What’s new?
We are a full one month into the outbreak, with the first cases of community tranmission announced on 17 June 2021. Today annoucement of 111 local cases (in the 24 hours up to 8 PM yesterday) is highly consistent with the trend and model, in the context that the model’s fit to the data hasn’t been terribly good. Case counts have bounced up and down somewhat. With the high level of uncertainty, I’m keeping projections to only 7 days. Long-term projections assume that current transmission dynamics remain static throughout, and this is clearly not likely to be a good assumption. The NSW Government has been ramping up the intensity of the stay-at-home orders with new announcements and futher restrictions announced today.
Entirely separate to the statistical model, we need to remember the actual generative mechanisms of the case counts, that is, “reality”. The highly transmissible nature of the delta variant of SARS-CoV-2, residual social movement of people in Greater Sydney leading to possible transmission events (e.g., in health facilities like pharmacies), and the burden of potentially unlinked community cases, means that the situation remains very concerning. Statistical models are at best a description and are not the reality itself.
Context and timeline of the Sydney 2021 outbreak
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.
Early in the week of 12 July 2021, even more restrictions were put into place, particularly for people living in Fairfield LGA, including the requirement for a COVID-19 swab every three days to work outside of the local area. On 15 July 2021, the lockdown was again extended until the end of the month (30 July 2021). On 17 July 2021, it was announced that only essential health and emergency service workers living in Fairfield, Liverpool, and Canterbury-Bankstown LGAs can leave these areas for work. The NSW Government also defined a narrow range of essential retail business that can continue to operate.
Projection of new daily cases, and cumulative counts of COVID-19 with data up to 17 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 7 days. It should be noted that estimates have high levels of uncertainty beyond a few days 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 17 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 a sudden increased rate of growth in cases, which represents the outbreak and community transmission in South Western Sydney.
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