Novel Coronavirus

Diagnostic Data Analysis for Submission Review Board

Aaron M. Hale
Director of Information
Mathematical Sciences Research Institute
Berkeley, CA
Etiologic Agent
• SARS-nCoV-2 is a positive-sense, single-stranded RNA virus.
• Multiple Genomes (38 as of 3/10/20).
• Genetic Sequence: 79.5% SARC-CoV-1, 96% coronavirus found in
horseshoe bat.
• First known infection early-December, 2019.
• Molecular clock suggest infections occurred as early as October 2019.
• Similar human-infecting viruses:
• SARS (2002)
• MERS (2012)
Range of Clinical Features
• Asymptomatic infection
• Mild self-limited fibril respiratory infection
• Life-threatening pulmonary infection
• Case fatality proportion: ? 1 – 3 % ?
CFR & IFR
• What fraction of detected cases die of the disease? (CFR). Unknown.
• What fraction of the infected individuals die of the disease? (IFR).
Unknown.
• WHO naively reports CFR @ 3.4%.
• We believe this rate will decline as serological testing ID’s
asymptomatic infected individuals.
CFR – Case Fatality Rate in SAR-nCoV-2
SEIR Mathematical Model
SEIR Model con’t…
SEIR Model con’t…
• Substantial undocumented infection facilitates the rapid
dissemination of this virus.
• We estimate that 86% of all infections have been undocumented.
• 95% CI: [82%-90%]prior to the Wuhan travel shutdown (January 23,
2020)
• Estimate CFR @ 5.5%
• Estimate 25 million critical care cases in 180 days in North America
(see my notes for Europe, Asia, and Africa)
How do we get those numbers?
• Using the following model:
Problem with mathematical models
• “The tendency of some modelers to present them as scientific predictions
of the future rather than models does not help. Models are widely used in
government, and some models have arguably too much influence. They are
generally most useful when they identify impacts of policy decisions which
are not predictable by commonsense; the key is usually not that they are
‘right’, but that they provide an unexpected insight.” (Chris Whitty, CMO
England, 2015)
• What we need to do:
• Provide projections of the likely future.
• Provide descriptions of history.
• Provide insight to the impact of possible interventions.
Predictive model Epidemiological features
• Incubation Period: 2 – 15 days.
• Routes of Transmission. Respiratory: Droplets and Aerosols.
• Skin Contact
• Fomites
• Virus is present in nasopharynx 1 – 2 days prior to symptoms.
R0 comparison
Input vectors to Prevention
• Diagnostics using n1 Primer improvements (attached to this invite)
• Isolation of cases
• Quarantine of exposed individuals
• Cordon Sanitaire and Protective Sequestration
• Masks
• Travel restrictions and border closings
• Social distancing
• Handwashing
• Environmental decontamination
• Closing of Live Animal Markets
Value of mitigation
Conclusions based on models
• I already mentioned math is flawed. It exists in a world separate from
our own and doesn’t always provide a framework on which we should
live our lives.
• I believe this math to be a near analog of our current situation.
• Acting quickly will save lives, mitigation is necessary.
• This will be the most significant worldwide event in the last 100 years.
Questions?
• I will only take questions on the mathematics of this study. I will defer
medical questions to Dr. Jewell.
• Predictive models are available on my GITHUB page.
• Proposed improvements to virus COVID-19 primer sets are available
upon request. These change daily as I work on this.