COVID-19

The Virus: SARS-CoV-2

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NY Times - April 30, 2020 How Coronavirus Mutates and Spreads J. Corum and C. Zimmer

The coronavirus is an oily membrane packed with genetic instructions to make millions of copies of itself. The instructions are encoded in 30,000 letters of RNA — a, c, g and u — which the infected cell reads and translates into many kinds of virus proteins.

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NY Times - April 3, 2020 Bad News Wrapped in Protein: Inside the Coronavirus Genome J. Corum and C. Zimmer

The genome of the new coronavirus is less than 30,000 letters long, while the human genome is over 3 billion. Scientists have identified genes for as many as 29 proteins, which carry out a range of jobs from making copies of the coronavirus to suppressing the body’s immune responses.

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NY Times - March 13, 2020 How Coronavirus Hijacks Your Cells J. Corum and C. Zimmer

The virus that causes Covid-19 is currently spreading around the world. At least six other types of coronavirus are known to infect humans, with some causing the common cold and two causing outbreaks: SARS and MERS.

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Treatment, Vaccine, Prevention

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NY Times - April 30, 2020 How Long Will a Vaccine Really Take? S. A. Thompson

A vaccine would be the ultimate weapon against the coronavirus and the best route back to normal life. Officials like Dr. Anthony S. Fauci, the top infectious disease expert on the US administration’s coronavirus task force, estimate a vaccine could arrive in at least 12 to 18 months.

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Data Sources (pandemic)

How do sources compare? by H. Ritchie et al., March 19, 2020 — Our World in Data

— There are three key sources providing regular updates of COVID-19 cases and deaths globally and by country.

1. World Health Organization
2. European Center for Disease Control and Prevention (ECDC)
3. Johns Hopkins University

Addendum

• Our World in Data — Global Change Data Lab
• Wolfram
• Worldometers
• Genetic Data for SARS-CoV-2 — Wolfram

NOTE: Script for downloading the CSV file into R

1 #these libraries need to be loaded
2 library(utils)
3 
4 #read the Dataset sheet into “R”. The dataset will be called "data".
5 data <- read.csv("https://opendata.ecdc.europa.eu/covid19/casedistribution/csv", na.strings = "", fileEncoding = "UTF-8-BOM")

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Data Sources (other)

• Mobility Trends Reports — Apple
  

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Datasets

• COVID-19 Open Research Dataset (CORD-19) — Semantic Scholar
• Coronavirus Database Search — Google
• CORD-19 Research Challenge — Kaggle

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Updates

• Outbreak Updates (Government of Canada)
• Coronavirus disease (COVID-19): Awareness resources (Government of Canada)
• The Centers for Disease Control and Prevention (CDC)
• Real-time estimation of the novel coronavirus incubation time
• The crystal structure of COVID-19
• The Coronavirus Outbreak — NY Times
• Flatten
• R Epidemics Consortium
• EndCoronavirus (ECV) — NECSI
• Awesome Coronavirus
• Genomic epidemiology of novel coronavirus (hCoV-19)
• DXY
• COVID-19 Scenarios
• Hospital Impact Model for Epidemics (CHIME)
• IHME COVID-19 Projections
• EpiRisk
• Infodemics Observatory
• 10 Day Forecast — University of Melbourne
• Global Tracker — REUTERS

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Dashboards

• Epidemic Calculator by G. Goh
• Observable Collection
  • Fatality Rate and Spreading Trends by Y. Ahn
  • EPi Curve by Niraj D
• Shiny
  • CoronaTacker by A. C. Valdez
  • A Dashboard by C. Schoenenberger
  • Modeling Spread and Capacity by A. Hill et al.
  • Flatten the Curve by M. Höhle
  • Explore the Spread by J. Gassen
  • WHO Covid-19 Explorer
• Tableau
  • Data Hub
  • Trend Tracker
  • Progression
  • Daily Updates

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Research

• Outbreak by K. Simler
• Contagiousness of COVID-19 Part I: Improvements of Mathematical Fitting by M. Weterings
• LitCovid — NCBI
• COVID-19 dataset clearinghouse — Polymath
• Modeling resources by J. Rickert — R Views
• Contagiousness of COVID-19 Part I: Improvements of Mathematical Fitting — Learning Machines
• Epidemiology: How contagious is Novel Coronavirus (2019-nCoV)? — Learning Machines
• COVID-19: Analyze Mobility Trends with R — Learning Machines

Self-check

• Covid-19 Progress in Turkey

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