Estimating effective reproduction number using generation time versus serial interval, with application to COVID-19 in the Greater Toronto Area, Canada

The effective reproductive number Re(t) is an important near-real-time indicator of intervention success and epidemic potential. Re(t) represents the average number of new infections generated by each infectious person, after accounting for interventions and the current context. Thus, Re(t)>1 leads to epidemic growth, and Re(t)<1 leads to fewer and fewer new infections. Re(t) is different from the basic reproduction number R0, which represents the average number of new infections generated by each infectious person in the absence of any interventions and in an entirely susceptible population. Thus, Re(t) will almost always be smaller than R0.

We estimate Re(t) over time for COVID-19 in Ontario and the GTA, and explore epidemic growth attributable to specific infection contexts, such as travel-related, long term care homes, and neighbourhood stratification. We also examine the influence of assumptions about the distribution of infectiousness on Re(t).

The preprint of the paper is available and there is also a GitHub repository related to this project.