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Coronavirus (COVID-19) Live Tracking, IIRESS Labs, 2020

COVID-19 Epidemiology & Transmission Information - History of Discovery

Dec. 2019/Jan. 2020 Archives | February 2020 Archives | March 2020 Archives | April 2020 Archives | May 2020 Archives

*Note: Pre-print articles have not yet been peer-reviewed and their results are subject to change or retraction. While they can be useful indicators of the direction of current research, waiting for full peer-review results is the best practice when making clinical or critical research decisions.

(Updated 05/25/2020)


COVID-19 Quick Stats

Quick Facts

Coronavirus disease 2019 (COVID-19) is the disease caused by the virus SARS-CoV-2
SARS-CoV-2 is closely related to the viruses that cause SARS and MERS, which have both caused severe outbreaks of respiratory disease.

Case Fatality Rate (CFR) in the US seems relatively stable at 5.6%, Italy/Spain/France at 10-14%.
⇒ Case fatality rate is the proportion of attributable number of deaths from a disease to reported (clinical) cases.

Infection Fatality Rate (IFR) in the US is still currently unknown with scientific certainty.
⇒ Infection fatality rate (IFR) is the proportion of attributable number of deaths to all those infected (includes sub-clinical and asymptomatic cases) and is expected to be lower than CFR. This number can be estimated during an epidemic/pandemic from antibody (by determining seroprevalence) studies.
⇒ SARS-CoV-2 has a very high asymptomatic rate that makes it difficult to estimate this number, meaning that estimates will vary widely between region and testing methodology.

Seroprevalence is the prevalence of antibodies in a population, meaning the percent of individuals that have or have recently had the disease, regardless of disease status (asymptomatic, sub-clinical, or full-clinical presentation).
⇒ Current seroprevalence estimates range from 1.5% up to 30%, varying from region and testing methodology (Levesque and Maybury, 2020).
⇒ Seroprevalence of SARS-CoV-2 antibodies is not currently known with scientific certainty in the US.

Mortality rate is the attributable rate of deaths due to a disease in a population (e.g., out of 100,000 people what is the risk of death for a particular disease).
⇒ This number is not typically estimated until after an epidemic/pandemic.
⇒ Mortality rate of COVID-19 is not currently known with scientific certainty in the US.

Table 1. IIRESS Labs running COVID-19 Estimated CFR (CFR) - 05/10/2020

Country Infections Deaths CFR 95% Confidence Interval
USA 1,329,799 79,528 5.98% (5.94 - 6.02%)
Spain 224,350 26,621 11.87% (11.73 - 12.00%)
UK 220,449 31,930 14.48% (14.34 - 14.63%)
Italy 219,070 30,560 13.95% (13.80 - 14.09%)
Russia 209,688 1,915 0.91% (0.87 - 0.95%)
France 177,094 26,383 14.90% (14.73 - 15.06%)
Germany 171,879 7,569 4.40% (4.31 - 4.50%)
China 84,010 4,637 5.52% (5.37 - 5.67%)
South Korea 10,909 256 2.35% (2.06 - 2.63%)
Australia 6,948 97 1.4% (1.12 - 1.67%)
Global 4,103,136 282,719 6.89% (6.87 - 6.91%)

Johns Hopkins Center for Systems Science and Engineering, Coronavirus (COVID-19) Live Map: Source


COVID-19 Special Report

Preliminary Data Suggests Stay-At-Home Orders Work (Original Analysis):

Outbreak risk modeling 5/24/2020

Quadrant 1 - High Risk for Disease Resurgence, Increasing Risk (Moderate → High)

Alabama, Georgia, Maine, Maryland, North Dakota, Rhode Island, South Dakota, Utah, Vermont, West Virginia

Quadrant 2 - Current Resurgence, Social distancing response, Decreasing Risk (High → Moderate)

Arkansas

Quadrant 3 - Decreasing Risk, Reduced Distancing (Moderate → Low)

Alaska, Arizona, California, Colorado, Connecticut, Delaware, District of Columbia, Florida, Hawaii, Indiana Iowa, Kansas, Kentucky, Louisiana, Massachusetts, Michigan, Minnesota, Mississippi, Missouri, Montana, Nebraska Nevada, New Hampshire, New Jersey, New Mexico, New York, North Carolina, Ohio, Oklahoma, Pennsylvania, South Carolina, Tennessee, Texas, Virginia, Wisconsin, Wyoming

Quadrant 4 - Decreasing Risk, Active Containment (Moderate → Low)

Idaho, Illinois, Oregon, Washington

Example States

Classification of quadrants

Updated 05/25/2020


Featured Report, May 2020

Center for Infectious Disease Research and Policy (CIDRAP) at University of Minnesota

  • CIDRAP has been a great resource for me during the pandemic and I would consider it a very high-trust source.
  • Recently, they have created a new section named “COVID-19: The CIDRAP Viewpoint”, which is a summary report from experts in the field.
  • Their first issue of the report, “The future of the COVID-19 pandemic: lessons learned from pandemic influenza” (Apr 30, 2020) contains some very pertinent estimates on the progression of the COVID-19 pandemic.
  • Researchers at CIDRAP estimate that the pandemic will continue for up to 18-24 months, and experience one of several potential disease curve patterns, pictured here below.

  • Recommendations from the report:
  • 1. States, territories, and tribal health authorities should plan for the worst-case scenario (Scenario 2), including no vaccine availability or herd immunity.
  • 2. Government agencies and healthcare delivery organizations should develop strategies to ensure adequate protection for healthcare workers when disease incidence surges.
  • 3. Government officials should develop concrete plans, including triggers for reinstituting mitigation measures, for dealing with disease peaks when they occur.
  • 4. Risk communication messaging from government officials should incorporate the concept that this pandemic will not be over soon and that people need to be prepared for possible periodic resurgences of disease over the next 2 years.
  • Follow-up for more CIDRAP reports here: https://www.cidrap.umn.edu/covid-19/covid-19-cidrap-viewpoint

Published estimates of COVID-19 CFR, IFR, and Mortality Rate

Estimates of Case Fatality Rate (CFR)

Estimates of Mortality Rate

Estimates of Infection Fatality Rate (IFR)

(Updated 05/09/2020)


Clinical Pathology of COVID-19

Clinical Pathology Archives

Immune System Function

Digestive Symptoms

Sensory Dysfunction (Loss of smell and taste)

Detection Assays

Corticosteroids

Patient-Derived Mutation Pathogenecity

News/Journal Shortname Key Guide

(Updated 04/19/2020)


COVID-19 Clinical Trials (Vaccine, Treatment, Testing, etc.)

Vaccine Development

Vaccine Trials

Testing Methodology

(Updated 05/02/2020)


Genetic Epidemiology of COVID-19

Genetic epidemiology of COVID-19, nextstrain.org

Figure 5. Sequence diversity of 3,170 SARS-CoV-2 strains during the 2019/2020 global coronavirus pandemic (Source: http://www.nextstrain.org)

(Updated 04/22/2020)


Coronavirus Specific Podcasts (The Planetary News Radio, an IIRESS Media Production)

The Planetary News Radio - Episode 19: Global Coronavirus (COVID-19) Pandemic Update 3 (3/31/2020)

The Planetary News Radio - Episode 18: Global Coronavirus (COVID-19) Pandemic Update 2 (3/20/2020)

The Planetary News Radio - Episode 17: Global Coronavirus (COVID-19) Pandemic Update 1 (3/14/2020)

Today's episode is a special feature episode of the Planetary News Radio. It is in times of great need that scientists and community members must join together to protect the community, whether that is at the national level, state level, city, or friends and family. As you all know, the coronavirus (COVID-19) has rapidly spread around the world, and we are seeing increasingly sweeping government responses to this outbreak, including quarantines, travel restrictions, and the bolstering of healthcare services. Listen to my status update on the pandemic here in Corvallis, Oregon, as well as a global perspective. For more coronavirus data analytics and updates, visit http://ncov.iiress.com. For transcripts and show notes, visit on the web at: http://www.iiress.com/planetary/podcasts.


COVID-19 General Information/Data Sources

Coronavirus E-mail Updates and GoFundMe info

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THANK YOU TO THE JUICE MEDIA FOR GILDING ME: https://youtu.be/Hks6Nq7g6P4

labs/coronavirus_live_tracking.txt · Last modified: 2020/05/27 06:16 by bpwhite