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 » Sun Jan 03, 2021 12:39 pm

bob sterman wrote:
Sun Jan 03, 2021 8:59 am
shpalman wrote:
Sun Jan 03, 2021 8:17 am
Why would you expect the prevalence to be higher among teenagers and young adults in the second wave as compared to the first one?
In the UK schools were closed and all face-to-face teaching at universities was stopped during first wave. Organised youth sport was also stopped.
Yes, plus the pubs were open for much of the autumn. But it's also a relative thing: A person who is infected now is more likely to be a younger person because the older people are keeping out of the way as much as possible.
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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Sun Jan 03, 2021 1:57 pm

sTeamTraen wrote:
Sun Jan 03, 2021 12:39 pm
bob sterman wrote:
Sun Jan 03, 2021 8:59 am
shpalman wrote:
Sun Jan 03, 2021 8:17 am
Why would you expect the prevalence to be higher among teenagers and young adults in the second wave as compared to the first one?
In the UK schools were closed and all face-to-face teaching at universities was stopped during first wave. Organised youth sport was also stopped.
Yes, plus the pubs were open for much of the autumn. But it's also a relative thing: A person who is infected now is more likely to be a younger person because the older people are keeping out of the way as much as possible.
I can't really follow your reasoning.

So the hospitals are now full of children in a way they weren't during the first wave because
(a) actually they aren't;
(i) someone who works in a children's ward notices more children than usual are in it but doesn't have an overview of the rest of the hospital i.e. hasn't noticed that there are actually way more adults in there than usual, and way more adults than children, in the hospital as a whole;
(b) they were full of children during the first wave too but we didn't notice because
(i) we didn't test them for covid ("out of every 100 people who got a positive there were probably only 1 or 2 children")
(ii) we were distracted by all the older people who were also 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)
(c) they are catching covid more because it's a variant of the virus which children are more likely to be infected by
(d) they are catching covid more because schools have been open i.e. child-child transmission rather than parent-child (so shouldn't we see more child-parent transmission too i.e. more infections in parent-age adults too so the age profile wouldn't stay biased towards only children)
(e) they are catching covid at the same rate as before but it's a variant of the virus which is more severe in children
(f) because the pubs were open, which children don't go to and parents probably haven't been going to, as compared to "teenagers and young adults [who] take more risks generally" but this somehow translates towards there being more children in hospital
?

Point (a) renders the whole discussion moot.

Point (b) makes no sense because like I said, we'd have noticed if lots of children had to go to hospital because of their symptoms, whether or not you'd manage to get covid tests for them. It has never been the policy to take someone to hospital just because they tested positive but were asymptomatic or mildly symptomatic. It was just that we generally didn't even pick up those cases the first time around.

Point (d) makes little sense to me because having schools open doesn't necessarily skew the age distribution that much towards children if parents and children can always catch it from each other. Having schools open just increases infection across the whole community (which is generally the result that we've seen) although maybe in the second wave people have learnt to keep the grandparents out of it
("the older people are keeping out of the way as much as possible").

Regarding point (e) we don't have evidence that the new variant is more severe in adults.

Point (f) has got nothing in particular to do with children, it's just another driver of general community transmission. The heatmap of cases in England clearly shows a high case rate in 15-19 year olds, and 20-24 year olds... at the beginning of October, before then spreading to everyone else. The late-December second half of the second wave seems distributed across all ages from 10 to 69 without one age group obviously leading.

So I'm only left with (c), if not (a).
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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Sun Jan 03, 2021 7:42 pm

SARS-CoV-2 escape in vitro from a highly neutralizing COVID-19 convalescent plasma
https://www.biorxiv.org/content/10.1101 ... 1.full.pdf

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Re: New Variant Covid-19 VUI 202012/01

Post by headshot » Sun Jan 03, 2021 8:04 pm

Woodchopper wrote:
Sun Jan 03, 2021 7:42 pm
SARS-CoV-2 escape in vitro from a highly neutralizing COVID-19 convalescent plasma
https://www.biorxiv.org/content/10.1101 ... 1.full.pdf
Ah f.ck.

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Re: New Variant Covid-19 VUI 202012/01

Post by sTeamTraen » Sun Jan 03, 2021 8:39 pm

shpalman wrote:
Sun Jan 03, 2021 1:57 pm
sTeamTraen wrote:
Sun Jan 03, 2021 12:39 pm
Yes, plus the pubs were open for much of the autumn. But it's also a relative thing: A person who is infected now is more likely to be a younger person because the older people are keeping out of the way as much as possible.
I can't really follow your reasoning.
My (only) point is that I don't find it unreasonable that for the same number of real (tested or not) cases as the first wave, the breakdown of ages would be different, for two main reasons:
1. Schools being open
2. Older people being more careful

If a lot of transmission is taking place in schools then we might indeed expect more parents to get ill, but the median age of the parents of school-age children (especially younger children, who are presumably less good at following distancing protocols) is probably below the median age of first wave patients. But presumably there is data on this.

I expected that in the first wave there would be a lot of stories of supermarket staff getting sick, but I didn't see very many --- although again it would be nice to have data rather than anecdotes. In this wave, I wonder if teachers are getting sick faster than other groups. I suppose we can calculate the relative risk of being in an classroom for X hours a day with 3 positive-but-asymptomatic 8-year-olds versus spending Y hours a week in the same house as one of them.

Overall I don't know if we have any sort of data to let us decide. I'm just mostly reasoning from the basic premise that if 100 people are sick in two samples (T1 and T2) and there are fewer older people in the latter, there must be more younger people by definition. That doesn't require anything else to be going on in the population.

(I also suspect this discussion needs more pencil & paper, and carefully-considered armwaving!)
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Re: New Variant Covid-19 VUI 202012/01

Post by Martin Y » Sun Jan 03, 2021 8:44 pm

headshot wrote:
Sun Jan 03, 2021 8:04 pm
Woodchopper wrote:
Sun Jan 03, 2021 7:42 pm
SARS-CoV-2 escape in vitro from a highly neutralizing COVID-19 convalescent plasma
https://www.biorxiv.org/content/10.1101 ... 1.full.pdf
Ah f.ck.
Ah f.ck indeed. Although I'm going to fall back on More Or Less's "is that a big number?" question. Having just glanced at the abstract, it's saying if you give Covid long enough it'll find a way around your immunity. So my question becomes how likely is it to get long enough?

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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Sun Jan 03, 2021 9:03 pm

sTeamTraen wrote:
Sun Jan 03, 2021 8:39 pm
shpalman wrote:
Sun Jan 03, 2021 1:57 pm
sTeamTraen wrote:
Sun Jan 03, 2021 12:39 pm
Yes, plus the pubs were open for much of the autumn. But it's also a relative thing: A person who is infected now is more likely to be a younger person because the older people are keeping out of the way as much as possible.
I can't really follow your reasoning.
My (only) point is that I don't find it unreasonable that for the same number of real (tested or not) cases as the first wave, the breakdown of ages would be different, for two main reasons:
1. Schools being open
2. Older people being more careful
If older people had been less careful we'd also have lots of old people in the hospitals; the only way this would have prevented the apparent increase in children in hospital is if the death rate would have gone higher earlier and led to a lockdown being properly enacted and enforced.
sTeamTraen wrote:
Sun Jan 03, 2021 8:39 pm
If a lot of transmission is taking place in schools then we might indeed expect more parents to get ill, but the median age of the parents of school-age children (especially younger children, who are presumably less good at following distancing protocols) is probably below the median age of first wave patients. But presumably there is data on this.
This isn't about the age of hospitalized covid patients being on average younger adults than before, this is about whether there are lots of children there which weren't there in the first wave.
sTeamTraen wrote:
Sun Jan 03, 2021 8:39 pm
I expected that in the first wave there would be a lot of stories of supermarket staff getting sick, but I didn't see very many --- although again it would be nice to have data rather than anecdotes.
In the first wave we missed probably about 90% of the cases just because test capacity was extremely limited, so the cases which did show up were the serious ones, more likely to be older patients, my point (b.ii). But this isn't about more children testing positive (see also point b.i) it's about there apparently being more children in the hospitals than the first time around (unless point a).
sTeamTraen wrote:
Sun Jan 03, 2021 8:39 pm
In this wave, I wonder if teachers are getting sick faster than other groups. I suppose we can calculate the relative risk of being in an classroom for X hours a day with 3 positive-but-asymptomatic 8-year-olds versus spending Y hours a week in the same house as one of them.

Overall I don't know if we have any sort of data to let us decide. I'm just mostly reasoning from the basic premise that if 100 people are sick in two samples (T1 and T2) and there are fewer older people in the latter, there must be more younger people by definition. That doesn't require anything else to be going on in the population.

(I also suspect this discussion needs more pencil & paper, and carefully-considered armwaving!)
If there are fewer older people in T2 then there's proportionally more of everyone else in there as compared to T1 and a relatively small number of more children, my point (a.i).

We have the age breakdown of positive tests but we don't have the age breakdown of patients in hospital.
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Re: New Variant Covid-19 VUI 202012/01

Post by sTeamTraen » Sun Jan 03, 2021 9:30 pm

shpalman wrote:
Sun Jan 03, 2021 9:03 pm
This isn't about the age of hospitalized covid patients being on average younger adults than before, this is about whether there are lots of children there which weren't there in the first wave.
Yeah, I think we need more data than a tweet to say whether the number of children per real case is higher this time. I trust NHS staff about a thousand more times than the "skeptics", but they are not always going to be completely objective about the situation (quite understandably, of course).
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Re: New Variant Covid-19 VUI 202012/01

Post by Millennie Al » Mon Jan 04, 2021 2:51 am

Martin Y wrote:
Sun Jan 03, 2021 8:44 pm
headshot wrote:
Sun Jan 03, 2021 8:04 pm
Woodchopper wrote:
Sun Jan 03, 2021 7:42 pm
SARS-CoV-2 escape in vitro from a highly neutralizing COVID-19 convalescent plasma
https://www.biorxiv.org/content/10.1101 ... 1.full.pdf
Ah f.ck.
Ah f.ck indeed. Although I'm going to fall back on More Or Less's "is that a big number?" question. Having just glanced at the abstract, it's saying if you give Covid long enough it'll find a way around your immunity. So my question becomes how likely is it to get long enough?
The simple answer is that it currently looks inevitable.

However, the situation is complicated. The experiment found that the necessary mutations occurred within 90 days, but that is in vitro where the test was (amongst other things) whether the plasma from one specific patient (selected as it was the best) could continue to defeat the virus. In a real patient, their immune system would not be passive as in the experiment and would try to recognise mutated variants as they arose. This means that such a mutated strain might not get spread to anyone else. However, in the real world we are seeing uncontrolled increase in the numbers of cases and each patient is a separate incubator which might produce a mutated variant, so as more people get infected the attempts to mutate run ever more in parallel, cutting down the time to the virus getting lucky.

I said inevitable because 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.
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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Mon Jan 04, 2021 1:48 pm

sTeamTraen wrote:
Sun Jan 03, 2021 9:30 pm
shpalman wrote:
Sun Jan 03, 2021 9:03 pm
This isn't about the age of hospitalized covid patients being on average younger adults than before, this is about whether there are lots of children there which weren't there in the first wave.
Yeah, I think we need more data than a tweet to say whether the number of children per real case is higher this time. I trust NHS staff about a thousand more times than the "skeptics", but they are not always going to be completely objective about the situation (quite understandably, of course).
Somebody made this graph

Image

https://twitter.com/ChristoPhraser/stat ... 1529487364

Of course it also depends on how many were tested, which would be related to how many showed symptoms (or had contact with someone who did, but the UK isn't currently interested in testing people just for having been in contact).
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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Mon Jan 04, 2021 4:30 pm

SAGE paper: TFC: Children and transmission - update paper, 17 December 2020
https://www.gov.uk/government/publicati ... ember-2020

May be of interest, I haven't had time to read it.

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Mon Jan 04, 2021 6:17 pm


South African coronavirus mutation may beat jabs

The South African variant is more likely to evade the vaccine than the new Kent variant, according to a key member of the Oxford vaccine team.

[...]

Sir John Bell, regius professor of medicine at Oxford, said that of the two, “I would worry a lot about the South African strain”.

[...]

“The mutations associated with the South African form are really pretty substantial changes in the structure of the protein,” he said.

Crucially, they are on the part of the virus that binds to human cells. “If you get an immune response that protects you, one of the ways it protects you is it gets in the way of that binding event. You rely on antibodies to bind to that domain to stop the virus entering your cells.”

If the virus changes, that mechanism may no longer work. “If you mess around with that you’re in trouble,” he said. “The real question is are the vaccines sufficient to neutralise the virus. Or, in the presence of the mutations, will they be disabled?”

Scientists have yet to determine the answer to that question.

My gut feeling is the vaccine will be still effective against the Kent strain,” Sir John said. “I don’t know about the South African strain — there’s a big question mark about that.”

If the virus does change, then it should be possible to tweak the vaccines without going through full regulatory approval. Sir John estimated that that would take a month to six weeks.

He added that this was to be expected and that manufacturers had anticipated it. “Everyone should stay calm. It’s going to be fine. We’re now in a game of cat and mouse. These are not the only two variants we will see. We are going to see lots of variants.”
https://www.thetimes.co.uk/article/sout ... -lrjtnhrgt

A month to six weeks to tweak the vaccine. But how long to revaccinate everyone again?

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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Mon Jan 04, 2021 7:20 pm

Woodchopper wrote:
Mon Jan 04, 2021 4:30 pm
SAGE paper: TFC: Children and transmission - update paper, 17 December 2020
https://www.gov.uk/government/publicati ... ember-2020

May be of interest, I haven't had time to read it.
I haven't read it either, but this post from Scientists for EU says
According to their own published works, the government has known since 17 December that school aged children are two to seven times more likely to catch and pass on Covid-19 than adults.
... while citing this tweet from Eric Feigl-Ding in which he helpfully circles all the words.
fucking-state-of-this.jpg
fucking-state-of-this.jpg (113.42 KiB) Viewed 196 times
  • Kids more likely to bring the virus into household than aged 17+
  • Young people 2-16 more likely to be first case in household—age 12-16 are 7x more likely.
  • 2-16 year olds more >2x as likely to pass on virus.
Last edited by shpalman on Mon Jan 04, 2021 7:26 pm, edited 1 time in total.
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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Mon Jan 04, 2021 7:24 pm

thats-better-fucks-sake.jpg
thats-better-fucks-sake.jpg (150.11 KiB) Viewed 193 times
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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Mon Jan 04, 2021 7:29 pm

This figure for example shows the effect of children under the age of 12 on a perfectly good graph when they get hold of the felt tips.
Eq10g1cW4A8bIIb.jpg
Eq10g1cW4A8bIIb.jpg (46.73 KiB) Viewed 187 times
WHY DOES HE DO THIS WHY
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Re: New Variant Covid-19 VUI 202012/01

Post by jimbob » Mon Jan 04, 2021 7:54 pm

lpm wrote:
Sat Jan 02, 2021 11:05 am
4-6 weeks lockdown is nothing like enough to get close to zero, even for the original version. You perhaps don't appreciate how high our cases are.

For the English variant maybe 4 months is needed to get back to test & traceable levels - something like 10% reduction per week.
Yes, we got down to the Australian peak around July, when we actually were lower than Australia for a short time - so instead of using this to really suppress the virus, decided to let it go.

I know that Ivor Cummins likes claiming the virus has "burnt itself out" and to be fair to him has predicted 5 of the last 0 times it has been eliminated from the UK, but to use his analogy, it's like getting the wildfire to a few flames, then packing up and stacking cardboard boxes nearby.
Have you considered stupidity as an explanation

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Re: New Variant Covid-19 VUI 202012/01

Post by Sciolus » Mon Jan 04, 2021 8:11 pm

Woodchopper wrote:
Mon Jan 04, 2021 6:17 pm
He added that this was to be expected and that manufacturers had anticipated it. “Everyone should stay calm. It’s going to be fine. We’re now in a game of cat and mouse. These are not the only two variants we will see. We are going to see lots of variants.”
https://www.thetimes.co.uk/article/sout ... -lrjtnhrgt

A month to six weeks to tweak the vaccine. But how long to revaccinate everyone again?
Is it possible for a new vaccine to protect against both/all variants of the virus? Presumably not intrinsically, if they are targetted at proteins that are different between variants, so it would have to be a mixture of two or more vaccines in a single dose? Any reason why that wouldn't work?

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Re: New Variant Covid-19 VUI 202012/01

Post by sTeamTraen » Mon Jan 04, 2021 8:18 pm

shpalman wrote:
Mon Jan 04, 2021 1:48 pm
Somebody made this graph
That would be a lot more helpful with other age groups on it...
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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Mon Jan 04, 2021 8:23 pm

sTeamTraen wrote:
Mon Jan 04, 2021 8:18 pm
shpalman wrote:
Mon Jan 04, 2021 1:48 pm
Somebody made this graph
That would be a lot more helpful with other age groups on it...
The data from the heatmap at https://coronavirus.data.gov.uk/details ... me=England can be downloaded.
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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Mon Jan 04, 2021 8:35 pm

Millennie Al wrote:
Mon Jan 04, 2021 2:51 am
However, the situation is complicated. The experiment found that the necessary mutations occurred within 90 days, but that is in vitro where the test was (amongst other things) whether the plasma from one specific patient (selected as it was the best) could continue to defeat the virus. In a real patient, their immune system would not be passive as in the experiment and would try to recognise mutated variants as they arose. This means that such a mutated strain might not get spread to anyone else.
This is one hypothesis for how this new variant arose, which I suppose is why we're talking about it in this thread.
However, in the real world we are seeing uncontrolled increase in the numbers of cases and each patient is a separate incubator which might produce a mutated variant, so as more people get infected the attempts to mutate run ever more in parallel, cutting down the time to the virus getting lucky.
The case in which a patient remains chronically ill for such a long period of time and then manages to infect someone else should hopefully remain very rare.

This is not how most people get infected.

But yes a situation with lots of cases and various incomplete containment measures is a great environment in which any more transmissible variant which happens to arise can suddenly gain an advantage.
I said inevitable because 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.
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Re: New Variant Covid-19 VUI 202012/01

Post by jdc » Mon Jan 04, 2021 8:44 pm

Sciolus wrote:
Mon Jan 04, 2021 8:11 pm
Woodchopper wrote:
Mon Jan 04, 2021 6:17 pm
He added that this was to be expected and that manufacturers had anticipated it. “Everyone should stay calm. It’s going to be fine. We’re now in a game of cat and mouse. These are not the only two variants we will see. We are going to see lots of variants.”
https://www.thetimes.co.uk/article/sout ... -lrjtnhrgt

A month to six weeks to tweak the vaccine. But how long to revaccinate everyone again?
Is it possible for a new vaccine to protect against both/all variants of the virus? Presumably not intrinsically, if they are targetted at proteins that are different between variants, so it would have to be a mixture of two or more vaccines in a single dose? Any reason why that wouldn't work?
Can't think of any offhand. I'd have assumed that if we can have a quadrivalent flu vaccine with two As and two Bs, and an MMR vaccine with three different vaccines in one shot, it should be feasible to vaccinate people with a vial of x2 covid vaccines targeting different strains.

I remember Boots saying I could get a pneumonia vaccine at the same time as my flu jab and the CDC says this of flu vaccines: "may be administered concurrently or sequentially with other inactivated or live vaccines. Injectable vaccines given simultaneously should be administered at separate anatomic sites." For the live flu vaccine, they say "may be administered simultaneously with other inactivated or live vaccines. If not given simultaneously, then ≥4 weeks should pass between administration of LAIV4 and another live vaccine".

So you have to be a wee bit careful with timing if it's live virus vaccines you're talking about but with the killed kind it's pretty much anything goes.

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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Mon Jan 04, 2021 9:01 pm

Since the Oxford vaccine doesn't even work properly if you give a full dose of one variant you'd probably not want to get two doses of two different variants at once. You'd need to use a different viral vector for each variant of the SARS-CoV-2 you wanted to target (and maybe in future different vectors for the first and second doses like what the Sputnik V has got).
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Re: New Variant Covid-19 VUI 202012/01

Post by jdc » Mon Jan 04, 2021 9:11 pm

shpalman wrote:
Mon Jan 04, 2021 9:01 pm
Since the Oxford vaccine doesn't even work properly if you give a full dose of one variant you'd probably not want to get two doses of two different variants at once. You'd need to use a different viral vector for each variant of the SARS-CoV-2 you wanted to target (and maybe in future different vectors for the first and second doses like what the Sputnik V has got).
sh.t, good point. Oxford will be an a..eh.le to work with if we're on to multivalent vaccines.

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Re: New Variant Covid-19 VUI 202012/01

Post by Little waster » 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? :?
People who use Godwin's Law are worse than Hitler.

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

Post by sTeamTraen » Mon Jan 04, 2021 11:44 pm

Little waster wrote:
Mon Jan 04, 2021 11:37 pm
Do you think we might be missing something? :?
There are some creationists who acknowledge that evolution takes place, as part of God's creation. They kind of have to because you can see it happening almost in real time in a lab. But for the, it just wasn't evolution that created yoomans.
Something something hammer something something nail

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