New evidence that amino acid mutations matter for contagiousness

It seems the virus mutated in Europe and became significantly more contagious (though not more dangerous per unit dose):

The Spike D614G amino acid change is caused by an A-to-G nucleotide mutation at position 23,403 in the Wuhan reference strain; it was the only site identified in our first Spike variation analysis in early March that met our threshold criterion. At that time, the G614 form was rare globally, but gaining prominence in Europe, and GISAID was also tracking the clade carrying the D614G substitution, designating it the “G clade”. The D614G change is almost always accompanied by three other mutations: a C-to-T mutation in the 5’ UTR (position 241 relative to the Wuhan reference sequence), a silent C-to-T mutation at position 3,037; and a C-to-T mutation at position 14,408 that results in an amino acid change in RNA-dependent RNA polymerase (RdRp P323L). The haplotype comprising these 4 genetically linked mutations is now the globally dominant form. Prior to March 1, it was found in 10% of 997 global sequences; between March 1- March 31, it represented 67% of 14,951 sequences; and between April 1- May 18 (the last data point available in our May 29th sample) it represented 78% of 12,194 sequences. The transition from D614 to G614 was occurred asynchronously in different regions throughout the world, beginning in Europe, followed by North America and Oceania, then Asia (Figs. 1-3, S2-S3).

That is from a new paper in Cell by B. Korber et.al., via Eric Topol.  You will note there is another recent paper suggesting the east and west coasts of the United States have faced different mutations and thus different levels of contagiousness, but that seems less well established.

The authors do not mention Taiwan, but if I understand their chronology correctly, it would seem that Taiwan has not significant been hit by the most contagious version of the virus.

In any case, I will repeat my general point: moralizing about the virus is premature.  And of course the main result presented in this new paper is subject to revision, further scrutiny, and possible reversal.

Addendum: Here is NYT coverage.

Comments

"moralizing about the virus is premature"

In case the code is unclear, ya'll look like a bunch of yokel racists for the "kung flu" crap.

If that's what it is, "moralizing" is a weird word choice.

that might be straussian jab at the nads to crazy uncle paulie
saying the virus is coming after white supremacists in florida golf carts

I don't know. If you read something like this, I don't think it is a pure morality play.

As with anything in real life there's a lot of moving parts. Maybe what jumps out at me at a first reading is that there were a lot of low information players.

might be referring to the marxist denver city council person who affirmed the idea of spreading covid to trump supporters

I would cite a lack of strong national messaging as contributing to those low information decisions.

At some point the decision to preach or not might become a moral one.

-----

I doubt very much that this relates to "which strain" has made it to Sacramento. Probably they all have.

Not sure whether we can put this no mask allowed restaurant(*) down to low information though.

There might be some flawed moral reasoning on that one.

* - this one is in my county

I don't understand. My wife and I were just joking about this. How do you eat in a restaurant with a mask? She came up with the idea of a little cloth door you could open and shovel the food in. My idea was a cloth bag covering your face that you toss the food in and eat it like a horse eats oats. But how do you have a mask and a restaurant???

To the extent that it's possible to have restaurants and best practices, it's got to be outdoor only, or take out only.

Here in Orange County it's pretty bad. Los Angeles is even worse. I read that if you do a normal day out in LA your chance of meeting somebody with COVID is essentially one hundred percent.

So outdoor dining here is probably out. Should we say take out food is okay? Or is that irrational bargaining?

“Here in Orange County it's pretty bad. Los Angeles is even worse. I read that if you do a normal day out in LA your chance of meeting somebody with COVID is essentially one hundred percent.”

Not likely : Here is why:
• The cumulative number in cases in LA is 105.5 K.
• The number infectious can only be those from the last 15 days after testing ~ 22 K.
• ~ Let’s be generous and say they are undercounted by a factor of 10 ( I doubt it’s this much btw) . but this was true in NYC because testing was scarce, so we have possibly 220 K positives
• At any time probably ½ of them are not out but are at home, probably some of them feel sick and have another reason to stay home, so worst case maybe 110k are walking around for you to potentially meet.
• LA has a population of 4 M , so we get about 1 in 36 walking around with Covid.
• It’s a Bernoulli trial. If you have 10 random encounters in your day, the probability of meeting one or more people with Covid is only 25 % and this is probably an over estimate. .

Interestingly enough, the article I read said 1 in 400, and that was enough to assure an interaction.

How many people are in that Costco with you?

Probably more than 10.

I in 400 is because they take the official number of infected at face value. It's almost certainly higher but maybe lower than my estimated number because I assumed a worst case.
Costco is a huge warehouse with a huge air volume and they mandate masks. From my experience, it doesn't feel crowded there.
You can't define an interaction as being in the same Costco store as an infected person, that risk is extremely low.
It's not rigorously defined and of course debatable but a meaningful interaction might be staying within 6 feet of someone indoors for at least a minute ( both not wearing masks)

That sounds like a lot of hand waving.

Remember the bottom line.

Cases per day are exploding.

Saying your chance of meeting a Covid person in an ordinary day is 100% is clearly false even assuming worse case.. Cases are not exploding from Costco shopping, Costco was never shut down And the bottom line is not cases. It's cases resulting in severe disease or deaths. As far as exploding the peak was June 25 in LA ( 2682 cases).
The death rate in nursing homes in LA has been declining since early May., indicating they're better at protecting the vulnerable which is the most important.
The newly infected are skewing younger. higher infection rates are a concern, but not a grave concern at this point.

http://publichealth.lacounty.gov/media/coronavirus/locations.htm#snf-deaths

One more. a CNN clip via Twitter.

Is it low information or is it low morality to deflect from the seriousness of the Texas surge?

Every location (city, state, country) with very low covid-19 cases simply hasn't experienced it yet. They will. They will eventually get the same statistical number of cases as the worst/average. To think that there is some right steps like wearing masks or social distancing or even shutdowns that will protect you forever is ludicrous. This is a highly contagious virus, eventually it will get to everyone (or perhaps 70% of everyone). Texas didn't do anything wrong EXCEPT believe that their early good luck was due to their brilliant efforts. Eventually it will be everywhere in every place that humans live. Simple as that! It is a virus, it does not know or care that you think you can prevent it. it simply does what viruses do; infects you.

Isn't this the classic low information response?

Most of the world avoided the American experience.

If One Guy is correct, the necessary caveat there would be "so far".

I'm not sure the perverse faith that New Zealand or Australia will someday experience New York or Houston level crises is useful.

Indeed it might be the very worst form of self-fulfilling prophecy.

You don't try, you get the worst, and then you say "see, we got the worst."

I would suggest looking at those situations and wondering why. Maybe there was a less virulent virus, or maybe the pacific rim saw one a while ago very similar and there is a certain immunity. Who knows. In about three years we will have figured it all out.

All I know is that we haven't seen the end of this yet.

Those who moralize think they know everything there is to know. I tend to favor information presented in a way that people will listen to (no one will listen to a self righteous Southern Baptist pontificating) so people can make decisions that they see as best for themselves. No one will get it right, lots will simply be lucky.

Nobody said they know everything.

You're actually arguing against the precautionary principle.

That is that we should exercise caution because we don't know everything.

My guess, Tyler means moralizing in the sense of thinking some countries that did well were just much better than countries that didn't do as well. That it's quite possible that some countries were lucky and had a mild strain(s) and other one's had a more contagious strain.

It's also possible that different strains account for the differences in the US where the North East got hammered but outbreaks in other areas seem to have a significantly lower death rate. OR that might be better hospital treatment.

It's too early to unpack all of that, because we don't have enough data yet.

Thanks JWatts for unpacking that. My paranoid mind goes to the below, from a private email where I argue C-19 virus is very possibly man-made. - RL

The issue is: given a certain four amino acid sequence (there are 20 amino acids in living cells, each amino acid having three nucleotides A, T (or U), G, C, see: https://en.wikipedia.org/wiki/Genetic_code ), can SARS-CoV-2, which has a unique "spike protein" (the little cap at the top which looks like a club) with the amino acid sequence RRAR (https://en.wikipedia.org/wiki/Amino_acid) be considered similar to the four amino acid sequence of RRKR, which is known to have come from a chimeric virus in 2019, as claimed by the Medium article? Or is the sequence RRAR radically different, as claimed by K. Andersen et al in the Nature Medicine article or the fivethirtyeight.com expert Dr. Robert Garry?

It's a one letter (one amino acid) difference. I side with the Medium article cited earlier [https://tinyurl.com/ybt2cv8w]. I say RRAR found in the C-19 virus is very similar to RRKR, which was designed in a lab.

Bonus trivia: At a party, even a "Catch Covid" party, if you want the one sentence Bluffer's Guide to whether or not the C-19 virus is chimeric or natural, simply say: "I agree that the consensus is the virus is natural, but the absence of an intermediate animal host is troubling, as animal hosts have been found for all past human infecting viruses". Then walk away. You're completely right in that statement and nobody can dispute you.

I thought the expert consensus was that it was that the Covid19 doesn't show any evidence of genetic manipulation. Of course that doesn't mean it wasn't lab cultured.

That doesn't mean it wasn't brought by recent UFOs.

I really doubt that it was designed, but totally willing to believe that a predecessor was chosen for gain of function research and induced into a humanly contagious virus.

Yes, if there's anything to the man made story, then it seems like it was being used for basic research and accidentally escaped containment.

It may not have been genetically modified but natural selection still happens in the lab environment and the lab may have caused the virus to mutate in such a way that it spreads among humans easier. For example, the lab was probably air conditioned and either humidified or dehumidified depending whatever the climate in Wuhan is so the virus may have adapted for certain kinds of temperatures and humidity levels. If they were testing on human cultures, it most certainly adapted to human biology as opposed to pangolin or whatever gremlin covid came from.

"It may not have been genetically modified but natural selection still happens in the lab environment "

It wouldn't be natural selection, it would almost certainly be viral culturing.

@JWatts - are your points are good ones but the difficulty you are having--and before I researched it I fell into the same trap--is that you think one can tell definitively whether a DNA sequence is "natural" or "artificial". In fact, you cannot (DNA is DNA). The Kristen G. Andersen et al Nature Medicine article of March 2020 argue that a gene jockey would not make such a design as found in C-19 virus, but this is nothing more than an opinion (as acknowledged as such by the authors). DNA is DNA. Can you tell whether a young child is IVF or not? Analogous issue, literally.

Ray there are signs indicating direct Genetic tampering with the common methods of gene work. As far as I know, Covid19 doesn't have those indicators. But clearly, you can culture a Virus (technically RNA) without tampering directly with the genes.

"is that you think one can tell definitively whether a DNA sequence is "natural" or "artificial"."

I don't think that because it's certainly not true. There's no way to tell if a Virus has been artificially cultured. And there might well be un-common methods of genetic tampering that scientists wouldn't know to look for. All that we know is that the common signs of genetic tampering are missing.

Thanks, J Watts! My thought precisely captured.

It's the same paper from April 20 from the Los Alamos team, just revised a little ( B Korber et al). They claim 614G overtook 614D pretty much everywhere in the world ( except Iceland strangely where the reverse is true).
This would seem to take care of the founder issue where a strain just expands faster just because by happenstance it found easier conditions enabling it to spread.
Their main claim : 614G required fewer PCR cycles to be detected indicating a higher viral load. This could mean higher infectiousness.
But they also found in a study in the Sheffield geographical area in the UK where he strains over time shifted from 614D to 614G
“no significant correlation found between D614G status and hospitalization status; although the G614 mutation was slightly enriched among the ICU subjects, this was not statistically significant”

At any rate, this is the main strain, we’re dealing with now.” I don’t think we should especially have a serious concern about it, just something to keep an eye on.

Well, "moralizing" could be a reference to the yokels in places like the Trump administration and in states such as Florida and Texas who declared victory and resumed their social (anti-social?) activities. Whatever. That we are seeing more infections but fewer deaths could be due to different mutations, or it could be due to the fact that the most vulnerable are, you know, already dead, or because young people were the first to resume their active social lives. I understand that conjecture can be productive, but it also can be highly misleading, rabbit- hole misleading.

Add to the yokels list British Columbia. Lots of tourists, restaurants are open with distancing. I got a desperately needed haircut today. The town looks like a normal early July day.

9 new cases today in the province.

I hope it stays like this. No is thinking this is over. Might as well enjoy a lull, make some money, get some things done. If there is another wave, we will deal with it. As they are dealing with it in Texas and Florida, making adjustments as necessary.

But keep in mind that all forms are highly contagious. The initial explosion of cases in Wuhan supposedly involved the less contagious version. I believe the same is true for the Korean religious group. Both China and Korea would have been devastated by Covid-19 without effective measures to control the virus.

+1

This is the logical conclusion. Strain might affect contagiousness on the margin but it’s not at the level where it changes what policy should be pursued.

OTOH I’m not sure policy will even be a statistically significant variable when controlling for Low trust / high trust society.

Do you pick a dentist at random? Because in our low trust society expertise doesn't matter?

You've got that exactly backward.

In a High Trust society you can just pick a dentist at random. They would all be competent. In a Low trust society you need to verify that the dentist is competent.

Okay, now do presidents.

Fine,

In a High Trust society, the Presidential pick doesn't matter very much, the likely picks are all going to be pretty good and it's likely any of the top contenders would be a competent President.

In a Low Trust society, the pick is far more important, because a particular candidate might make for an incompetent President. Furthermore, even all the top candidates could be flawed and represent a plethora of bad options. There might, not be a good choice.

This makes me reflect on the elections of 1948, 1952, 1956, 1960, and many others where it didn't much matter who won because both of the candidates were fine. We were demographically a different country then, but most importantly we had party regulars pick the candidates. Anyone want to go back to that system? After 2020, I do.

I would think it was the opposite. In a High Trust society laws are enforced and obeyed. So picking the President is important because even mildly bad laws will be enforced. In Low Trust societies picking the President is less important because the law is widely ignored. Whatever laws he passes, life will go on because everyone knows that the President is a corrupt buffoon.

Consider Italy since World War Two. No one pays their taxes much less stops at traffic lights. As long as the Communists were kept out of power what difference did it make? In Latin America it hardly matters if the President is incompetent or corrupt - unless they are Venezuelan-level incompetent - because it hardly matters if somewhere like Argentina is under a radical or a liberal or a crypto-Fascist regime. They are all more or less equally useless and the only hope is that the Army will step in sooner or later.

Now consider Germany during World War Two. The tragedy of the Holocaust is that all the good aspects of Northern European society - an orderly society with good record keeping and low corruption - meant that the round up of Jews could take place and they could be killed in an orderly fashion. It was much harder for the Germans to do in Italy or Bulgaria or even Greece because no one had good records, and the bureaucracy was unreliable and corrupt.

"In a High Trust society laws are enforced and obeyed. So picking the President is important because even mildly bad laws will be enforced."

Yes, but as long as the laws are enforced fairly and across the board, that's a matter for the Judicial branch.

"In Low Trust societies picking the President is less important because the law is widely ignored. "

No, in a Low Trust society one would fear that the President would enforce the law selectively. For example, deciding to grant favored groups exemption from the Law. (ie the Dreamers) but strictly enforce Laws against political opponents (ie denying consverative groups tax exemptions 10x more than progressive groups via the IRS across two critical elections, thus handicapping the othersides Fund raising).

I intentionally picked examples from the Obama administration. Not because Obama was worse than Trump. Indeed his administration was better. However to the point, both sides have been doing this increasingly for decades. And both sides want to claim that the other guy started, or the other guy is worse, etc. Which again, is a sign of a Low Trust society.

" Both China and Korea would have been devastated by Covid-19 without effective measures to control the virus."

Again, what about Japan, which tested less than the U.S. and didn't have a lockdown but social distancing after April 7th?

975 Japanese deaths (80 deaths in June) and cases increasing 0.5% a day.

The Japanese obviously took effective measures. Imagine if what happened in Wuhan had happened all over China.

Was Wuhan an infected primary health care system, as was Italy? They can be particularly nasty as by definition anyone exposed has either a health issue, or the practitioners getting very high virus loads.

New York and the first wave in the US and Canada were worst in elder care homes. They were vigorous about protecting the primary health facilities, and were successful, but the costs were born by the facilities less able to handle infection control.

Maybe what we are seeing in the southern states is when you get those things right; high numbers, but fewer deaths.

Scott, If what happened in Wuhan also happened all over China, then China would still have a death by capita much lower than Western Europe,
the US, most Latin America, Iran, etc.

Hubei province
Official death rate from Covid19 : 4,512
Population: 58.5 million

So 77 per million. Which puts the epicenter of the virus substantially less than every country in Western Europe or North America.

However, I'm inclined to believe the Chinese deliberately lied about the results. I suspect that Scott is referring to what probably happened and not what the Chinese are saying happened.

Not sure I agree that policy won't be statistically significant. I think a key divergence between East Asia and the West (including the US) was that in East Asia, public health authorities consistently advised people to wear masks, given that it looked like a contagious respiratory disease. In contrast, in much of the West, experts inside and outside the government spent the first three or four months of the pandemic advising that people affirmatively should not wear masks. I think that's one reason Japan has had such a low case load, despite not responding particularly aggressively. Sure, a high trust society in which people are cooperative and defer to public health authorities is helpful on the margin. But it won't help if public health authorities give bad advice, and people follow it to their deaths.

Japan had a low percentage of mask wearers in Asia at 65% in February that increased to 75% in April whereas Taiwan and Hong Kong were up to 90%. But maybe 65% was enough - not sure. Australia only had 100 deaths and only 25% wore masks.

"In contrast, in much of the West, experts inside and outside the government spent the first three or four months of the pandemic advising that people affirmatively should not wear masks. "

+1, this seems to be the single most obvious reason for the differences in spread

Yes, though effective measures probably largely means "knowing where you are with the virus and the risk level and informing people early enough to make behavioural changes that allow most introductions to fizzle out, and catch the remaining few". As most evident in Japan. With a side order of preventing virus introduction from multiple vectors (easy if it's in one country recognised early, or lots far away, hard if many countries, close by).

(Public trust, a la skeptical comment might matter, but I think trust in medicine is high enough across range of countries that it wouldn't, once early/late tracking of virus progress / risk is accounted for. But that's testable.)

What happened in Japan?

I thought I rather expressed what I thought had? No?

Also, a relevant tweet - https://mobile.twitter.com/NahasNewman/status/1277646382686515201

I still don't get it. "Informing the people early enough"? The South Korean government asked people to say home in late February but the Japanese government only asked that from April 7 for large cities and from April 16 for the rest of the country.

The tweet is wrong to say restaurants didn't close as many did in Tokyo as there were fewer and fewer customers from early April.

I don't know that the Japanese knew the risk level as the April 7th announcement came after an increase from 8% a day to 12% a day and was already coming back down to 8% before the April 16th national emergency was announced. (The mayor of Tokyo said on March 23 that people should stay home as much as possible but that didn't seem to have much of an effect until at least a week later.)

Hey, if the characterisation of Japan as the government raising awareness of citizens to avoid "3 C" situations very early on and thoroughgly is wrong, then I guess it's wrong. I'm working off second hand information here. Objective measures of behavioural change would be good.

Honestly I can't see what else is likely other than early, voluntary, mass scale behavioural change that altered R0.

Tang et al pointed this out in early March. In English. Oscar MacLean in Glasgow came down hard on their paper, nitpicking their methods and demanding a retraction.
Four months later, I think the English-speaking world should be demanding an apology from Dr. MacLean for doing his best to shut down this line of research.

What line of research was shutdown?

The driver of research is the lack of acceptance of an idea, not universal agreement something is true, with the exception of dogmatic training in research process. Eg, teaching lab testing by measuring gravity with pendulums and balls rolling down ramps. No one is allowed to question anything about gravity, even when the student is required to write the lab question as if gravity is subject to debate.

Great job on keeping the heterogeneity thread going, too few public intellectuals helping on this front! On moralizing, 100% agree with you Tyler. The sliver lining of this unique moment in history is premature moralizing helps the public separate the true scholars from the hacks. The wheel is still in spin and the hacks will lose their hand trying to grab it.

"The sliver lining of this unique moment in history is premature moralizing helps the public separate the true scholars from the hacks. "

+1

Because it seems to be lacking in all of the countries where the pandemic is currently reasonably enough under control to start reopening - without any appreciable increase in the number of new cases.

+10! This post is a perfect example of just the sort of moralizing Tyler was referring to in his comment.

Why is it moralizing to point out that the pandemic has been brought under control in many countries that are currently reopening? There is one outlier among rich nations, a simple observation based on reported numbers. Go far enough in any direction, and everything is moralizing in the eyes of those interested in moralizing.

Do you have some concrete suggestions - which are not moralizing - about how the U.S. can approach the sort of pandemic performance seen in the Netherlands or Canada?

Don't make me bring out the Crikey hammer, and start talking about traditional public health measures, whose effectiveness only decreases the more moralizing is involved.

Oh you are sooo right, because all those countries are just like a racially/ethnically/culturally diverse superpower of 330,000,000 living in quasi autonomous states in a republic protected by a bill of rights, the first of which is freedom of speech, press, and religion.

The USA is a generic nation, just like all the others.

It's kind of suspicious when you only abandon national leadership when you need it.

In diet authoritarian countries like Germany, France, Spain or Italy its way easier to tell a bunch of half free people to go sit inside.

They’re half free people. In a country like the US where people are 4/5ths free it is far harder.

Why is that so hard to comprehend?

It’s even easier in China where people are 1/10th free or Taiwan or South Korea where people are 3/10ths free....

The US has actually done better than France, Spain and Italy as measured by Deaths per capita.

Those three countries had 14, 5 and 30 deaths yesterday (respectively), the USA had 619. Those countries are at a very different place in their pandemic trajectory compared to the USA - the USA is more similar to Sweden. See this graph - http://shorturl.at/fkFQY

Yes, it's possible the US will end up worse. But currently it's better.

+1. My favorite theory!

Now the follow-up question is why was there so much moralizing about this virus? I don’t recall a similar level of moralizing in previous pandemics or would-be pandemics such as Ebola, swine flu, etc. This time around, it seems that everyone’s first instinct was to moralize about Chinese hygienic practices and containment policies and brag about how jobs were coming back to North America rather than fight the virus...

Reasons for difference, either:

1) the poor PRC's selfless and heroic Communist bureaucracy were so unfairly persecuted by evil and biased Western media (those people who simply want to frustrate China's rise to it's natural greatness!), who could not see that they behaved openly, honestly and with complete transparency, telling the WHO absolutely everything they needed to know, like the ultra-competent technocrats they are (not some sort of one party state authoritarian incompetents, no!).

Or...

2) the PRC were simply not open, not transparent and did not usefully warn or act to help to contain the disease in China very well, or early enough.

China was even slower to warn the world about SARS in 2002, and did not provoke as much moralizing.

People talk about things that lead to lots of impact, generally.

Because the president kept lying about it. He lies about everything, of course, but this was the first one that had consequences for the entire country. The left has been angry at Trump’s lying for years. This time he has no escape so critics are reveling in it. (Me included)

Always check what Francois Balloux has to say on studies like this:

"I remain personally unconvinced the D614G variant is directly associated to higher viral loads. The correlation behind that claim was not controlled for any possible confounder. There is also no [evidence] whatsoever it is associated to transmissibility or virulence."

https://twitter.com/BallouxFrancois/status/1278732863110877187?s=20

Because of the CCP's pattern of malfeasance and incompetence in dealing with previous outbreaks, and this time it became a major pandemic.

What to say about Beijing's savage regime's aggressions against its peaceful neighbours, India, Nepal, Vietnam, Myanmar, the Phillippines, etc.? What to say about its support for terrorism? https://www.hindustantimes.com/india-news/myanmar-calls-out-china-for-arming-terror-groups-asks-world-to-help/story-fzb8ADXt1VgS9ofZMMWdWO.html

What about its invasion of the Soviet Union in 1969? What about its criminal support for the genocidal Khmer Rouge regime before the liberation of Cambodia by the Socialist Republic of Vietnam's gallant forces? What about its several invasions of Indian territory?

It is time to put an end to it. China's current regime is a criminal enterprise. Once again, the drum sounds call the world to Peking to school its savage, arrogant oligarchy and civilize the country.

https://youtu.be/9rMbxmQmo94

...."moralizing about the virus is premature."

True but no harm in calling out those who are proudly claiming their great achievement in stopping flights from China while the virus merrily continued to come from Europe.
I went to South Asia in march; there were temperature checks everywhere except on return to the US. Temperature check may not be the best solution , but atleast there was concern elsewhere.

There is concern a-plenty in the US. Look at all the mask shaming memes.

The problem with moralizing and your perceived lack of “concern elsewhere” not observed here is it distracts from things that would really help with COVID like a massive testing regime or a stronger economy.

Of course we need a national testing strategy. People have been saying that since early March.

But instead of providing it, Trump spent all his time blaming others and whining that governors weren’t being nice to him. Less than two weeks ago at the Tulsa rally he said he told host staff not to do so much testing.

When you see someone acting so mendaciously then of course people are going to have a morally valenced sense of disgust for Trump and anyone who supports him.

I like how the Democrats and the media, but I repeat myself, went from "Trump is evil because travel bans are racist" to "Trump is evil because he did not impose enough travel bans fast enough".

The fact is the media and the Democrats, alas again I repeat myself, are determined to blame Trump for everything, something, anything. It doesn't matter. As long as they can run TDS 24/7.

After all, they have thrown everything at Trump and none of it has stuck. If burning down cities and destroying the economy doesn't work what have they got left? Really the only thing the Democrats have not tried is firing on Fort Sumter and that did not work out well the last time they did it.

As everyone knows, criticism of the president renders him incapable of doing his job.

Like when Obama was getting so much heat from Fox and Trump about Ebola after seven cases made it into the country, there was nothing he could do anymore and so now we’re all dead.

This is entirely irrelevant to anything I said. Trump is doing an excellent job by not doing very much. Good for him.

Obama also did not very much. Although the CDC was busy making it as likely to have an Ebola outbreak as they could manage at the time.

Even without studies like this, the virus has persistently defied efforts to find a definition of virtue that it respects. That may put it too strongly; I suspect effort does correlate with success when it comes to reducing infections. But there's a lot of obvious variance that effort (or policy) doesn't seem to explain, and it's been that way for many weeks. Just to be clear, this isn't an anti-lockdown comment. It's a pro-epistemic-modesty comment.

"It's a pro-epistemic-modesty comment."

Quite right! It's a novel virus so no bugger knows.

The virus keeps validating the worst conspiracy theories.

I recall that this blog was extremely critical of epidemiologists for having forecasts that did not always predict outcomes well. Who is moralizing?

They say this was the stand that was recently found in Beijing and was why they went ape. People like to say China’s policy response has been more effective, but it’s just sort of luck I think. Three things at play really. It’s easy to track people down and isolate them because of hotel registration requirements, cell phone data, and grid management policing. Second, low trust society so we all assumed at first that things were a hell of a lot worse than the government was telling us. Third, the Party loves a strike hard campaign, and it seems like a strike hard campaign just so happens to be the exact response required. Aside from that, the Party doesn’t give a shit about the economy. They just want to maintain power. I think the initial analysis was that a bad pandemic was a greater threat than a recession. Hopefully the whack a mole strategy continues to work and we don’t have to find out if they have changed their minds.

Read in the Times that EU will only let Chinese travel to Europe if China reciprocates. Hah. No way in hell. Precisely because we’re all scared shitless of the European strain. Anyways, two and a half more years of this nightmare to go — if we’re lucky.

Criticism was more for advocating extremely unusual restrictions of normal civil rights, on the basis of models that did *not* predict much, and which the person's making predictions knew full well would not be borne out. Less than "Why can't you useless lot predict this novel virus!!!?". Epistemic humility.

This to RM.

The models predicted that things were going to be bad. What the heck else did we want? Zip code level data? Exact demographic breakdowns? Was it not clear that there were huge uncertainties associated with the pandemic that we should err on the side of caution?

"Criticism was more for advocating extremely unusual restrictions of normal civil right". Huh? Not sure where you got that from. I believe I saw criticisms that policy makers needed advice to understand how the public would react to policies, such as lockdowns, which I agree with, that would have made those efforts more successful.

The models by Imperial, the only ones that explicitly modelled impact of shutdowns IRC, had unrealistic assumptions about the impact of lockdowns/shutdowns vs traditional mitigation and advice strategies. We should have erred on the side of following the tested science, not unprecedented and untested measures. That would have been a cautious and conservative route.

That would have been moronic in the context of a novel virus we didn't (and still don't understand).
If anything, the models underestimate the danger as they look only at deaths when it's already obvious that long-term disability will be a far more significant consequence of this infection.

When they said it was the polio of our generation, they were actually optimistic as this is worse than polio. Interesting whether there were polio-denying morons in the first half of the 20 century (hence, moronism is just part of the human condition) or if there is something peculiar about our dysfunctional culture that brings this stupidity about.

We didn’t need precise models to argue for a shutdown. All we had to do is look at what was happening in Italy and France, then overlay our own data.

I knew it was going to get bad here when Italy shit down. They went from fewer than 100 cases to overwhelmed in just two weeks.

Yeah, you need a model of what a shutdown would do relative to no shutdown. At least the debacle of the shutdowns will make it clear through subsequent analysis what limited effect they had, and sway against them in future.

Here are models that explicitly test what shutdowns did to people's behaviour, before and after:

https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(20)30553-3/fulltext - analysis of 25 US counties most affected in initial wave finds extensive, ubiquitous voluntary social distancing before lockdown orders, little to no additional effect on mobility from lockdown date itself on mobility or transmission.

Sweden and UK - https://mobile.twitter.com/BallouxFrancois/status/1271111312530178049

So shutdowns were unnecessary because people have taken actions themselves so they did nothing but simultaneously they were harmful and we shouldn't do them again.

Do you realize how big of a moron you are?

They're probably economically harmful on the margin, and harmful to civ liberties, you panicking ad hom slinging chimp. I'm not proposing anything internally contradictory.

My point has been that the difference in outcomes is overly dramatised, and the impact of shutdown orders is marginal and probably negative, if we have a wider concern than obsessively minimising Covid infections at all costs.

The difference hasn't been overly dramatized, all European countries that had lockdowns managed to reduced the measured number of cases by ~ an order of magnitude (probably more, given that testing was unavailable for many in March) and the one country that didn't do any lockdowns - Sweden - hasn't managed to achieve that.

So, yes, lockdowns work. Cry me a river for your imaginary bullshit civil liberties who are nothing but fiction written on paper.

'Criticism was more for advocating extremely unusual restrictions of normal civil rights'

The U.S. lockdown criticism was never directed toward what various EU states were capable of. "Anthony S. Fauci, the United States’ top infectious-disease expert, attributed rising case numbers in the United States at least partially to American lockdown measures being more lenient than those in some European countries that have since managed to turn the tide on the coronavirus.

“If you look at the different curves between the European Union, the U.K. and others, how they’ve handled the outbreak, they’ve had big spikes and then they’ve brought it down almost or even to baseline in some countries,” Fauci said in an interview the BBC released Thursday. “The situation in the United States has been more problematic.”

Fauci, the director of the National Institute of Allergy and Infectious Diseases, said while some countries in Europe locked down around 97 percent of activity to control the virus, even the strictest U.S. lockdowns only shut down about 50 percent.

“That allowed the perpetuation of the outbreak that we never did get under very good control,” he said.

You may have a better argument to make pointing out the difference between lockdowns that are followed by an orders of magnitude decline in new infections, ones that even fit your definition of unusual restrictions of civil rights for a couple of months, and what happened in the U.S., prompting assault weapon carrying protesters to demonstrate against the restrictions they felt too burdensome. Protesting against the fairly lax measures taken before the current massive rise in cases in large parts of the U.S.

The U.S. is so, so messed up.

Fauci is probably incorrect. See the Lancet published study on the independence of shutdown orders from social distancing behaviour in US counties, that you bizarrely responded to with a non sequitur about Greece and Finland.

Simply everybody is incorrect when they present information that contradicts the proper truth.

Now Fauci is probably incorrect too. We will see if he is also incorrect about 100,000 new infections per day. Just because he has decades of public health experience, and is actually responsible for handling projections and responding to the implications, is no reason to think he any expertise worth paying any attention to in this area.

However, his observation that a number of countries had large spikes and then brought the disease under control is indisputable. It is also indisputable that all of those countries only started reopening after they had the disease under control, not before.

The U.S. is so, so messed up.

Settle down lol. There are tons of different opinions among epidemiologists and working statisticians in the topic. Balloux, Wood, Tegnell, the authors of the Lancet study etc have far more doubts about the efficacy of the lockdowns. You are leaping to a moral story of American decline and then trying to mangle reality into shape to fit your predecided moral. The US is not messed up.

These are base pair mutations in the core genome, not amino acid mutations. Yes, they lead to changes in subsequently encoded amino acids in proteins/enzymes, but just want to be clear on terminology.

> The D614G change is almost always accompanied by three other mutations:

There seems to be many SJWonk-ers virologists that demand equality of outcomes and denied that D614G mutation is significant especially on population lines, and they also mentioned the co-mutations. Statistically in multi-variable analysis if there are highly correlated "independent" variables it is best to drop some of them through stepwise method, or use principle component analysis. None of these were mentioned in the paper. By not isolating them out the same effects are distributed to the correlated variables and sometimes they all become not significant, their often slite of hand trick.

Some even go to the extend of objecting to the use of words "explosive growth". I see NYTimes did use those words. If so what were happening in Italy, Spain, NewYork, Sweden, etc ?? In Sweden the Nextstrain clade 20s from the D614G mutation are almost the totality of the strains starting from 0%, almost totally replacing the early clade 19 strains. From the Nextstrain mid June dataset the last detected clade 19s in Sweden was on 2020-04-27.

https://i.ibb.co/k3SCF5Z/dsequsaca.png

The worsening situation in California is that killer clade 20s is displacing the early clade 19s. The recent Beijing outbreak set back the infection rate to the March level because someone with clade 20B sneezed at the frozen salmons exported to China. Prior to that Beijing has only 3 detected clade 20B all from foreign visitors. The clade 20B from the salmons are genetically much older and so are not the descendants of the earlier imports.

> it would seem that Taiwan has not significant been hit by the most contagious version of the virus.

https://i.ibb.co/d2h6pwt/dseqtw.png

Taiwan like Singapore was hit by clade 20s earlier and like SG managed to suppress/eliminat them. Clade 20s are easier to suppress in different populations?? I speculate that blood groups might be a significant factor in that 23andMe has now shown with large sample size that those in blood group A are more subceptible and most Europeans are in blood group A while Asians are mostly blood group O. Beijing as well as Wuhan has relatively higher blood group A pop because of the ancient assimilated notherners. A research group (not from China, need time to dig that out) has more explicitly through GWAS to identify the demarcation SNP marker rs35074065-deletion. From the 1KGP the allele frequency,

http://grch37.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=21:42833020-42834020;submit=Go;v=rs35074065;vdb=Variation;vf=539539913

EUR 0.433
SAS 0.350
AMR 0.269
AFR 0.079
EAS 0.006
CHS 0 (Southern Chinese, the majority in TW and SG)

The usual SJWonk-ers trick with U shape effects is by ignoring population line effects and pooling all populations together, any inconvenient effects will be reduced or eliminated.

All the more reason to roll out massive testing of tens of millions of people per day. Find the infected and isolate them. Then the pandemic would stop.

"In Arizona, where the virus appears to be spreading out of control, hospitals rushed to expand capacity and adopted practices similar to those employed at the height of the outbreak in New York City and Italy, including doubling up hospital beds in rooms, pausing elective surgeries and bringing in health-care workers from other states.

Perhaps most chillingly, at the urging of doctors and advisers, state officials this week activated “crisis standards of care” protocols, which determine for hospitals which patients get ventilators and care as the system becomes overwhelmed under the crush of patients."

For some strange reason, nobody talks about exponential growth anymore, even as it happens right in front of everyone - again.

"For some strange reason, nobody talks about exponential growth anymore, even as it happens right in front of everyone - again."

Go away Troll!

“You look at what happened in Lombardy, Italy. What happened in New York. That’s what is about to happen here. People are going to die because our system is overwhelmed,” said Will Humble, who was director of Arizona’s Department of Health Services for six years under its previous Republican governor. “It’s important for other states to learn from us. This wasn’t bad luck. It was avoidable. Don’t let this happen to you. You look back at the past few months and we’re an example of what not to do.”

"Pat Herlihy recalled transforming one of Baylor St. Luke’s Medical Center’s units in Houston into one that could receive coronavirus patients when he received the advice he needed.

Herlihy got a call from a doctor at New York-Presbyterian/Columbia University Medical Center who had seen the worst of the novel coronavirus as it swamped New York’s health-care system with tragic consequences.

The first three words out of the New York doctor’s mouth stuck with Herlihy: “Prepare. Prepare. Prepare.”

The reopening of the state worried public health officials who believed it was too fast, prompting medical directors to plan for a possible wave of cases.

Texas doctors including Herlihy communicated in real time with colleagues elsewhere, scoured social media, studied YouTube videos from around the world and reviewed articles for anything that could help them get ready. The state and municipalities had time to streamline supply chains for personal protective equipment (PPE) and scale up staff numbers. State officials used their robust emergency management apparatus to deliver ventilators, medicine and test kits.

Abbott restricted elective surgeries to help conserve PPE, and he ordered health-care institutions to reserve beds for covid-19 patients. Doctors in New York passed on what they had learned then and now.

“It was very important to communicate in real time because we were learning in real time,” said David Greenwald, director of clinical gastroenterology and endoscopy at Mount Sinai in New York.

“We are hearing from people in Texas,” he said. “All of that information that we created in March, we memorialized and we have been offering all those resources back out.”

Health-care workers in Texas have been trying to stay abreast of a flood of information on phone calls, Zoom lectures, in published papers and through medical societies."

It was always about the virus, and never about stupid colors. Luckily for Texans, they have a health care system that knows that, and has done its best to meet a challenge that other places with less time to prepare have failed. Sadly, they were not in a position to keep it from happening in the first place, as Texas started reopening May 1, more than 3 weeks before the first Floyd protest.

thanks for your input Moron!

But "moralizing" about failures: not creating the capacity to randomly test trace and isolate, closing down institutions by category rather than by how they can and do operate, refusal to wear mask to prevent infecting others, failure to prioritize elder care facilities, IS appropriate.

But "moralizing" about failures is just another sign of TDS. As many commenters here are more than welcome to tell you.

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