What’s new?
Today’s announcement of 633 new local cases in NSW was a shocking jump in case numbers. It is substantially higher than the model estimate. The Gompertz model remains somewhat stable, though the Richards’ growth curve model has had difficulty fitting the data. Both the models are performing okay though are biased towards underestimating.
The projections for the cumulative number of local cases for today, from the Gompertz and Richards’ growth models 7 days ago underestimated by 9% and 7% respectively. The same from 14 days ago underestimated by 18% and 14% respectively.
The model projections suggest that the outbreak is continuing to grow, with the rate of growth increasing. We are likely to see around 3000-4000 new cases over the coming week. The current lock down conditions in Greater Sydney have been extended to the end of August 2021, but it is implausible that the outbreak will be at a stage where these conditions can be lifted, something that has now been acknowledged by the NSW Government. The commencement of the recent state-wide lockdown and some enhanced restrictions in Greater Sydney will hopefully make a difference in the medium term.
Context and timeline of the Sydney 2021 outbreak
I started these analysis in early July with the new COVID-19 (delta variant) outbreak 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.
By 9 July 2021, there were early signs that COVID-19 transmission was worsening. On 15 July 2021, the lockdown was again extended until the end of July, and then extended again, this time for four weeks on 28 July 2021. Conditions at the end of the month for people living with South Western, and Western Sydney included a limit to travelling only 5 km from home, masks at all times outside, with only essential workers allowed to leave the local government area, with the requirement of a COVID-19 swab every 72 hours.
On 14 August 2021, in the setting of rapidly rising case counts, further restrictions were announced. The 5 km radius limit (from 10 km) was extended to all residents in Greater Sydney, starting 16 August 2021. Permits were also now required to leave the Greater Sydney area. Furthermore, stay-at-home orders were extended to across the entire state of NSW.
Projection of new daily cases, and cumulative counts of COVID-19 with data up to 18 August 2021
What is this?
The top image is a chart of the cumulative (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 Gompertz curve using non-linear regression. The dark central dashed lines are the model estimates, with 95% confidence intervals of the estimate. On the lower chart, the blue gradations can be understood as the degree of uncertainty in the model projections.
Gompertz and Richards’ growth curve
The Gompertz function is a type of sigmoid, or “S”-shaped curve. It’s been around since the early 19th century and was initially used to describe and model demographic mortality curves, and hence, well known to actuaries. The Gompertz function can also be used to accurately model biological growth (e.g., epidemics, tumour size, enzymatic reactions). I have chosen to use this model to help with creating insights as earlier in the pandemic, it was found to be useful in modelling cumulative cases of COVID-19 from the Chinese outbreaks (Jia et al. arXiv:2003.05447v2 [q-bio.PE]).
I had previously used the Richards’ growth curve (or the generalised logistic function), which 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).
Why the change?
It was clear that both models were not fitting the data that well, but the Richards’ curve model was performing especially poorly in mid-July 2021, with estimates that were obviously implausible. I’ve undertaken some assessment of the degree of predictive error in both the Gompertz and Richards’ growth curve models. These charts compare the 7- and 14-day total case projections of the models, to what actually occurred in reality 7 and 14 days later. For interpretation, above the 0% error line means that the model provided an over-estimate compared to reality, and below the 0% error line an underestimate.
Both models were in early July providing substantial underestimates, which is what I suspected when I started this series. The Richards’ growth curve model has struggled with the fit to the data, with poor predictive accuracy in July. Both models have been gradually underestimating further since the beginning of August.
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 18 August 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. The odd looking confidence intervals on the Richards’ curve is due to the degree of uncertainty in that regression model.
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.