SARS CoV-2 coronavirus / Covid-19 (No tin foil hat silliness please)

Penna

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Totally agreed. Just get vaccinated you idiotic selfish pricks.

And to the idiots in charge help vaccinate the entire world out of self interest if nothing else.
There was a vaccine drive in one of the Georgia (USA) counties today, loads of people turned up because they were giving out $100 gift cards with every vaccination. Why didn't they get vaccinated before? Presumably because many of them just couldn't be bothered, as it's free and very easy to get in the USA. But they'll do it for $100.
 

Wibble

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There was a vaccine drive in one of the Georgia (USA) counties today, loads of people turned up because they were giving out $100 gift cards with every vaccination. Why didn't they get vaccinated before? Presumably because many of them just couldn't be bothered, as it's free and very easy to get in the USA. But they'll do it for $100.
Mind numbingly dumb. Doubly so when people with very genuine reasons to be wary of getting vaccinated, like yourself, have taken the time and effort to seem medical advice and then decide to take the risk for yourself and the greater good.
 

Pogue Mahone

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After another 24 hours obsessively thinking about this fecking thing something is bothering me.

Even before omicron (and feck know how transmissible it will turn out to be) SARS-CoV-2 has quickly evolved to become much more infectious than flu. How come flu (and other resp viruses) haven’t mutated to become more and more infectious over the decades (millennia?) we’ve shared the planet with them? They all mutate too. Why has this virus become turbo-charged in less than two years while none of the rest of them have done the same over centuries? Does this virus have some unique innate qualities that allows it “upgrade” way more than other endemic viruses?

Transmissibility aside. What’s to stop other viruses mutating to become much more deadly? A future where this thing is endemic and could mutate to become much more lethal at any moment is pretty fecking grim. How come we aren’t staring down that same gun barrel with other common respiratory viruses?

@jojojo
@Anustart89
@africanspur
@mav_9me

@ any other scientists/medics that my shitty memory can’t recall right now…
 
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Wibble

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After another 24 hours obsessively thinking about this fecking thing something is bothering me.

Even before omicron (and feck know how transmissible it will turn out to be) SARS-CoV-2 has quickly evolved to become much more infectious than flu. How come flu (and other resp viruses) haven’t mutated to become more and more infectious over the decades (millennia?) we’ve shared the planet with them? They all mutate too. Why has this virus become turbo-charged in less than two years while none of the rest of them have done the same over centuries? Does this virus have some unique innate qualities that allows it “upgrade” way more than other endemic viruses?

Transmissibility aside. What’s to stop other viruses mutating to become much more deadly? A future where this thing is endemic and could mutate to become much more lethal at any moment is pretty fecking grim. How come we aren’t staring down that same gun barrel with other common respiratory viruses?

@jojojo
@Anustart89
@africanspur

@ any other scientists/medics that my shitty memory can’t recall right now…
I'd be guessing that it is because viruses like flu tends to change through antigen drift, with antigen shift (recombination) being quite rare and selection pressure acts on what it has to work with. Probably why we have flu with a quite low R and measles with a very high one - largely down to how a particular virus is configured (e.g. viral particle size and things like differing incubation period) and random chance regarding how it evolves and interacts with the host (as R isn't the only factor involved) particularly when they are novel. Once they exist in a population that has been widely exposed to it then they will tend to change by antigen drift which means infectiousness doesn't tend to change very much/quickly - so flu stays around an Ro of 1.2 and Measles an Ro of 12+. Antigen shift can still occur and cause pandemics but so far flu pandemics haven't been novel enough (in the modern era) to create anywhere near the shit show we currently have. With covid being created by antigen shift and essentially entirely novel we are still in that initial phase where antigen drift changes are much bigger due to the sheer number of infections (and thus opportunities to mutate) and possibly due to immune compromised people being mutation incubators (jury is still out). I hope that eventually, when almost everyone is vaccinated or has been infected we will settle down to a more stable situation where antigen shifts are less dramatic. How this progresses will detriment if we need annual or less frequent boosters to adapt for viral changes and/or boost the speed of response to infection.

So there is no reason that an existing virus couldn't become more, even far more infectious except as long as a virus isn't fatal before it is transmitted as increased (or decreased) fatality/severity isn't that much of a selection pressure to cause change by antigen drift I'd say. So once is a stable state in the population dramatic changes are less common. And as we have seen antigen shift can happen.

@Tony Babangida might well know if I'm barking up the wrong tree.
 
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jojojo

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After another 24 hours obsessively thinking about this fecking thing something is bothering me.

Even before omicron (and feck know how transmissible it will turn out to be) SARS-CoV-2 has quickly evolved to become much more infectious than flu. How come flu (and other resp viruses) haven’t mutated to become more and more infectious over the decades (millennia?) we’ve shared the planet with them? They all mutate too. Why has this virus become turbo-charged in less than two years while none of the rest of them have done the same over centuries? Does this virus have some unique innate qualities that allows it “upgrade” way more than other endemic viruses?

Transmissibility aside. What’s to stop other viruses mutating to become much more deadly? A future where this thing is endemic and could mutate to become much more lethal at any moment is pretty fecking grim. How come we aren’t staring down that same gun barrel with other common respiratory viruses?

@jojojo
@Anustart89
@africanspur

@ any other scientists/medics that my shitty memory can’t recall right now…
Not a virus scientist or a medic but I have some ideas that I wouldn't rate high enough to call theories. :smirk:

Pandemic viruses have more (naive to the virus) people to infect than ever before and better transport links to move them around.

I suspect being a coronavirus is a great start when it comes to being able to mutate to new levels of infectious. We live with lots of them and mostly ignore them - we don't even notice when they become more infectious. This one is trouble because it's not staying in the nose and throat like a nice sensible cold.

I do wonder if SARS2 is also an odd beneficiary of improved healthcare. The frail elderly and the immune compromised (whether they have that status as a result of disease, another virus or because of medication) are living longer and living more normal lives than ever before, previously healthy people with severe covid sometimes recover very slowly - sometimes only after multiple rounds of treatment. In other words most people now survive infection, even protracted and severe infection - but some are maybe remaining infected for longer, with the virus at a low level but still alive and mutating, until it hits another viral load high and infects more people.
 

Tony Babangida

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I'd be guessing that it is because viruses like flu tends to change through antigen drift, with antigen shift (recombination) being quite rare and selection pressure acts on what it has to work with. Probably why we have flu with a quite low R and measles with a very high one - largely down to how a particular virus is configured (e.g. viral particle size and things like differing incubation period) and random chance regarding how it evolves and interacts with the host (as R isn't the only factor involved) particularly when they are novel. Once they exist in a population that has been widely exposed to it then they will tend to change by antigen drift which means infectiousness doesn't tend to change very much/quickly - so flu stays around an Ro of 1.2 and Measles an Ro of 12+. Antigen shift can still occur and cause pandemics but so far flu pandemics haven't been novel enough (in the modern era) to create anywhere near the shit show we currently have. With covid being created by antigen shift and essentially entirely novel we are still in that initial phase where antigen drift changes are much bigger due to the sheer number of infections (and thus opportunities to mutate) and possibly due to immune compromised people being mutation incubators (jury is still out). I hope that eventually, when almost everyone is vaccinated or has been infected we will settle down to a more stable situation where antigen shifts are less dramatic. How this progresses will detriment if we need annual or less frequent boosters to adapt for viral changes and/or boost the speed of response to infection.

So there is no reason that an existing virus couldn't become more, even far more infectious except as long as a virus isn't fatal before it is transmitted as increased (or decreased) fatality/severity isn't that much of a selection pressure to cause change by antigen drift I'd say. So once is a stable state in the population dramatic changes are less common. And as we have seen antigen shift can happen.

@Tony Babangida might well know if I'm barking up the wrong tree.
Yeah sounds about right. I asked a flu expert that I know and this is what they said:
So, flu crossed the host-species barrier >100 years ago.

Following a cross species transmission event, we expect a high rate of evolution for some time as the virus becomes more "optimised".. ie, selection for variants that have better binding affinity, or increased transmission.... once "optimised", selection is slower as there are fewer opportunities for significant fitness advantages

so... for COVID... we would, in a few years, expect selection opportunities to be more limited (ie vaccine escape mutants)... the same as we have for flu now.

An intersting example for flu is H7N9.... in early 2013 we saw rapid evolution of this virus as it became more optimised to infecting humans... and then limited change for the following 7 years. Thankfully this one has "disappeared" due to mass vaccination of poultry.

I think that this is the paper that describes the original selection process : https://www.eurosurveillance.org/content/10.2807/1560-7917.ES2014.19.25.20836?crawler=true

Oh, also! I forgot. The evolutionary distance of "delta" to "omicron" is about what we see in H3 influenza every ~2 years... hence a vaccine update. Its just that most people don't care that this year it was 3c2a flu vs A1b. You can see all the "variants" of H3N2 influenza here : https://nextstrain.org/flu/seasonal/h3n2/ha/2y This explains why sometimes we have a really BAD flu year (ie 2017) - new variant, one that was not in the vaccine
 

rcoobc

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In the classic example of infection to cowpox offering some protection to smallpox, how far away are those two?

Are we talking Delta to Omicron or common cold vs Covid?
 

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If every unvaccinated adult died tomorrow...what would the short, medium and long term consequences be?

I started reasoning that most far-right and pious zealots would die, along with about 91 of every 100 people with a low income. Africa would be almost completely unpopulated. Then I realized there would be millions of decomposing corpses all over the place, and an unavoidable collapse of law and order would follow suit. Sheer panic would take over and most of the vaccinated people would also die as civilization quickly imploded. This has not been a nice train of thought.
 

Tony Babangida

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In the classic example of infection to cowpox offering some protection to smallpox, how far away are those two?

Are we talking Delta to Omicron or common cold vs Covid?
They are different species in the same genus, so yeah like common cold vs covid.
 

golden_blunder

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If every unvaccinated adult died tomorrow...what would the short, medium and long term consequences be?

I started reasoning that most far-right and pious zealots would die, along with about 91 of every 100 people with a low income. Africa would be almost completely unpopulated. Then I realized there would be millions of decomposing corpses all over the place, and an unavoidable collapse of law and order would follow suit. Sheer panic would take over and most of the vaccinated people would also die as civilization quickly imploded. This has not been a nice train of thought.
The walking dead
 

11101

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After another 24 hours obsessively thinking about this fecking thing something is bothering me.

Even before omicron (and feck know how transmissible it will turn out to be) SARS-CoV-2 has quickly evolved to become much more infectious than flu. How come flu (and other resp viruses) haven’t mutated to become more and more infectious over the decades (millennia?) we’ve shared the planet with them? They all mutate too. Why has this virus become turbo-charged in less than two years while none of the rest of them have done the same over centuries? Does this virus have some unique innate qualities that allows it “upgrade” way more than other endemic viruses?

Transmissibility aside. What’s to stop other viruses mutating to become much more deadly? A future where this thing is endemic and could mutate to become much more lethal at any moment is pretty fecking grim. How come we aren’t staring down that same gun barrel with other common respiratory viruses?

@jojojo
@Anustart89
@africanspur
@mav_9me

@ any other scientists/medics that my shitty memory can’t recall right now…
How do you know it didn't? Influenza is at least 2,000 years old, who knows what mutations it's undertaken in that time. What mutations did it go through in 1918 when it spread across the globe in weeks and killed far more than Covid? The biggest difference with Covid is we have the ability to track it step by step.

People have just slowly built up immunity to other respiratory viruses over time. I'd be willing to bet money that when the common cold first appeared thousands of years ago it too was a killer.
 

Sparky Rhiwabon

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The Welsh government are already talking about potentially extending the Covid passes to all hospitality (not just those that play loud music after midnight as at present). Wales has consistently been more cautious than England so I expect this to happen.
 
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After another 24 hours obsessively thinking about this fecking thing something is bothering me.

Even before omicron (and feck know how transmissible it will turn out to be) SARS-CoV-2 has quickly evolved to become much more infectious than flu. How come flu (and other resp viruses) haven’t mutated to become more and more infectious over the decades (millennia?) we’ve shared the planet with them? They all mutate too. Why has this virus become turbo-charged in less than two years while none of the rest of them have done the same over centuries? Does this virus have some unique innate qualities that allows it “upgrade” way more than other endemic viruses?

Transmissibility aside. What’s to stop other viruses mutating to become much more deadly? A future where this thing is endemic and could mutate to become much more lethal at any moment is pretty fecking grim. How come we aren’t staring down that same gun barrel with other common respiratory viruses?

@jojojo
@Anustart89
@africanspur
@mav_9me

@ any other scientists/medics that my shitty memory can’t recall right now…
None scientist weirdo wonders if we’ve ever tried making it so difficult for the flu, RS and other viruses to transmit before?
We are fighting nature here after all, and this virus wants to survive and replicate.
What was it Jeff Goldblum said again?
 

Pogue Mahone

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None scientist weirdo wonders if we’ve ever tried making it so difficult for the flu, RS and other viruses to transmit before?
We are fighting nature here after all, and this virus wants to survive and replicate.
What was it Jeff Goldblum said again?
Yes is the answer to that question. We’ve been vaccinating against flu for a very long time.
 

Pogue Mahone

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How do you know it didn't? Influenza is at least 2,000 years old, who knows what mutations it's undertaken in that time. What mutations did it go through in 1918 when it spread across the globe in weeks and killed far more than Covid? The biggest difference with Covid is we have the ability to track it step by step.

People have just slowly built up immunity to other respiratory viruses over time. I'd be willing to bet money that when the common cold first appeared thousands of years ago it too was a killer.
We track flu mutations too. I’m just curious about what it takes to end up relatively stable. The answer from @Tony Babangida was great. It will get “optimised” over a period of several years and from then on the changes will be fairly minor. It’s just a little unsettling wondering what the fully optimised version will look like a few years down the road, considering how much nastier it’s got in just 24 months existence.
 

11101

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We track flu mutations too. I’m just curious about what it takes to end up relatively stable. The answer from @Tony Babangida was great. It will get “optimised” over a period of several years and from then on the changes will be fairly minor. It’s just a little unsettling wondering what the fully optimised version will look like a few years down the road, considering how much nastier it’s got in just 24 months existence.
We didn't track flu mutations in 1918 and we definitely didn't track them 2000 years ago. We have no idea what flu back then looked like or how it evolved. We still have a few bits of lung tissue from 1918 to look back at but that's about it.

Point is this is a virus that has been with us for 2 years. The impact and the mutations will be greater now than they ever will be. From here it could either get more transmissible, or more deadly, but if any variant appears that does both it wont last too long.
 

Pogue Mahone

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We didn't track flu mutations in 1918 and we definitely didn't track them 2000 years ago. We have no idea what flu back then looked like or how it evolved. We still have a few bits of lung tissue from 1918 to look back at but that's about it.

Point is this is a virus that has been with us for 2 years. The impact and the mutations will be greater now than they ever will be. From here it could either get more transmissible, or more deadly, but if any variant appears that does both it wont last too long.
The last sentence is wrong. It could get a hell of a lot more deadly without any negative impact on fitness (i.e. ability to reproduce/transmit) We even have an example of this already in delta, that was both more transmissible and (slightly) more virulent.
 

Pogue Mahone

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Have you got any for non sciencey really stupid folk? Asking for a friend.
The tl;dr non sciencey bit is that it’s got a load of mutations that, individually, could make the virus less viable but when combined together have the opposite effect and might radically change how it interacts with the antibodies that are supposed to give us protection. Which is shit luck but there you go.
 
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Yes is the answer to that question. We’ve been vaccinating against flu for a very long time.
But surely we haven’t vaccinated at these levels?
We’ve given 7 bn vaccine shots Worldwide in the past 12 or so months.
Pre Covid the only people I knew who took flu jabs were the +70s? Nor have we done lockdown, closed borders etc.
I mean, surely we’ve made it much harder for Covid to spread right?
 

711

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After another 24 hours obsessively thinking about this fecking thing something is bothering me.

Even before omicron (and feck know how transmissible it will turn out to be) SARS-CoV-2 has quickly evolved to become much more infectious than flu. How come flu (and other resp viruses) haven’t mutated to become more and more infectious over the decades (millennia?) we’ve shared the planet with them? They all mutate too. Why has this virus become turbo-charged in less than two years while none of the rest of them have done the same over centuries? Does this virus have some unique innate qualities that allows it “upgrade” way more than other endemic viruses?

Transmissibility aside. What’s to stop other viruses mutating to become much more deadly? A future where this thing is endemic and could mutate to become much more lethal at any moment is pretty fecking grim. How come we aren’t staring down that same gun barrel with other common respiratory viruses?

@jojojo
@Anustart89
@africanspur
@mav_9me

@ any other scientists/medics that my shitty memory can’t recall right now…
Population density might come into it. Go back a couple of centuries and there just wasn't the the sheer number of humans all densely packed into the same places as there is now. Can we look forward to more infectious disease and more mutation as time goes on, I don't know?

I once read all human infectious disease originated in animals, simply because there were never enough humans on the planet for their own to evolve. I might have misunderstood or it might be bollocks of course.
 

Pogue Mahone

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But surely we haven’t vaccinated at these levels?
We’ve given 7 bn vaccine shots Worldwide in the past 12 or so months.
Pre Covid the only people I knew who took flu jabs were the +70s? Nor have we done lockdown, closed borders etc.
I mean, surely we’ve made it much harder for Covid to spread right?
Lockdowns and closed borders will have zero effect on virus evolution (other than if they slow down spread, which slows down evolution). The extensive vaccination program might but doubtful it would put more pressure on the virus to evolve than our own immune responses.

The one area where modern medicine might be accelerating virus evolution is when we keep immune suppressed covid patients alive for a long time, giving them monoclonal antibody treatments. There are plausible theories about this being the background for delta and omicron. Although there are equally plausible theories about it happening when the virus bounces in and out of animal hosts. So feck knows really.

All I can say for certain is that your obsession with blaming lockdowns for everything bad about the pandemic is wide of the mark here.

It’s also worth noting that (potentially) immune evading new variants like omicron show the foolishness of strategies based on “letting it rip” on the assumption that immunity after infection is permanent (or even very long term) South Africa got through their delta wave without much (any?) lockdowns because they had a very young population so could afford to let the virus spread without mitigation and not experience too many excess deaths. And now look at them….

At this stage the pattern where all of these new variants emerged in countries that either couldn’t or wouldn’t keep community transmission below extremely high levels is fairly fecking obvious.
 
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All I can say for certain is that your obsession with blaming lockdowns for everything bad about the pandemic is wide of the mark here. It’s also worth noting that (potentially) immune evading new variants like this show the foolishness of “letting it rip” on the basis that immunity after infection is permanent (or even very long term)
I’ve never once declared we should “let it rip” and the bolded is severely misrepresenting me.

And your final paragraph does give some excellent food for thought in fairness.
 
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Zehner

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We track flu mutations too. I’m just curious about what it takes to end up relatively stable. The answer from @Tony Babangida was great. It will get “optimised” over a period of several years and from then on the changes will be fairly minor. It’s just a little unsettling wondering what the fully optimised version will look like a few years down the road, considering how much nastier it’s got in just 24 months existence.
Maybe it has to do with the overall population, too? We're approaching 8 billion human beings on the planet right now. Influenza probably never had that many hosts and I could imagine that each host increases the speed at which the virus mutates. I mean, I'm by no means an expert, far from it, but I recently read an article that claimed that the industrial nations actually harmed themselves by hoarding vaccine doses and not giving them to poorer countries because the virus can freely transmit over there and thus quickly develop new variants/mutations. Which is more or less what we're witnessing with Omicron right now.

Also, even if the vaccines don't protect to the same extent against Omicron as they do against Delta, you're still more resistant to it and far less likely to end up hospitalized which is essentially what it's all about: On the route from the pandemic to an endemic, keep the graph flat and try to not overstrain the capacities of our health care infrastructure.
 

Pogue Mahone

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I’ve never once declared we should “let it rip” and the bolded is severely misrepresenting me.

And your final paragraph does give some excellent food for thought in fairness.
Ok. Apologies. I know how annoying it is to be misrepresented.

I wasn’t really aiming at you personally so much as the various (legitimate) experts who advocated strategies around letting the virus spread freely among the less vulnerable.

With hindsight, the best approach would have been to do everything possible to keep community spread as low as possible, for as long as possible. Then hope that vaccines can stamp transmission down even further. Which might have avoided these most recent variants. Vaccines vs original covid (or even alpha) would crush the hell out of it. Obviously a fecking nightmare (probably impossible?) to keep transmission low all over the world for as long as we needed. But arguably less of a long term nightmare than what we’re facing now.
 
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Maybe it has to do with the overall population, too? We're approaching 8 billion human beings on the planet right now. Influenza probably never had that many hosts and I could imagine that each host increases the speed at which the virus mutates. I mean, I'm by no means an expert, far from it, but I recently read an article that claimed that the industrial nations actually harmed themselves by hoarding vaccine doses and not giving them to poorer countries because the virus can freely transmit over there and thus quickly develop new variants/mutations. Which is more or less what we're witnessing with Omicron right now.

Also, even if the vaccines don't protect to the same extent against Omicron as they do against Delta, you're still more resistant to it and far less likely to end up hospitalized which is essentially what it's all about: On the route from the pandemic to an endemic, keep the graph flat and try to not overstrain the capacities of our health care infrastructure.
The WHO warned against the hoarding of vaccines from the off with this as one of the main reasons right?

Your final paragraph here represents my thoughts much better than Pogue’s claim.
 
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With hindsight, the best approach would have been to do everything possible to keep community spread as low as possible, for as long as possible. Then hope that vaccines can stamp transmission down even further. Obviously a fecking nightmare to implement all over the world. But arguably less of a long term nightmare than what we’re facing now.
I get that, but my argument has always been about an inevitability factor. I think we all could have done everything “right” and still end up here in a year, or two or three. Because we’ll never be able to do everything “right” for long enough.
I certainly can’t say it with any certainty obviously and you’d hope there’s a possibility we could have been in a better position, especially for future pandemics.
 

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From here it could either get more transmissible, or more deadly, but if any variant appears that does both it wont last too long.
I'm afraid that isn't true. It could become more transmissible and more deadly as long as the incubation period remains so long.

It could also become less deadly.
 

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I get that, but my argument has always been about an inevitability factor. I think we all could have done everything “right” and still end up here in a year, or two or three. Because we’ll never be able to do everything “right” for long enough.
I certainly can’t say it with any certainty obviously and you’d hope there’s a possibility we could have been in a better position, especially for future pandemics.
surely the vaccines make this argument a non-starter?
 

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It's possible that evolution has played a part in previous pandemics which we are disrupting now.

In 1918 an estimated 50,000,000 died and you can make assumptions that proportionally they were the most vulnerable and had the least effective immune systems to fight that strain of influenza. The remaining population who had been infected (which was estimated at two thirds of the population) had immune systems which fought off the virus and that would have been passed genetically through families which may have an impact on the virus becoming less virulent through generations.

It's interesting that this will be the first pandemic that we've fought off with vaccines and it could even lead to it going on longer (but with lower mortality)?
 

Pogue Mahone

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Also, even if the vaccines don't protect to the same extent against Omicron as they do against Delta, you're still more resistant to it and far less likely to end up hospitalized which is essentially what it's all about: On the route from the pandemic to an endemic, keep the graph flat and try to not overstrain the capacities of our health care infrastructure.
That is by no means certain. But fingers crossed. We’ll know more in a few weeks.

What makes the next few weeks/months likely to be shitty is that even if vaccines gives us the exact same protection against omicron as they do against delta (which is highly unlikely but hope springs eternal!) and the only difference is increased transmissibility then we’re still in for a world of hurt, considering how many problems the delta wave is already causing.

Omicron specific vaccine boosters could be the game changer here. They might get vaccine efficacy right back up to original covid levels. And then we have to hope we don’t get another variant with such radical changes to its structure. And that is possible. The fecking thing can’t keep changing shape this much and still fulfil its primary function.