Tracking the Covid-19 spread: Monitoring the effective reproduction number

Rt is the effective reproduction rate – a real-time monitoring metric of how fast the virus is growing.

When Rt is above 1.0, each infection causes more than one infection (virus spreads quickly). For example, Rt = 2 indicates one infected patient will yield two other infected patients on average.

When Rt is below 1.0, each infection causes less than one infection (virus will stop spreading).

World Health Organization and leading epidemiological research have shown real-time estimates of Rt as an important parameter to guide the selection and timings of lockdown measures. As we aim to relax lockdown measures, it is important to continuously monitor Rt to understand implications of measures on the virus spread. learn more

Calculating Rt

Rt is the effective reproduction rate of COVID-19 calculated for each region/country. It gives an up-to-date snapshot of the current epidemic situation by estimating the average secondary infections per one case in a population over time. This will change over time and can be used as an indication of real-time transmissibility.

Calculating Rt is a mathematical modeling exercise. Our Rt tracking model is inspired by the work of Bettencourt & Ribeiro (2008) and Systrom (2020), and calibrated to represent the COVID-19 situation in Indonesia. Park et al (2020) has estimated the incubation period to be 4-6 days and the serial interval to be 4-8 days. In our model, we have used a serial interval of 7 days as an input.

The grey band shows that there is a 90% chance that the true Rt estimate exists within the range. Higher testing rates can contribute to a narrower grey band as we have more confidence in the estimates.

While we make our best effort to accurately calculate Rt, our model (just like every mathematical model) has its limitations.

references

COVID-19, G. (2020). Gugus Tugas Percepatan Penanganan COVID-19. Retrieved from https://covid19.go.id

Bettencourt, L., & Ribeiro, R. (2008). Real Time Bayesian Estimation of the Epidemic Potential of Emerging Infectious Diseases. Plos ONE, 3(5), e2185. doi: 10.1371/journal.pone.0002185

Systrom, K. (2020). The Metric We Need to Manage COVID-19. Retrieved from http://systrom.com/blog/the-metric-we-need-to-manage-covid-19/

Rt Covid-19. (2020). Retrieved 24 May 2020, from https://rt.live/

Park, M., Cook, A., Lim, J., Sun, Y., & Dickens, B. (2020). A Systematic Review of COVID-19 Epidemiology Based on Current Evidence. Journal Of Clinical Medicine, 9(4), 967. doi: 10.3390/jcm9040967

Inglesby, T. (2020). Public Health Measures and the Reproduction Number of SARS-CoV-2. JAMA. doi: 10.1001/jama.2020.7878

HKUMed WHO Collaborating Centre for Infectious Disease Epidemiology and Control releases real-time situation report by the instantaneous effective reproductive number (Rt) of COVID-19. (2020). Retrieved from https://sph.hku.hk/en/news/press-releases/2020/hkumed-who-collaborating-centre-for-infectious-disease-epidemiology-and-control-releases-real-time-situation-report-by-the-instantaneous-effective-reproductive-number-rt-of-covid-19

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