Difference between revisions of "COVID-19"


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__NOTOC__
 
__NOTOC__
[[Covid-19 Progress in Turkey]]
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==The Virus: SARS-CoV-2==
  
==SARS-CoV-2, The Virus==
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{{Post-summary
 +
| summary-category =
 +
| summary-title = [https://www.nytimes.com/interactive/2020/04/30/science/coronavirus-mutations.html How Coronavirus Mutates and Spreads]
 +
| summary-author = ''J. Corum'' and ''C. Zimmer''
 +
| summary-institution = NY Times
 +
| summary-date = April 30, 2020
 +
| summary-text = 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.
 +
}}
  
[https://www.nytimes.com/interactive/2020/04/30/science/coronavirus-mutations.html How Coronavirus Mutates and Spreads] by ''J. Corum'' and ''C. Zimmer'', April 30, 2020 — <span class="is-all-small-caps">NY Times</span>
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{{Post-summary
 +
| summary-category = https://static01.nyt.com/newsgraphics/2020/03/10/coronavirus-pathogen/0ee8f1a44b1932072653a0a75ff96486feb6f36d/covid-vaccine.png
 +
| summary-title = [https://www.nytimes.com/interactive/2020/04/03/science/coronavirus-genome-bad-news-wrapped-in-protein.html Bad News Wrapped in Protein: Inside the Coronavirus Genome]
 +
| summary-author = ''J. Corum'' and ''C. Zimmer''
 +
| summary-institution = NY Times
 +
| summary-date = April 3, 2020
 +
| summary-text = 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.
 +
}}
  
— 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.
+
{{Post-summary
 
+
| summary-category = https://static01.nyt.com/newsgraphics/2020/03/10/coronavirus-pathogen/0ee8f1a44b1932072653a0a75ff96486feb6f36d/covid-soap.png
[https://www.nytimes.com/interactive/2020/04/03/science/coronavirus-genome-bad-news-wrapped-in-protein.html Inside the Coronavirus Genome] by ''J. Corum'' and ''C. Zimmer'', April 3, 2020 —  <span class="is-all-small-caps">NY Times</span>
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| summary-title = [https://www.nytimes.com/interactive/2020/03/11/science/how-coronavirus-hijacks-your-cells.html How Coronavirus Hijacks Your Cells]
 
+
| summary-author = ''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.
+
| summary-institution = NY Times
 
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| summary-date = March 13, 2020
[https://www.nytimes.com/interactive/2020/03/11/science/how-coronavirus-hijacks-your-cells.html How Coronavirus Hijacks Your Cells] by ''J. Corum'' and ''C. Zimmer'', March 13, 2020 —  <span class="is-all-small-caps">NY Times</span>
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| summary-text = 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.
 
+
}}
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.
 
 
 
[https://www.wolframcloud.com/obj/examples/COVID19Gene Genetic Data for SARS-CoV-2], April 12, 2020  —  <span class="is-all-small-caps">Wolfram</span>
 
 
 
— This interactive dashboard displays recent information on the COVID-19 (coronavirus) pandemic, patient symptoms and outcomes, and the genetic makeup of the novel coronavirus (SARS-CoV-2).
 
  
 
<hr class="stylish2">
 
<hr class="stylish2">
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==Treatment, Vaccine, Prevention==
 
==Treatment, Vaccine, Prevention==
  
[https://www.nytimes.com/interactive/2020/04/30/opinion/coronavirus-covid-vaccine.html How Long Will a Vaccine Really Take?] by ''S. A. Thompson'', April 30, 2020 —  <span class="is-all-small-caps">NY Times</span>
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{{Post-summary
 
+
| summary-category = https://static01.nyt.com/newsgraphics/2020/04/08/opinion-covid-timeline/b006abb8ec5ece8b419f2ad57b88ceee5b576856/vaccine-success-Artboard_1.png
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.
+
| summary-title = [https://www.nytimes.com/interactive/2020/04/30/opinion/coronavirus-covid-vaccine.html How Long Will a Vaccine Really Take?]
 +
| summary-author = ''S. A. Thompson''
 +
| summary-institution = NY Times
 +
| summary-date = April 30, 2020
 +
| summary-text = 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.
 +
}}
  
 
<hr class="stylish2">
 
<hr class="stylish2">
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==Data Sources (pandemic)==
 
==Data Sources (pandemic)==
  
[https://ourworldindata.org/covid-sources-comparison How do sources compare?] by ''H. Ritchie et al.'', March 19, 2020 — <span class="is-all-small-caps">Our World in Data</span>
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[https://ourworldindata.org/covid-sources-comparison How do sources compare?] by ''H. Ritchie et al.'', March 19, 2020 — <span class="is-all-small-caps">Our World in Data</span>
  
 
— There are three key sources providing regular updates of COVID-19 cases and deaths globally and by country.
 
— There are three key sources providing regular updates of COVID-19 cases and deaths globally and by country.
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'''Addendum'''
 
'''Addendum'''
  
 +
* [https://ourworldindata.org/coronavirus Our World in Data] — <span class="is-all-small-caps">Global Change Data Lab</span>
 
* [https://wolfr.am/COVID19Dashboard Wolfram]
 
* [https://wolfr.am/COVID19Dashboard Wolfram]
 
* [https://www.worldometers.info/coronavirus/ Worldometers]
 
* [https://www.worldometers.info/coronavirus/ Worldometers]
 +
* [https://www.wolframcloud.com/obj/examples/COVID19Gene Genetic Data for SARS-CoV-2] — <span class="is-all-small-caps il-sans-serif">Wolfram</span>
 +
  
 
'''NOTE:''' [https://www.ecdc.europa.eu/en/publications-data/download-todays-data-geographic-distribution-covid-19-cases-worldwide Script] for downloading the CSV file into '''R'''  
 
'''NOTE:''' [https://www.ecdc.europa.eu/en/publications-data/download-todays-data-geographic-distribution-covid-19-cases-worldwide Script] for downloading the CSV file into '''R'''  
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==Data Sources (other)==
 
==Data Sources (other)==
  
* [https://www.apple.com/covid19/mobility Mobility Trends Reports] —  <span class="is-all-small-caps">Apple</span><br>
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* [https://www.apple.com/covid19/mobility Mobility Trends Reports] —  <span class="is-all-small-caps il-sans-serif">Apple</span><br>
  
 
<hr class="stylish2">
 
<hr class="stylish2">
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* [https://github.com/HopkinsIDD/ncov_incubation Real-time estimation of the novel coronavirus incubation time]
 
* [https://github.com/HopkinsIDD/ncov_incubation Real-time estimation of the novel coronavirus incubation time]
 
* [https://www.rcsb.org/structure/6LU7 The crystal structure of COVID-19]
 
* [https://www.rcsb.org/structure/6LU7 The crystal structure of COVID-19]
* [https://ourworldindata.org/coronavirus-source-data Our World in Data]
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* [https://nyti.ms/31jGhk2 The Coronavirus Outbreak] — <span class="is-all-small-caps">NY Times</span>
* [https://nyti.ms/31jGhk2 The Coronavirus Outbreak] — <span class="is-all-small-caps">NY Times</span>
 
 
* [https://flatten.ca/ Flatten]
 
* [https://flatten.ca/ Flatten]
 
* [https://www.repidemicsconsortium.org/projects/ R Epidemics Consortium]
 
* [https://www.repidemicsconsortium.org/projects/ R Epidemics Consortium]
* [https://ourworldindata.org/coronavirus Our World of Data]
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* [https://www.endcoronavirus.org EndCoronavirus (ECV)] <span class="is-all-small-caps">NECSI </span>
 
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* [https://github.com/soroushchehresa/awesome-coronavirus Awesome Coronavirus]
<hr class="stylish2">
 
 
 
===Observable===
 
* [https://observablehq.com/collection/@observablehq/coronavirus Observable Collection]
 
* [https://observablehq.com/@yy/covid-19-fatality-rate Fatality Rate and Spreading Trends] by ''Y. Ahn''
 
* [https://observablehq.com/@nirajd/sars2-cov-epi-curve EPi Curve] by ''Niraj D''
 
 
 
<hr class="stylish2">
 
 
 
===Shiny===
 
 
 
* [https://andrecalerovaldez.shinyapps.io/CovidTimeSeries/ CoronaTacker] by ''A. C. Valdez''
 
* [https://chschoenenberger.shinyapps.io/covid19_dashboard/ A Dashboard] by ''C. Schoenenberger''
 
* [https://alhill.shinyapps.io/COVID19seir/ Modeling Spread and Capacity] by ''A. Hill et al.''
 
* [https://tinu.shinyapps.io/Flatten_the_Curve/ Flatten the Curve] by ''M. Höhle''
 
* [https://jgassen.shinyapps.io/tidycovid19/ Explore the Spread] by ''J. Gassen''
 
 
 
<hr class="stylish2">
 
 
 
===Tableau===
 
* [https://www.tableau.com/covid-19-coronavirus-data-resources Data Hub]
 
* [https://public.tableau.com/profile/jonas.nart#!/vizhome/COVID19_15844962693420/COVID19-TrendTracker Trend Tracker]
 
* [https://public.tableau.com/profile/marc.psaila#!/vizhome/Coronavirusfortableaupublic/Coronaviruscasesbycountry Progression]
 
* [https://public.tableau.com/profile/daminda.de.silva#!/vizhome/corona-virusspreadingacrosstheworld/Dashboard33 Daily Updates]
 
 
 
<hr class="stylish2">
 
 
 
 
* [https://nextstrain.org/ncov Genomic epidemiology of novel coronavirus (hCoV-19)]
 
* [https://nextstrain.org/ncov Genomic epidemiology of novel coronavirus (hCoV-19)]
 
* [https://ncov.dxy.cn/ncovh5/view/en_pneumonia?from=dxy&source=&link=&share= DXY]
 
* [https://ncov.dxy.cn/ncovh5/view/en_pneumonia?from=dxy&source=&link=&share= DXY]
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* [https://covid19obs.fbk.eu/  Infodemics Observatory]
 
* [https://covid19obs.fbk.eu/  Infodemics Observatory]
 
* [http://covid19.science.unimelb.edu.au/ 10 Day Forecast] —  <span class="is-all-small-caps">University of Melbourne</span>
 
* [http://covid19.science.unimelb.edu.au/ 10 Day Forecast] —  <span class="is-all-small-caps">University of Melbourne</span>
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<hr class="stylish2">
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==Dashboards==
 +
 +
* [https://gabgoh.github.io/COVID/index.html Epidemic Calculator] by ''G. Goh''
 +
* [https://observablehq.com/collection/@observablehq/coronavirus Observable Collection]
 +
** [https://observablehq.com/@yy/covid-19-fatality-rate Fatality Rate and Spreading Trends] by ''Y. Ahn''
 +
** [https://observablehq.com/@nirajd/sars2-cov-epi-curve EPi Curve] by ''Niraj D''
 +
* Shiny
 +
** [https://andrecalerovaldez.shinyapps.io/CovidTimeSeries/ CoronaTacker] by ''A. C. Valdez''
 +
** [https://chschoenenberger.shinyapps.io/covid19_dashboard/ A Dashboard] by ''C. Schoenenberger''
 +
** [https://alhill.shinyapps.io/COVID19seir/ Modeling Spread and Capacity] by ''A. Hill et al.''
 +
** [https://tinu.shinyapps.io/Flatten_the_Curve/ Flatten the Curve] by ''M. Höhle''
 +
** [https://jgassen.shinyapps.io/tidycovid19/ Explore the Spread] by ''J. Gassen''
 +
* Tableau
 +
** [https://www.tableau.com/covid-19-coronavirus-data-resources Data Hub]
 +
** [https://public.tableau.com/profile/jonas.nart#!/vizhome/COVID19_15844962693420/COVID19-TrendTracker Trend Tracker]
 +
** [https://public.tableau.com/profile/marc.psaila#!/vizhome/Coronavirusfortableaupublic/Coronaviruscasesbycountry Progression]
 +
** [https://public.tableau.com/profile/daminda.de.silva#!/vizhome/corona-virusspreadingacrosstheworld/Dashboard33 Daily Updates]
  
 
<hr class="stylish2">
 
<hr class="stylish2">
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* [https://meltingasphalt.com/interactive/outbreak/ Outbreak] by ''K. Simler''
 
* [https://meltingasphalt.com/interactive/outbreak/ Outbreak] by ''K. Simler''
 
* [https://blog.ephorie.de/contagiousness-of-covid-19-part-i-improvements-of-mathematical-fitting-guest-post Contagiousness of COVID-19 Part I: Improvements of Mathematical Fitting] by ''M. Weterings''
 
* [https://blog.ephorie.de/contagiousness-of-covid-19-part-i-improvements-of-mathematical-fitting-guest-post Contagiousness of COVID-19 Part I: Improvements of Mathematical Fitting] by ''M. Weterings''
 +
* [https://www.ncbi.nlm.nih.gov/research/coronavirus/ LitCovid] — <span class="is-all-small-caps">NCBI</span>
 +
* [https://asone.ai/polymath/index.php?title=COVID-19_dataset_clearinghouse COVID-19 dataset clearinghouse] — <span class="is-all-small-caps">Polymath</span>
 +
* [https://rviews.rstudio.com/2020/04/07/some-select-covid-19-modeling-resources/ Modeling resources] by ''J. Rickert'' — <span class="is-all-small-caps">R Views</span>
 +
* [https://blog.ephorie.de/contagiousness-of-covid-19-part-i-improvements-of-mathematical-fitting-guest-post Contagiousness of COVID-19 Part I: Improvements of Mathematical Fitting] — <span class="is-all-small-caps">Learning Machines</span>
 +
* [https://blog.ephorie.de/epidemiology-how-contagious-is-novel-coronavirus-2019-ncov Epidemiology: How contagious is Novel Coronavirus (2019-nCoV)?] — <span class="is-all-small-caps">Learning Machines</span>
 +
* [https://blog.ephorie.de/covid-19-analyze-mobility-trends-with-r COVID-19: Analyze Mobility Trends with R] — <span class="is-all-small-caps">Learning Machines</span>
 +
 +
==Self-check==
 +
 +
* [[Covid-19 Progress in Turkey]]
 +
 +
{{Top}}

Revision as of 10:28, 11 May 2020

The Virus: SARS-CoV-2

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.

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.
covid-vaccine.png

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.
covid-soap.png

Treatment, Vaccine, Prevention

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.
vaccine-success-Artboard_1.png

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


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")

Data Sources (other)


Datasets


Updates


Dashboards


Research

Self-check