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The case reproduction number is the expected number of secondary infections actually generated by a person infected at time $t$, allowing transmission conditions to change during that person's infectious lifetime. It follows an infection cohort through the subsequent conditions it experiences. The instantaneous reproduction number instead freezes conditions at the reference time. Cori and colleagues distinguish these two constructions in their framework for time-varying reproduction numbers. ^[ref].

An effective reproduction number describes transmission in the current population, accounting for available susceptibility and transmission conditions. The phrase is used with different time conventions, so a definition must specify whether it means an instantaneous reproduction number or a case reproduction number. The CDC uses a time-varying effective quantity $R_t$ to describe the direction of community transmission. ^[ref].

For the closed, homogeneous SIR model with constant $\beta ,\gamma$, the instantaneous convention givesThus the infectious compartment grows when $R_{\mathrm{eff}}>1$ and declines when $R_{\mathrm{eff}}<1$, provided $i>0$. At the SIR infection peak it equals one. This freezes the current susceptible fraction; it does not count a newly infected person's actual future secondary infections while $s$ continues to decrease. The distinction comes directly from the SIR model equations and the two time conventions above.

The instantaneous reproduction number at time $t$ isIt is the expected number of secondary infections that one infected individual would produce if the transmission conditions at time $t$ applied throughout that individual's infectious life. The case reproduction number, also called the effective reproduction number in this question, isthe expected number actually produced by a person infected at $t$ as calendar-time conditions subsequently change. The instantaneous quantity is easier to estimate in real time because it depends on current and past incidence; the case quantity depends on future conditions.