Estimating the increased transmissibility of the B.1.1.7 strain over previously circulating strains in England using fractions of GISAID sequences and the distribution of serial intervals

Piantham, C.; Ito, K.

The B.1.1.7 strain, a variant strain of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is thought to have higher transmissibility than previously circulating strains in England. The fraction of the B.1.1.7 strain among SARS-CoV-2 viruses in England have grown rapidly. In this paper, we propose a method to estimate the selective advantage of a mutant strain over previously circulating strains using the time course of the fraction of B.1.1.7 strains. Based on Wallinga-Teunis's method to estimate the instantaneous reproduction numbers, our method allows the reproduction number to change during the target period of analysis. Our approach is also based on the Maynard Smith's model of allele frequencies in adaptive evolution, which assumes that the selective advantage of a mutant strain over previously circulating strains is constant over time. Applying this method to the sequence data in England using serial intervals of COVID-19, we found that the transmissibility of the B.1.1.7 strain is 40% (with a 95% confidence interval (CI) from 40% to 41%) higher than previously circulating strains in England. The date of the emergence of B.1.1.7 strains in England was estimated to be September 20, 2020 with its 95% CI from September 11 to September 20, 2020. The result indicated that the control measure against the B.1.1.7 strain needs to be strengthened by 40% from that against previously circulating strains. To get the same control effect, contact rates between individuals need to be restricted to 0.71 of the contact rates that have been achieved form the control measure taken for previously circulating strains.