SIR+B applied to Victoria, Australia
Updated: Aug 2, 2020
Victoria, Australia, is currently suffering an outbreak of COVID-19 and the state government is increasing social distance restrictions in order to keep the epidemic under control. Social distance restrictions are highly effective at reducing Reff - which we have seen in the global data set. Currently, in Victoria, Reff > 2. We are yet to see the new social distance policies having an impact in our model.
Lets look at the data.
We have included the epidemiological events (in green boxes) and policy actions (in red boxes) into a timeline. The Reff values have been calculated using CloseAssociate's SIR+B method as described here, using the daily case data for Victoria, Australia from Johns Hopkins CSSE data set. The original data and charts are in this spreadsheet. The chart shows
Reff from noisy daily case data (as black squares)
50% and 95% confidence intervals from statistical bootstrapping (in light gray and dark gray respectively)
Critical line of Reff = 1 (as a dashed red line - remember above 1.0 and the epidemic is increasing and below 1.0 it is decreasing)
Timeline events have been taken from news agency Australian Associated Press
Positive daily case data (as blue columns) taken from JHU CSSE
To see the chart above in more detail click on it to see an expanded view.
What the information is in this chart?
The SIR+B data and timeline allow us to conclude the following points.
There was a mini-outbreak starting on or about the 20 April 2020, which resulted in a small spike in 22 positive daily cases on 4 May (approx. 14 days later). Reff increased over 1.0 on 27 April but decreased to less than 1.0 by 5 May (8 days later). This outbreak event was contained. There are no timeline events associated with it but signals an early warning that Victoria was susceptible.
The first major outbreak identified starts on 25 May from "Rydges on Swanston" and it results in a rapid rise in Reff peaking at 2.0 on 12 June (approx. 14 days later)
The Stamford outbreak occurs on 17 June resulting in a further increase in Reff to 2.5 on or about 1 July (approx. 14 days later)
Since these outbreaks Reff has remained 2.7±0.2 and the implementation of social distance policies on 29 June (local lockdown), 4 July (extension of local lockdown), 6 July (border closure), 8 July (extension of local lockdown) are not seen in any reduction in the Reff value.
In general what we are seeing is outbreaks occurring and 14 days later spikes appearing in daily case data. Our new method is showing increased detail compared with other methods and this information is vital to understanding the epidemic. We are not claiming that the method is predictive of outbreaks but it certainly provides early warnings of Reff approaching epidemic values. What we are also seeing is increased detail and information about the progression of the epidemic. That information is of vital importance to the people of Victoria, Australia. We should expect to see the effects of the recent social distance policies taking effect by now. If Reff doesn't start to decrease below 1.0 soon then we can expect increasing daily case counts for the rest of this week.
You can track this information for yourself on our public website here. The information is updated daily.
The benefits of the SIR+B method
Globally, various countries and regions have different COVID-19 policy responses. We are not interested in criticizing the policy actions of any particular government especially when so much is yet to be learned about this epidemic. Rather we are interested in applying new research to practically inform and increase our knowledge of the disease.
We have developed an original SIR+B method for calculating the Effective Reproduction Number for COVID-19. As is often the case with new research, the value is not easily accessible to lay people, and this is especially true in the field of mathematics and data science when the concepts are complex.
Therefore it is critical that we present information to the public, public health officials and policy analysts that is consumable. The Victoria, Australia outbreak offers an opportunity to apply new science and mathematics to an outbreak and to demonstrate its effectiveness in a way that does not require post-graduate level mathematics.
The timeline of Victoria, Australia shows the value of the SIR+B method of the new science and methods. The value of this method over others, is that it is responsive and detailed and it is theoretically simple and computationally fast.