April Coronavirus Open Thread

by Elizabeth1 min read31st Mar 2020140 comments

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CoronavirusOpen Threads
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Last month’s Coronavirus Open Thread did a fantastic job at being a place for coronavirus-related information and questions that didn’t merit a top level post, but at almost 400 comments, many of which were great at the time but are now obsolete, it’s getting a little creaky. So for the next month (probably. Who knows what’s going to happen in that month) this is the new spot for comments and questions about coronavirus that don’t fit anywhere else and aren’t worth a top level post.

Wondering what happened in last month’s thread? Here are the timeless and not-yet-eclipsed-by-events highlights:

  • Spiracular on why SARS-Cov-2 is unlikely to be lab-created.
  • Two documents collating estimates of basic epidemiological parameters, in response to this thread
  • Discussion on whether the tuberculosis vaccine provides protection against COVID-19.
  • Suggestive evidence that COVID-19 removes sense of taste and smell.
  • Could copper tape be net harmful?

Want to know what’s coming up in the future? Check out the Coronavirus Research Agenda and its related questions.

Wondering why the April thread is going up on 3/31? Because everything’s a little more confusing on 4/1 and I didn’t want the extra hassle.

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In most major countries, daily case growth has switched from exponential to linear, an important first step towards the infection being under control. See https://ourworldindata.org/grapher/daily-covid-cases-3-day-average for more, you can change which countries are on the graph for more detail. The growth rate in the world as a whole has also turned linear, https://ourworldindata.org/grapher/daily-covid-cases-3-day-average?country=USA+CHN+KOR+ITA+ESP+DEU+GBR+IRN+OWID_WRL . Since this is growth per day, a horizontal line represents a linear growth rate.

If it was just one country, I would worry it was an artifact of reduced testing. Given almost every country at once, I say it's real.

The time course doesn't really match lockdowns, which were instituted at different times in different countries anyway. Sweden and Brazil, which are infamous for not taking any real coordinated efforts to stop the epidemic, are showing some of the same positive signs as everyone else - see https://ourworldindata.org/grapher/daily-covid-cases-3-day-average?country=BRA+SWE - though the graph is a little hard to interpret.

My guess is that this represents increased awareness of social distancing ... (read more)

I'd like to point out that the growth in India is still exponential (linear on the log-scale) https://www.worldometers.info/coronavirus/country/india/. This could be or become true of other developing countries.

India and other developing countries probably have a harder time controlling the outbreak (and governments and the young, food-insecure populations may judge the economic cost of social distancing to be higher than the risk of the virus).

There was a time when the number of worldwide cases appeared to stagnate because of the Chinese lockdown, but this number just hid the exponential growth of the European+US outbreaks.

What I said doesn't contradict any explicit statement in your comment, I just want to argue against the hypothetical deduction from "the growth rate of the world as a whole has also turned linear" to "and this means that the world is over the hill".

I would like this to be true, but two days on from the above comment, I am not seeing any linearity in the world growth rate (second link above), just three points in a nearly horizontal line a few days ago. The link for BRA+SWE shows the same thing for Brazil even more dramatically. New daily cases is a noisy enough measurement that I wouldn't entertain hope that we are past the exponential phase until seeing at least a week of a flat or declining rate.

The site I usually look for stats on is https://gisanddata.maps.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6

The graph at the bottom right still looks like exponential runaway, even when you switch to daily instead of cumulative cases. And just like the above links, a few days ago there was a period of a few days of seeming flatness in new cases, but it didn't mean anything.

Edit: corrected corrupted URL to the arcgis.com site.

9CellBioGuy8moHow much of that is a delayed effect of distancing and how much is saturation of test capacity? American capacity hasn't increased in days, and by both my and the Imperial College of London's calculations, at least 3 million Italians are probably already infected...
5Davidmanheim8moI've been forecasting a high probability that almost all of the low case count growth in Africa and Southeast Asia as limited testing.
4Bucky8moI think there's a decent amount of correlation with between lockdown dates and entering linear growth. Below are the lockdown dates and starts of the linear phase for some of the worst hit countries. China 23rd Jan -> 5th Feb S. Korea 20th Feb -> 1st March (This wasn't a mandated government lockdown but people did seem to stay inside [https://www.reuters.com/article/us-china-health-southkorea-cases/like-a-zombie-apocalypse-residents-on-edge-as-coronavirus-cases-surge-in-south-korea-idUSKBN20E04F] in the worst hit areas) March: Italy 9th -> 21st Spain 15th -> 26th Germany 16th -> 27th France 17th -> not yet linear (last 2 days have been high) Switzerland 20th -> 21st US 22nd (NY) -> not yet linear UK 23rd -> approaching linear? Possibly already there These are remarkably consistent at 10-14 days, apart from Switzerland (very fast) and France (looked like it had gone linear at about the normal time but has increased again). This graph [https://chart-studio.plotly.com/~Bucky13/9] shows the same data but is annotated with containment steps taken by each country (it isn't averaged over 3 days so the exact numbers don't match up but the same pattern applies).

New post by Tomas Pueyo, the author of 'Coronavirus: The Hammer and the Dance':

'Coronavirus: Out of Many, One'

Here’s what we’re going to cover today, with a lot of data, charts and sources:
1. What’s the situation in the US and its states
2. Why the coronavirus should be a bipartisan issue
3. The economics of controlling the virus
4. Which decisions should be left to the federal government or to states
Here’s what you’ll take away:
The coronavirus is growing everywhere in the US.
Some states are on their way to controlling it.
Others have massive outbreaks that make China’s outbreak pale in comparison.
Many are unprepared, and will suffer some of the worst outbreaks.
All voters care about this, Democrats and Republicans.
Democrats were hit first.
But Republicans have more to lose.
They’re older and more likely to die.
Most hesitation comes from the perceived cost of suppressing the virus.
Fortunately, it’s cheaper to suppress it than to let it run loose.
We should do it.
But right now, states are left fending for themselves. It’s a mess.
They are competing against each other instead of collaborating.
They might be forc
... (read more)

There's a fascinating post by Patrick McKenzie (software engineer at Stripe, American living in Japan) on the Covid-19 situation in Japan.

With others, he did independent research into the issue when public sentiment stated the virus was well under control. They circulated this research privately and publically (anonymously), and the story even involves a cryptographic hash to pre-register their research (reasoning).

The whole post is interesting, and contains this gem that reminded me of LW concepts like a Crisis of Faith or Yudkowsky's Civilizational Inadequacy:

I know the exact moment that I got worried for Japan: [...]
I didn’t do anything major, for a while.
I assumed everyone in a position to act had reached this conclusion. Surely, talented epidemiologists understand exponential growth and already know the shape of things to come. Surely, there is a department of people working day and night on the national response effort. Surely, all professionals understand how to parse official communications. Surely, in a hundred thousand rooms, responsible professionals have told their leadership what would soon happen. Surely, in a hundred thousand rooms, people in positio
... (read more)

[EDIT: Bucky points out that these cases make up too high a proportion of new cases for novel reinfection to be the primary mechanism, which means that there's negligible evidence to move the basic prior that general immunity should persist for a while (once the virus is well and truly defeated by the immune system).]

In South Korea, 2% of previously recovered patients have again tested positive and are again in isolation. There are several other explanations besides a general lack of acquired immunity (which would be the worst possible case, from a public health standpoint). But it seems critical that someone look at the evidence for the most dangerous possibility.

The magnitude of the numbers here seem wrong to represent people being infected twice.

From April 9-17 there were 74 newly discovered positive tests in those who had previously recovered. Over the same period there were only 203 new cases discovered. If the 74 received a new infection then they are getting infected at 2000x the rate of the general population.

Obviously there are a fair few reasons why they might be getting reinfected at a higher rate but I can’t think of a way it would be that much more. The reoccurrence of an existing infection would make a lot more sense.

4orthonormal7moGreat point. And South Korea is one of the few places I trust to have counted almost all of their cases, so that calculation has to be basically right. I think that completely settles it.

I've seen an image on social media that suggests postural drainage, a physical therapy practice used mostly for cystic fibrosis, as a way to cope with COVID-19 at a sub-hospitalization stage; the shared image suggests that draining the mucus can keep a patient from needing a ventilator. (I'll transcribe the actual text attached to the image in a subthread, but it's of pretty low quality; I've written here what I think is the only interesting point.)

Unfortunately, Googling "postural drainage coronavirus" just gets me all the medical pages on postural drainage (because they now have headers about coronavirus).

It's a very cheap intervention for patients not on ventilators, the mechanism seems at least plausible, and it's the sort of thing that medical professionals might fail to consider. Is it worth taking a closer look?

This is the link I was looking for (but couldn't find!) for my previous answer:

Proning the non-intubated patient

Written by Josh Farkas assistant professor of Pulmonary and Critical Care Medicine at the University of Vermont.

Some general comments.

  • Positioning affects lung capacity and function.

Images (figure 1) and information to see the effects of gravity and compression of the lungs here and here.

Definitions:

supine ~ "facing up"

prone ~ "facing down"

More info: prone-ventilation-for-adult-patients-with-acute-respiratory-distress-syndrome

Proning the non-intubated patient

  • Movement is also important to help prevent congestion and keep the lungs inflated, for example post-op care for thoracotomy patients (where the chest wall has been opened which collapses the lung) is mainly about mobilisation - getting out of bed and walking around as soon as possible.

So yes, definitely worth a closer look.

9Andrew_Clough8moOn TWiV 595 they did an interview with a doctor who said he'd been able to get the survival rate of intubated patients up to 50% by using proning, though I don't recall them going into the details.
5leggi8moSupine positioning is the easiest position for intubation but once the endotracheal tube is in-situ it makes physiological sense to turn the patient over if possible. Assuming the tube is secured in place - which it should be. Main issues with a prone intubated patient are medical staff accessing/assessing/maintaining the tube - requiring suitable facilities or having to kneel on the floor! Supine and immobile for days - not good.
2MichaelGR7moSome more on proning in this NYT article [https://www.nytimes.com/2020/04/14/nyregion/new-york-coronavirus.html]:
5orthonormal7moSo wow, something like this (just the basic version like leggi was discussing, putting patients on their belly instead of their back) is proving to be strikingly effective [https://www.nytimes.com/2020/04/14/nyregion/new-york-coronavirus.html]:
4orthonormal8moText of the shared image; don't say I didn't warn you about the quality of the writing, and [sic] for the whole thing. It does read like it could really be from an elderly physical therapist. ...and there the image ends.
2orthonormal7moSo wow, something like this (just the basic version, putting patients on their belly instead of their back) is proving to be strikingly effective [https://www.nytimes.com/2020/04/14/nyregion/new-york-coronavirus.html]:

Thanks for the shout-out, but I don't think the thing I proposed there is quite the same as hammer and dance. I proposed lockdown, then gradual titration of lockdown level to build herd immunity. Pueyo and others are proposing lockdown, then stopping lockdown in favor of better strategies that prevent transmission. The hammer and dance idea is better, and if I had understood it at the time of writing I would have been in favor of that instead.

(there was an ICL paper that proposed the same thing I did, and I did brag about preempting them, which might be what you saw)

3Lanrian8moLink to paper [https://www.imperial.ac.uk/media/imperial-college/medicine/sph/ide/gida-fellowships/Imperial-College-COVID19-NPI-modelling-16-03-2020.pdf] , the relevant figure is on page 12.
2Elizabeth8moI think you're being too modest, but I've removed it since you think it's been eclipsed by something better.

I've written a blog post on "Body Mass and Risk from COVID-19 and Influenza", available at https://radfordneal.wordpress.com/2020/04/06/body-mass-and-risk-from-covid-19-and-influenza/

Here's the intro:

Understanding the factors affecting whether someone infected with COVID-19 will become seriously ill is important for treatment of patients, for forecasting and planning, and — with factors that can be changed — for personal decisions aimed at reducing risk. Despite our current focus, influenza also remains a serious disease, so understanding its risk factors is also important.

Here, I’ll look at some of the evidence on how body mass — formalized as Body Mass Index (BMI, weight in kilograms divided by squared height in metres) — influences prognosis for respiratory diseases. Information specific to COVID-19 is still scant, but there is more data on influenza and on other respiratory infections (which includes coronaviruses other than COVID-19). Information on how BMI relates to general mortality should also be helpful.

Below, I’ll look at two relevant papers, plus a preliminary report on COVID-19. To preview my concl... (read more)

8Elizabeth8moThis is fantastic. Can I encourage you to make it a top level post?
1Radford Neal8moThanks for the suggestion. I've put it up as a post now.
2Raemon8mo(meta note: you can make posts "link posts", by clicking the link icon in the Edit Post page. I did that for your post so its now a proper link post)

Some points from an interview with virologist Hendrik Streeck who is leading a systematic study in the German town of Gangelt in the county of Heinsberg, one of the epicenters of Corona in Germany (https://www.zeit.de/wissen/gesundheit/2020-04/hendrik-streeck-covid-19-heinsberg-symptome-infektionsschutz-massnahmen-studie/komplettansicht, ZEIT online, April 6, interviewed by Jakob Simmank and Florian Schumann):

  • The team is testing, for the first time, a representative sample (1,000 from 500 households) for Germany on whether they are infected with Corona virus (smear test and antibody blood test).
  • There was a famous carnival event in Heinsberg and in Germany it is kind of common knowledge by now that the large outbreak in Heinsberg can be traced back to that event. In the study, people were asked whether they attended that event, whether they had pre-existing conditions or take any medications; and all participants of that event were finally tested, and the researchers are reconstructing who sat next to whom and talked to whom. People had assumed that infection had spread via insufficiently clean draft-beer glasses; this seems to be wrong, most people had bottled beer. Moreover, peop
... (read more)
4ChristianKl7moIf they have a different pattern that might mean that their local strain has a mutation and actually there's a different pattern.
1Ramiro P.7moI've seen news [https://www.businessinsider.com/death-rate-german-laboratory-city-5x-less-than-national-average-2020-4] about this study, but no preprint. It'd be really helpful if we could get it.

https://en.wikipedia.org/wiki/Pneumocystis_pneumonia

Could the coronavirus be interfering with the immune system in a way that is allowing Pneumocystis pneumonia to thrive?

My understanding is that Pneumocystis pneumonia, otherwise known as PJP or PCP, is caused by a fungus. It is highly opportunistic, and is rarely seen in people with healthy immune systems. It is highly associated with AIDS/HIV.

The fungus that causes it is widespread, and likely exists in the lungs of most healthy people.

I'm not sure about this one, but it seems relatively difficult to test for. Given it's rarity, it seems it is most are assumed to have it if they present symptoms and are positive for HIV/AIDS. If they are suspected, it seems they test for HIV/AIDS first.

Symptoms sound similar, if not the same as coronavirus

CT scans of those suffering from coronavirus and PJP are very similar, and both are very different from more typical pneumonia.

I have seen some papers that indicated the coronavirus may lower CD4 T-Cell counts, which is one of the reasons PJP is seen in HIV/AIDS patients. Not sure if this has been well studied and peer reviewed yet.

There exists a very effective treatment for PJ... (read more)

I emailed this comment and my reply to Elodie Ghedin, a molecular parasitologist and virologist at NYU for her thoughts on this. Here is her reply (posted with permission):

"Thanks for reaching out. 

To my knowledge, there has not been an association of PCP with COVID-19. The percentages compared in that comment are not really comparing the same thing.

In severe COVID-19 cases there is indeed pneumonia but that's a general term indicating inflammation due to the virus itself. It can however be followed by an opportunistic infection, mostly from bacteria.

At first blush SARS-CoV-2 is not doing anything all that different to the immune system than any other acute virus infection. "

1Nicholas Campbell7mo'' At first blush SARS-CoV-2 is not doing anything all that different to the immune system than any other acute virus infection. '' Not sure about this, it does seem to create a cytokine storm and lypmphopenia in a minority.
4Nicholas Campbell7moMD here. Could the coronavirus be interfering with the immune system in a way that is allowing Pneumocystis pneumonia to thrive? A: Yes. COVID has been linked to CD4+ (T helper) lymphopenia, possible via cytokine storm. The main risk factor for PCP is CD4+ lymphoooenia caused by HIV. My understanding is that Pneumocystis pneumonia, otherwise known as PJP or PCP, is caused by a fungus. It is highly opportunistic, and is rarely seen in people with healthy immune systems. It is highly associated with AIDS/HIV. A: Its actually rarely seen with HIV these days (due to ART), useally in transplant or immunosupressed patients. The fungus that causes it is widespread, and likely exists in the lungs of most healthy people. I'm not sure about this one, but it seems relatively difficult to test for. Given it's rarity, it seems it is most are assumed to have it if they present symptoms and are positive for HIV/AIDS. If they are suspected, it seems they test for HIV/AIDS first. A: It is easy to test for (PCR for the gene or antibody based assays), but a bronchoscopy is needed to get fluid from the lung. As this causes aerosolization, this shouldn't be done in a COVID patient. You are right to say that a positive test cannot distinguish between colonization or infection, although infectious burden (DNA copy number by PCR) is becoming a useful marker. Symptoms sound similar, if not the same as coronavirus. A: Yes, although PCP doesn't cause a quick and spectacular deterioration like COVID. CT scans of those suffering from coronavirus and PJP are very similar, and both are very different from more typical pneumonia. A: Yes, but the image is really not specific and can be caused by any atypical infection, drug reaction or auto-immunity. I have seen some papers that indicated the coronavirus may lower CD4 T-Cell counts, which is one of the reasons PJP is seen in HIV/AIDS patients. Not sure if this has been well studied and peer reviewed yet. There exists a very effective
3Dokler8moI have no medical background, but wanted to add that the prevalence of Pneumocystis colonization in the general population [https://academic.oup.com/cid/article/50/3/347/393968] is approximately the proportion of cases of COVID-19 that are symptomatic [https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2020.25.10.2000180] (~70%). We don't know either of these numbers with great confidence or precision, but these estimates appear consistent with your hypothesis. Edit: additional source showing 68% of COVID-19 cases have a dry cough (page 4) [https://www.ecdc.europa.eu/sites/default/files/documents/RRA-sixth-update-Outbreak-of-novel-coronavirus-disease-2019-COVID-19.pdf]
  • A laboratory study (preprint) showed that covid could live in cat and ferret respiratory systems, but not dogs, pigs, chickens, or ducks. It further found that covid could be passed to from an infected to an uninfected cat in an adjacent cage (doesn't look like they tested transmission in ferrets).
  • A survey (preprint) of Wuhan cats indicated 15% of cats surveyed after the outbreak had antibodies to covid. 0 of 39 cats caught before the outbreak had antibodies. (ETA 4/9: They don't mention what they were sampling from, from what they imply I think 15% is an overestimate but still enough to establish the possibility).
  • At least one zoo tiger has test-confirmed covid, and several big cats at the zoo are showing symptoms

So it seems pretty likely cats are vulnerable to covid, and may be able to pass it to humans.

3mfoley7moDoes the fact that 15% of cats had antibodies suggest that far more Wuhan residents were infected than the official totals? Officially I think only around 1 in 200 Wuhan residents were infected. It says that the cats were sampled from animal shelters or pet hospitals so maybe the workers there had to keep coming in every day to care for the animals even during lockdown and thus were more at risk.
4Elizabeth7moWhere do you get that the cats were sampled from shelters and hospitals? I see So hospitals and shelters were certainly part of the sample, but it seems like they also tested some human patients' cats.

I've been playing with the Kinsa Health weathermap data to get a sense of how effective US lockdowns have been at reducing US fever. The main thing I am interested in is the question of whether lockdown has reduced coronavirus's r0 below 1 (stopping the spread) or not (reducing spread-rate but not stopping it). I've seen evidence that Spain's complete lockdown has not worked so my expectation is that this is probably the case here. Also, Kinsa's data has two important caveats:

  • People who own smart thermometers are more likely to be health conscious which makes them more likely to be health conscious than the overall population. Kinsa may therefore overstate the effect of the lockdown by not effectively sampling the health apathetic people more likely to get the virus.
  • Kinsa data cannot separate coronavirus fever symptoms with flu fever symptoms. At the early stages of coronavirus spread, seasonal flu illness dominates coronavirus illness and seasonal flu r0 is between 1-2. This means that a lockdown can easily eliminate symptoms caused by seasonal flu illness by reducing flu r0 below zero without reducing coronavirus's r0 below zero.
    • I'm addressing
... (read more)

The Kinsa data is barely even weak evidence in favor of R0 < 1. The downward trend in fever readings are confounded, likely severely, by their thermometers having to be actively used vs. being a passive wearable. It seems plausible that more people will check their temperature when they are concerned about COVID-19, and since most people are healthy this will spuriously drive average fever readings down. Plausibly the timing of increased thermometer use will coincide somewhat with shelter-in-place orders since they correlate with severity & awareness of the local outbreak.

Their FAQ notes that they have seen 2-3x normal usage of their thermometers (this was as of March 29, they haven't updated this part of their FAQ since) and consider this "healthcare seeking behavior" a potential driver of their trends. This has not stopped them from promoting their data to government agencies and NYT, without mentioning this or any other limitations whatsoever (at least to the NYT).

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4AlexSchell7moI was completely wrong, I don't think their data is subject to this worry. They now have a preprint [https://www.medrxiv.org/content/10.1101/2020.04.06.20039909v1] up. From supplementary methods: So lots of repeat readings shouldn't affect the gauge, and neither should more of their user base taking readings. Unless they are seeing a lot of new users, or lots of returning users that haven't used the thermometer in over a year, both of which seem somewhat unlikely, their metric should be fine.
3Isnasene8moThanks for pointing this out. Having recently looked at Ohio County KY [https://www.healthweather.us/?regionId=21183&mode=Trends], I think this is correct. %ill there max'd out at above 1% the typical range but has since dropped below 0.4% of the typical range and started rising again (which is notable in contrast with seasonal trends) [Edit to point out that this is true for many counties in the Kentucky/Tennessee area]. This basically demonstrates that having a reported %ill now that is lower than previous in the Kinsa database is insufficient to show r0<1. Probably best to stick with the prior of containment failure.

Hydroxychloroquine update!

A smart friend pointed me to this study that explains that mediocre antivirals only work if administered right after infection. By the onset of symptoms the effect is already much reduced. (The study isn't clear as to what counts as "symptoms" except that they occurred 3 days before hospitalization, so maybe early warning signs like loss of smell don't count). HCQ is, at best, a mediocre antiviral.
https://www.medrxiv.org/content/10.1101/2020.04.04.20047886v1

This model agrees with a new study from China (N=150) that showed zero effect when giving patients HCQ 16-17 days after the onset of the disease. Of note, the study compared Standard of Care to SOC+HCQ, and I have no idea what the Chinese SOC is beyond the minimal requirement of intravenous fluids, oxygen, and monitoring that's mentioned in the paper. In particular, there's no info on whether it includes antibiotics like azithromycin, and whether it includes zinc. It's hypothesized that HCQ works partly by easing the entry of zinc into cells where it slows viral replication, and so they work well in conjunction.
https://www.medrxiv.org/content/10.1101/2020.04.10.2006... (read more)

Scott talked some days ago about how Brazil didn't take real coordinated efforts, and as a brazillian living in the country's largest city, I'm here to both defend my country and say that things are much worse than a lack of coordination.


The government, both at federal and state level, took quarantine measures earlier than other countries did (according to the Johns Hopkins institute), compared to number of confirmed cases. We officially closed schools at about 100~ confirmed cases, with parents refusing to take their kids to school much earlier. (Per comparison, Lombardy closed at about 200 cases or so).

They're also taking measures to have a semi-UBI going on so people have spending money for basics and utilities. Brazil also has much more robust work laws than US, thus people aren't at such a risk of sudden unemployment without social safety nets that can last them through this pandemic. They're also pushing for landlords and companies to open negotiations for rent and utilities.

BUT

The biggest factor here is the brazillian people, which are simply not caring about what the media has to tell them. Barely two weeks of quarantine in, and people a... (read more)

I'm personally quite worried about disruptions to the food supply chain severe enough to cause food shortages in e.g. the Bay Area in the next few months but not sure what to do with that worry other than to stock up more on non-perishables. Would very much appreciate seeing more people thinking and researching about this.

3BECA7moThe shift of the supply chain from commercial food supply to residential is part of the problem, and is being highlighted right now with producers destroying milk and produce while food banks face severe shortages. These commercial supply chains aren’t easily converted to being direct to consumer, but the government should be purchasing and diverting these excesses to food banks. As individuals, we could all sign up for local CSA veggie boxes, which could contract with commercial suppliers to augment their produce to meet the increased demand. This would reduce collective demand on the direct consumer supply lines (ie: grocery stores). We could also purchase food in bulk from commercial suppliers, and coordinate with neighbors if a single bulk unit is too much to consume before it spoils. The other part of the equation is a potential food shortage in the fall due to farmers being unable to get temporary migrant workers in the spring planting season and projecting that same difficulty for the fall harvest, so they’ve elected to further reduce their spring planting. Unfortunately, I think this has already happened across Europe and North America. https://www.theglobeandmail.com/world/article-abrupt-shortage-of-seasonal-farm-workers-threatens-to-create-food/ [https://www.theglobeandmail.com/world/article-abrupt-shortage-of-seasonal-farm-workers-threatens-to-create-food/] As individuals, we could all plant subsistence gardens right now to help reduce the collective demand for food in the fall.
2Vaniver7moThe various things I've seen about this claim that food banks aren't processors (who take industrial-sized portions of foodstuffs and pack it into commercial or individual-sized portions), and so aren't able to handle a 55-gallon drum of milk better than anyone else.
3BECA7moFor things like milk, I’d expect that’d pose a problem. But for things like fresh produce, food banks can handle industrial-sized portions of these, or at least I’ve seen it handled at my local food bank, and my local food bank probably isn’t unique in this.

Summarizing an article on gloves: https://www.n-tv.de/panorama/Einweghandschuhe-so-wichtig-wie-Masken-article21689035.html (April 2)


First, about virus survival on surfaces in general:

Germany's (kind of celebrity) virologist Christian Drosten's (Berliner Charité hospital) opinion on the study about survival rates of Sars-CoV-2 on surfaces and the possibility of smear infection:

He hypothesizes that for the experiment, dass für den Versuch Viruses in a larger drop were put on the surface, and even though in this way you can verify infecti... (read more)

The Imperial college model (yes, that one) has just been released, open-source, for anyone to look at. We don't actually know what the model's precise projections were (thanks to the UK governments lack of transparency), but we do know that ever since the UK's lockdown was declared the model had been predicting a peak on Easter weekend, which was, in fact, what happened in the UK. Imperial supposedly has the best infectious disease modellers in the world, and this is the code of the model that led the UK to dramatically reverse course, so its probably pretty accurate. Here's the GitHub.

5Lukas_Gloor7moI've heard people with good judgment criticize the Imperial College modelling for countries outside the UK because the forecasts proved to be too pessimistic repeatedly. That's interesting because I know that their UK forecasts were slightly too optimistic. They predicted 20k deaths for the UK initially, then updated to "probably a bit less than that" shortly afterward. And now we're at 21k deaths already (but daily deaths slowed down a lot). I would imagine that their forecasting is the most accurate for the UK numbers because that's what their main task is about.
5SDM7moI don't understand that either - its like they got the shape and timing of the epidemic right but had a mistake in the scaling factor. The other models I've been looking at that seem sensible - Covid-19 projections [https://covid19-projections.com/united-kingdom]and the FHI [http://epidemicforecasting.org/?region=united+kingdom&scenario=4W_None]both try to model scenarios where social distancing is relaxed to various degrees at the start of June, which is realistic. Both actually look decently optimistic to me, with no giant second wave anytime soon (instead more of a 'slow burn' with R about 1) even with 'weak mitigation' - which is basically what happens by default when people say 'Morituri Nolmus Mori' [https://www.lesswrong.com/posts/ijd2TsoGrhcriAeNs/my-covid-19-thinking-4-23-pre-cuomo-data?commentId=89eTNPy5acBrdLZPR] . With moderate to strong mitigation imposed constantly (a big ask, admittedly) it stays gone. Those roughly agree with the Imperial model, at least based on what we've heard of it - all of them agree that R is currently decently below 1 so we have a bit of headroom to relax restrictions in June without it blowing up in our faces immediately.

I might later write a more indepth post, but for now the core idea. Controling a building to have between 50% and 60% humidity might reduce the amount of spread of corona. There are multiple studies that you can reduce the spread of infections in schools and hospitals that way.

There was also a paper out that suggested COVID-19 to spread less in climates with high moisture and temperature.

If anyone wants to collaborate with me on writing a post about this, please contact me.

5gwillen8moCan you link whatever you have on this, even before you write it up? Articles, the paper you mentioned, the studies about reducing infections this way, where you get the idea in general? (Everyone, please do this! It is really helpful, and it's probably easier for you to re-find things than for people to try to find them based on your comment! I wish LW had a rule about doing this!)
2ChristianKl8moI think it would be really stupid to have such a rule that you should have to put effort into asking for help to write a post. I think downvoting a post that asks for help to flash out a given case more because the post doesn't flash out the case enough is rather demotivating to the actual production of the case getting written up.

For what it's worth, I upvoted your comment.

But since you stated that you had a source already, I don't see how it's asking much for you to post a link to the source you already said you had.

[EDIT: After a couple days, I regret the tone of my comments here. I don't want to discourage anybody from writing posts, or asking for help in composing posts. And I think "there oughta be a rule" was a poor summary of my position and sounded pretty hostile. I think it would be nice if people mentioning the existence of sources would link the sources they mention, and in general I'd like it if people linked source more often. But that wasn't really directed at you personally, it was spillover from elsewhere.]

1silverdrake118moThis suggests that a humidity between 50-60% is optimal https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2863430/ [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2863430/]
2rhollerith_dot_com8moIf you are wondering what the typical humidity is where you live, note that almost any build that is 10 deg F or more warmer than its surrounding because it is heated will have relative humidity (which is what parent means by "humidity") well below .6. Relative humidity is expensive to control partly because it is expensive for an automated system to measure. My guess is that on the margin, distributing fresh surgical masks to everyone entering the building would be much cheaper (and more effective) even when we adjust for the fact that an emergency ramp-up of mask production is much more expensive than normal, "peacetime" mask production. (I added "on the margin" to adjust for the fact that surgical masks are most efficiently produced in a facility that can supply many orders of magnitude of buildings.)
3ChristianKl8moMeasuring humidity is cheap. You only have to pay 2,86 € [https://www.amazon.de/Level-Great-Digital-Hallenrunde-Thermometer-Feuchtigkeitsmessger%C3%A4t/dp/B07TC9HY85/ref=sr_1_26?__mk_de_DE=%C3%85M%C3%85%C5%BD%C3%95%C3%91&dchild=1&keywords=humidity+meter&qid=1585764968&sr=8-26] for the cheapest one on Amazon. Automated systems are more expensive but even a non-automated system could do the job with a bit on manual effort. Effort-wise I think it's less effort to do manual humidity control then to wear a surgical mask. My first experience with wearing a surgical mask for longer was to wear it 5 hours for a SlateStarCodex meetup I organized for the 8.3. Afterwards, I had a headache and didn't wear my masks in a meeting the next day even through I'm a well-prepared rationalist who brought his masks a year in advance. Comparing it to mask wearing however misses the point. It's quite likely that we want to do multiple interventions to keep down infection rates.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4420971/ is skeptical of cloth masks. Does anyone have any thoughts on it, or know any other studies investigating this question?

4ChristianKl8moIt seems the primary argument for clothing masks that's made is that if an infected person wears them it's less likely that they will infect others. That's not the purpose that was tested in "A cluster randomised trial of cloth masks compared with medical masks in healthcare workers" [https://www.researchgate.net/publication/275360639_A_cluster_randomised_trial_of_cloth_masks_compared_with_medical_masks_in_healthcare_workers] that study seemed more about whether or not the masks have protective qualities for the wearer.
2cata8moIt seems only skeptical of cloth masks as compared to surgical masks, which isn't really very interesting to me in the current circumstances, since most people don't have access to surgical masks.
8Scott Alexander8moNo, it says:
6cata8moMea culpa, that's more of a condemnation than I thought.
3silverdrake118moI noticed this too. When wearing a bandana as a mask, humidity is building up while exhaling, causing it to be slightly damp.

Should there be a non-coronavirus Open Thread?

Some potentially useful numbers I've been working on estimating:

1. The number of days lag between registered cases and deaths

2. The adjusted CFR for each country taking this into account

The method is essentially to try different lags (dividing current deaths by cases from x days ago) and see which length of lag gives a constant CFR over time (normally CFR increases with time as the growth rate of cases slows earlier than that of deaths).

Here are the results for a few countries:

China: 9 day lag, CFR=4%

USA: 7 day lag, CFR=6.5%

Italy: 4 day lag, CFR=14.5%... (read more)

6Spiracular7moHere's a snippet from it... It also links to WHO's spreadsheet of COVID-19 candidate vaccines [https://www.who.int/blueprint/priority-diseases/key-action/novel-coronavirus-landscape-ncov.pdf] , which looks like a good resource in its own right (although this particular copy is probably a bit old).
2micpie7moA nice graphical guide on COVID-19 vaccines: https://www.nature.com/articles/d41586-020-01221-y [https://www.nature.com/articles/d41586-020-01221-y]

Metaculus is running a competition for accurate, publicly-posted, well-reasoned predictions about how COVID-19 will hit El Paso, Texas, in order to help the city with its disaster response. The top prize is $1,000.

Dr. Birx said in the press conference today that the US is counting any patient who dies with COVID-19 as dying of COVID-19. Are deaths during pandemics normally counted this way? Is it legitimate to call this number inflation--i.e., is there something fishy going on here--or is this standard practice?

2Taran8moNot a doctor, but it doesn't seem fishy to me: most people do not die, most of the time. If you sample a random person it's highly likely that they'll survive the next two weeks. This is true even among high-risk groups (the elderly, obese, etc.). If you hear that someone died, and that they had a CV19 diagnosis, you should not put much weight on the hypothesis that they died of something unrelated, just because of this low base rate. It makes more sense to worry about the opposite thing: people dying without formal CV19 diagnoses being excluded from the official statistics. For example, right now in New York about 200 people are dying at home each day, up from a baseline of 20 to 25, according to the city's department of health: https://gothamist.com/news/surge-number-new-yorkers-dying-home-officials-suspect-undercount-covid-19-related-deaths [https://gothamist.com/news/surge-number-new-yorkers-dying-home-officials-suspect-undercount-covid-19-related-deaths] These are not presently counted as CV19 deaths, but probably a lot of them are.

Cardboard and plastic: Tottori Prefecture goes low-tech to protect officials from COVID-19

This made my day.

  • Cheap, low-tech prevention measures.
  • ‘“I hope this system will send out a message that even Tottori, where no infections have been reported yet, is being very vigilant.”’ – Yes!

I want Tottori spirit everywhere.

Is the Chinese coronavirus data fake?

If so, what's a good estimate of the actual number of Chinese cases & actual number of Chinese deaths?

5ChristianKl8moIt would be interesting to look at Apple or Fitbit [https://www.thelancet.com/journals/landig/article/PIIS2589-7500(19)30222-5/fulltext] data to see patterns of ILI in China but I doubt they will be willing to share given the politics of it.

Hi all,

Does anyone know why US cases and deaths tend to be lower on Sundays and (especially) Mondays, compared to other days of the week? Is it something with the timing of how the data are processed?

I put up some quick plots here:

https://twitter.com/Nick_Lutsko/status/1254067996990959616

Apologies if this has been explained before and I missed it.

What should be the relative importance of natural herd immunity vs vaccination, in anti-corona strategy?

Scott Atlas argues that mass isolation prolongs the problem by delaying natural herd immunity. Meanwhile, countries like Australia and New Zealand have engaged in national isolation as well, creating entire national populations where natural immunity will be rare.

Will we see the world divided between countries that rely on natural herd immunity, and those which rely on the artificial herd immunity of vaccination? Does it make sense to have a differenti... (read more)

Hi,

I need your input on something. Sweden, as many of you know they are going for the herd immunity. Choosing to walk an unorthodox way.

They are still only reporting around ten thousand cases but with a death toll of 600 and rising. Probably the true number of infections is around 40k-100k depending on what mortality/asymptomatic cases we assume. The current rate, as in the number of hospitalizations per day is still within the the limits. It could probably go as high as double the death rate, before breaching the limit.

To reach heard immunity they need 60

... (read more)

Video explaining the Czech Republic's experience of having everyone make home-made masks in about 10 days, from a starting point of almost no masks being worn in public in the country.


Here is their COVID19 infection curves on a log chart (seems to be flattening).

With noticeably different governance and social reactions in different locations, I wonder if this situation will spur migration in the coming few years. At what point is it worth moving to somewhere with more sane (still broken; nowhere is perfect) government and social behaviors, even if it's more distant from your personal networks?

Seattle and the Bay Area are looking pretty good compared to New York and Florida (this could reverse over the next few months, but it's unlikely that by end of year there'll be no difference in terms how we ... (read more)

9CheerfulWarrior8moMy response here is pretty useless but I have relevant personal experience and not many human interactions recently so I might as well... I'm an EU citizen and as such I benefit from almost 30 sovereign countries competing over my presence (I could also move to a non-EU country but staying within EU is much easier). This has been my perspective for quite a few years. I have recently moved to a new country mostly because it offers low taxation for high-income individuals and the bureaucracy is generally friendly towards expat entrepreneurs and freelancers. I keep my investments/savings and even current accounts in more dependable countries. Following reports of how different countries respond to the pandemic, I've been also considering moving to another EU country for a month or two and staying there in an AirBnB. The primary criteria would be the political response to the crisis (the more rational the better; the less constraining individual freedom the better) and expected quality of healthcare, should I require it. (Another factor is possible barriers when I try to come back to my country of residence.) The one thing stopping me from doing that is lack of reliable data that would help me estimate the risks.
1Sherrinford8moSo how much of the differences between the Bay Area and NY do you attribute to a difference in government action?
3gwillen8moI have heard, and give some credit to, the theory that silicon valley tech company culture played a role in the bay area's response being relatively early. Tech companies were making contingency plans and sending their employees home, well before there was any kind of government action here. I don't know what fraction of employees / day-to-day interactions that represents. But e.g. all Google employees working from home seems like it could have played a nontrivial role in Mountain View, which was the epicenter of the bay area coronavirus outbreak.
1Dagon8moHard to separate government from cultural/behavioral issues - they reinforce each other. But variance in behaviors regionally (differences in how quickly governments signaled action and how well populations complied) seems likely to be a significant driver of variation of outcomes. Wild guesses: 30% from different patterns of trade and interaction with the broader infected world, 25% from different social structures and living situations (types of corner store and shopping/entertainment mechanisms), 45% from behavioral differences and reaction time. I don't think I can defend these guesses, and would be interested to hear other perspectives and missing causes of variation. Note that we don't actually know yet if NYC is all that much worse off than San Francisco. It looks that way currently, but a lot can change in a few weeks.

Late Edit: Pangolins with this viral infection have been found from smuggled ones from both Guangxi and Guangdong provinces, but do not show up in wild pangolin populations in general.

Despite the virus being characterized in pangolins, after looking into this, I now think it is basically incorrect to think of this as primarily a "pangolin virus." The pangolins were a dying canary in a coal mine, and probably caught it from something else that serves as the real reservoir species for this nCOV precursor*.

These pangolins were being smuggled when they were ca... (read more)

I think the brief era of me looking at Kinsa weathermap data has ended for now. My best guess is that that covid spread among Kinsa users has been almost completely mitigated by the lockdown and current estimatess of r0 are being driven almost exclusively by other demographics. Otherwise, the data doesn't really line up:

  • As of now, Kinsa reports 0% ill for the United States (this is likely just a matter of misleading rounding: New York county has 0.73% ill)
  • New York's trend is a much more aggressive drop than what would be anticipated by Cuomo&apos
... (read more)

[Years of life lost due to C19]

A recent meta-analysis looks at C-19-related mortality by age groups in Europe and finds the following age distribution:

< 40: 0.1%

40-69: 12.8%

≥ 70: 84.8%

In this spreadsheet model I combine this data with Metaculus predictions to get at the years of life lost (YLLs) due to C19.

I find C19 might cause 6m - 87m YYLs (highly dependending on # of deaths). For comparison, substance abuse causes 13m, diarrhea causes 85m YLLs.

Countries often spend 1-3x GDP per capita to avert a DALY, and so the world might want to spend $2-... (read more)

In addition to prediction markets, there are also, y'know, normal financial markets, which implicitly predict lots of things. But I don't personally know how to speak the language. For example, does the market say anything about the price of food, or possibility of shortages, in three months? Like, shouldn't there be some future / option / something whose price corresponds to a prediction about that? Or shortages of other things? Does anyone know?

A US study looking for recruits: NIH begins study to quantify undetected cases of coronavirus infection

A new study has begun recruiting at the National Institutes of Health .... to determine how many adults in the United States without a confirmed history of infection with SARS-CoV-2 have antibodies to the virus.
After enrollment, study participants will attend a virtual clinic visit, complete a health assessment questionnaire and provide basic demographic information—including race, ethnicity, sex, age and occupation—before submitting s
... (read more)

Why does recovery data seem so sparse? I only seem to be able to find that data for the global dashboards but that means it should be available. I would think that would be easily found as reporting only deaths is, to be nice, creating a situation where people will be misinformed and overly fearful.

I took a quick look on the links database but nothing jumping out for me there.

New data out of Germany using serological testing found 14 % of the population presented antigens against COVID19. This is massive if nearly 1/7 of the population has already contracted the disease and developed some type of immunity. This is only one piece of data, however, and is even much higher than the Iceland estimates of 50% asymptomatic and 50% symptomatic.

German study

https://www.land.nrw/sites/default/files/asset/document/zwischenergebnis_covid19_case_study_gangelt_0.pdf


Iceland information

https://www.cnn.com/2020/04/01/europe/iceland-testing-... (read more)

1Primer7moThat German study only refers to Germany's COVID-19 hotspot area and does not apply at all to the larger population. There are also connections to a PR agency and one of that agency's founders was the former head of the notorious "Bild" tabloid newspaper. Given the fact that on the one hand a PR agency should be able to provide a correct narrative, and on the other hand the study's results have been reported wrongly quite often, you should take that study with a grain of salt. (German) source: https://www.zeit.de/wissen/gesundheit/2020-04/heinsberg-studie-coronavirus-hendrik-streeck-storymachine-kai-diekmann/komplettansicht [https://www.zeit.de/wissen/gesundheit/2020-04/heinsberg-studie-coronavirus-hendrik-streeck-storymachine-kai-diekmann/komplettansicht]

I'm trying to make some educated guess about the situation, but it looks like the data are very lacking. Could someone validate my logic please?

1. Some people claim that SARS-CoV-19 could have been around for ages, "everybody's bad flu last autumn was this thing" and basically nothing is happening except panic. People are dying not because of the virus, but because everybody is going to hospitals making them overcrowded. People dying of other reasons just happen to also have almost-harmless COVID-19. When I've heard this couple wee... (read more)

8Lukas_Gloor8moIf you go through my LW comment history you'll find that I'm in the camp of "The IFR is definitely >0.3%, and very plausibly >0.8%" and that I seem to care somewhat strongly about conveying this to others. :) Maybe you'll find some of the discussions (or links therein) useful. (Unfortunately I can't recommend any single resource that looks super convincing all on its own.) Edit: By "very plausibly" I mean 25% likely rather than 50% likely. By "definitely" I mean 97% likely.
7mfoley8moWe're finally getting some results on this [https://twitter.com/TabulaFour/status/1247487723470020608]. An antibody test in an Italian town an hour outside Milan has been done. 2000 people out of a population of 6169 have been tested. Results: 13-14% of the population tested positive for the antibodies (~832 people). The town had 27 confirmed cases, with 4 confirmed deaths. 6 deaths of all causes were recorded in March. So this is arguably good news. It implies an IFR of about .5%. If the population here is older/unhealthier than average, as seems to be true for Northern Italy as a whole, then we could see that number dipping down further. Covid being less than an order of magnitude worse than the flu is starting to look likely but there is still a long way to go to reach herd immunity and I personally think that they should at least try for actual suppression unless we get really good numbers on the death rate and are more confident that survivors won't have lasting side effects.
5Lukas_Gloor8moSomeone in that twitter thread points out that with subtracting false positives, it implies that 10% would be the better guess, as opposed to 13-14%. Does that make sense? Then 4 Covid-confirmed deaths per 620 people would be 0.66%. And what about sampling bias? I read that the tests were voluntary. Unless someone was extremely meticulous about trying to somehow get a representative sample, I don't think it's reasonable to treat this as random. It's really quite obvious that people who had flu-like symptoms for a couple of days will be more curious to go among people and have a needle stuck into them. .
6Bucky8moI share your rough estimates of IFR in your other comment here although I was concerned about how high IFR might be with overwhelmed hospitals. Sampling bias at its worst here would mean that IFR is 3 times more than those calculations (i.e. 1.5-2%). If this is the worst case in Lombardy where the hospitals are overwhelmed then it is something of a relief to me that higher rates are unlikely.
1mfoley8moBoth good points. Hopefully we get more tests of the sort reported soon.
1Remoddy8moVery interesting, thanks. I think it's 13% of tests, not 13% of entire population of 6'169, so not 832. I don't speak Italian and struggle to find any details. Actually they didn't mention that all 2'000 samples were processed. On 5th April the mayor of the town posted [https://www.facebook.com/pg/robertofrancese.it/posts/] a photo of newspaper mentioning "29% of 38 persons" positive. So I would not be surprised if they have taken blood from 2'000 people, processed 100 of them so far and this results got it to newspaper. Very promising (we get more test data!), but I wouldn't draw any conclusions on this yet.

IHME published a dashboard with state-by-state projections of coronavirus peaks: http://covid19.healthdata.org/projections

The accompanying FAQ is also interesting: http://www.healthdata.org/covid/faqs

6Wei_Dai8moThe IHME Covid19 Model is Dangerously Flawed [https://medium.com/@robertbracco1/the-ihme-covid19-model-is-dangerously-flawed-c19928464db1] :
2ioannes_shade8moThanks, hadn't seen that. Also just saw this, which makes a lot of the same points: https://westhunt.wordpress.com/2020/04/04/ihme-projections/ [https://westhunt.wordpress.com/2020/04/04/ihme-projections/]
4Wei_Dai8moI was suspicious of the IHME model several days ago when I first saw it, but couldn't find a detailed description of their methodology. (It's really well hidden, and doesn't even appear in their FAQ section.) Finally found it [https://www.medrxiv.org/content/10.1101/2020.03.27.20043752v1] yesterday, noticed the "similar to Wuhan" assumption, then saw the page criticizing it linked in the comments section for the paper.
1cian8moCan anyone help me to understand these graphs? The 'deaths per day' graphs seem to incorporate actual data up to April 1st and to be projections from there, which suggests that they are using the actual death rates to calibrate some parameters of their model. But the 'hospitalization' graphs don't seem to incorporate any actual data, and seem to be very different from the reality: for example, for April 1st (when the models were last updated), the "all beds needed" and "ICU beds needed" numbers for New York State are 50,962 and 10,050; but it looks like the actual number of people in hospital for Covid in NYS on that date was about 12,500, with about 3,000 in the ICU (source: 'NYS total hospitalized' graphs here [https://gothamist.com/news/coronavirus-statistics-tracking-epidemic-new-york]). [[https://gothamist.com/news/coronavirus-statistics-tracking-epidemic-new-york]).] Does that mean that they are not trying to fit their model to actual hospitalization data at all? If so that seems like a problem: hospitalization rates should be much better than death rates for estimating what effect social distancing measures are having, since there is so much time between infection and death.

Does anyone have any idea / info on what proportion of the infected cases are getting Covid19 inside hospitals? This seems to have been a real issue for previous coronavirus.

I'd say there might be a stark difference between countries / regions in this area. Italian health workers seem to have taken a heavy blow. Also, 79 deaths in Brazil (total: 200) came from only one Hospital chain/ health insurer, which focus on aging customers (so, yeah, maybe it's just selection bias?).

(Epistemic status: low, but I didin't find any research on that aft... (read more)

South Korea, as always, are a treasure trove on information - they publish details every day which includes major outbreak clusters, some of which are hospitals. Of the non-cult related cases where they have managed to identify the source of the infection, hospital based infections account for 20%. If you include cases where they haven't identified the source then it's more like 10% which is probably a fairer reflection as hospital clusters probably mainly do get identified.

(They changed their reporting layout on March 25th and the new version doesn't quite contain as much information so I've based this on the 24th)

This article and the linked study propose that smokers are getting infected less often due to the nicotine rather than the smoking. Is it worth getting nicotine gum and patches?

Oxford COVID-19 vaccine begins human trial stage

The vaccine is based on an adenovirus vaccine vector and the SARS-CoV-2 spike protein,

I'm trying to formulate a response to, what at least in my circle of friends and acquaintances, is an increasing insistence that people had Covid-19 in November 2019.

If we assume someone did have Covid-19 in upstate NY for instance what else would have to be true?

I think mainly, that a novel virus made its way around the world without detection would be pretty major. And then it mutated in Wuhan, China unleashing this second, more virulent strain, meaning that the pattern of outbreak that we all witnessed beginning in Wuhan was some kind of 'sec... (read more)

TL;DR: No. The earliest I'd buy for pandemic-track COVID is early-to-mid December, and in China or maybe Australia. Otherwise, it'd have to be a non-pandemic substrain that died out early, and left no children behind except the first Wuhan strain. The theory loses in an Occam's Razor fight with "your friends probably had something else back then."

ETA: This post mentions a second independent line of evidence on the matter (using antibodies), and also dates the first COVID-19 cases to no earlier than December.

I'm going to be basing most of this on nextstrain's COVID-19 phylogeny data and their accompanying chart.*

The earliest sequenced US case we have came from Washington. The Washington strain's earliest sequenced sample was 5 weeks of mutation out from the Wuhan strain at the time, leading to the inference that it arrived (or at least split off from the Wuhan gene-pool) in about mid-January. Australia seems to have a divergent strain that might have broken off even earlier, possibly as far back as mid-December.

Going on their graph, they dated the Wuhan last common-ancestor (LCA) strain to roughly mid-December, and the all-strain LCA is the same one.

(I'm not going to detail all of h

... (read more)
3vidro37moThanks for this, I was not aware of the Bedford lab's work. Wondering if you (or any other LW reader) has any thoughts on on the emotional aspect of this. Seems folks are very attached to the idea that they had Covid-19 earlier than it was identified. It's starting to get into that 'can't be reasoned out of something they haven't reasoned into' area. I'm curious why people are so adamant that an extremely unlikely scenario is actually the most likely explanation. But i guess this cuts across all kinds of mental models and not just covid-19.
4Spiracular7moI don't really know, I wouldn't do this. Here are a couple of possibilities that ran through my mind. * COVID's symptoms are basically "see: undefined flu-like symptoms." This might just be an equivalent of "I looked up my symptoms on WebMD and it's definitely cancer," only with COVID. * There was that revelation that Washington got it earlier than expected. Maybe they're pattern-matching blindly to this. It's really easy to do so, especially if there was another nasty flu or cold going around back then (which there probably was). * Motivated reasoning * People want an excuse to go about their life as normal (or to complain if they're not) * People especially hate taking the possibility of their own death seriously * Nobody wants to deal with the guilt of knowing that their "normal" actions may be endangering others (cough asymptomatic transmission), and they would rather believe something potentially-false than contend with that It's probably a mix of all three, or even more. With all due affection, I've heard that New Yorkers as a whole are fairly prone to contrarianism. So the frequency with which you're hearing this might also partially be local variance.

Ok, a question of which I assume that people here can quickly provide the answer:

How certain are we that age groups with low likelihood of developing symptoms - in particular, children - are actually infectious? Sure, there is asymptomatic spread in general, but I guess being asymptomatic also correlates with the ability to quickly kill the virus and thus not transfer it to others. So the first question is HOW infectious are people who are and stay asymptomatic? Is there good evidence on this?

Harvard published a study on link between PM2.5 pollution and mortality.

We found that an increase of only 1 μg/m3 in PM2.5 is associated with a 15% increase in the COVID-19 death rate, 95% confidence interval (CI) (5%, 25%)

Places most hit so far are on the more polluted side so one can expect final CFR/IFR be lower than estimated from current data.

How much do we know about gender differences?

I saw a reddit thread suggesting that women have different symptoms than men, though it was super anecdotal and I can't find it now. I know women have a lower death rate, and I understand that was originally suspected to be because men smoke more but more recently maybe that turns out not to explain the whole difference? This paper suggests that men have more ACE2 than women, which is the enzyme the virus binds to.

Is this a thread that's been well explored by others?

Something to keep an eye out for:

we also predict that the virus may invade multiple brain tissues, which may help explain to the loss of taste and smell in infected individuals. Has anyone seen evidence of further brain damage in COVID-19 patients? Please share if you do!
Also unexpected is the prediction that the virus may be able to invade the reproductive system (vagina, uterus, testis, cervix, ovary). Has anyone seen evidence for this? Please share if you do.
The COVID-19 targets do not show significant overlap with any major disease module (we tested it
... (read more)

"The Case for Universal Cloth Mask Adoption & Policies to Increase the Supply of Medical Masks for Health Workers"

Excerpt from Twitter thread summarizing it:

We have very good evidence that universal adoption of cloth masks will combat the spread of the virus. Specifically, we know that 1) asymptomatic people spread the virus, 2) mask wearing by infected people prevents them from transmitting the virus (the report provides citations).
How large are the benefits? Even if masks reduce transmission probabilities by only 10% (and as you'll see
... (read more)

Innoculate GI tract with live virus. Suffer GI symptoms. Get immunity. Avoid respiratory complications.

4gwillen8moThis is an interesting idea but would benefit from more elaboration. Why the GI tract in particular -- do you have evidence that this will significantly reduce the risk of respiratory symptoms, or just speculation / "common sense"? Is there evidence that the GI tract as the initial site of exposure will produce an infection / an immune response, but with a reduced chance of the infection spreading to the lungs / respiratory tract? Or with it taking longer to get there, similar to Robin Hanson's thoughts about deliberate exposure with a low dose, like variolation of old? If you have any links/references, please definitely post them. If it's just speculation, it's interesting speculation but tell us what it's based on.

Exactly like variolation, except you do it intelligently to minimize lung infection.

SARS and SARS-Cov2 are both ACE2 dependent for cell entry.

ACE2 expression in AT2 cells in the lower respiratory track is known to be on the apical surface, that is the side of the cell facing airspace, not the basal surface facing vasculature. Hypothesis would be that lung infection is much more efficient and virulent by droplet delivery rather than by virus circulating in blood stream. I am also under the understanding that the kidney and heart complications are due to poor oxygenation due to the respiratory distress, not a primary viremia in those organs.


https://www.ncbi.nlm.nih.gov/pubmed/15141377

Tissue distribution of ACE2 protein, the functional receptor for SARS coronavirus. A first step in understanding SARS pathogenesis.

"In conclusion, ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, which might provide possible routes of entry for the SARS-CoV. "


ACE2 expression by colonic epithelial cells is associated with viral infection, immunity and energy metabolism

https://www.medrxiv.org/content/10.1101/2020.02.05.20020545v1.full.pdf


The digestive system... (read more)

2gwillen8moCool, thanks for expanding on that. You might want to link this comment in your other comments about this idea, so people have some details to read. It's a lot more informative than the one I was responding to!
1Nicholas Campbell7moNeat idea, although immune responses can be tissue specific (to a certain degree).

Swiss cardiologist Nils Kucher is going to start a study to check whether blood thinners help covid-19 patients, suspecting that lung embolisms play a role in hospitalization and mortality. (https://www.n-tv.de/wissen/Helfen-Blutverduenner-bei-Corona-Infektion-article21722726.html)

I am not sure how it is possible that there are reports in the media claiming a low IFR (0.1%) when Lombardy has an official population fatality rate (i.e official COVID19 deaths over total population) of 0.12%, and unofficial one of 0.22% (measuring March and April all cause mortality there are ~10000 excess deaths) and a variability of up to 10x of casualties between towns more or less hit, indicating that only a small fraction (~10-20% imho) of the entire population was infected. I am pretty confident that the IFR is around 1% on average: it’s p... (read more)

Hi all. I haven't been to LessWrong in a while...but the mess in the world has reminded me how important it is for us to strive for clear thinking as a community. With that, I'd like to share a Coronavirus pandemic information site that has really good analysis for tracking the progress of the pandemic. It's here: https://ourworldindata.org/grapher/daily-covid-cases-3-day-average

(it seems that I cannot embed or add images)

<iframe src="https://ourworldindata.org/grapher/covid-confirmed-daily-cases-epidemiological-trajectory" style="width: 100%; height: 600px; border: 0px none;"></iframe>

How Large is the Iceberg? New Evidence from Kansas City

The details are currently vague, but I have tried to report key information, as this is one of the few efforts at random sampling that I am aware of. My main hope is to inspire someone with more expertise and ability to access details to expand the analysis.


Basics:
Johnson County, with a population of 602k, has reported on preliminary results from an effort to test a representative sample of its residents. I have been unable to find details about how they constructed the sample, so cannot assess how re... (read more)

1muchcharles7moHow would 0.1% IFR square with New York’s state fatality rate of .08%? Seems unlikely it is representative, or it Johnson city was at earlier stage and had more recent exponential growth.

Why are surgical or self-made masks supposed to be better at protecting others than at protecting oneself? Naively, it seems to me that the percentage of filtered droplets/aerosol should be the same regardless of the direction in which it is breathed.

5clone of saturn8moI think it's mostly because the mask slows down the flow of exhaled air, which reduces the distance the droplets travel before they evaporate or fall to the ground. You can see this illustrated here [https://youtube.com/watch?v=kYJvU81DKgk] and what happens without a mask here [https://vimeo.com/402577241].
1muchcharles7moAerosolization maybe happens more after exposure to air where water evaporates off of the lipid/protein shell. On exhale into mask it hasn’t had as much time to evaporate and is in humid environment, on inhale brought mask it has made its way over from another person and has had more time to aerosolize in drier air.
1muchcharles7moAnd as mentioned below, large droplets would be caught and kept off surfaces reducing hand to face transfer.
1Remoddy8moDon't know about percentage of filtered droplets/aerosol in both directions, but I would guess the reasons include: 1. A mask doesn't protect your eyes 2. You are likely to touch contaminated outer surface of your mask (and then touch your mouth, scratch your eye etc and get infected), but other people probably won't touch the inner surface of your mask.

Mass testing seems like a promising brute force strategy that can keep R < 1 after lockdown, without requiring contact tracing. I'm pretty early in thinking about this but wanted to share my thoughts to encourage parallel efforts. A few possibilities (not mutually exclusive):

1) RNA testing: If everyone is given a daily RNA test and positives are isolated, transmission will likely be very close to 0. The US is still a factor of 1000 away from doing this (for comparison, RNA testing has scaled by 400x in the last month). However it seems likely that ... (read more)

1AlexSchell7moSome very encouraging developments. There is a PCR protocol [https://www.biorxiv.org/content/10.1101/2020.04.06.025635v1] that can test 100,000 samples in a single machine run, making millions of samples per day feasible, ignoring sample collection capacity. On that front, FDA just approved (EUA, limited scope for now) a sample collection protocol [https://www.rutgers.edu/news/new-rutgers-saliva-test-coronavirus-gets-fda-approval] relying on saliva samples rather than nasopharyngeal swabs (would mean enormous increase in sample collection capacity). The prospects for plan #1 look dramatically better. On plan #3, I was hoping this would work as a backup or low-tech option for poor countries but it looks like most estimates tend to put asymptomatic + presymptomatic transmission at 50%+ of all transmission, which makes this pretty limited.

Idris Elba and his wife, two weeks after testing positive for the coronavirus, say they still have experienced no symptoms

The pool of people who 1. received a test while asymptomatic 2. tested positive and 3. are updating the public about their condition through mass media seems very small to me. The fact that two of them are turning out to remain fully asymptomatic seems to indicate that this is in fact likely to be a common thing. Somewhat surprising imo.

2Joe_Collman7moInteresting. I suppose another possibility is that both tests were false positives. Unlikely assuming that false positives are independent - but is that a reasonable assumption here? It seems possible they'd be correlated - e.g. if the tests were picking up some other infection. Does anyone have a good understanding of this (in general, needn't be SARS-cov-2 specific)? Under what circumstances is it (un)reasonable to assume that false positives are independent?
2leggi7moTest reliability: * Sensitivity and specificity of the test. an image here [https://qph.fs.quoracdn.net/main-qimg-4e6846605de48c4b372265b47e32ac15] sensitivity = number of true positives / number of true positives + number of false negatives (true positives that test negative) specificity = number of true negatives / number of true negatives + number of false positives (cross-reactions, other infections giving positive result) Some info. I found here [https://www.fda.gov/media/136151/download] about covid19 PCR test. (It might not be the test that was was used but as far as I'm aware all current covid virus testing is via PCR so the tests should be of a very high specificity - 100%?!) A bio-optical laser sensor [https://www.technologynetworks.com/diagnostics/news/new-saliva-test-to-instantly-detect-coronavirus-333236] for COVID testing is under development. * Technique/testing protocol. Contamination of swabs is a possibility for positive results in a negative patient. (e.g. test personal is positive and contaminates sample, contamination in lab.) Poor technique on sampling, 'bad luck' just missing the virus on sampling, using the wrong type of swab, poor handing of sample will give a negative result for a positive case.

Seems like a good model for estimating total infections, from my quick look: https://observablehq.com/@danyx/estimating-sars-cov-2-infections

I haven't poked its methodology.

Which US federal agencies should receive more funding in response to coronavirus? Which should receive less?

From the Center for Health Security's covid19 brief:

PANAMA IMPLEMENTS GENDER-SPECIFIC SOCIAL DISTANCING In an effort to further enforce nationwide social distancing measures, Panama recently announced that it is implementing gender-specific rules for when people can leave their homes. Women will be allowed to be outside on Mondays, Wednesdays, and Fridays, and men will be allowed on Tuesdays, Thursdays, and Saturdays. On Sundays, everyone must remain indoors.

More info here. Maybe someone was listening to Scott's surname-based lockdown suggestion.