Realized generation times: contraction and impact of infectious period, reproduction number and population size

Andrea Torneri; Amin Azmon; Christel Faes; Eben Kenah; Gianpaolo Scalia Tomba; Jacco Wallinga; Niel Hens

In In the competition scenario, we increase competition in the time interval (3, 7) , for a 266 population of size N = 1000 and a reproduction number of value R 0 = 1.5. In Table 6 267 we report the epidemic characteristics; we notice that the mean value of the generation 268 time is smaller compared to the one in the baseline scenario (Table 1) , both for the 269 forward and the backward scheme. We also notice that the mean number of generation 270 affected by competition and the mean number of competitors is higher respect to the 271 baseline scenario with same reproduction number (Table 2) . 272 Table 6 . Epidemic characteristics -Competition scenario The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/568485 doi: bioRxiv preprint time contracts around the interval in which the competition intensity is increased. Competition also affects the generation time distribution but its effect is directed to 295 a single generation. To have a similar impact on the mean forward generation time as 296 caused by depletion, competition should affect most of all the generations that an 297 individual makes. This is simulated in the scenario where competition is increased and 298 results show a potentially large impact of competition on the forward generation time. 299 However, in a baseline scenario where competition is not increased rarely more than one 300 generation per single individual is affected by competition and the mean number of 301 competitors is not particularly high to be able to explain a decreasing mean forward 302 generation time (Fig 3) . Furthermore, the effect of competition is strongly dependent on 303 March 5, 2019 12/23 the competitor's infection time and does not not always affect the considered generation. 304 The contact interval that leads to the generation time can be the longest one among the 305 contact intervals proposed by the infectors since the next generation is the minimum of 306 the set given by the infection times plus the proposed contact times. Competition is 307 slightly affecting the forward and backward generation time: Table 6 shows a small 308 decrease probably due to the competition effect.