Fig. 2.

Method performance on simulated data. We assessed the performance of MV-EpiEstim on a range of scenarios. In each panel, the $x$-axis shows the true value of the effective transmission advantage (on categorical scale). The $y$-axis shows the bias i.e., the difference between the posterior mean estimate of the transmission advantage and the true value. The solid dots represent the mean bias (across 100 simulations) and the vertical bars show the standard deviation (SD) of the bias. Each panel corresponds to a different simulation scenario. In all scenarios, the $R_t$ for the reference variant was 1.1 and the $R_t$ for the new variant was $ϵ$ times the reference $R_t$ (see Suppl Sec. 5 for details). (A) In the baseline scenario, we assumed no superspreading and the same natural history for both variants. (B) As (A), but with low (overdispersion parameter $\kappa$ = 1), moderate ($\kappa$$=$ 0.5) and high ($\kappa$$=$ 0.1) levels of superspreading. (C) As (A), but the mean serial interval of the new variant is 0.5 (low), 1.5 (moderate) or 2 (high) times that of the reference and is correctly specified during estimation. (D) As (C), but the mean serial interval of both variants are assumed to be the same during estimation. (E) As (A), but the coefficient of variation (CV, ratio of standard deviation to mean) of the serial interval distribution of the new variant is 0.5 (low), 1.5 (moderate) or 2 (high) times that of the reference and is correctly specified during estimation. (F) As (E), but the CV of the serial interval distribution of the reference and new variants are assumed to be the same during estimation. Note that the $y$-axis range is different for panel D. Results using $R_t=1.6$ for the reference and using fewer days of data are presented in Suppl Secs. 5.3 to 5.9. Results using time-varying reference $R_t$ in one or two locations are shown in Suppl Secs. 5.10 and 5.11.