Richard Sprague

My personal website

Wuhan COVID19 ncov2019 Coronavirus: Best Resources

Created: 2020-01-31 ; Updated: 2020-05-21

My list of links and information I find most useful in trying to understand the COVID19 outbreak.

Latest important news

Half of COVID19 deaths happen in nursing homes: freopp.org

OpenSAFELY: factors associated with COVID-19-related hospital death in the linked electronic health records of 17 million adult NHS patients A big open source project using NHS data to compute risk hazards

My favorite links

Compare locations based on number of days since first n cases: e.g. WA, CA, LA, MI

Coronavirus Map lets you zoom in to the county level. (@embrein)

Another good map also tracks every news article and lets you filter by state: 1Point3Acres

Rather than wade through all the daily posts and articles out there, save time with this 97 page summary by some professors at the London Business School. The full site includes key charts and statistics, plus various forecasts about the economic implications. Updated regularly.

Report your own COVID19 status on the crowd-sourced COVID Near You.

BMJ Best Practice: COVID19 Highly-respected guidelines for physicians, researchers, patients and more from The BMJ (formerly known as the British Medical Journal)

The Coronavirus Tech Handbook is a crowd-sourced lengthy set of curated links and documents. Unfortunately its popularity makes the site slow sometimes. If you can, try to subscribe to some of the WhatsApp channels, where smaller groups of people discuss new events in real time.

My favorite list of curated, well-thought links is from Lesswrong: Coronavirus Link Database

Slate Star Codex posts thoughtful, well-researched summaries. All of the entries are good, but especially see the one recommending Face Masks and also March 19 which points to an open source Google Doc, Pandemic Preparedness, with crowd-sourced details about the virus and what to do.

New England Journal of Medicine (Feb 28) had this well-balanced summary, but it’ll take months before we know whether this was extremely prescient or naive:

the overall clinical consequences of Covid-19 may ultimately be more akin to those of a severe seasonal influenza (which has a case fatality rate of approximately 0.1%) or a pandemic influenza (similar to those in 1957 and 1968) rather than a disease similar to SARS or MERS, which have had case fatality rates of 9 to 10% and 36%, respectively” https://www.nejm.org/doi/full/10.1056/NEJMe2002387?query=RP

The medical lecture site MedCram has a series of short videos with experts explaining the latest situation.

Amateur epidemiologist Tomas Pueyo’s detailed Medium post (free) was the most widely-viewed summary of the need for drastic measures: “Coronavirus: Why You Must Act Now”

Reopening

Covid Exit Strategy by researchers from Duke University, United States of Care and elsewhere. Charts each US State by its performance on metrics like 14-day average number of cases, % of ICU utilization, etc.

#OpenSafely is a site run by former politicians, and various public policy experts including Eric Topol.

Scenarios for the Covid-19 Future PDF by UC Berkeley collaborators using the futurist scenario approach to map the space of what may happen based on how deadly the disease is versus its impact on the economy.

Compare reopening scenarios taking into account both health and economic factors: Wharton policy response simulator

Statistics

It’s no longer possible to count all the zillions of Coronavirus tracking web sites

Our World in Data is best at showing the data in context.

nCov2019.live Build by a Mercer Island teenager, this is the official” website for r/Coronavirus

USA only map from Andrzej Leszkiewicz. USA by state and county: another one, from USAFacts.org.

Worldometer breaks it down by age/sex/etc. (though CNN questions the site’s accuracy)

The Johns-Hopkins CSEE site is the Granddaddy site that everyone uses (and they publish the raw data as a Google Sheet)

If you read Chinese, the best summary is here. (now in English too]) See a map of cases near you

Also Korea

The official WHO map and situation reports. Also take their 3-module course about preparing for COVID19.

Projections

Healthdata.org has good interactive models, including one showing the number of days remaining till full hospitalization usage.

Estimate the projected number of cases in your area using the Nehrer Lab COVID-19 Scenarios calculator. (or this hardcore one by Gabe Goh)

Data

Institute for Health Metrics and Evaluation (IHME) at University of Washington keeps a CSV file of all COVID19 cases updated daily.

Amazon publishes a A public data lake for analysis of COVID-19 data.

API Collections to Help in the COVID-19 Fight easily accessible using the Postman service.

Science

Many scientific journals have made their (normally outrageously priced) articles free:

The specialist site http://virological.org/ has up-to-date commentary and links from practicing virologists. Great source for deep scientific info as it happens.

Harvard Med School graphical summary. and a curriculum being compiled by Harvard Med Students.

“Analysis of Wuhan Coronovirus”: (Feb 7) 90-page eBook by LSU emeritus professor and virologist William Gallaher is a technical introduction for curious non-experts who want to understand details of this virus. free download

Mapping the Landscape of Artificial Intelligence Applications against COVID-19: a summary of AI-related solutions for imaging, epidemiology, therapeutics, and more.

The Biohackers Flu Guide is a free download from the makers of the European Biohackers Summit. While I find much of the “science-based” suggestions a bit dubious and far-fetched, they present some interesting new ideas for followup if you approach with an open mind.

If you prefer traditional Chinese medicine (TCM), see How COVID-19 (2019-nCoV) is Currently Treated in China with TCM:

Hardcore science

Several groups are sharing detailed information about the virus in hopes of crowd-sourcing a diagnostic or even a cure:

COVID19 Hackpad biohackers exchange all the information we know.

Coronavirus: Digital Health Projects and Resources links by n-of-1 expert Eric Daza.

#OpenCovid19Test on JOGL: Developing a safe & open source DIY Covid-19 diagnosis test

Coronavirus Method Development Community is part of the well-established protocols.io group that has been supporting distributed science for many years.

MIDAS 2019 Novel Coronavirus Repository University of Pittsburgh-based open source modeling library.

Phylogenetic analysis from the open source Github-based nextstrain.

The primers you’ll need for COVID19 PCR. [see more from Yale Epidemiologist @Nathan Grubaugh]

COVID19 antivirals regularly-updated list from longtime quantitative clinician Peter D’Adamo about molecules known to have an effect on the virus.

Microbiome connection

See my up-to-date report: Coronavirus and the Microbiome

News

Up-to-date headlines on Jerry Brito’s Coronafeed

@naval’s Twitter list of trustworthy public information about COVID19: https://twitter.com/i/lists/1221004646656835585

Mainstream news has been fully-engaged since mid-March, so their reporting is often as good as you’ll find anywhere. For example, The New York Times map and list of incidents is updated in real time.

Highly-respected healthtech news site STAT has lifted the paywall for all their coronavirus news. Updated daily.

Singularity University hosted COVID-19: The State & Future of Pandemics free online event on March 16.

A summary of the report by 25 WHO experts who visited China for 9 days:

The vast majority of those infected sooner or later develop symptoms. Cases of people in whom the virus has been detected and who do not have symptoms at that time are rare - and most of them fall ill in the next few days.

The most common symptoms are fever (88%) and dry cough (68%). Exhaustion (38%), expectoration of mucus when coughing (33%), shortness of breath (18%), sore throat (14%), headaches (14%), muscle aches (14%), chills (11%) are also common. Less frequent are nausea and vomiting (5%), stuffy nose (5%) and diarrhoea (4%). Running nose is not a symptom of Covid.

The Reddit forum r/Coronavirus is a lightly-moderated source for news and rumors. See especially r/china_flu for the best independent expert summary of what is currently known.

Alternative

RANT: Real experts question everything, including the comments of other experts. I find it patronizing and appalling when sites like Twitter or Medium or Google pick and choose the ideas they think are worthwhile and censor the rest. Nobody at this point really knows all that much, which is why it’s even more important to look at a broader space of ideas, many of which will turn out to be flat out wrong, perhaps even deliberately deceptive. If you read me, then I trust you to have the intelligence to decide for yourself, which is why I include the following links.

The National Review’s Robert Verbruggen wrote a complete summary on Do Lockdowns Work?

Lockdown Skeptics careful breakdown of the reasons maybe a forced quarantine isn’t the best solution.

Can We Discuss Flatten-the-Curve in COVID19? My Eight Assertions: well-written summary of the case for loosening up by John Mandrola, M.D.

People and governments are taking it very seriously now, but we should remember that it’s possible to overreact in a panic.

Aaron Ginn @aginnt wrote a post that received more than 1M views before it was censored on Medium “Evidence over hysteria” for saying:

China, Singapore, and South Korea’s containment efforts worked because community-based and airborne transmission aren’t common. The most common form of transmission is person-to-person or surface-based.

See the brief refutation by Carl Bergstrom, which frankly is exactly what should happen. If you disagree with somebody, speak up about it, but don’t censor. People are smart enough to make up their own minds.

In the beginning, Japan was an odd outlier, though by mid-April it was becoming the same public emergency as it is in other countries. A 24-April BMJ feature warned that the early lapse in public vigilance was escalating out of control, though by mid-May it was becoming harder to make that argument, as cases were flattening again. (My theory is that Japanese has fewer phonetic aspirants than other languages, making it harder to spit the virus into the air. See this video tweet from @rumireports)

If you are more paranoid, Peak Prosperity is a site that summarizes the day’s Coronavirus news with Youtube videos. Note: Youtube has demonetized the channel because it apparently thinks the information is questionable. But for that very reason I think it’s a worthwhile look at a broader space of ideas (many of them incorrect) that are floating out there.

Another prepper site, theprepared.com does daily updates.

The Market Ticker makes a daily case for why the news isn’t as bad as the mainstream says it is.

Similarly, the non-mainstream news site Fabius Maximus has up-to-date detailed posts and links worth reading.

Local

Most local health departments have an up-to-date page describing the situation in your area:

Seattle

Test results from the UV Virology lab (updated in real time) Test results in Washington State

Michigan

China

A recent (early May 2020) account of a friend who experienced the Wuhan lockdown and finally made it back to his home in Seattle: Jeff Zhang on Amid the coronavirus pandemic, from Wuhan back to Seattle

I’ve been following the China news since the start of the outbreak. The best summaries are Sinocism Bill Bishop’s newsletters: (latest: May 21

Coronavirus treatment manual(English translation): required reading for doctors there.

An anonymous Chinese journalist wrote a lengthy perspective that argues the Chinese government’s “dramatic action” to fight the virus comes second after the need to maintain the Communist Party’s grip on power. [via @benthompson]

Videos

Liveleak has an 8-minute video of shocking scenes taken around Wuhan.

No doubt out of boredom from being cooped up all day, several people (mostly students) in Wuhan are uploading vlog diaries to Youtube. In Chinese, there’s a very well-produced one here.

Warnings

China Law Blog warns:

“Coronavirus likely will constitute a force majeure event for your Chinese counter-parties and this will mean they can breach their contracts with you without much if any legal repercussion. This also likely means some Chinese companies that are not yet truly impacted by the coronavirus will seek to use the virus as a basis for terminating or breaching or revising their contract with you.”

Keep in mind that all Chinese numbers are estimates. Barrons is only one of many publications that question the accuracy of these statistics.

A (now-censored) article by the respected Chinese business magazine Caijing argues that the death statistics out of Wuhan are grossly underreported. A shortage of test kits combined with a systemic fear by officials to report bad news results in automatic cremation and mislabeling of the cause of death. Google Translate version

Scary news, possibly fake, from a Taiwan website that claims a Tencent site briefly listed 10x the number of infections and deaths, hinting that the government keeps two sets of statistics.

After the outbreak

How will the pandemic end?

Coronavirus vaccines and Treatments: Businessinsider keeps track.

John Hewitt at Inference Review writes another summary of the current status of diagnostics and treatments.