On reproductive and respiratory syndrome virus dissemination across pig production systems in the United States

Manuel Jara; David A. Rasmussen; Cesar A. Corzo; Gustavo Machado

We estimated the contribution of local transmission (i.e., between farms within a production system) 132 versus external introductions (i.e., between farms across production systems) using a structured 133 coalescent model. Due to computational demand, we used PRRSv alignment from MEGA software 134 MASCOT, we estimated the effective population size in the local and external population and the 142 migration rates between them, which was allowed to be asymmetric. This analysis was replicated three 143 times, each time using one of the three pig systems as local and the other two as external. We also 144 calculated the posterior probability of each internal node in the tree being in each state (i.e., local or 145 external) using the forwards/backwards approach implemented in MASCOT (Müller et al., 2018) . 146