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

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

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background.The effective reproduction number Re(t) is a critical measure of epidemic potential.Re(t) can be calculated in near real time using an incidence time series and the generation time distribution: the time between infection events in an infector-infectee pair.

In calculating Re(t), the Horse Shampoo generation time distribution is often approximated by the serial interval distribution: the time between symptom onset in an infector-infectee pair.However, while generation time must be positive by definition, serial interval can be negative if transmission can occur before symptoms, such as in covid-19, rendering such an approximation improper in some contexts.methods.

We developed a method to infer the generation time distribution from parametric definitions of the serial interval and incubation period distributions.We then compared estimates of Re(t) for covid-19 in the Greater Toronto Area of Canada using: negative-permitting versus non-negative serial interval distributions, versus the inferred generation time distribution.results.

We estimated the generation time of covid-19 to be Gamma-distributed with mean 3.99 and standard deviation 2.96 days.

Relative to the generation time distribution, non-negative Robot Replicas serial interval distribution caused overestimation of Re(t) due to larger mean, while negative-permitting serial interval distribution caused underestimation of Re(t) due to larger variance.implications.Approximation of the generation time distribution of covid-19 with non-negative or negative-permitting serial interval distributions when calculating Re(t) may result in over or underestimation of transmission potential, respectively.