New Variant Covid-19 VUI 202012/01

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sTeamTraen
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Re: New Variant Covid-19 VUI 202012/01

Post by sTeamTraen » Tue Jan 05, 2021 12:10 am

shpalman wrote:
Mon Jan 04, 2021 8:23 pm
The data from the heatmap at https://coronavirus.data.gov.uk/details ... me=England can be downloaded.
I tried that. The CSV file contained one record per line, in JSON format. :roll: Now patching it up with a text editor...
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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Tue Jan 05, 2021 7:11 am

sTeamTraen wrote:
Tue Jan 05, 2021 12:10 am
shpalman wrote:
Mon Jan 04, 2021 8:23 pm
The data from the heatmap at https://coronavirus.data.gov.uk/details ... me=England can be downloaded.
I tried that. The CSV file contained one record per line, in JSON format. :roll: Now patching it up with a text editor...
Yeah LibreOffice's import filter failed to separate it, but I cut & pasted the JSON bit into a text editor then pasted it back into a new sheet, and LibreOffice was then able to separate it into columns.

The point is that I made the graph but it's a mess, you'll get further with figuring out what's going on with it if you make your own which you can play with.

Or else it doesn't tell you anything you couldn't have got from the colourmap (for example you can see how the second wave started with young people back in mid September), just with a quantitative scale.
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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Tue Jan 05, 2021 7:56 am

Structure-function investigation of a new VUI-202012/01 SARS-CoV-2 variant
https://www.biorxiv.org/content/10.1101 ... 1.425028v1

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Tue Jan 05, 2021 12:12 pm

South Africa testing whether vaccines work against variant
Scientists in South Africa are urgently testing to see if the vaccines for COVID-19 will be effective against the country’s variant virus

[...]

“This is the most pressing question facing us right now,” said Dr. Richard Lessells, an infectious diseases expert who is working on the country's genomic studies of the variant.

“We are urgently doing experiments in the laboratory to test the variant," against the blood of people with antibodies and against the blood of people who have received vaccines, Lessells told The Associated Press Monday.

The tests, called neutralizing assays, will help determine the reliability of vaccines against the variant, he said.
https://abcnews.go.com/Health/wireStory ... t-75034535

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Re: New Variant Covid-19 VUI 202012/01

Post by lpm » Tue Jan 05, 2021 12:46 pm

Little waster wrote:
Mon Jan 04, 2021 11:37 pm
Can I just doublecheck the timelines.

4000BC God makes the COVID-19 virus, for some ineffable reason. It then hides for a few centuries.

3500BC It sneaks out long enough to hide in one (or both) of Noah’s bats so it isn’t killed in the Flood but refrains from infecting Noah or his family. It doesn’t kill the bats either and they don’t develop any immunity. After 40 days the bats are released with all the other birds and fly to China from Turkey. In China most of the bats’ descendants don’t have COVID, these fly to all the other parts of the world and turn into all the 1400+ different species of bats which look completely different and can’t interbreed but definitely haven’t descended with modifications over time. The original COVID bats hide in China for a few millennia.

2020AD One day COVID suddenly decides to start a world tour. It rapidly spreads around the world. Some people are naturally immune, some people catch it and barely notice, other people catch it and are severely ill, some even die. NOTHING must be read into any of that. Within a year it is everywhere. Humans collectively take action to reduce its transmission.

2021AD God intelligently designs a new version of COVID because he loves us which just happens to have a single mutation which makes it a lot better at transmitting itself. It only turns up in one place (possibly the UK) and quickly spreads everywhere. Through some unknown mechanism this new version quickly supplants the old version, because God loves us. Humans develop vaccines through a strict regime of closing our eyes and kneeling and giving the men with the funny hats a tenth of our money and our children to molest. Gods love sticks three mutations in yet another version of COVID, one of which might get round the vaccine and two which may not do anything, this one he bestows only on South Africa.

You know I’ve read my Bible from cover to cover and I can’t make any sense of it.

Do you think we might be missing something? :?
You missed the bit where God raped a girl and made her pregnant, not physical rape just virtual like over Zoom or something, and then Baby Jesus was born and took all the sin and got Christmas presents, and God then killed Baby Jesus but promised with a rainbow to never to collective-punish humans with a virus ever again, but 666 is the number of the beast and Satan and all his little goblins have come back with Covid riding the four bats of the apocolypse and so it all makes perfect sense, actually.
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Re: New Variant Covid-19 VUI 202012/01

Post by tenchboy » Tue Jan 05, 2021 12:55 pm

lpm wrote:
Tue Jan 05, 2021 12:46 pm
Little waster wrote:
Mon Jan 04, 2021 11:37 pm
Can I just doublecheck the timelines.

4000BC God makes the COVID-19 virus, for some ineffable reason. It then hides for a few centuries.

3500BC It sneaks out long enough to hide in one (or both) of Noah’s bats so it isn’t killed in the Flood but refrains from infecting Noah or his family. It doesn’t kill the bats either and they don’t develop any immunity. After 40 days the bats are released with all the other birds and fly to China from Turkey. In China most of the bats’ descendants don’t have COVID, these fly to all the other parts of the world and turn into all the 1400+ different species of bats which look completely different and can’t interbreed but definitely haven’t descended with modifications over time. The original COVID bats hide in China for a few millennia.

2020AD One day COVID suddenly decides to start a world tour. It rapidly spreads around the world. Some people are naturally immune, some people catch it and barely notice, other people catch it and are severely ill, some even die. NOTHING must be read into any of that. Within a year it is everywhere. Humans collectively take action to reduce its transmission.

2021AD God intelligently designs a new version of COVID because he loves us which just happens to have a single mutation which makes it a lot better at transmitting itself. It only turns up in one place (possibly the UK) and quickly spreads everywhere. Through some unknown mechanism this new version quickly supplants the old version, because God loves us. Humans develop vaccines through a strict regime of closing our eyes and kneeling and giving the men with the funny hats a tenth of our money and our children to molest. Gods love sticks three mutations in yet another version of COVID, one of which might get round the vaccine and two which may not do anything, this one he bestows only on South Africa.

You know I’ve read my Bible from cover to cover and I can’t make any sense of it.

Do you think we might be missing something? :?
You missed the bit where God raped a girl and made her pregnant, not physical rape just virtual like over Zoom or something, and then Baby Jesus was born and took all the sin and got Christmas presents, and God then killed Baby Jesus but promised with a rainbow to never to collective-punish humans with a virus ever again, but 666 is the number of the beast and Satan and all his little goblins have come back with Covid riding the four bats of the apocolypse and so it all makes perfect sense, actually.
So why does my sleeve fall down at the very moment I put my hands in the water to do the washing up?
Eh?
Not so f.cking smart now, are yer?

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Tue Jan 05, 2021 3:16 pm

Denmark moves to (top) level 5 Covid alert, government believes that the UK variant will be dominant by mid-February.

Danish:
Fra midten af februar vil den britiske coronamutation være den dominerende i Danmark, forventer sundhedsmyndighederne
https://nyheder.tv2.dk/samfund/2021-01- ... inerende-i

English:
Denmark moves to highest Covid-19 alert level amid concerns over more infectious variant
https://www.thelocal.dk/20210105/latest ... 17-variant

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Tue Jan 05, 2021 3:18 pm

I think that by now we can drop the suggestion that the prevalence of the new variant is all due to a founder effect. That might have happened in Kent and London, Scotland was stretching it. Difficult to see how that could also be happening in Denmark.

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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Tue Jan 05, 2021 3:35 pm

Woodchopper wrote:
Tue Jan 05, 2021 3:18 pm
I think that by now we can drop the suggestion that the prevalence of the new variant is all due to a founder effect. That might have happened in Kent and London, Scotland was stretching it. Difficult to see how that could also be happening in Denmark.
What I'm still waiting to see (and hoping not to see) is any country apart from the UK having a third wave kick off because of it.
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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Tue Jan 05, 2021 3:44 pm

shpalman wrote:
Tue Jan 05, 2021 3:35 pm
Woodchopper wrote:
Tue Jan 05, 2021 3:18 pm
I think that by now we can drop the suggestion that the prevalence of the new variant is all due to a founder effect. That might have happened in Kent and London, Scotland was stretching it. Difficult to see how that could also be happening in Denmark.
What I'm still waiting to see (and hoping not to see) is any country apart from the UK having a third wave kick off because of it.

daily-new-cases-Denmark.png
The Danes appear to think that it will, unless checked. Info is in Danish, but Google will help you, the number of hospital admissions isn't looking good (Indlagte patienter): https://www.sst.dk/da/corona/tal-og-overvaagning

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Tue Jan 05, 2021 3:58 pm

shpalman wrote:
Tue Jan 05, 2021 3:35 pm
Woodchopper wrote:
Tue Jan 05, 2021 3:18 pm
I think that by now we can drop the suggestion that the prevalence of the new variant is all due to a founder effect. That might have happened in Kent and London, Scotland was stretching it. Difficult to see how that could also be happening in Denmark.
What I'm still waiting to see (and hoping not to see) is any country apart from the UK having a third wave kick off because of it.

daily-new-cases-Denmark.png
Anyway, new UK variant will still be less than 5% of cases now. Its too early for it to show up in the total numbers of cases.

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Re: New Variant Covid-19 VUI 202012/01

Post by sTeamTraen » Tue Jan 05, 2021 4:17 pm

Woodchopper wrote:
Tue Jan 05, 2021 3:44 pm
shpalman wrote:
Tue Jan 05, 2021 3:35 pm
Woodchopper wrote:
Tue Jan 05, 2021 3:18 pm
I think that by now we can drop the suggestion that the prevalence of the new variant is all due to a founder effect. That might have happened in Kent and London, Scotland was stretching it. Difficult to see how that could also be happening in Denmark.
What I'm still waiting to see (and hoping not to see) is any country apart from the UK having a third wave kick off because of it.

daily-new-cases-Denmark.png
The Danes appear to think that it will, unless checked. Info is in Danish, but Google will help you, the number of hospital admissions isn't looking good (Indlagte patienter): https://www.sst.dk/da/corona/tal-og-overvaagning
As usual, deaths are following cases closely, with a lag. Cases peaked 15 days ago, so I guess the deaths curve has a week or so of further growth before it turns.

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Re: New Variant Covid-19 VUI 202012/01

Post by sTeamTraen » Tue Jan 05, 2021 4:58 pm

shpalman wrote:
Tue Jan 05, 2021 7:11 am
The point is that I made the graph but it's a mess, you'll get further with figuring out what's going on with it if you make your own which you can play with.

Or else it doesn't tell you anything you couldn't have got from the colourmap (for example you can see how the second wave started with young people back in mid September), just with a quantitative scale.
It also probably needs adjustment for the number of people in each category. That won't matter too much between, say, 20-24 and 40-44, but the spike from March seems to show that the largest number of people who died were aged 75-79, presumably because there aren't nearly as many people in the older age groups.
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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Tue Jan 05, 2021 5:39 pm

sTeamTraen wrote:
Tue Jan 05, 2021 4:58 pm
shpalman wrote:
Tue Jan 05, 2021 7:11 am
The point is that I made the graph but it's a mess, you'll get further with figuring out what's going on with it if you make your own which you can play with.

Or else it doesn't tell you anything you couldn't have got from the colourmap (for example you can see how the second wave started with young people back in mid September), just with a quantitative scale.
It also probably needs adjustment for the number of people in each category. That won't matter too much between, say, 20-24 and 40-44, but the spike from March seems to show that the largest number of people who died were aged 75-79, presumably because there aren't nearly as many people in the older age groups.
The data is given both in terms of the number of cases that day, and of the rolling rate (new cases per week per 100,000), which is what I've plotted and what is plotted in the colourmaps at uk dot govid.

Also, it's the case rate, not the deaths, so doesn't tell you anything about ages of the "number of people who died".
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Re: New Variant Covid-19 VUI 202012/01

Post by sTeamTraen » Tue Jan 05, 2021 7:27 pm

shpalman wrote:
Tue Jan 05, 2021 5:39 pm
Also, it's the case rate, not the deaths, so doesn't tell you anything about ages of the "number of people who died".
Apologies. But my point about population adjustment is still relevant, I think.

If we ignore that for a moment and assume that every 5-year cohort has similar population, I wonder why so many 75-79 year olds tested positive. They seem a bit young to be in care homes in large numbers. But perhaps the age distribution of testing was highly skewed in the spring (or, as we should probably start saying, the spring of 2020).
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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Tue Jan 05, 2021 7:38 pm

sTeamTraen wrote:
Tue Jan 05, 2021 7:27 pm
shpalman wrote:
Tue Jan 05, 2021 5:39 pm
Also, it's the case rate, not the deaths, so doesn't tell you anything about ages of the "number of people who died".
Apologies. But my point about population adjustment is still relevant, I think.

If we ignore that for a moment and assume that every 5-year cohort has similar population, I wonder why so many 75-79 year olds tested positive. They seem a bit young to be in care homes in large numbers. But perhaps the age distribution of testing was highly skewed in the spring (or, as we should probably start saying, the spring of 2020).
shpalman wrote:
Sun Jan 03, 2021 1:57 pm
...(b.ii) ... all the older people [were] in hospital (the first wave seemed to skew towards older people because they all caught it in nursing homes or hospitals and/or tests were only carried out on patients severe enough to end up in hospital, who would have been more likely to be older)
You can get the 2011 age structure and the 2020 one won't be that different, except for maybe fewer in the oldest bands.
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Re: New Variant Covid-19 VUI 202012/01

Post by sTeamTraen » Tue Jan 05, 2021 7:45 pm

shpalman wrote:
Tue Jan 05, 2021 7:38 pm
You can get the 2011 age structure and the 2020 one won't be that different, except for maybe fewer in the oldest bands.
Presumably I can just move everyone up two bands. ;)
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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Tue Jan 05, 2021 9:24 pm

The Irish Government was briefed today that 25% of cases in a recent sampling contained the variant
https://www.rte.ie/news/primetime/2021/ ... iant-b117/

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Re: New Variant Covid-19 VUI 202012/01

Post by nekomatic » Tue Jan 05, 2021 11:40 pm

sTeamTraen wrote:
Tue Jan 05, 2021 7:45 pm
Presumably I can just move everyone up two bands. ;)
Apart from the ones who emigrated because of Brexit.

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Wed Jan 06, 2021 6:42 am

Viral mutations may cause another ‘very, very bad’ COVID-19 wave, scientists warn
https://www.sciencemag.org/news/2021/01 ... tists-warn

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Wed Jan 06, 2021 7:17 am

Comprehensive mapping of mutations to the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human serum antibodies
https://www.biorxiv.org/content/10.1101 ... 1.425021v1

Summary thread
https://twitter.com/jbloom_lab/status/1 ... 80098?s=21

tl;dr South Africa variant may be better at escaping antibody response, not so UK. Current vaccines will still be useful for years.

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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Wed Jan 06, 2021 8:15 am

Woodchopper wrote:
Tue Jan 05, 2021 3:44 pm
shpalman wrote:
Tue Jan 05, 2021 3:35 pm
Woodchopper wrote:
Tue Jan 05, 2021 3:18 pm
I think that by now we can drop the suggestion that the prevalence of the new variant is all due to a founder effect. That might have happened in Kent and London, Scotland was stretching it. Difficult to see how that could also be happening in Denmark.
What I'm still waiting to see (and hoping not to see) is any country apart from the UK having a third wave kick off because of it.

daily-new-cases-Denmark.png
The Danes appear to think that it will, unless checked. Info is in Danish, but Google will help you, the number of hospital admissions isn't looking good (Indlagte patienter): https://www.sst.dk/da/corona/tal-og-overvaagning
https://www.sst.dk/en/English/Corona-en ... and-charts

With a bit of luck, it might have just peaked.
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Re: New Variant Covid-19 VUI 202012/01

Post by Millennie Al » Thu Jan 07, 2021 2:04 am

shpalman wrote:
Mon Jan 04, 2021 8:35 pm
Millennie Al wrote:
Mon Jan 04, 2021 2:51 am
I am starting to doubt that SARS-COV-2 can be exterminated. If it gets down to a low enough level, I think that there will not be enough determination worldwide to completely stamp it out. That means that it will turn into a disease like the flu whereby it keeps killing some people, but at a level where it is considered not worth the effort to completely eliminate it. Maybe we will have to get a new vaccine every so often, as is the case for flu, when it mutates, but at any one time there will be enough susceptible people worldwide that it persists.
It's easier to try to stamp it out, once it gets low enough, than it is to try to maintain it low enough without stamping it out. It won't take much for it to flare up again and it seems it's usually a couple of weeks too late by the time anyone decided to do anything about it.
From a technical and scientific perspective, yes; but maybe not from a political one. One of the properties of exponential decay is that if it takes (for example) four weeks to get from 50,000 cases to 5,000, it will take another four to get to 500, and another to 50 (assuming all else stays the same). I think that once people have spent the eight weeks to get to 500 cases they will feel that it's not worth another four weeks merely to get rid of 450 cases (and will start saying the measures aren't working because the same measures produces a reduction of 45,000 earlier). This is why effective trace and quarantine is so vital - it takes over when the numbers are small enough so all else isn't the same.

In the absence of enough determination to completely stamp it out, it will keep flaring up and getting suppressed, but never hit zero.
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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Thu Jan 07, 2021 10:02 am

Millennie Al wrote:
Thu Jan 07, 2021 2:04 am
shpalman wrote:
Mon Jan 04, 2021 8:35 pm
Millennie Al wrote:
Mon Jan 04, 2021 2:51 am
I am starting to doubt that SARS-COV-2 can be exterminated. If it gets down to a low enough level, I think that there will not be enough determination worldwide to completely stamp it out. That means that it will turn into a disease like the flu whereby it keeps killing some people, but at a level where it is considered not worth the effort to completely eliminate it. Maybe we will have to get a new vaccine every so often, as is the case for flu, when it mutates, but at any one time there will be enough susceptible people worldwide that it persists.
It's easier to try to stamp it out, once it gets low enough, than it is to try to maintain it low enough without stamping it out. It won't take much for it to flare up again and it seems it's usually a couple of weeks too late by the time anyone decided to do anything about it.
From a technical and scientific perspective, yes; but maybe not from a political one. One of the properties of exponential decay is that if it takes (for example) four weeks to get from 50,000 cases to 5,000, it will take another four to get to 500, and another to 50 (assuming all else stays the same). I think that once people have spent the eight weeks to get to 500 cases they will feel that it's not worth another four weeks merely to get rid of 450 cases (and will start saying the measures aren't working because the same measures produces a reduction of 45,000 earlier). This is why effective trace and quarantine is so vital - it takes over when the numbers are small enough so all else isn't the same.

In the absence of enough determination to completely stamp it out, it will keep flaring up and getting suppressed, but never hit zero.
I agree in general. Test, trace and isolate is an effective means to eradicate infection. But it appears to only function properly at low levels of infection.

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Thu Jan 07, 2021 10:33 am

MK Lighthouse Lab @Biocentre_UK covid testing continues to show a significant increase in positive test rate and B117 'new variant', as detected by PCR S (spike) gene target failure (SGTF), now represents ~90% of all positives.
https://twitter.com/The_Soup_Dragon/sta ... 66688?s=20

Tweet by the head of the lab.

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