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

After that, to investigate the phenomenon of contraction, next to the baseline 153 scenario, we study two scenarios that increase the effect of, respectively, depletion and 154 competition on the generation time distribution. In the former scenario susceptible 155 persons are vaccinated at a specific moment in time during the epidemic, referred to as 156 the vaccination scenario, and in the latter scenario infectious individuals are forced to 157 compete for the same susceptible, referred to as the competition scenario. We also study 158 a scenario in which the competition among infectors is not present: individual are 159 forced to proposed a contact only to susceptible persons who no one already proposed 160 an infectious contact to. We refer to this scenario as the pure depletion scenario. In all 161 of these scenarios the infectious period is set here to be constant to avoid that the 162 stochasticity of the infectious period distribution affects the results. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder.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 Vaccination of susceptible persons 164 We study simulations in which 30%, 60% and 90% of the susceptible population is 165 vaccinated during the epidemic. In a population of size N = 1000 and R 0 = 1.5 we do 166 so by vaccinating the remaining susceptible persons at a specific time called vaccination 167 time and indicated with t v . In this way we change the depletion effect: both augmenting 168 the intensity and changing the time at which depletion occurs. We consider simulations 169 with different vaccination times representing the initial phase (t v = 2), the main phase 170 (t v = 3, 5, 7) and the last phase (t v = 9) of the epidemic and we compute the value of the 171 epidemic characteristics. We do not report the depletion entity because of the instant Average values of duration (T max ), final size (F S), mean forward (ω f ) and mean backward (ω b ) generation times.