haven't had the result. I'm not really in much doubt about having the infection, particularly after the last few days, but it would be nice to get the confirmation. I guess that the PCR testing system really is under such a lot of stress at the moment that they are struggling to keep up with the exceptionally high numbers.

The good news for me (and for her as well) is that my wife is still testing negative. She had her booster several weeks after me, so perhaps she still has peak immunity at the moment. Just as well as she can at least get out to do some shopping when necessary.

 

[Hop_it]

If anybody is interested in an easy to follow explanation of viruses, testing, transmission, mathematical modelling techniques etc, I recommend watching the Royal Institution Christmas Lectures, hosted by Prof. JVT. The three one hour programmes were shown live on BBC4 just after Christmas, but are still available on the BBC iPlayer.
I know that the Christmas lectures are traditionally aimed primarily at children, but they are very well presented, and the guest experts explain a lot of complex information in a very easy to follow way. I've watched the first two so far, and I've found them to be very informative

 

[Chippy_Tea]

IKEA announce anyone not vaccinated going off sick with Covid will only get statuary sick pay.

 

[Hop_it]

IKEA announce anyone not vaccinated going off sick with Covid will only get statuary sick pay.

I guess that there will be a lot of IKEA employees looking very closely at their contracts of employment.