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Watsisname
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Coronavirus (COVID-19) Thread

01 May 2021 02:10

midtskogen wrote:
Source of the post My other point was, if we understand so well how these viruses spread, why do we have these large waves?  Most have been living with restrictions for more than a year, and we can hardly explain those waves by assuming that there were times when people simply ignored the restrictions and recommendations and other times when people were compliant.  The favourite answer seems to be mutations, but it seems to me as an oversimplification.

In two words, human behaviorRestrictions in most places have not been like a binary on-off switch, but a matter of varying degree, and people do behave differently over time regardless of restrictions ("pandemic fatigue"). I think this is the most important effect overall for causing regular/repeated waves. But there are also many other effects of varying level of importance and depending on the region and timeframe, which we should explore as well.

First, why repeated waves? A good way to think about it is by analogy to oscillations. An oscillation happens if when a quantity is big, there is a mechanism to reduce it, and when the quantity is small, there is a mechanism to increase it. And that's exactly what happens with human behavior during a pandemic.

When the effective reproduction number R is greater than 1, the virus spreads exponentially. This leads to a faster and faster rate of new cases, until eventually it cannot be ignored any further and society takes action. Either government steps in to limit social activities, or people become more careful of their own will. (Often both.) If the increased caution and reduced interaction manages to push R below 1, then new cases decline exponentially. Then when the rate of new cases falls low enough (especially in comparison to where it had been), then people gradually begin to relax, and more restrictions get lifted. 

But even if restrictions stay the same, people tend to become less careful, even if they are not aware of it. This has often been called "pandemic fatigue". If R had been only slightly less than 1, then it does not take much change in behavior to get it above 1 again, and this triggers a new wave of exponential growth until people are forced to react again. The cycle repeats, until either the virus is eradicated or an effective immunity is reached. (And if mutations continue to occur and force us to do repeated vaccinations, which appears increasingly likely, then this cycle might go on for a long time to come, just like with influenza.)

It is interesting to examine this effect in different regions. Let's look at Washington State in particular. Here are the rates of new cases (per day per 100k people), and the reconstructed curve for R(t) based on the cases and hospitalizations:

► Show Spoiler


There are four distinct waves (we are currently still in the fourth, and most people have only barely started noticing or reacting to it.) Each wave corresponds to R(t) becoming slightly greater than 1 (or much greater than 1 for the first one, with the behavior of pre-COVID society.) What's interesting is that the waves appear somewhat periodic. Each wave occurs approximately 4 months after the previous one. 

Seasonal effect? Virus mutation effect? Random chance? I don't think so. I think this is mostly the above effect of human/societal behavior. In Washington State, we get a wave, then we react to it, then it takes about 4 months for us to 'get tired of it' and act in a way slightly closer to normal. And it's such a small change in R that causes it, that most aren't even necessarily aware of it. Even as we keep masks on and avoid large groups (especially indoors), people are on average just becoming slightly less careful over time, and that's all it takes. The effect creeps up over time.

Seasonal effects:
I think the seasonal effect is real, in the sense that when the weather is colder, more people stay inside longer, which is where it is easier for the virus to spread through the air. This is why the pandemic appears to be stronger in each hemisphere's winter. But it cannot be the only or even most important effect, because there are waves in many regions despite the season. I think this effect just makes waves easier to occur or larger than they would be otherwise (basically like a small increase to R on top of anything else that happens.) And it really is human behavior in response to the weather, more so than the weather affecting the virus directly (because we now know infection outdoors or through surfaces is not the dominant means of transmission.)

Holidays and Religious events:
I think these play a huge role for some waves in many countries. In the US, and even in the above figures for Washington, you can see two separate peaks in the third wave. The first peak is Thanksgiving, the second peak is Christmas and New Years. Both peaks involve a huge amount of travel and family getting together, which is a great way to spread the virus. The American public was warned about this repeatedly with every major holiday of 2020, yet so many people traveled and socialized anyway. Every time, the event was followed shortly after by a surge in cases and hospitalizations and deaths. Totally sad. Totally avoidable. 

Holidays and religious gatherings also explain a number of major waves in Israel, according to a friend there. And I'm sure we can find many more examples.

Mutations:
There is now no doubt that more infectious variants have caused more severe waves. One of the most powerful demonstrations of this is to look at the fraction of sequenced cases that belong to a particular clade over time:

► Show Spoiler


The figure at top left shows the genetic diversity across sequences (angle) over time (radially), in a similar way as the tree of life graphics. The bottom colormap figure indicates the fraction of sequenced cases that correspond to each clade. Notice how after November 2020, the orange group labelled "20I/501Y.V1" rapidly grows, and now accounts for about half of all sequenced cases. That is the UK variant (also called B.1.1.7). It takes up a growing proportion of cases because it is more infectious and outcompetes the others. As more infectious variants grow to dominate, this increases the R value (if all else stays the same).

I think the severity of the current wave in India is largely due to more infectious variants combined with poor ability of their government to control it. (Rather, they did an outstanding job of controlling it throughout most of 2020, but then they relaxed, and because the early restrictions caused such economic harm it is now even harder to going back to controlling it, especially in the face of the more infectious variants.) The rate of growth is much more rapid for a given number of cases, indicating a larger effective R. Sequencing there also shows several variants that are more infectious than the original, including the UK variant. There is also a new variant with two mutations to the spike protein, the exact effects of which remain to be seen.

Another problem in India: they have fallen far behind much of the rest of the world for vaccinations per capita.
 
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Coronavirus (COVID-19) Thread

02 May 2021 05:09

Since the NYTimes deaths above normal page doesn't seem to be updating anymore (last update was February 9th), I've looked for others. The Economist has a nice one:

https://www.economist.com/graphic-detai ... hs-tracker

Of the countries listed, Russia appears to have the largest gap between deaths above normal and the official COVID-19 deaths: 373,000. 

I added up the data for all the countries in the list, and come up with about 3.39 million deaths above normal, and 2.16 million official COVID-19 deaths. That leaves about 1.23 million deaths above normal that are unaccounted for and likely due to COVID-19. (I also included the negative values for some countries for which deaths were below normal, perhaps due to the diminished seasonal flu.) 

Globally, the official COVID-19 deaths to date is about 3.2 million, so true death toll must be at least 4.4 million. If the ratio between reported figures and deaths above normal is the same globally as for the set of countries for which we have data, then that comes to more than 5 million... consistent with my suspicions a couple pages ago. The incompleteness of the data for the most recent several weeks also implies the true toll is higher.
 
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Coronavirus (COVID-19) Thread

02 May 2021 21:55

this oscillating scenario sounds very similar to rabbit population booms.  So basically when predators are around rabbits can control their birth rates.  So if there are many coyotes in the area, rabbits reproduce less, and with less rabbits available, the coyotes move on to a different area.  When they are gone the rabbits experience a population explosion, and then the coyotes come back, rinse and repeat.
 
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Coronavirus (COVID-19) Thread

03 May 2021 03:45

A-L-E-X wrote:
Source of the post this oscillating scenario sounds very similar to rabbit population booms.

Yes, similar effect. In the predator-prey example, more prey means more food for predators, so the number of predators increases. Then when there are many predators, the prey get eaten up more quickly than they can reproduce, and their numbers decline. When the number of prey gets too low to sustain the predators, the predators' numbers crash, too (or they go somewhere else, or whatever.) Then the prey's population is able to recover, and the cycle repeats.

So here there are two populations whose birth and death rates are coupled together, and mathematically a good way to model it is with a set of coupled differential equations (the Lotka-Volterra equations). That is, the rates at which each population changes depends on the sizes of both populations, which allows them to influence each other and produce a regular repeating cycle.
 
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Coronavirus (COVID-19) Thread

03 May 2021 08:52

Nature favours an R number around and close to 1.  If it stays much lower, the virus dies out.  If it stays much higher, the hosts quickly develops immunity or dies out.  In either case the virus fails, and the successful and persistent viruses manage to have an R near 1.  I agree that the simple answer to the waves is the nature of exponential changes.  One small change can completely turn the tables.  The balance is highly unstable.  India is highly overpopulated, becoming extra sensitive.  Not even the strictest lockdown gives any guarantees.

Countries with ample space not having a strong culture for socialising seem to be the least hit or dodging excessive deaths altogether.  Over here the introvert's joke goes "I look forward to the abolishment of the 6 feet rule so we can go back to the normal 20 feet rule".
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Coronavirus (COVID-19) Thread

05 May 2021 14:05

Watsisname wrote:
A-L-E-X wrote:
Source of the post this oscillating scenario sounds very similar to rabbit population booms.

Yes, similar effect. In the predator-prey example, more prey means more food for predators, so the number of predators increases. Then when there are many predators, the prey get eaten up more quickly than they can reproduce, and their numbers decline. When the number of prey gets too low to sustain the predators, the predators' numbers crash, too (or they go somewhere else, or whatever.) Then the prey's population is able to recover, and the cycle repeats.

So here there are two populations whose birth and death rates are coupled together, and mathematically a good way to model it is with a set of coupled differential equations (the Lotka-Volterra equations). That is, the rates at which each population changes depends on the sizes of both populations, which allows them to influence each other and produce a regular repeating cycle.

Thanks for the equations, Wat!  I'm always interested in mathematical predictions of populations (human populations too)....by the way did you see the data showing that the predicted "baby boom" did not occur (thank goodness)....US new births down 4% in 2020 (lowest since 1979) and December births down 8%.

Also, did you all see that now it's being predicted that "herd immunity" will not be reached because of the slow adoption of the vaccines and there's an 80% chance that this will be a regular part of our lives, just like the flu is?  We'll probably need an annual shot, just like for the flu, Pfizer has already announced this.  The only way I see around the annual shot is when and if that universal coronavirus vaccine is developed, just like we're developing a universal flu vaccine....give it 5 years or so for both. :)
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Coronavirus (COVID-19) Thread

05 May 2021 14:07

midtskogen wrote:
Nature favours an R number around and close to 1.  If it stays much lower, the virus dies out.  If it stays much higher, the hosts quickly develops immunity or dies out.  In either case the virus fails, and the successful and persistent viruses manage to have an R near 1.  I agree that the simple answer to the waves is the nature of exponential changes.  One small change can completely turn the tables.  The balance is highly unstable.  India is highly overpopulated, becoming extra sensitive.  Not even the strictest lockdown gives any guarantees.

Countries with ample space not having a strong culture for socialising seem to be the least hit or dodging excessive deaths altogether.  Over here the introvert's joke goes "I look forward to the abolishment of the 6 feet rule so we can go back to the normal 20 feet rule".

India and Brazil have both had awful responses.  India was always a ticking time bomb because of the extreme density of the population and I think the high levels of air pollution there also exacerbate the outcome.  I've heard Australia has decided not to take back its citizens who were in India at the time, so they will be stranded there for the time being.

The exponential nature and graph describes it well; with exponents if the base is 1, 1^x=1, if the base is less than 1, it exponentially decreases, and if the base is greater than 1, it exponentially increases.

Being an introvert myself (INFP-T if it matters), that introvert's joke is completely on point. :)
 
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Coronavirus (COVID-19) Thread

05 May 2021 22:23

A-L-E-X wrote:
Source of the post I've heard Australia has decided not to take back its citizens who were in India at the time, so they will be stranded there for the time being.

Which makes me wonder whether law and basic citizen rights are amongst the victims of covid-19.  Though governmental responses to a pandemic are required, there are several juridical questions.  Governments have implemented restrictions which might not have a solid foundation in their country's laws, or new laws have been passed through a fast track also not quite through regular procedure.  Now, all this has much support, but if we want a lesson in how dictatorships are born, the covid-19 response is instructive.  Western civilisations are not immune to policies that we usually associate with dictatorships, and the notion that dictatorships are results of evil people seizing power against the will of the people, is not accurate.  Dictators rise to power often with massive support.  If not in numbers, then by voice.  I do think western countries will return to apparent normality when this pandemic is over, but the thresholds for drastic measures, declaring emergencies and making exceptions have been moved.
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Coronavirus (COVID-19) Thread

06 May 2021 00:20

midtskogen wrote:
A-L-E-X wrote:
Source of the post I've heard Australia has decided not to take back its citizens who were in India at the time, so they will be stranded there for the time being.

Which makes me wonder whether law and basic citizen rights are amongst the victims of covid-19.  Though governmental responses to a pandemic are required, there are several juridical questions.  Governments have implemented restrictions which might not have a solid foundation in their country's laws, or new laws have been passed through a fast track also not quite through regular procedure.  Now, all this has much support, but if we want a lesson in how dictatorships are born, the covid-19 response is instructive.  Western civilisations are not immune to policies that we usually associate with dictatorships, and the notion that dictatorships are results of evil people seizing power against the will of the people, is not accurate.  Dictators rise to power often with massive support.  If not in numbers, then by voice.  I do think western countries will return to apparent normality when this pandemic is over, but the thresholds for drastic measures, declaring emergencies and making exceptions have been moved.

It makes me wonder about this too.  Historically speaking, when the needle moves in the direction of authoritarianism, it's very difficult to make it move back to where it was before, even when there are reasonable precautionary measures taken for public health (and the draconian measures taken by the Australian govt are not reasonable, reasonable would be establishing a 2 week mandatory quarantine for Australians returning from India.)
I am seeing some hesitancy over vaccine passports in the US, as usual it looks like some states will require them (NY) for attendance in indoor venues, while others will not.
NY has decided to create vaccinated vs unvaccinated zones in sports stadiums, so people will be separated into these two categories and likely treated differently (and more than just spacing differences.)  I hope we get as many vaccinated as we can, because in the current atmosphere, segregation is certainly worse than whatever minor side effects the vaccine may cause for the vast majority of people  Looks like we will start vaccinating the 12-16 age group soon, Canada has begun to already.
 
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Coronavirus (COVID-19) Thread

06 May 2021 03:05

There are reasons to worry.  We see a good share of protests against covid restrictions, and I think it's a sign of a healthy society that there are critical voices against the authorities, but, which is a bit sad, these critical voices tend to come from conspiracy theorists and various crackpots.  People with more well founded critical opinions wisely tend to stay silent, partly not to be associated with the crackpots, partly because of a growing cancel culture.  It's definitely on the rise.  Trump banned from social media?  Political censorship exists in many countries, and contrary to popular belief perhaps, most censorship is not state initiated, but organised by the state's eager private citizens to protect stability of the nation.  Decolonisation of science.  Reinterpretation of history.  It's coming everywhere.  Everything can be offensive now, not only things related to religion, sexuality, ethnicity, but in general whatever is at odds with people's worldviews and self-realisation.  If this swings further, we're heading back to the dark ages under the yoke of dogmas.

I don't know the details of what's going on in Australia, but denying entry for own citizens is not worthy a respectable country.  Usually, people who overstay their visas or are illegal aliens are considered to be from defunct countries if they are not returnable.  Apparently, Australia added itself to the list of such countries.
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Coronavirus (COVID-19) Thread

06 May 2021 18:47

Yep, while he is a very controversial figure and has incited violence, Trump being banned from social media brings up serious issues about Big Tech and free speech implications.  People dont notice this but Big Tech (talking about facebook in this instance) has been banning a lot more than just Trump.  They have been banning Native American peaceful protest groups who were organizing against pipelines that run through their reservations and where Native women have gone missing (the implication is it is the pipeline workers doing it; across three states, 2,300 women have disappeared over a period of 10 years.)  The reason facebook has banned these peaceful protest organizing groups is because they collect a lot of ad revenue from pipeline companies who spread their own propaganda on there.  So anyone who says they did this Trump ban for the greater good is naive, they do everything for their own profits and for no other reason.  Big Tech has already been doing bad things in the realm of collecting personal and private data and surveillance (as do many supposedly "democratic" governments).  You wont see me bring up the free speech issue on social media though, because then there would be a mob to deal with (an issue in itself.)  There needs to be a better way to deal with problems  than conspiracy nuts on the one hand and big indignant mobs on the other hand.  Our society is bipolar, literally and figuratively.  The pandemic isn't the only illness that afflicts society on a global level.  I see the authoritarians taking advantage of it and using it to achieve their own selfish ends, divide and conquer as they say.  There are even certain states have passed laws against peaceful protests.

A good example of a healthy protest was what doctors and other healthcare professionals did in Canada when the restrictions that came out recently included a weird ban against outdoor activities in wide open spaces.  That was against medical advice and counterproductive, people need the therapy right now that being in the great outdoors provides and being outside in low density areas actually promotes better health and a lower infection rate.  The protests really worked and those draconian measures were rescinded.
 
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Coronavirus (COVID-19) Thread

09 May 2021 00:13

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Coronavirus (COVID-19) Thread

09 May 2021 02:16

I dont understand why it took them so long to acknowledge this....this is one of the most contagious viruses we've ever seen, it was apparent that it could be spread in a variety of ways and 6 feet was an outdated term from the 1918 outbreak, this is far more contagious than that was.
 
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Coronavirus (COVID-19) Thread

09 May 2021 15:17

A-L-E-X wrote:
Source of the post I dont understand why it took them so long to acknowledge this...


Indeed, it was known and should have been acknowledged a year ago (actually it was briefly acknowledged and then retracted last summer).

On the SE Discord I had mentioned how I thought that the CDC language regarding transmission and prevention was mostly because of administrative or political pressure. Their fear may be that many people don't understand what airborne transmission really means, and could incorrectly conclude that they can just get it from anywhere, or that masks or other measures won't be effective. We also later learned that Trump had been made aware of airborne spread, and then downplayed it, in his words "to prevent a panic".

Image

Personally, I would rather people better understand the reality. I said in the OP and still strongly believe that a good public awareness leads to better preparations and a better response. Whereas if people see that things are getting bad, and their government appears inept or unprepared, that only increases the panic. Last spring was a fiasco in the US. It didn't need to be.
 
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Coronavirus (COVID-19) Thread

09 May 2021 16:32

Yes, I think this was also shown during the 1918 Pandemic, cities that downplayed it had a worse outcome than those were honest with their people.  Trust goes both ways.....

Wat, did you see the interview where Fauci said that we're going to find that a lot more people died from this than we know about so far?  I tend to agree.  Statistics bear this out too.

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