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

The contraction of the mean forward generation time seems counter-intuitive since 50 one would expect generations to happen faster in the initial phase of the epidemic, when 51 the population is mostly susceptible. The principal aim of this paper is to clarify the 52 epidemiological mechanisms that cause contraction. Researchers typically assign to the 53 phenomenon of contraction only one among two explanations: competition among 54 infectors [8] and depletion of susceptible individuals [5, 20] . Both explanations are 55 reasonable, but a study that clearly shows which of these hypotheses are responsible for 56 the contraction of the mean forward generation time is not present in literature. The We distinguish between three time intervals that determine the between-host 89 transmission of infection. The first one is the contact interval Ï„ i,j , defined to be the Our simulation models are based on two algorithms previously introduced in literature. 103 The stepwise algorithm was proposed by Kenah et al. (2008) ; it is based on the notion 104 contact interval [22] and it was implemented to illustrate the competition among Appendix. Since results are similar for both algorithms we report results based on the 113 parallel algorithm and defer results based on the stepwise algorithm to S1 Appendix (S1 114 Fig and S1 Table) .