COVID-19 Reproduction Rates
Published:
COVID-19 - Keeping an Eye on Reopening of Countries and States
This notebook is intended to serve as a reference of the various partial economic reopenings occurring around the world. With the arrival rate of new cases dropping in almost every country, many countries are relaxing social distancing practices and allowing the reopening of local businesses. This is an exciting and nervous time - no one wants another hot reignition of the spread of the virus.
In addition to monitoring growth rates in the re-opened countries and states, a new section of the notebook now calculates the reproduction rate $R_t$, which is a key indicator of the safety of reopening.
Background
I think it is important for everyone to understand the nature of the growth patterns of pandemics. There is an excellent Youtube video from 3Blue1Brown that offers a great explanation.
Understanding Growth Video Link
Purpose of This Document
This document will maintain a dynamic list of countries and states as they reopen local businesses. It will track the daily and logistic growth patterns to identify any flair-ups of the virus.
In addition to the visual tracking of new cases, active cases, and growth rates, this notebook now incorporates the calculation of the effective reproduction number R. This is a key variable to track in determining when the situation is really safe to reopen public venues. We will track changes in R over time. As R becomes < 1, it is much safer to resume normal activities, because the virus will not spread.
The addition of the R modeling is inspired by the work from Kevin Systrom, Estimating COVID-19’s $R_t$ in Real-Time here.
Starting Observations
As of April 22, 2020, there are about 6 European countries that have some form of reopening in place.
- Denmark - reopened daycare and primary schools on April 14. April 20 saw reopening of hairdressers, tattooists, and psychologists.
- Austria - April 14 non-essintial shops with floor space < 400 square meters. May 1, this extended to shopping centers.
- Norway - April 20 - kindergartens. Primary and some high schools on April 27, along with universities, beauty salons. Domestic travel is allowed but discouraged.
- Germany - April 20, shops < 800 square meters, along with car showrooms, bookstores, and bicycle shops. Schools on May 4th.
- Switzerland - April 27 hairdressers, hardware stores, beauty salons and flower shops. Also non-essential medical care.
- Sweden - Never closed down so it is included as a reference point.
- Georgia - First US state to reopen. It includes hair and nail salons, barber shops, massage businesses and gyms.
In the next two weeks, several US states are scheduled to reopen. They will be added as the reopening occurs.
Observation Log
- 2020-04-26 - European reopening countries are all ok, although Germany’s R value has moved above 1. Sweden still shows increasing cases; they probably have not reached an inflection point.
Change History
- 2020-03-18 - Addressed a problem with some of the curve fitting not converging. Because some of the countries, like the US, had a long period of days with no increases of cases, the tracking start date.
- 2020-03-18 - Added US “hot” states, NY, CA, and WA. Also added Germany, which has shown rapid recent growth.
- 2020-03-19 - Added Colorado, per friend request. Also added France and 2 high density countries, Monaco and Singapore
- 2020-03-20 - Removed Monaco, not enough cases
- 2020-03-21 - Added Switzerland, New Jersey, Louisiana, and 12 ‘hot’ European countries as a group
- 2020-03-22 - Added United Kingdom and UK to hot European group
- 2020-03-23 - Changed South Korea extract, due to a data change in source; moved Iran to the logistic curve section;
- 2020-03-24 - Changed dataset source due to issues with corona-virus- report/covid_19_clean_complete.csv; United Kingdom is called UK on this dataset
- 2020-03-27 - Added more US states: Massachusetts, Florida, Michigan, Illinois. Add new cases tracking graph. Removed Iran from logistic graph.
- 2020-03-30 - Added Sweden to country tracking because they are not enforcing any social distancing rules. Also added India because of population size.
- 2020-03-31 - Moved Italy, Spain, Hot European, and New York to the logistic plot.
- 2020-04-02 - Added Washington to logistic plot. Corrected error with negative growth rates.
- 2020-04-05 - Added Germany, California, Washington to logistic plot. Corrected error with negative growth rates.
- 2020-04-06 - Added Louisiana, Massachusetts, Florida, and the rest of the world without China to logistic plots.
- 2020-04-08 - Added United States to logistic plots.
- 2020-04-22 - Converted this to a reopening tracker
- 2020-04-22 - Added Rt tracking
About Coronavirus
- Coronaviruses are zoonotic viruses (means transmitted between animals and people).
- Symptoms include from fever, cough, respiratory symptoms, and breathing difficulties.
- In severe cases, it can cause pneumonia, severe acute respiratory syndrome (SARS), kidney failure and even death.
- Coronaviruses are also asymptomatic, means a person can be a carrier for the infection but experiences no symptoms
Novel coronavirus (nCoV)
- A novel coronavirus (nCoV) is a new strain that has not been previously identified in humans.
COVID-19 (Corona Virus Disease 2019)
- Caused by a SARS-COV-2 corona virus.
- First identified in Wuhan, Hubei, China. Earliest reported symptoms reported in November 2019.
- First cases were linked to contact with the Huanan Seafood Wholesale Market, which sold live animals.
- On 30 January the WHO declared the outbreak to be a Public Health Emergency of International Concern
Acknowledgements
This effort was inspired by an excellent Youtube video from 3Blue1Brown