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Watsisname
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Coronavirus (COVID-19) Thread

17 Oct 2021 02:19

A-L-E-X wrote:
Source of the post Wat, what happened to those variations that were supposed to be worse than Delta? One was Lambda I think and the other was Mu?

Outside of inflated media headlines, I don't think there was ever any serious prediction that they would be worse. They were never considered variants of concern, just of interest or monitoring.

There was limited evidence that they might be able to evade prior immunity or vaccines a little bit more than other variants. However, delta had the huge advantage in transmissibility, so delta quickly made up the vast majority of new cases. Now we have a large fraction of the population that is either vaccinated or recovered, so any variants have to either be extremely transmissible, extremely immune evading, or both, in order to continue to spread. Delta clearly has the former going for it, but the others don't evade immunity enough to be able to compete with it.

This is kind of a catch-22 with predicting the behavior of variants: we identify them when they show up often enough in sequenced cases, but then we can't really know their properties well until they demonstrate them by how they spread and compete with the others. It was because of how quickly delta outcompeted the other variants that we could tell it was so much more transmissible (though there were other hints from contact tracing). We couldn't just know that it would do that when it was first detected.
 
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Coronavirus (COVID-19) Thread

17 Oct 2021 10:41

Watsisname wrote:
A-L-E-X wrote:
Source of the post Wat, what happened to those variations that were supposed to be worse than Delta? One was Lambda I think and the other was Mu?

Outside of inflated media headlines, I don't think there was ever any serious prediction that they would be worse. They were never considered variants of concern, just of interest or monitoring.

There was limited evidence that they might be able to evade prior immunity or vaccines a little bit more than other variants. However, delta had the huge advantage in transmissibility, so delta quickly made up the vast majority of new cases. Now we have a large fraction of the population that is either vaccinated or recovered, so any variants have to either be extremely transmissible, extremely immune evading, or both, in order to continue to spread. Delta clearly has the former going for it, but the others don't evade immunity enough to be able to compete with it.

This is kind of a catch-22 with predicting the behavior of variants: we identify them when they show up often enough in sequenced cases, but then we can't really know their properties well until they demonstrate them by how they spread and compete with the others. It was because of how quickly delta outcompeted the other variants that we could tell it was so much more transmissible (though there were other hints from contact tracing). We couldn't just know that it would do that when it was first detected.

Yes thats what I heard too, they were saying that the vaccines can't handle Lambda and Mu was a new one that showed up in NYC but has lessened now.

Is it possible that the predominance of Delta is a good thing? It has such a high bar that it will be hard for a new variant to overcome it and be worse?
 
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Coronavirus (COVID-19) Thread

17 Oct 2021 14:11

A-L-E-X wrote:
Source of the post Is it possible that the predominance of Delta is a good thing? It has such a high bar that it will be hard for a new variant to overcome it and be worse?

Yes and no. The good news is the competitive advantage of delta did mean that all the other variants that were around at the time died out. Among them, any variants that were better than delta at evading prior immunity, but not transmissible enough. Now the virus has to "relearn" immune evasion.

The bad news is that this isn't that unlikely, because the selective pressure for mutations which help evade immunity is growing larger, and the virus is still circulating a lot so many mutations are still happening. Now any new variant that arises will be an offshoot of delta, because delta makes up nearly all new cases. So it is likely any that new variant that is good at evading immunity will also be very transmissible.


We're now in a difficult to predict moment of the pandemic (not that any moment was particularly easy to predict except early on that there would be continued exponential growth until lockdowns), where it's hard to know if delta will be the last severe wave and then the virus fizzles out, or if the virus continues bouncing around like seasonal colds and flu. If the latter, at least we now have vaccines and treatments to help keep it under control, rather than having to resort to lockdowns.
 
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Coronavirus (COVID-19) Thread

17 Oct 2021 21:11

Watsisname wrote:
A-L-E-X wrote:
Source of the post Is it possible that the predominance of Delta is a good thing? It has such a high bar that it will be hard for a new variant to overcome it and be worse?

Yes and no. The good news is the competitive advantage of delta did mean that all the other variants that were around at the time died out. Among them, any variants that were better than delta at evading prior immunity, but not transmissible enough. Now the virus has to "relearn" immune evasion.

The bad news is that this isn't that unlikely, because the selective pressure for mutations which help evade immunity is growing larger, and the virus is still circulating a lot so many mutations are still happening. Now any new variant that arises will be an offshoot of delta, because delta makes up nearly all new cases. So it is likely any that new variant that is good at evading immunity will also be very transmissible.


We're now in a difficult to predict moment of the pandemic (not that any moment was particularly easy to predict except early on that there would be continued exponential growth until lockdowns), where it's hard to know if delta will be the last severe wave and then the virus fizzles out, or if the virus continues bouncing around like seasonal colds and flu. If the latter, at least we now have vaccines and treatments to help keep it under control, rather than having to resort to lockdowns.

Wat, are there any good computer programs that can model how viruses evolve? It would be fascinating if this was the case and could have some predictive value.  I really hope that it's the latter, it sounds like that's what happened with the 1918 pandemic too?  That one lasted for 3 years so if this one has a similar longevity, we have one more year of this.
 
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Coronavirus (COVID-19) Thread

17 Oct 2021 23:12

There are good models for how a virus spreads (like the SIR model I used earlier, and models involving interacting particles), but for simulating variant evolution... not so much. The problem is there are so many possible mutations that can happen, and each one may change how a protein behaves, but understanding that typically requires a supercomputer simulation. (See for example the [email protected] distributed computing service to solve specific protein folding problems).
 
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Coronavirus (COVID-19) Thread

18 Oct 2021 10:09

I can imagine it would be, it reminds me of the supercomputer models used to simulate the future expansion of the universe and all the unknowns involved (how much dark matter, dark energy, etc.)  [email protected] does good work, I think SETI has a similar program which makes use of cpu idle time to do research!
 
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Coronavirus (COVID-19) Thread

18 Oct 2021 12:40

Watsisname wrote:
Source of the post The bad news is that this isn't that unlikely, because the selective pressure for mutations which help evade immunity is growing larger, and the virus is still circulating a lot so many mutations are still happening. Now any new variant that arises will be an offshoot of delta, because delta makes up nearly all new cases. So it is likely any that new variant that is good at evading immunity will also be very transmissible.

On the other hand, the diversity has been greatly reduced, which makes the virus more vulnerable.  Delta is more transmissible, but apparently no more dangerous than alpha (according to the Norwegian study):
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The pandemic has been called off in Norway.  Transmission is still widespread, but the disease is no longer considered particularly dangerous.  Will it backfire?
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Coronavirus (COVID-19) Thread

20 Oct 2021 01:41

midtskogen wrote:
Source of the post The pandemic has been called off in Norway.  Transmission is still widespread, but the disease is no longer considered particularly dangerous.  Will it backfire?

Maybe not, but continued surveillance is probably important.

The high rate of vaccination combined with the sort of "normal social distancing" in Norway helps a lot. With that the virus is unlikely to severely sicken a lot of people as quickly as it could before vaccines. We're seeing the effect across the US, too. The delta wave, by cases, hospitalizations, and by deaths, is consistently lower and slower where vaccination rates are higher. Even if a variant should suddenly appear that is so evasive as to make current vaccines mostly ineffective (which I don't think is impossible, but I think it's less likely than observing a gradation of diminishing effectiveness), I imagine there would be time to monitor it and adjust tactics as needed.
 
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Coronavirus (COVID-19) Thread

06 Nov 2021 11:54

So a new drug will be available next year that is even better than Merck's antiviral.  It's from Pfizer and is 90 pct effective in reducing hospitalizations and out of 600 sick covid patients none died when they took this drug in the first five days of showing symptoms.  A real gamechanger and lots are excited about it.
 
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Coronavirus (COVID-19) Thread

07 Nov 2021 23:29

midtskogen wrote:
Source of the post The pandemic has been called off in Norway.  Transmission is still widespread, but the disease is no longer considered particularly dangerous.  Will it backfire?

It now appears many European countries are following suit (or are otherwise failing to prevent delta from spiking with their current level of restrictions). The new case rates are growing rapidly across them, making Europe the current global hotspot. However, the vaccination rates across these countries varies quite a bit. Perhaps the most important metric (for which I don't have data offhand) is the percentage of population vaccinated at higher ages, but otherwise as examples, according to Our World in Data, Norway has about 77% of its population with at least one dose, and 69% are fully vaccinated. In Hungary those percentages are 62% and 60%, respectively. In Croatia: just 48% and 45%. 

This may have enormous implications for the severity of the wave. I basically expect a repeat of what we saw in the US. The states that had the lowest vaccination rates and lowest restrictions peaked earlier -- at the cost of higher hospital loads and more deaths per capita.
 
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Coronavirus (COVID-19) Thread

08 Nov 2021 00:29

The latest vaccination numbers are 78% and 70% in Norway.  Only a few in the 12 - 17 age group have got two doses, and a third dose as been rolled out for the elderly who got vaccinated more than 6 months ago and now appear to have much less protection.  The number of new cases is now at the highest for the entire pandemic, but since close contacts no longer have to go into a quarantine, not even if you live in the same house as one infected (partially vaccinated or unvaccinated are recommended to test themselves every few days for 10 days, though), everyday life appears normal and covid has mostly been forgotten.  The hospital admissions are also on the rise, currently about half the level during the peak in spring 2020.  Most of them are fully vaccinated.  That might be a concern.
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Coronavirus (COVID-19) Thread

08 Nov 2021 01:30

An interesting opinion on whether Sweden was doing an experiment or the rest of the world written in Swedish. Do lockdowns really work that well?  The Google translation seems pretty good (with a few exceptions, one even reversing the meaning).
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Coronavirus (COVID-19) Thread

08 Nov 2021 10:49

midtskogen wrote:
Source of the post An interesting opinion on whether Sweden was doing an experiment or the rest of the world written in Swedish. Do lockdowns really work that well?  The Google translation seems pretty good (with a few exceptions, one even reversing the meaning).

Interesting in the sense of how many wrong claims can be in an opinion piece. Measures such as closing schools and banning meetings were newly invented for coronavirus? No they weren't. Look at what cities did in the US during the Spanish Flu. Lockdowns are not effective? Look at all the times exponential growth has been traded for exponential decay. Sweden's method was the better one? Well, that would actually be an opinion and hence can't really be wrong, but it's worth remembering Sweden has 1475 deaths per million residents, vs. Norway's 168.

It's also worth remembering Sweden's original approach for herd immunity wasn't maintained for very long. They imposed heavier restrictions (though nothing like a complete lockdown) when the cases grew too high. The same is true in most countries and here in the US, with a varying and adaptive strategy depending on where you are and how high the cases are at the time. Public health measures during a pandemic are not an on-off switch. They are a set of dials.
 
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Coronavirus (COVID-19) Thread

08 Nov 2021 11:34

I think the main argument was that Sweden fared pretty well compared to countries that went for lockdowns because you can shut down a society for only so long.  You can postpone the waves, not stop them.  So we're back to flatten the curve again, rather than to kill it, and a lockdown is somewhat overkill as a flattener.  Yes, Sweden was much harder hit than Norway, but demographic differences can explain some of that and it's difficult to account for random factors.  So comparing to a larger set of countries is fair.  And the conclusion is quite correct that the disaster that the other countries to a large degree justified the lockdowns with, did not happen in Sweden.  I do not fully agree with the author, but I think it should be discussed why Sweden was no worse hit than most countries, and I don't think it's right to dismiss the arguments.  I wouldn't say that lockdowns don't work at all, but rather not so often the best tool.  You can shoot sparrows with a cannon, but less intrusive weapons can do the same, or even better. To me the lockdowns seem like a symptom of a world that has become more and more polarised.  We're getting more and more on-off switches, fewer dials.

Social distancing has surely been effective.  I haven't had a cold in two years.  I find it kind of scary, worried that when it comes, it will hit hard.
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Coronavirus (COVID-19) Thread

09 Nov 2021 07:36

On the topic of vaccine effectiveness (especially by age, by vaccine type, over time, and against delta), my university recently forwarded this study, which I thought had both a good method and good presentation of the data. Quite a lot of data: the study followed 780,000 US veterans from February to October 2021.

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