New variants

[GrahamPlatt]

Of antibodies: https://theconversation.com/coronavirus ... ies-156810?

Quite heartening.

[Julian]

Interesting. As well as protection against potential new variants I see it says...

A recent preprint (a study that is yet to undergo peer review) also found that some antibodies present six months after infection were starting to be able to recognise related, but entirely distinct viruses, such as the coronavirus that causes Sars.

One of admittedly a very large number of theories(*) about why South Africa hasn't been as catastrophically badly affected by this pandemic as some feared given the cramped conditions in the townships and the high incidence of things like diabetes & TB is that exposure to previous novel viruses might have given the population some level of protection against SARS-CoV-2 where the original SARS virus is one such previous novel virus often cited. The above is suggesting that antibodies generated due to a SARS-CoV-2 infection might also work against SARS so it isn't too much of a leap to imagine that antibodies generated due to a SARS infection might indeed still be at least partially protective against SARS-CoV-2. The paper is of course not addressing it that way round at all but maybe offers some encouragement that people supporting that explanation might be on to something.

It would be really interesting to see equivalent practical (presumably in-vitro) research on whether SARS antibodies do have residual effect against SARS-CoV-2. I know that's looking backwards and not forwards but the more we can use this pandemic to advance our understanding of the immune system in general the better prepared we will be for any future pandemics.

- Julian

(*) And one of the less exciting theories is simply that the in-country data collection isn't good enough and the statistics being reported aren't catching all Covid-19 deaths.

[redsturgeon]

Interesting. As well as protection against potential new variants I see it says...

A recent preprint (a study that is yet to undergo peer review) also found that some antibodies present six months after infection were starting to be able to recognise related, but entirely distinct viruses, such as the coronavirus that causes Sars.

One of admittedly a very large number of theories(*) about why South Africa hasn't been as catastrophically badly affected by this pandemic as some feared given the cramped conditions in the townships and the high incidence of things like diabetes & TB is that exposure to previous novel viruses might have given the population some level of protection against SARS-CoV-2 where the original SARS virus is one such previous novel virus often cited. The above is suggesting that antibodies generated due to a SARS-CoV-2 infection might also work against SARS so it isn't too much of a leap to imagine that antibodies generated due to a SARS infection might indeed still be at least partially protective against SARS-CoV-2. The paper is of course not addressing it that way round at all but maybe offers some encouragement that people supporting that explanation might be on to something.

It would be really interesting to see equivalent practical (presumably in-vitro) research on whether SARS antibodies do have residual effect against SARS-CoV-2. I know that's looking backwards and not forwards but the more we can use this pandemic to advance our understanding of the immune system in general the better prepared we will be for any future pandemics.

- Julian

(*) And one of the less exciting theories is simply that the in-country data collection isn't good enough and the statistics being reported aren't catching all Covid-19 deaths.

South Africa has the worst record in all Africa and at over 800 deaths per million population is hardly getting away lightly. This may be less interesting than the other theories though.

John

[ursaminortaur]

There are reports that the UK's Kent variant is causing heart problems in cats and dogs.

https://www.theguardian.com/science/2021/mar/21/vets-warn-new-covid-variant-heart-problems-pets-cats-dogs

Vets are warning of a possible link between a new variant of coronavirus and heart problems in cats and dogs after a increase in pets presenting with myocarditis at a specialist veterinary hospital in Buckinghamshire during the pandemic’s second wave.

“We don’t want to spread panic unnecessarily, especially because at the moment we have a strong suspicion of transmission from human to pet, but not vice versa – and we don’t know this for sure. But vets ought to be aware of this so that they can start testing if they suspect a potential case of Covid infection,” said Luca Ferasin, a cardiologist at the Ralph Veterinary Referral Centre (RVRC) in Marlow, who led the research, which has not yet been peer reviewed.

The highly transmissible B117 variant was first detected in Kent in December, and has rapidly become the dominant circulating variant in the UK, accounting for about 95% of infections.

[zico]

Dr. John Lee is attracting a lot of attention for a recent article in the Mail arguing that lockdown is a cure worse than the disease.

Here's an interesting article he wrote for the Spectator in May 2020, arguing that lockdown could make the virus more deadly, because it stops viruses mutating, and he argues that milder versions of Covid will be more likely to spread. He also argues that vaccination are very unlikely to provide a way out of lockdown because mutations will be resistant to any vaccine developed, so he prefers attempts to reach "herd immunity" without vaccination. In his words "Should we be rapidly reversing lockdown to let the virus help us?"

It's a reasonably well-argued article, with some logic behind it and (although crucially, it's just a theory, not based on any evidence or data) his theory may well have turned out to be correct.
However, as we now know, it was wrong on the 3 main points.
Mutations have become the biggest danger, and the Kent variant is more deadly than the original virus.
Vaccinations are an effective way out.
The rapid reversal of lockdown he advocatedwould have led to many more thousands of deaths than actually happened.

https://www.spectator.co.uk/article/cov ... ore-deadly

[GrahamPlatt]

I am reminded of a quote from Charles Bukowski
"The trouble with the world is that the intelligent people are full of doubts, while the stupid ones are full of confidence."

[XFool]

Pardon my prejudice(?).

Dr. John Lee is attracting a lot of attention for a recent article in the Mail arguing that lockdown is a cure worse than the disease.

Here's an interesting article he wrote for the Spectator in May 2020

Oh dear! That doesn't inspire confidence. At least, not with me.

https://www.spectator.co.uk/article/ten-reasons-to-end-the-lockdown-now

Sounds like all the usual tosh to me:

Lockdown was enacted on a prediction of 500,000 deaths in the UK, rapidly reduced to 250,000 and then to 20,000.

There goes that 5000,000 "prediction" again - Whoosh!

But even if you assume 40,000 Covid deaths, its death toll is in the same ballpark as diseases we live with, not something so extraordinary as to justify the lockdown reaction.

Um... even "40,000"? We should be so lucky.

2. The policy response to the virus has been driven by modelling of Covid – not other factors

Now where have I heard that "driven by modelling" critique before? Oh yes - Global Warming deniers.

... arguing that lockdown could make the virus more deadly, because it stops viruses mutating, and he argues that milder versions of Covid will be more likely to spread.

I wonder how he now explains the current Kent variety?

He also argues that vaccination are very unlikely to provide a way out of lockdown because mutations will be resistant to any vaccine developed, so he prefers attempts to reach "herd immunity" without vaccination.

1. Oh that "herd immunity" 'thing' again... (Well it was still May 2020)

2. Err... but ANY virus which has jumped species is a "mutation" (definitionally) and viruses do mutate, so that 'logic' seems to lead to the conclusion that any vaccine against the coronavirus is inherently useless. Then again, given mutations, how can the human immune system ever succeed against any natural infection, "herd immunity" or not? (But then, Mike Yeadon told us is you survived any virus you were immune to any even similar one for the remainder of your natural...)

- There' s certainly more I could quote, but it would be against TLF policy.

Sound like most of the other Spectator contributors to me.
I also notice, like Mike Yeadon, he is retired...

[UncleEbenezer]

I wonder how he now explains the current Kent variety?

Oh, that's easily explained: it's a natural response to lockdown. As posted here.

[XFool]

I wonder how he now explains the current Kent variety?

Oh, that's easily explained: it's a natural response to lockdown. As posted here.

Right. But, unfortunately - quoting zico - Lee's argument was that lockdown stopped the virus mutating...

Can't have it both ways. Then again, maybe he can.

[UncleEbenezer]

I wonder how he now explains the current Kent variety?

Oh, that's easily explained: it's a natural response to lockdown. As posted here.

Right. But, unfortunately - quoting zico - Lee's argument was that lockdown stopped the virus mutating...

Can't have it both ways. Then again, maybe he can.

Not wishing to take either side here, but maybe he can indeed. Lockdown - or more accurately social distancing - creates an environment in which there may be fewer mutations, but much stronger natural selection in favour of those that can most easily (in a metaphorical sense) jump two metres.

[XFool]

Right. But, unfortunately - quoting zico - Lee's argument was that lockdown stopped the virus mutating...

Can't have it both ways. Then again, maybe he can.

Not wishing to take either side here, but maybe he can indeed. Lockdown - or more accurately social distancing - creates an environment in which there may be fewer mutations, but much stronger natural selection in favour of those that can most easily (in a metaphorical sense) jump two metres.

Um. Perhaps. To my mind, more convincing sounding is still: More spread, more cases. More cases more viruses. More viruses more mutations.

[dealtn]

Right. But, unfortunately - quoting zico - Lee's argument was that lockdown stopped the virus mutating...

Can't have it both ways. Then again, maybe he can.

Not wishing to take either side here, but maybe he can indeed. Lockdown - or more accurately social distancing - creates an environment in which there may be fewer mutations, but much stronger natural selection in favour of those that can most easily (in a metaphorical sense) jump two metres.

Um. Perhaps. To my mind, more convincing sounding is still: More spread, more cases. More cases more viruses. More viruses more mutations.

But the point is from an evolutionary perspective if you limit the conditions, such as by reducing, or increasing, distance between potential carriers, then the mutants that can be created, and survive, are the ones that are better suited to "jump" that distance (regardless of other factors).

That's not to say there will be less or more mutants, or that they will be deadlier or not, just that the variants you get are dependent on the conditions for their creation. It isn't as simple as saying "more" = "more" = "more" etc.

Evolution is a strange, yet simple, concept. Change the conditions and you get "different". That needs taking into account to, not just the absolute numbers.

To be clear my views on lockdown, or any other policy response, are unimportant here, and not part of the argument being made. This is just a scientific matter of evolutionary progress

[XFool]

Not wishing to take either side here, but maybe he can indeed. Lockdown - or more accurately social distancing - creates an environment in which there may be fewer mutations, but much stronger natural selection in favour of those that can most easily (in a metaphorical sense) jump two metres.

Um. Perhaps. To my mind, more convincing sounding is still: More spread, more cases. More cases more viruses. More viruses more mutations.

But the point is from an evolutionary perspective if you limit the conditions, such as by reducing, or increasing, distance between potential carriers, then the mutants that can be created, and survive, are the ones that are better suited to "jump" that distance (regardless of other factors).

But don't the mutations just happen (at duplication/reproduction)? The more mutations, the more there are to select from. Surely the outside environment effectively selects the viable mutations, it doesn't create them - leaving aside chemicals/radiation.

[zico]

Um. Perhaps. To my mind, more convincing sounding is still: More spread, more cases. More cases more viruses. More viruses more mutations.

But the point is from an evolutionary perspective if you limit the conditions, such as by reducing, or increasing, distance between potential carriers, then the mutants that can be created, and survive, are the ones that are better suited to "jump" that distance (regardless of other factors).

But don't the mutations just happen (at duplication/reproduction)? The more mutations, the more there are to select from. Surely the outside environment effectively selects the viable mutations, it doesn't create them - leaving aside chemicals/radiation.

More infected people give more opportunities for mutations. That's a compelling argument for me.
The point about this virus is that if we take measures to stop the spread, we're less likely to get mutations, so the vaccines against the original Wuhan variant are much more likely to be able to polish off all Covid cases.

The problem with an argument that (for example) having 2 metre social distancing forces the vaccine to evolve to jump 5 metres or more, is that viruses don't work like that - they're not actually intelligent.
If they were, then the polio virus would have arranged a conference between its main strain and any variants, to discuss the threat of the polio vaccine, and worked out exactly how to mutate to stop the polio vaccine killing it off. But the virus wasn't an intelligent entity capable of forward planning, so it just got wiped out.

[dealtn]

Um. Perhaps. To my mind, more convincing sounding is still: More spread, more cases. More cases more viruses. More viruses more mutations.

But the point is from an evolutionary perspective if you limit the conditions, such as by reducing, or increasing, distance between potential carriers, then the mutants that can be created, and survive, are the ones that are better suited to "jump" that distance (regardless of other factors).

But don't the mutations just happen (at duplication/reproduction)? The more mutations, the more there are to select from. Surely the outside environment effectively selects the viable mutations, it doesn't create them - leaving aside chemicals/radiation.

"create, and survive" is what I said.

So if Covid only existed in places that were sub-zero in temperature, or >40 degrees, then random mutation might "create" variation, but only those variations able to survive those extreme temperatures, for instance, would survive (and be able to replicate, and potentially dominate and take over from existing strains etc.)

[dealtn]

But the point is from an evolutionary perspective if you limit the conditions, such as by reducing, or increasing, distance between potential carriers, then the mutants that can be created, and survive, are the ones that are better suited to "jump" that distance (regardless of other factors).

But don't the mutations just happen (at duplication/reproduction)? The more mutations, the more there are to select from. Surely the outside environment effectively selects the viable mutations, it doesn't create them - leaving aside chemicals/radiation.

More infected people give more opportunities for mutations. That's a compelling argument for me.
The point about this virus is that if we take measures to stop the spread, we're less likely to get mutations, so the vaccines against the original Wuhan variant are much more likely to be able to polish off all Covid cases.

The problem with an argument that (for example) having 2 metre social distancing forces the vaccine to evolve to jump 5 metres or more, is that viruses don't work like that - they're not actually intelligent.
If they were, then the polio virus would have arranged a conference between its main strain and any variants, to discuss the threat of the polio vaccine, and worked out exactly how to mutate to stop the polio vaccine killing it off. But the virus wasn't an intelligent entity capable of forward planning, so it just got wiped out.

This is genetics. Perhaps read something such as The Selfish Gene. Genes don't rely on "intelligence" in the sense you are describing.

You are absolutely right. The more there is of "it" the more the chances of mutations, and potential nasty ones at that. I am not disputing that in any way. All I have added is that the likely mutations that succeed will be the ones best suited to the environment.

So you might have less variation, but an extremely successful one at "large distance transmission" between people coming to dominate, were lockdown "working". You would also likely have much less of "it around" and presumably we all agree that's a good thing. I am making no claim that having no lockdown would have been better, only that potentially different variations and mutations will exist and survive under different environments.

[servodude]

But don't the mutations just happen (at duplication/reproduction)? The more mutations, the more there are to select from. Surely the outside environment effectively selects the viable mutations, it doesn't create them - leaving aside chemicals/radiation.

More infected people give more opportunities for mutations. That's a compelling argument for me.
The point about this virus is that if we take measures to stop the spread, we're less likely to get mutations, so the vaccines against the original Wuhan variant are much more likely to be able to polish off all Covid cases.

The problem with an argument that (for example) having 2 metre social distancing forces the vaccine to evolve to jump 5 metres or more, is that viruses don't work like that - they're not actually intelligent.
If they were, then the polio virus would have arranged a conference between its main strain and any variants, to discuss the threat of the polio vaccine, and worked out exactly how to mutate to stop the polio vaccine killing it off. But the virus wasn't an intelligent entity capable of forward planning, so it just got wiped out.

This is genetics. Perhaps read something such as The Selfish Gene. Genes don't rely on "intelligence" in the sense you are describing.

You are absolutely right. The more there is of "it" the more the chances of mutations, and potential nasty ones at that. I am not disputing that in any way. All I have added is that the likely mutations that succeed will be the ones best suited to the environment.

So you might have less variation, but an extremely successful one at "large distance transmission" between people coming to dominate, were lockdown "working". You would also likely have much less of "it around" and presumably we all agree that's a good thing. I am making no claim that having no lockdown would have been better, only that potentially different variations and mutations will exist and survive under different environments.

Sounds like crossed wires a bit?
Both of the lasts two posts are in agreement that gene's aren't intelligent; but the latter is written like a rebuttal

Anyways with this stuff the language is important and subtle
- framing it as "survival of the fittest" back in the day was a shite tag line
- the only thing the environment does is remove the unviable (no direction, no intent) (<-- colleagues misrepresenting this was such a bugbear of mine when I used to use GALib/genetic algorithms as a postgrad)

having said that... it's a bit of a worry with RNA viruses if you let them hang around in the vicinity of other things as they can swap data

here's an interesting paper:
Are RNA Viruses Candidate Agents for the Next Global Pandemic? A Review
https://academic.oup.com/ilarjournal/article/58/3/343/4107390
Even though the high mutation rate caused by the lack of proofreading mechanisms is the main engine in RNA viral evolution, recombination and reassortment have also shown to play a key role. Recombination can be defined as the synthesis of chimeric RNA molecules from two different progeny genomes. Per se, recombination occurs in a single genomic segment. Recombination can be intra-genomic when the two segments come from the same origin, that is, the same infecting virus, or inter-genomic when the two segments come from different origins, that is, different viruses infecting the same cell.
- 2017 ! - that aged well

but on the point of NPIs exerting "evolutionary pressure"
- how do you think a vaccine programme would push things? and what if you then implemented it in a way that the manufacturer said you shouldn't (because it reduced efficacy)?
- this is part of my discontent with the decision to not issue the Pfizer as it should have been (the other part being it fuels the "its being rushed" brigade)

- sd

[zico]

Interesting new research from a BMJ webinar, showing a very strong correlation between people flying out of London & prevalence of Kent variant in other countries.

The top 8 destinations also have the most Kent variant, in exact order (e.g. Turkey 7th most popular destination, 7th most Covid)
Top destinations are in order - Spain, Italy, Greece, Poland, Germany, Portugal, Turkey, Romania.

New variants don't just "lap up on the shores", they are carried in by people arriving from areas/countries with high numbers of new variants.

[9873210]

Re: effective lockdowns create mutations.

This is why the variants of concern are named after Melbourne, Canberra and Auckland, rather than Brazil, California, UK or RSA.

[zico]

Re: effective lockdowns create mutations.

This is why the variants of concern are named after Melbourne, Canberra and Auckland, rather than Brazil, California, UK or RSA.

Hang on, the 3 main variants of concern - Kent (UK), South Africa, Brazil. (Your RSA is presumably Republic of South Africa).