Coronavirus information and analysis bleg

What are the best things to read to estimate what’s going to happen from here?

In particular, what is the best way to think about how to make inferences, or not, from extrapolating current trends about case and death numbers?

What is “what happens from here” going to be most sensitive to in terms of potential best remedies? Regulatory decisions of some kind? Which features of local public health infrastructure will matter the most? Will any of it matter at all?

Which variables should we focus on to best predict expected severity?

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Right now the best news sources are 75% emerging information and 25% experts speaking in relative generalities (which is currently the best they can do). I suppose a reliable source is one that makes that clear.

This is a test case for authoritarian efficacy in China and institutional trust in the West. I doubt China will decide that transparency and public engagement, or expressive freedom for experts, will prevent this in the future. Who knows about the rest? I dread hearing that the virus has landed in India or Lagos.

It has landed in India

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Ostensibly, these folks are monitoring the situations reasonably closely:

https://www.who.int/emergencies/diseases/novel-coronavirus-2019

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Check out Maria Ma, MPH (@guacamolebio):

https://twitter.com/guacamolebio?s=09

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I recommend these reports:

https://www.imperial.ac.uk/mrc-global-infectious-disease-analysis/news--wuhan-coronavirus/

http://www.centerforhealthsecurity.org/resources/2019-nCoV/index.html

Abstract from most recent MRC Centre report:

We estimate that, on average, each case infected 2.6 (uncertainty range: 1.5-3.5) other people up to 18th January 2020, based on an analysis combining our past estimates of the size of the outbreak in Wuhan with computational modelling of potential epidemic trajectories. This implies that control measures need to block well over 60% of transmission to be effective in controlling the outbreak. It is likely, based on the experience of SARS and MERS-CoV, that the number of secondary cases caused by a case of 2019-nCoV is highly variable – with many cases causing no secondary infections, and a few causing many. Whether transmission is continuing at the same rate currently depends on the effectiveness of current control measures implemented in China and the extent to which the populations of affected areas have adopted risk-reducing behaviours. In the absence of antiviral drugs or vaccines, control relies upon the prompt detection and isolation of symptomatic cases. It is unclear at the current time whether this outbreak can be contained within China; uncertainties include the severity spectrum of the disease caused by this virus and whether cases with relatively mild symptoms are able to transmit the virus efficiently. Identification and testing of potential cases need to be as extensive as is permitted by healthcare and diagnostic testing capacity – including the identification, testing and isolation of suspected cases with only mild to moderate disease (e.g. influenza-like illness), when logistically feasible.

Should the news reports indicating that healthcare providers have been infected change one’s estimates that it is the most serious cases that are the most virulent, and the more mild cases do not lead to many more infections? I suspect not, or otherwise the disease wouldn’t be spreading like it is.

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Watch the markets. Various categories of travel in China are down 25+%. Wuhan virus going to slow the global economy regardless of the death toll.
https://www.cnbc.com/2020/01/26/how-coronavirus-is-beginning-to-hit-chinas-economy.html

If the virus establishes outside of China then it will spread in less well managed countries, and possibly in industrialized countries which are unwilling or unable to apply restrictions of the sort that Xi Jinping can easily order.

Start thinking about this at a personal level. Start acting on this at a personal level. More hand washing throughout your day. Become aware of coughing people and avoid them. I bought lots of bottles of hand sanitizer yesterday. Store brands are way cheap. Act now.

Can you work from home some days? Dial back your exposure to all respiratory viruses. You could at least avoid a cold or flu.

--but observe how the prudent utility of wearing protective masks over noses and mouths conflicts with face-recognition surveillance preferences that have emerged in our surveillance era.

(Who manufactures standard-issue respiratory-protection masks?)

How insistent can tech surveillance advocates be as a consequence? Do they need to refine eye-scanning to compensate for partial face-covering?

Gait recognition. And at some point, machine learning bloodhound-on-a-chip or real-time DNA sniffing of the cloud trail of dead cells that is constantly floating off everyone. Or why get fancy... your phone is a tracking device.

It's a moot point anyway. You could easily still recognize your friend despite the covering, so why would machines have a problem? It's a surgical mask, not a Halloween mask.

Would gait recognition begin to fail when bipeds begin staggering or become afflicted with severely labored breathing?

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A standard respiratory mask won't protect you from this virus. You need to get an N95 rated mask.

As a bonus, those masks will obscure even more of your face.

I've already got my boxes of N95 masks. Got some N100 too in case the pandemic is here and I have to go to a high risk zone like a hospital.

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At a policy level: we need much bigger and more efforts to develop vaccines.

We also need to scale up production of protective gear for health workers so that they don't abandon their jobs or get sick in large numbers. Treat this as an opportunity to push for a big decrease in nosocomial infections.

College professors should be pushing for the ability to deliver all lectures over video connections. You profs are targets at which rooms full of coughers aim. Get yourselves out of the line of fire.

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I don’t know how serious this virus is, but isn’t some epidemic inevitable sooner or later? The plague, influenza, smallpox, syphilis, and tuberculosis caused serious illnesses and deaths in the past. The microbes have not stopped evolving. We should probably plan for some outbreaks every fifty years.

Funny how the modern plagues usually come from Red China. I wonder why.

@Frederick Miller - it's quite trivial once you understand this, actually, see: https://en.wikipedia.org/wiki/Lanchester%27s_laws

It's also the same reason why you can get laid in the Philippines more easily than say the USA, which has a larger population. Or for that reason why electric cars are inferior to fossil fuel cars for most tasks (or why batteries are inferior to fuel). Density is the key, also known as availability in energy. Solve for the equilibrium.

Live game (animal meat) markets.

"The coronavirus that has spread from Wuhan has been linked to the sale of live wildlife at a market that experts describe as a perfect incubator for novel pathogens."

https://www.nytimes.com/2020/01/25/world/asia/china-markets-coronavirus-sars.html

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Ray, you've really got to try an electric car. Even the American ones are good:

https://www.solarquotes.com.au/blog/tesla-model-s-review/

They're good as a flashy way of showing off wealth, but do not meet the average persons need, and are not affordable.

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+1 Thread winner! It's true. And pigs share a lot of the same anatomy as humans, so arguably the recent coronavirus was a mutation of the pig virus that wiped out 25% of China's swine recently.

Bonus trivia: fear not fast acting viruses like Ebola, that kill the carrier before they infect others, but fear the slow acting "SARS" type viruses and the 1918 viruses that take a long time to incubate. Those closing credits of the modern Planet of the Apes film comes to mind... vectors via airplane travel and the mass movement of people.

I remember being told to fear the SARS virus. For about five minutes.

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2019-nCoV didn't come from the pig virus (e.g. Coronavirus is a RNA virus, African Swine Fever is DNA, they are very different).

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Aside from things like tapeworms that have lifecycles that need organs, anatomy is irrelevant. It's genetic similarity that matters.

China keeps popping these viruses out because of their population density, and the way they keep their animals

"...the way they keep their animals” being code for the gender imbalance that prevents a lot of poor country men from finding human female companionship.

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I have no expertise but from what I’m reading: The key variable is contagiousness during the asymptomatic incubation period. If not very contagious at that time, than screening measures and quarantines should be effective and we have a SARS type scenario. Otherwise, screening will not work and we have something like than 1918 Spanish flu until a vaccine is developed.

https://www.ecdc.europa.eu/sites/default/files/documents/Risk-assessment-pneumonia-Wuhan-China-26-Jan-2020_0.pdf

Second-order effects are a big question. What is the impact on supply chains? Does the US have shortages of medicines in general because of manufacturing stoppages in China? Is there social unrest in the densely populated developing cities of Asia? What happens if you have something like the Black Death but just for a year until a vaccine is deployed, rather than for decades and centuries?

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China’s health minister is reporting that it is contagious during the incubation period, though some experts are skeptical.

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I do not hesitate to cast a vote here for Daniel Defoe's Journal of the Plague Year.

Another MIE, this one a fashion statement for 2020/Year of Rat, whatever your calendrical nomenclature preference:

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

I second your vote for "Journal of the Plague Year". A vivid account of the Black Death, and wonderfully readable, like just about everything by Defoe.

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The classic American fiction concerning pestilence remains Poe's "Masque of the Red Death", "classic" because its reading has permitted nuance and adaptation to all kinds of specifically American ills in the decades since it appeared in 1842.

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Even the Chinese are saying it is spreading faster than SARS. Problem is estimating fatality and true contagiousness. Only hope is to rely on proven data outside of China for rigorous estimates.

"Only hope is to rely on proven data outside of China for rigorous estimates"

Yes, exactly. The Lancet's ICU and fatality rate based on early Chinese data seems quite high (32% and 15% respectively). The R0 being ~2.7 is believable in the overall context. Hopefully we get more info from these cases outside of China.

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You should know that infectious disease and public health academics tend to be very left wing and insist on very tendentious and week research grounds that any attempt to restrict travel "doesn't work because science."

So, for instance, if flu is transmitted at an exponential pace, and the first week or so of an epidemic sees a certain amount of disorganization and chaos until everyone at health institutions gets on the same page, then would restricting travel (maybe from certain countries) for a week or two or at least a few days maybe help hold down infections and deaths? "No, it doesn't work, Nazi!"

During the SARS epidemic these guys drove me crazy. I think economists could do a better job in this field.

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Now the impeachment stuff is finished the wonderful media organizations can start doing their week long 24 hour coverage. We will surely be adequately informed. Maybe we should be thankful that almost no one is watching.

I'd watch for indications of mutation. It is obviously contagious and will spread. So far the death rate is not extreme. A change in that rate over time is useful to know. As it spreads the incubation times will become known.

Unless it mutates it seems to be bad not catastrophic so far.

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Likely the best answer is time. Early speculations will be weeded through, and as correct information is determined, it will be distributed though sources that are interested in providing reliable and useful information.

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Wuhan has 11 million inhabitants. Quarantine of such scale have never been imposed. The Communist Party will not shoot people trying to escape. The cat (tiger) is out of the sack. Taking Bocaccio's Decameron as a precedent, we shall have fun and then, maybe, die.

Do you promise to check in next month so we can laugh at your prediction about our imminent demise?

...he won't be able to.

Bocaccio is more optimist. His Decameron was written during the Black Death epidemy in Florence. Seven young ladies, ranging in age from eighteen to twenty-eight, meet at mass. and they are all of genteel birth. Let’s get out of here, the eldest, says. Let’s go to our country estates. The other women say that they’d love to, but they think they should bring some men along. They assemble three gentlemen linked to them and the ten young people decamp for the countryside. TV was yet uninvented but they manage to have great fun and no one dies.

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I just saw this, apparently it is spreading before the symptoms are obvious.
https://www.youtube.com/watch?v=0jAWPcyPFQc

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Relax. So far it is propagating and killing at a far lower rate than SARS, inside and outside China.

So far it's hard to know. Could be that a LOT of people have been exposed, are asymptomatic, and only very few have died so it's actually a mild version of a normal flu. Or maybe relatively few have been exposed and it's lethal. So far I'm leaning toward standard flu + hysteria, but could be wrong.

Problem is that even if it is only somewhat worse than the flu, if it spreads far enough and fast enough, it will overwhelm medical providers in certain parts of the globe, including China. So even if it isn’t super deadly or severe on a case by case basis, there could well be enough cases to cause havoc and devastate the world’s largest economy, and probably several other countries as well.

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normally i would say examine social media, web searches for symptoms by geography, etc. however this is China. The "great firewall" will play a large part in the post analysis blame game for this outbreak.

yeah those guys are great in a crisis - remember World War 3!

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> In particular, what is the best way to think about how to make inferences, or not, from extrapolating current trends about case and death numbers?

Current numbers are nearly worthless. You don't get cases popping up all over the world when at the time there were only, reportedly, a few hundred cases at the epicenter. Outbreak was far more widespread at that point. Very contagious. Most contagious sub-types are being selected for.

> Which variables should we focus on to best predict expected severity?

Reportedly discovered in early December. Not many deaths since then. So probably a dud. At least, not approaching "Spanish flu"-like impact. If more contagious sub-types are outracing more deadly sub-types then more deadly sub-types may not get a chance to spread, since people will have developed some immunity.

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> What are the best things to read to estimate what’s going to happen from here?

https://www.biorxiv.org/search/2019-nCoV%20numresults%3A10%20sort%3Apublication-date%20direction%3Adescending

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Given that Marginal Revolution is old for a blog, try looking back at your own previous posts:
https://marginalrevolution.com/?s=%22avian+flu%22
https://marginalrevolution.com/?s=sars (more irrelevant hits than the first)

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Here is Taleb's paper on your questions:

https://twitter.com/nntaleb/status/1221486205847646208

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If the virus is new to human-to-human transmission, you will need a sort of discontinuity analysis to look for major adaptive shifts...

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Garbage In, Garbage out - if you can't trust numbers from China, you got nothing right now.

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Adam R tried to submit the following, it would not clear the software:
Here are the reliable sources of information I’ve found so far and some of their analysis:

Tom Inglesby, Director, Johns Hopkins SPH Center for Health Security
https://twitter.com/T_Inglesby
See thread this morning on necessity of making preparations for possibility containment will fail: https://twitter.com/T_Inglesby/status/1221434570714669056

Michael Osterholm, Director, Center for Infectious Disease Research and Policy at the University of Minnesota, on possible economic impact and shortages in US medical supplies/drugs from areas in China that are under quarantine:
https://twitter.com/CNBCTheExchange/status/1220814002894360579

Maia Majumder, researcher at Harvard on probabilistic modeling, data science, and systems epidemiology. Released a preprint study transmission of this virus:
https://twitter.com/maiamajumder
Explainer thread on study: https://twitter.com/maiamajumder/status/1220501403057229824

Christian Althaus, computational epidemiologist, released a “preprint” study on transmission of this virus:
https://twitter.com/C_Althaus

Helen Branswell, infectious diseases & global health for
@statnews
https://twitter.com/HelenBranswell

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"This Week in Virology" podcast to hear what real virologists are thinking.

http://www.microbe.tv/twiv/

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If I were an epidemiologist by trade, I would of course have contact with Russian epidemiologists.

I guarantee you there are textbooks on epidemiology from the old Soviet Union that have a few worthwhile observations in their chapters on contagious diseases that started the way the current bugaboo virus started.

Remember, there was an awful lot of technical skill in the old Soviet Union, and they had lots more information on epidemiology than they would have if they had lived in a less deleterious environment.

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According to wikipedia, some of the first research on MERS was posted on https://promedmail.org/. So that could be a source to check this time around.

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Wouldn't super forecasters look at evaluations of public health organizations and officials attempting to contain the SARS outbreak?
https://www.ncbi.nlm.nih.gov/books/NBK92460/
Good luck.

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Well, it's the right time to think once again of air pollution in the name of economic development.

Ozone and nitrogen and sulfur oxides in polluted air contribute to chronic irritation of respiratory tracts making people more susceptible to contagion of any flu virus, including the new one.

So, when will air pollution matter?

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The predictors at Metaculus are aggressively keeping up with this, and are very good about filtering and sharing new information. See the salient questions at https://www.metaculus.com/questions/?search=cat:bio--infectious-disease--novel-coronavirus

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https://promedmail.org/promed-post/?id=20200126.6918012
https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)30183-5/fulltext#seccestitle170
https://blogs.sciencemag.org/pipeline/archives/2020/01/27/coronavirus

Hat tip to the excellect always excellect https://twitter.com/pkedrosky?ref_src=twsrc%5Egoogle%7Ctwcamp%5Eserp%7Ctwgr%5Eauthor

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Wierdly enough, last June I experienced an illness which strongly resembles the symptoms of this coronavirus: low-grade fever for 1 week, dry cough, progressing to bronchitis after a week, resolved on it's own after 3 weeks. I went to an urgent care and they just said that something was "going around". Got it from my daughter via preschool. One of the other kids was hospitalized with pneumonia (but was ok). The urgent care doctor said it was viral so they couldn't really tell what it was, but that it was just circulating at a low level. Given the bronchitis, I can totally see how it could kill people (and even predicted "next winter, this is going to kill people". I just didn't think it would be in *China*. )

So I sort of suspect maybe this thing has been out there for longer and just hasn't hit the public health radar until now.

The incubation period is also pretty consistent. My daughter got it first, then 2 weeks later I got it, than 2 weeks after that my other child got it (probably from me). Which makes it wierd if it was the flu because the flu usually travels faster than that.

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Hope this helps:)
https://www.xuntang.net/welcome/china-novel-coronavirus-n-cov-and-the-stupefyingly-soothing-effect-of-statistics-modelling

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You're welcome! https://www.wikiwand.com/en/Mathematical_modelling_of_infectious_disease

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Mr Dalio's take. Proceed with caution, graphs ahead.

https://www.linkedin.com/pulse/our-early-thinking-coronavirus-pandemics-ray-dalio/?published=t

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