COVID-19 reproduction number
Description
The reproduction number R indicates the average number of people infected by one person with COVID-19. For the estimation of this reproductive number, we use the number of reported COVID-19 hospitalisations per day in the Netherlands. Because a hospitalisation of a COVID-19 patient is passed on with some delay in the reporting system, we correct the number of hospitalisations for this delay [1]. For a large part of the reported patients, the first day of disease is known. This information is used to estimate the first day of disease for the other patients. By showing the number of patients admitted to the hospital as of the first day of illness, you can immediately see whether the number of infections is increasing, peaking or decreasing. In order to calculate the reproductive number, it is also necessary to know the length of time between the first day of disease of a COVID-19 patient and the first day of illness of his or her contagious person. This duration is on average 4 days, calculated on the basis of COVID-19 notifications to the GGD. If the number of new hospitalisations is low, we calculate the reproduction number R based on the number of reports of COVID-19 patients. This number of reports is kept by the GGDs. This information calculates the value of the reproduction number as described in Wallinga & Lipsitch 2007 [2].
From the Kassteele J, Eilers PHC, Wallinga J. Nowcasting the Number of New Symptomatic Cases During Infectious Disease Outbreaks Using Constrained P-spline Smoothing. Epidemiology. 2019;30(5):737-745. doi:10.1097/EDE.0000000000001050.
Wallinga J, Lipsitch M. How generation intervals shape the relationship between growth rates and reproductive numbers. Proc Biol Sci. 2007;274(1609):599-604. doi:10.1098/rspb.2006.3754.
Description of the variables
Version: Version number of the dataset. If the content of the dataset is changed structurally (i.e. not the daily update or a record level correction), the version number will be adjusted (+ 1) and also the corresponding metadata in RIVMdata (https://data.rivm.nl).
Version 2 update (8 February 2022):
— In the calculation of the reproduction number, instead of the GGD notification date, the date of positive test result is now used.
Version 3 update (17 February 2022):
— The calculation of the reproduction number now takes into account different generation times for different variants. For the variants up to Delta, the average generation time is 4 days, from Omikron that is 3.5 days. The reproduction number published here is a weighted average of the reproduction numbers per variant.
Version 4 update (1 September 2022):
— From 1 September 2022, this dataset has been split into two parts. The first part contains the dates from the beginning of the pandemic until 3 October 2021 (week 39) and contains ‘tm’ in the file name. This data is no longer updated. The second part contains the dates from 4 October 2021 (week 40) and is updated every Tuesday and Friday.
— Until 31 August, the published reproduction number was calculated with the dates of the day before publication. From 1 September, the published reproduction number has been calculated with the dates of the day of publication.
Date: Date for which the reproduction number has been estimated
Rt_low: Lower limit 95 % confidence interval
Rt_avg: Estimated reproduction number
Rt_up: Upper limit 95 % confidence interval
population: patient population valued “hosp” for hospitalised patients or “testpos” for test positive patients
For recent R estimates, reliability is not high, as reliability depends on the time between infection and getting sick and the time between getting sick and reporting. Therefore, the variable Rt_avg is absent in the last two weeks.
Resources
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Description |
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0 |
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https://data.rivm.nl/covid-19/COVID-19_reproductiegetal.json |
Tags
- reproductiegetal
- sars-cov-2
- infectieziekten
- gezondheid
- infectious-diseases
- health
- covid-19
- reproduction-number