A practical generation interval-based approach to inferring the strength of epidemics from their speed

Sang Woo Park; David Champredon; Joshua S. Weitz; Jonathan Dushoff

The generation interval is the amount of time between when an individual is infected by an infector, and the time that the infector was infected [39] . While r measures the speed of the disease at the population level, the generation interval measures speed at the individual level. Generation interval distributions are typically inferred from contact tracing, sometimes in combination with clinical data [7, 20, 16] . Generation interval distributions can be difficult to ascertain empirically [29, 8] , and the generation-function approach depends on an entire distribution. Multiple studies have explored how general-interval distributions affect the r-R relationship (summarized in Table 1 ). However, the use of an entire distribution makes it difficult to determine which features of the distributions are essential to connect measurements of the rate of spread r, with the reproductive number, R. Moreover, different assumptions about the shape of generation interval distributions