Inferring pandemic growth rates from sequence data

de Silva, Eric; Ferguson, Neil M.; Fraser, Christophe

population size and variance of offspring distribution [4, 30, 31] . Using the formula for the negative binomial distribution given earlier, the ratio of effective population size (N e ) to census population size (N ) is equivalent to the reciprocal of the variance (s 2 ), which can be written in terms of the reproduction rate (R) and offspring distribution (k): Figure 2 indicates that estimates of the effective population size obtained using BEAST tend to be biased upwards in the early phase of the epidemic, before they tend to level off. The red curves in figure 2 are BSPs generated via uniform sampling. While these estimates effectively capture epidemic dynamics over the earlier generations, by the halfway point of the epidemic, growth in the BSP curves begin to slow down significantly. The final effective population size is thus significantly less (this discrepancy being more pronounced for higher R-values) than the actual size of the simulated infected population, leading to a false inference of a slowing epidemic.