Author Topic: Coronavirus  (Read 239756 times)

ProfessorDavey

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Re: Coronavirus
« Reply #4350 on: July 09, 2021, 01:35:33 PM »
Re mutation: I've read stuff to the effect of if there is a lot of virus it may mutate, yes, but the mutations won't be selected for, since the original strain is surviving. But if that strain is under pressure and is being neutralised by vaccine-induced antibodies, and mutated strains are more resistant to those antibodies, a new variant will survive and replicate until it becomes the dominant one. (It will be 'selected for').
It is basic evolutionary theory.

Mutations are random events which occur when the virus is being replicated in a host human - the more the level of the virus in the population the more mutation events will occur.

The mutations may, or may not, change the characteristic of the virus - specifically making it more or less transmissible than the virus before the mutation or more or less dangerous in terms of severity of disease than the virus before the mutation.

If the mutation is more transmissible it will be more likely to infect people and more likely to infect more people and therefore there will be greater overall replication of the new mutant and it will replicant and survive better and therefore become dominant. It its transmissibility is less than the pre-mutation variant it will do the reverse and will likely disappear fairly rapidly. If there is no difference in transmissibility than the original virus it will likely just transmit itself alongside the original.

The issue of severity of disease is different as it doesn't impact on replication unless it it so severe that it kills the host before replicating or is retained for much longer in the body before the immune response deals with it.

So in terms of a pandemic your worst nightmare is the combination of a virus mutation that is more transmissible and causes more severe disease. But your friend (up to a point) it a virus that is more transmissible because causes less serious disease, allowing transmission (and population level immunity to develop) while only causing very mild illness.

Spud

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Re: Coronavirus
« Reply #4351 on: July 09, 2021, 02:30:08 PM »
It is basic evolutionary theory.

Mutations are random events which occur when the virus is being replicated in a host human - the more the level of the virus in the population the more mutation events will occur.

The mutations may, or may not, change the characteristic of the virus - specifically making it more or less transmissible than the virus before the mutation or more or less dangerous in terms of severity of disease than the virus before the mutation.

If the mutation is more transmissible it will be more likely to infect people and more likely to infect more people and therefore there will be greater overall replication of the new mutant and it will replicant and survive better and therefore become dominant. It its transmissibility is less than the pre-mutation variant it will do the reverse and will likely disappear fairly rapidly. If there is no difference in transmissibility than the original virus it will likely just transmit itself alongside the original.

The issue of severity of disease is different as it doesn't impact on replication unless it it so severe that it kills the host before replicating or is retained for much longer in the body before the immune response deals with it.

So in terms of a pandemic your worst nightmare is the combination of a virus mutation that is more transmissible and causes more severe disease. But your friend (up to a point) it a virus that is more transmissible because causes less serious disease, allowing transmission (and population level immunity to develop) while only causing very mild illness.
Interesting. So iirc the Delta variant is more transmissible, but is its apparent lower morbidity and mortality more due to the host population being younger people and those with 'suboptimal' antibodies from recent vaccination or previous infection or generally good innate immunity because they are younger?
« Last Edit: July 09, 2021, 06:24:50 PM by Spud »

ProfessorDavey

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Re: Coronavirus
« Reply #4352 on: July 09, 2021, 03:47:24 PM »
Interesting. So iirc the Delta variant is more transmissible, but is its apparent lower morbidity and mortality more due to the host population being younger and those with 'suboptimal' antibodies from recent vaccination or previous infection or generally good innate immunity because they are younger?
The delta variant is more transmissible.

Whether is causes more serious disease isn't so clear - I don't think your assertion is valid as it is based on a different population demographic for people most likely to be infected now (younger) as most older people have been vaccinated.

The assessment of seriousness is how likely it is to cause serious disease compared to the earlier variant on the basis that the population at risk is the same.

You can then factor in any differences in the population likely to become infected, but that isn't a feature of the virus itself.
« Last Edit: July 09, 2021, 03:59:30 PM by ProfessorDavey »

SusanDoris

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Re: Coronavirus
« Reply #4353 on: July 09, 2021, 03:57:05 PM »
it's not a question of the date. It's a question of what is reasonable on the date.

I am all in favour of opening up as much as we can, but to get rid of the mandate for mask wearing is irresponsible in the extreme.

Mask wearing is such an easy win in terms of controlling the spread of the virus. It allows for most things to be done as normal and yet it significantly reduces infection if all adhere to that one restriction. What so many people appear to miss is the virus's capability to mutate and that in order to mutate it is much easier if there is a lot of virus in circulation which is the case now, and will be even more so when we open with no safeguards in place.

Johnson has made it sound like an either/or decision. That is nonsense. We can open up with a few safeguards in place.

All the government are doing at the moment is taking a huge gamble, a gamble that risks making England a world beater in variant creation and also risks significant numbers of people being affected by long covid.

This government is appalling.
Okay - |I agree about wearing of masks and sensible social distancing, but there are so many other things that can't be held back for ever. The economy, mental health, llearning to live with the new normal whatever that turns out to be. I don't pretend to know anywhere near enough to offer any better solutions though.
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Spud

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Re: Coronavirus
« Reply #4354 on: July 09, 2021, 06:35:00 PM »
The delta variant is more transmissible.

Whether is causes more serious disease isn't so clear - I don't think your assertion is valid as it is based on a different population demographic for people most likely to be infected now (younger) as most older people have been vaccinated.

The assessment of seriousness is how likely it is to cause serious disease compared to the earlier variant on the basis that the population at risk is the same.

You can then factor in any differences in the population likely to become infected, but that isn't a feature of the virus itself.
I guess it would be hard to know how serious disease from the Delta is compared with the alpha variant, since it is affecting a younger host age. What I was focussing on in my earlier post was whether human infection prevention measures such as lockdown and vaccination were responsible for mutated strains being selected for. The measures make it hard for the original strain to survive, and thus the variants are more likely to become dominant.
This is the opposite of the refrain that the more people are vaccinated, the less chance the virus has to spread.
« Last Edit: July 09, 2021, 06:37:11 PM by Spud »

ProfessorDavey

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Re: Coronavirus
« Reply #4355 on: July 09, 2021, 06:41:07 PM »
I guess it would be hard to know how serious disease from the Delta is compared with the alpha variant, since it is affecting a younger host age.
Not really, you just look at the likelihood of developing serious illness with age etc matched cohorts infected with the alpha and delta variants. It may take a little more time to get the data as there will be less people developing serious illness if you are looking at a younger cohort of people.

What I was focussing on in my earlier post was whether human infection prevention measures such as lockdown and vaccination were responsible for mutated strains being selected for. Since they make it hard for the original strain to survive, and thus are more likely to become dominant.
No - the lockdown etc will only affect the levels of transmission and therefore number of mutations some of which may be variants of concern.

I think you may be confusing the infection with a virus with concerns about antibiotic use driving antibiotic resistant strains, which is a real concern.

This is the opposite of the refrain that the more people are vaccinated, the less chance the virus has to spread.
But not born out by the science.

Nearly Sane

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Nearly Sane

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Re: Coronavirus
« Reply #4357 on: July 12, 2021, 10:01:47 PM »
So Macron hinting at a further lockdown but Johnson still sort of full steam ahead for freedom day despite hospital numbers up 48% in a week. The lying incompetent racist thug PM....
« Last Edit: July 12, 2021, 10:39:00 PM by Nearly Sane »

Nearly Sane

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Re: Coronavirus
« Reply #4358 on: July 13, 2021, 08:29:13 PM »

Aruntraveller

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Re: Coronavirus
« Reply #4359 on: July 13, 2021, 08:36:22 PM »
He is a murderous, ignorant, stupid idiot. Driven by greed. We all knew some of this and yet sufficient of us voted for him to make this scenario possible.

Those that did vote for him should hang their heads in absolute shame.
Before we work on Artificial Intelligence shouldn't we address the problem of natural stupidity.

Roses

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Re: Coronavirus
« Reply #4360 on: July 14, 2021, 11:15:43 AM »
I hope the Welsh Government will be much more circumspect about lifting the lockdown restrictions. It is no good relying on the public to be sensible as that idiot, Boris, is hoping they will be. ::) Facemasks and social distancing should remain mandatory whilst the latest spike in the virus is going ever upwards.
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Spud

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Re: Coronavirus
« Reply #4361 on: July 14, 2021, 12:15:06 PM »
View from New Zealand on our policy.



https://www.newsroom.co.nz/uks-awful-experiment-will-threaten-nz
The virus would still eventually evade the vaccine because the vaccine is not 100% effective. And it would be a more virulent strain that evaded it. If we relax restrictions the current strain will continue to be the dominant one.

jeremyp

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Re: Coronavirus
« Reply #4362 on: July 14, 2021, 12:46:16 PM »
Looking at the current daily figures, I am sorry to say, I think it would be reckless to lift the current restrictions on July 19th. In fact, it looks like a further lock down will be needed.

I'm really looking forward to my festivals in August, but if the figures carry on as they are, it would be insane to allow them to go ahead.
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jeremyp

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Re: Coronavirus
« Reply #4363 on: July 14, 2021, 12:49:07 PM »
The virus would still eventually evade the vaccine because the vaccine is not 100% effective. And it would be a more virulent strain that evaded it. If we relax restrictions the current strain will continue to be the dominant one.

Unfortunately, that's not true. The more people who get the virus, the more opportunity there is for a strain to develop that has immunity to our vaccines. If it does develop, it will become the dominant strain fairly quickly. 
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ProfessorDavey

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Re: Coronavirus
« Reply #4364 on: July 14, 2021, 01:23:31 PM »
The virus would still eventually evade the vaccine because the vaccine is not 100% effective. And it would be a more virulent strain that evaded it. If we relax restrictions the current strain will continue to be the dominant one.
That isn't true at all - in fact the reverse is true.

Mutations are random events and the number of mutations is directly linked to the number of replication events of the virus. This in turn links to the number of infections. So if you relax restrictions there will be more infections and therefore more mutations and therefore a greater likelihood that one of those mutations evades the vaccine.

The best way to avoid dangerous variants arising is to keep infections as low as possible (hence reducing the number of replication events) through both vaccines and restrictions.

Nearly Sane

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Re: Coronavirus
« Reply #4365 on: July 14, 2021, 06:13:27 PM »

jeremyp

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Re: Coronavirus
« Reply #4366 on: July 14, 2021, 06:23:00 PM »
42k new cases today



https://coronavirus.data.gov.uk/

That's actually good news. The rate of increase is only 27% compared to last week. The rate of increase in cases is not rising exponentially anymore.

It's hospital admissions that is the real bad news at the moment: 53% more compared to last week. It won't take too many weeks of rising at 50% to overwhelm the NHS.
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Nearly Sane

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Re: Coronavirus
« Reply #4367 on: July 14, 2021, 06:32:38 PM »
That's actually good news. The rate of increase is only 27% compared to last week. The rate of increase in cases is not rising exponentially anymore.

It's hospital admissions that is the real bad news at the moment: 53% more compared to last week. It won't take too many weeks of rising at 50% to overwhelm the NHS.
Neither of then are figures that you would use to justify 'Freedom Day'

jeremyp

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Re: Coronavirus
« Reply #4368 on: July 14, 2021, 06:41:44 PM »
Neither of then are figures that you would use to justify 'Freedom Day'
Of course not. It's insane to continue with the removal of current measures.
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ProfessorDavey

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Re: Coronavirus
« Reply #4369 on: July 14, 2021, 07:10:58 PM »
That's actually good news. The rate of increase is only 27% compared to last week. The rate of increase in cases is not rising exponentially anymore.
But surely the point about an exponential increase is that, in % terms, it remains the same over time.

So if you have a 25% increase per week and the starting point is 100, in one week you have 125, another week you have 156, the next week 195, then 244, 305 etc. So in the first week your absolute increase is only 25, by week 6 it is over 60.

There may be some evidence that the rate of increase is slowing, but i think you need to follow that over a longer period of time than just one week to see a real effect, as it can be particularly influenced by a single daily value that is anomalously high or low.

It's hospital admissions that is the real bad news at the moment: 53% more compared to last week. It won't take too many weeks of rising at 50% to overwhelm the NHS.
True

Gordon

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Re: Coronavirus
« Reply #4370 on: July 14, 2021, 08:59:41 PM »
The situation in England is already looking shambolic as regards wearing masks on public transport with various 'mayors' (which we don't have here in Scotland) doing different things, and it seems they have varying local powers where some can require masks be worn and other just encourage the wearing of masks.

You'd have thought that the strategy of the UK government as regards changes in England would have anticipated this scenario: unless, of course, the strategy is to encourage chaos and, no doubt, then blame everyone else (which presumes there is a strategy). Alternatively it could be down to the incompetence of a bunch of  incompetents.

https://www.theguardian.com/uk-news/2021/jul/14/passengers-face-patchwork-of-mask-rules-on-public-transport-after-19-july

Nearly Sane

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Re: Coronavirus
« Reply #4371 on: July 14, 2021, 09:15:26 PM »
The situation in England is already looking shambolic as regards wearing masks on public transport with various 'mayors' (which we don't have here in Scotland) doing different things, and it seems they have varying local powers where some can require masks be worn and other just encourage the wearing of masks.

You'd have thought that the strategy of the UK government as regards changes in England would have anticipated this scenario: unless, of course, the strategy is to encourage chaos and, no doubt, then blame everyone else (which presumes there is a strategy). Alternatively it could be down to the incompetence of a bunch of  incompetents.

https://www.theguardian.com/uk-news/2021/jul/14/passengers-face-patchwork-of-mask-rules-on-public-transport-after-19-july
To be fair, while we aren't going for Freedom Day, we are in Scotland reducing restrictioms while hospital.cases rise. Overall I would give the Scottish govt 3 out of 10 handling this, as opposed to 2 for UK govt, if I ignore the corruption. Sturgeon has communicated better but the actual different decisions have been marginal.
« Last Edit: July 14, 2021, 09:54:18 PM by Nearly Sane »

jeremyp

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Re: Coronavirus
« Reply #4372 on: July 15, 2021, 08:49:15 AM »
But surely the point about an exponential increase is that, in % terms, it remains the same over time.

So if you have a 25% increase per week and the starting point is 100, in one week you have 125, another week you have 156, the next week 195, then 244, 305 etc. So in the first week your absolute increase is only 25, by week 6 it is over 60.

There may be some evidence that the rate of increase is slowing, but i think you need to follow that over a longer period of time than just one week to see a real effect, as it can be particularly influenced by a single daily value that is anomalously high or low.
True

Until recently, the % rate of increase was in the 50's. It came down first to the 30's and now it's below 30. It's not just one week. So I think the evidence is that the rate of increase of infections is slowing. It's the one piece of good news in an otherwise grim situation.
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ProfessorDavey

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Re: Coronavirus
« Reply #4373 on: July 15, 2021, 09:34:58 AM »
Until recently, the % rate of increase was in the 50's. It came down first to the 30's and now it's below 30. It's not just one week. So I think the evidence is that the rate of increase of infections is slowing. It's the one piece of good news in an otherwise grim situation.
The problem with 7 day rolling data is that is can be affected by a single anomalous day's data depending on whether that is in the 7-day figures or when it drops out. Have a look at the graph - scroll down to 'Cases - people testing positive'.

https://coronavirus.data.gov.uk

My reading of this was that there was some evidence of a slowing - the early part of the 'red' line compared to the 'black' line, but that there is now a stronger increase (look at the trend within the red line). So your 'now below 30' is because the rolling 7 day average is comparing the red to the black. Once those first few days of 'red' drop out of the system and are part of the comparison I think we may see the rolling average percentage rising again.

I hope I'm wrong.

jeremyp

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Re: Coronavirus
« Reply #4374 on: July 15, 2021, 10:35:17 AM »
The problem with 7 day rolling data is that is can be affected by a single anomalous day's data depending on whether that is in the 7-day figures or when it drops out. Have a look at the graph - scroll down to 'Cases - people testing positive'.
The rate has been dropping for a while. I'm not just looking at this week's figures. Look at the shape of the black line

https://coronavirus.data.gov.uk/details/cases

It's not an exponential curve.

Of course, I expect an increase following the last week of the Euros and, if July 19th goes ahead as planned, I expect the rate to go exponential again, at least for a while.
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