What’s new?
The last three days has seen a rapid rise in case numbers, particularly in South Western Sydney, especially in the Fairfield Local Government Area. These new cases appear to be part of an outbreak not evident 1-2 weeks earlier.
It is important to note that it is very likely that the current model estimates are significant underestimates. Acknowledging this direction of bias, the near term estimates and trend could be seen as a lower boundary of plausibility – it’s not likely to be any better than this.
From that perspective, the situation is very concerning. The enhanced lockdown has occurred for no more than 3 days, and the rapidly rising case counts are due to transmission events from a week ago. Case counts may look a lot worse before they improve.
Context
I started these analysis in early July with the new COVID-19 (delta variant) oubreak in Sydney NSW. The purpose of these charts is that they provide some projections into the near future. Hopefully this allows for some data driven expectations. The Sydney 2021 series starts on 12 July 2021 and are available here: https://vitualis.com/?page_id=4071
The current Sydney outbreak started on 17 June 2021 – the first day with reports of community cases in Bondi. The NSW Government formally commenced stay-at-home orders (“lockdown”) for a number of inner-Sydney regions on 25 June 2021 at 2359, having announced this earlier in the day. This was then broadened 18 hours later to cover the whole of Greater Sydney. The initial plan was a two-week lockdown, with it potentially being lifted on 9 July 2021.
After one-and-a-half weeks, it was evident that new case numbers were not reducing, and a one week extension to the lockdown was announced. By 9 July 2021, there were early signs that COVID-19 transmission was worsening, particularly in Western and South-Western Sydney and the NSW Government intensified lockdown restrictions.
Projection of new daily cases, and cumulative counts of COVID-19 with data up to 13 July 2021
What is this?
The top image is a chart of the culmulative (total) COVID-19 cases in NSW, starting from 17 June 2021, and the lower image is a chart of the daily new cases. Only local cases are included (i.e., excluding cases identified in quarantine). Projections are given for the next 2 weeks. It should be noted that estimates have high levels of uncertainty at around a week and must be interpreted cautiously.
The projections are made using a model by fitting the cumulative case data since 17 June 2021 to a Richards’ growth curve using non-linear regression. The dark central dashed lines are the model estimates, with 95% prediction intervals. On the lower chart, the green gradations can be understood as the degree of uncertainty in the model projections.
Richards’ growth curve
The Richards’ growth curve (or the generalised logistic function) is a broad family of sigmoid (S-shaped) curves that can describe well many types of growth, including epidemics. It has been demonstrated to have utility in modelling COVID-19 outbreaks in 2020 (Lee et al. PLoS One 2020 doi: 10.1371/journal.pone.0236860). My experience with the Melbourne 2020 outbreak was that the Richards’ growth curve was able to model the cumulative case numbers extremely well (see the second image). It should be noted, however, that when I used the Richards’ growth curve to model data from earlier in the Melbourne outbreak, it tended to result in very wide prediction intervals in near future projections, with an estimate that biases towards under-estimates. It performed particularly well after the inflexion point of the total case count (that is, the peak of the daily case count) had passed.
Daily case trends
Comparison between the Gompertz and Richards’ growth curve model projections, along with smoothed data trends (7-day simple moving average, and GAM) with data up to 13 July 2021
The generalised additive model gives a descriptive “reality check” to the models. The GAM can be considered as an advanced smoothed trend of the daily counts. My interpretation is that the initial lockdown did reduce the grow rate in cases, but did not reverse the trend. In early July 2021, we see an “exponential” looking growth in cases, which probably represents a new area of sustained community transmission in South Western Sydney. When we look at the most recent new daily cases data counts and the GAM, it is apparent that the growth model projections (both Gompertz and Richards’) are likely underestimates – probably due to the change in recent transmission dynamics.
Want to know more?
Primary data source is from NSW Health for daily new cases. The analysis is performed using RStudio Cloud using R version 4.1.0.
Today’s charts
Data: au_covid
R code: richards_model