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Novel Coronavirus General Info

An ad hoc and unofficial collection of resources. I live in Illinois, so I'm including Illinois-specific resources. - Hal Snyder, M.D.

Contents:

Update on face masks

Note: This information is about face coverings worn to prevent infecting others, sometimes known as "source control" measures. See the PPE topic below for info about masks to protect the wearer.

Several recent publications indicating universal wearing of face masks, even homemade masks and simple cloth coverings, can prevent spread of the pandemic.

Health Affairs: JUNE 16, 2020 Community Use Of Face Masks And COVID-19: Evidence From A Natural Experiment Of State Mandates In The US

  • EFFECTS OF MANDATES FOR FACE COVERING IN PUBLIC
    • no evidence of declines in daily COVID-19 growth rates with the employee-only mandates
    • direct evidence on the effectiveness of widespread community use of face masks
    • 230,000–450,000 COVID-19 cases may have been averted based on when states passed these [community use of face masks] mandates

Proceedings of the National Academy of Sciences (PNAS): June 11, 2020: Identifying airborne transmission as the dominant route for the spread of COVID-19

Our analysis reveals that the difference with and without mandated face covering represents the determinant in shaping the trends of the pandemic. This protective measure significantly reduces the number of infections. Other mitigation measures, such as social distancing implemented in the United States, are insufficient by themselves in protecting the public.

Proceedings of the Royal Society A 10 June 2020: A modelling framework to assess the likely effectiveness of facemasks in combination with ‘lock-down’ in managing the COVID-19 pandemic

We show that, when facemasks are used by the public all the time (not just from when symptoms first appear), the effective reproduction number, ReR_e, can be decreased below 1, leading to the mitigation of epidemic spread. Under certain conditions, when lock-down periods are implemented in combination with 100% facemask use, there is vastly less disease spread, secondary and tertiary waves are flattened and the epidemic is brought under control. The effect occurs even when it is assumed that facemasks are only 50% effective at capturing exhaled virus inoculum with an equal or lower efficiency on inhalation.

IZA – Institute of Labor Economics JUNE 2020: Face Masks Considerably Reduce COVID-19 Cases in Germany: A Synthetic Control Method Approach

early introduction of face masks in Jena has resulted in a reduction of almost 25% in the cumulative number of reported Covid-19 cases after 20 days. The drop is greatest, larger than 50%, for the age group 60 years and above. ... After the introduction of the mandatory masks, "the number of new infections fell almost to zero"

Science 27 May 2020: Reducing transmission of SARS-CoV-2

Masks and testing are necessary to combat asymptomatic spread in aerosols and droplets

Vanity Fair MAY 8, 2020 If 80% of Americans Wore Masks, COVID-19 Infections Would Plummet, New Study Says refers to the following paper, I think - Hal

arXiv.org physics.soc-ph 22 Apr 2020: Universal Masking is Urgent in the COVID-19 Pandemic: SEIR and Agent Based Models, Empirical Validation, Policy Recommendations : alternate link

These effects hold even at the lower filtering rates of homemade masks

Reopening

How We Reopen Safely CovidExitStrategy.org Tracking states as they make progress towards gating criteria.

We are a group of public health & crisis experts with experience working at the White House, Department of Health & Human Services, and on the Ebola epidemic in West Africa.

2020-05-06 The Risks - Know Them - Avoid Them Erin Bromage

As states reopen, and we give the virus more fuel, all bets are off. I understand the reasons for reopening the economy, but I've said before, if you don't solve the biology, the economy won't recover.

2020-04-15 Our Pandemic Summer

The fight against the coronavirus won’t be over when the U.S. reopens. Here’s how the nation must prepare itself.

2020-04-06 Lockdown Can’t Last Forever. Here’s How to Lift It By Gabriel Leung

  • Dr. Leung is an infectious disease epidemiologist and dean of medicine at the University of Hong Kong.
  • We need to hit and release the brakes on physical distancing, again and again, until we safely get to immunity.
  • Note: for some reason, NYT kept this important article behind their paywall.

Stanford Survey

Please consider participating in the Stanford Medicine National Daily Health Survey. The goal is to learn and predict which geographical areas will be most impacted by coronavirus. It takes a minute or two the first day and just seconds on following days.

Terminology

--

The disease: COVID-19 - coronavirus disease.

The virus: SARS-CoV-2 - severe acute respiratory syndrome coronavirus 2.

Reference:

public health terms: containment, mitigation, suppression

See "Impact of non-pharmaceutical interventions (NPIs)..." and "The Hammer and the Dance" below for use of these terms.

sensory changes with COVID-19

anosmia: loss of sense of smell

  • also hyposmia, reduced ability to smell things

ageusia: loss of sense of taste

  • also hypogeusia, reduced ability to taste things

NOTE: 2020-03-21 ENT UK: Loss of sense of smell as marker of COVID-19 infection (slow link)

there have been a rapidly growing number of reports of a significant increase in the number of patients presenting with anosmia in the absence of other symptoms

Two Purposes for Masks

Thanks to Carl T. Bergstrom (see twitter feeds below) for this clarification. Wording here is from Bergstrom's 2020-04-03 thread.

receiver protection: your mask protects you from others. A properly fitted N95 provides effective receiver protection, but fitting is very difficult and not easily achieved by members of the public without training and equipment.

source control: your mask protects others from you. A basic surgical-type face covering provides effective source control.

Personal Protective Equipment (PPE)

CDC recommends wearing cloth face coverings in public settings where other social distancing measures are difficult to maintain (e.g., grocery stores and pharmacies) especially in areas of significant community-based transmission.

  • 2020-03-03 Leora Horwitz let’s have a chat about masks

    • Director, Center for Healthcare Innovation and Delivery Science @nyulangone ; general internist; mom of 3 boys.

    Let me tell you what my hospital makes me do EVERY YEAR to make sure my N95 mask fits (yes, they come in sizes)...

  • OHSHA: COVID-19 Control and Prevention

    Measures for protecting workers from exposure to, and infection with, the novel coronavirus, COVID-19 depend on the type of work being performed and exposure risk, including potential for interaction with infectious people and contamination of the work environment...

  • WHO: How to Put on and Take Off Personal Protective Equipment (PPE)

Making PPE

Smart Air: What Are The Best Materials for Making DIY Masks?

South China Morning Post: How to make your own mask: Hong Kong scientists reveal temporary solution

  • Lab tests by City University find home-made masks achieve 80 to 90 per cent function of regular ones in terms of filtration of aerosol and droplets

Prusa Protective Face Shield - RC2 - 3D printing

  • A prototype face shield that we developed. In three days, we went through dozens of prototypes and two verifications with the Czech Ministry of Health.

Dr. Lauren Streicher A Surgeon's Guide to Sewing a Surgical Mask

Organizations

American Medical Association (AMA)COVID-19 (2019 novel coronavirus) resource center for physicians

World Health Organization

US CDC

Center for Communicable Disease Dynamics at Harvard (CCDD)

Illinois Department of Public Health

Journals and Other Publications

Publishers provide the following content without a paywall.

Springer Nature SARS-CoV-2 and COVID-19

Elsevier Novel Coronavirus Information Center

The Lancet: COVID-19 Resource Centre

JAMA (Journal of the American Medical Association) Network: Coronavirus Disease 2019 (COVID-19)

NeJM (New England Journal of Medicine): Coronavirus (Covid-19)

MIT Technology Review: Coronavirus

Financial Times: Coronavirus: free to read

Frequently-updated Maps & Statistics

Nextstrain.org - Real-time tracking of pathogen evolution

Nextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data. We provide a continually-updated view of publicly available data alongside powerful analytic and visualization tools for use by the community.

Rt Covid-19

These are up-to-date values for Rt, a key measure of how fast the virus is growing. It’s the average number of people who become infected by an infectious person. If Rt is above 1.0, the virus will spread quickly. When Rt is below 1.0, the virus will stop spreading.

ESRI Impact Planning for COVID-19

Google See how your community is moving around differently due to COVID-19

  • community mobility reports

Visual Capitalist Visualizing the History of Pandemics

  • This post and infographic are meant to provide historical context, and we will continue to update it as time goes on to maintain its accuracy.

Time Magazine Is the U.S. 'Flattening the Curve?' Check Our Coronavirus Chart for Daily Updates


the US and South Korea reported their first cases on the same day

Washington Post daily counts for coronavirus in the U.S.

  • Daily charts of confirmed cases and reported deaths for all US and for each state.

Citymapper Mobility Index (CMI) % of city moving compared to usual

Dadax Worldometer COVID-19 CORONAVIRUS PANDEMIC

  • includes table of Confirmed Cases and Deaths by Country, Territory, or Conveyance

COVID ACT NOW TEAM: Why you must act now

  • This model predicts the last day each state can act before the point of no return
  • Here is is the model as of 2020-03-25 for outcomes for Illinois:

Johns Hopkins CSSE: Coronavirus COVID-19 Global Cases map

Our World in Data: Coronavirus Disease (COVID-19) – Statistics and Research also listed under "Data and Notebooks" below

The Atlantic: COVID19 Tracker

  • test results from across the country. Maintained by The Atlantic since CDC stopped reporting number of tests.

    The COVID Tracking Project collects information from 50 US states and the District of Columbia to provide the most comprehensive public data we can on state-level testing for the novel coronavirus, SARS-CoV-2.

HealthMap: Novel Coronavirus (COVID-19)

  • HealthMap, a team of researchers, epidemiologists and software developers at Boston Children's Hospital founded in 2006, is an established global leader in utilizing online informal sources for disease outbreak monitoring and real-time surveillance of emerging public health threats - from about

Financial Times: Coronavirus tracked: the latest figures as the pandemic spreads

  • The countries affected, the number of deaths and the economic impact

Avi Schiffmann: nCoV2019.live - impressive work by high school student

  • This site was created by Avi Schiffmann. I am a high schooler in Washington State, USA.

Illinois Persons Under Investigation (PUI) for COVID-19

MOOCs (massive open online courses)

Coursera

All of these may be taken for free. Some also have a paid option.

Institut Pasteur

Imperial College London

HKU (University of Hong Kong)

3-Hour Workshop Joint SPH-JMSC Workshop for Journalists on COVID-19 and other infectious diseases

This workshop is a pilot programme jointly presented by The University of Hong Kong’s School of Public Health of HKUMed and Journalism and Media Studies Centre as part of an initiative to enable journalists to develop greater insight related to public health and science. The kick-off session addresses the basics of infectious diseases, which is highly relevant for COVID-19 and other infectious disease outbreaks.

program starts about 5 minutes into the video

OpenWHO - Responding to COVID-19

  • Real-time training during global emergencies is critical for effective preparedness and response. The COVID-19 Channel provides learning resources for health professionals, decision-makers and the public for the outbreak of coronavirus disease (COVID-19).
  • https://openwho.org/channels/covid-19

Twitter feeds

Larry Brilliant, MD, MPH

Carl Bergstrom

Marc Lipsitch

  • Infectious disease epidemiologist and microbiologist, aspirational barista. Director @CCDD_HSPH
  • https://twitter.com/mlipsitch
  • 2020-03-26 https://twitter.com/mlipsitch/status/1243347447537115136

    Tonight #DeborahBirx stated that models anticipating large-scale transmission of COVID-19 do not match reality on the ground...

    It is a fundamental scientific error to take the current success of containment in some places as a sign that permanent containment is possible. We should work to make it possible, but 1918 flu and, frankly, the germ theory of disease show that containment is a temporary victory

Dr. Dena Grayson

Trevor Bedford

Liz Specht

Andy Slavit

  • Former Medicare, Medicaid & ACA head for Obama. Founded @usofcare & @townhallvntrs to make health care work. Never broke a website, only fixed a big one.
  • https://twitter.com/ASlavitt
  • 2020-04-04 Oxygen and COVID-19

    The amount of oxygen to it takes to keep a COVID-19 patient alive is absolutely startling... Apparently 8 or more of those massive oxygen cylinders/day to keep someone alive.

  • 2020-03-14 COVID-19 Prep Update

    Last night I was on with state & local officials around the US well into the night. By March 23 many of our largest cities & hospitals are on course to be overrun with cases.

Important Articles and Graphics

3Blue1Brown

  • 2020-03-27 Simulating an epidemic
  • Andy Slavitt takeaways from video
    • Quarantine is most effective at flattening
    • Quarantine plus contact tracing wins
    • Hand washing & social distance very helpful
    • Half measures, non-compliance weaken effectiveness
    • Central markets or city to city travel hurts
    • Quarantine length saves lives

  • 2020-03-08 About exponential and logistic functions

Imperial College London, Ferguson, Laydon, et al.

Kurzgesagt

  • 2020-03-19 The Coronavirus Explained & What You Should Do

Harry Stevens

Tomas Pueyo

1. Confirmed cases (orange) lagged behind actual cases (grey) by about 10 days.
2. The curve in actual cases turned down when lockdown started.

Alanna Shaikh | TEDxSMU

Dylan Matthews/Vox.com

Carl Bergstrom/Drew Harris

Luca Dellanna

In blue, ICU & deaths from the flu. In yellow & red, from the virus

Mortality % does not matter yet because the higher the yellow line, the higher the mortality OF ALL CONDITIONS you might visit a hospital for

But the real problem is resource saturation (translated) - Francesco Menegalli

Trevor Bedford

on average every other step in the transmission chain will have a mutation and so would look something like:

Systems Theory

Wicked problem Summary article in Wikipedia. Severe global pandemics are wicked problems.

How Complex Systems Fail, by Richard I. Cook, MD, Cognitive technologies Laboratory University of Chicago: Classic paper from 1998.

First-person Accounts

2020-03-27 London (?), Shiraz Maher

2020-03-25 New York City, Dr. Ashley Bray

2020-03-23 New York City, Craig Spencer MD MPH, Director of Global Health in Emergency Medicine @ColumbiaMed / @NYPhospital and Faculty in Forced Migration & Health @ColumbiaMSPH | @MSF_USA BoD |#Ebola survivor

2020-03-21 London, Natalie Silvey, Anaesthetic registrar, dabbles in healthcare policy and healthcare data geek. Proud Girly Swot, Feminist & European

2020-03-15 West Michigan, Dr. Rob Davidson, Dad, husband, ER doc, and Exec Dir of the Committee to Protect Medicare because ALL Americans need affordable healthcare, ,

2020-03-11 Western Europe, Physician

  • Newsweek: YOUNG AND UNAFRAID OF THE CORONAVIRUS PANDEMIC? GOOD FOR YOU. NOW STOP KILLING PEOPLE | OPINION

    Here is how it looks in practice. Most of my childhood friends are now doctors working in north Italy. In Milan, in Bergamo, in Padua, they are having to choose between intubating a 40-year-old with two kids, a 40-year old who is fit and healthy with no co-morbidities, and a 60-year-old with high blood pressure, because they don't have enough beds. In the hallway, meanwhile, there are another 15 people waiting who are already hardly breathing and need oxygen.

2020-03-09 Bergamo, Italy, Silvia Stringhini, Social and lifecourse epidemiologist. Studies biological consequences of social inequalities / Dr. Daniele Macchini author of original Italian posting

Data and Notebooks

IHME COVID-19 Projections

  • projected hospital resource use for all US and individual states
  • The projections assume the continuation of strong social distancing measures and other protective measures.

New York Times We’re Sharing Coronavirus Case Data for Every U.S. County

  • Download county-level data for coronavirus cases in the United States from The New York Times on GitHub.

Covid Near You
Excellent! Citizen Science joins the battle against COVID-19 - Hal

Created by epidemiologists and software developers at Harvard, Boston Children's Hospital and a group of volunteers from across the technology industry. Covid Near You uses crowdsourced data to visualize maps to help citizens and public health agencies identify current and potential hotspots for the recent pandemic coronavirus, COVID-19.

Corona Data Scraper

Corona Data Scraper pulls COVID-19 Coronavirus case data from verified sources, finds the corresponding GeoJSON features, and adds population data.

  • includes county-level stats with time series for much of the US
  • 2D and 3D visualizations as well as access to the raw data
  • github project lazd / coronadatascraper
  • maintained by lazd (Larry Davis), twitter bio: Engineer, teacher, designer of drones. Senior Design Engineer on @Adobe’s design system, creator of Spectrum CSS. Fighting COVID-19 with data.

Unacast: Social Distancing Scoreboard based on mobile device data

Kinsa US Health Weather Map

The U.S. Health Weather Map is a visualization of seasonal illness linked to fever - specifically influenza-like illness. The aggregate, anonymized data visualized here is a product of Kinsa’s network of Smart Thermometers and the accompanying mobile applications.

  • Enter a zip code or US county name and see map and timeline for observed and atypical illness levels.

Our World in Data: Coronavirus Disease (COVID-19) – Statistics and Research

  • The mission of Our World in Data is to make data and research on the world’s largest problems understandable and accessible.
  • this article focuses on a new, emerging global problem: the ongoing outbreak of the coronavirus disease [COVID-19]

Semantic Scholar: CORD-19 COVID-19 Open Research Dataset

  • Updated 3/27. Highlights include:
    • Launched the easy-to-use CORD-19 Explorer for quick searching
    • Opened up CORD-19 Discourse, a forum for ideas and discussions
    • Added nearly 5,000 new full-text papers

Example notebooks by the CoCalc Team

2019 Novel Coronavirus COVID-19 (2019-nCoV) Data Repository by Johns Hopkins CSSE

THE [email protected] CONSORTIUM (FAHC) Coronavirus – What we’re doing and how you can help

  • Donate home computing power to run simulations of how all the atoms in selected viral proteins move. This can reveal potential binding sites for new anti-viral drugs.

Food Safety

Dr. Jeffrey VanWingen

  • PSA Safe Grocery Shopping in COVID-19 Pandemic – UPDATED!!!

Illinois Resources

Cook County Dept of Public Health (CCDPH) COVID-19 Surveillance Data

This data represents all confirmed cases of COVID-19 reported to the Cook County Department of Public Health (CCDPH). The jurisdiction of CCDPH includes all municipalities and portions of municipalities within Cook County, except for Chicago, Evanston, Oak Park, Skokie and Stickney Township, each of which has its own state-certified local health department.

IRMA: COVID-19 Special Shopping Hours For senior citizens and other vulnerable populations

United Way of Illinois, Alliance of Illinois Community Foundations, et al: Illinois COVID-19 Response Fund

Celebrity videos to cheer us up

Arnold Schwarzenegger

Patton Oswalt

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