Basic reproduction number as a measure of the rapidity of the inter-farm spread of porcine epidemic diarrhea during the initial phase of the epidemic in Japan in 2013-2014

The Japanese swine industry was heavily affected by the global porcine epidemic diarrhea (PED) outbreaks, started in the country in 2013. This study was conducted to quantify the infectivity of PED at the farm level in the initial phase of an epidemic in Kagoshima Prefecture, the largest swine producing area in Japan. A compartmental model was developed with the following five components of farm status according to the situation of within-farm PED infection : susceptible with no infected pig (S) ; exposed with at least one infected pig but no pig showing clinical symptoms (E) ; infectious with at least one pig showing symptoms, but the farmer has not yet reported it to the veterinary authorities, whether intentionally or unintentionally (In) ; infectious with pigs showing symptoms, and recognized by the veterinary authorities as an infected farm (Id) ; and recovered with all pigs having recovered from PED (R). Parameters were solved to maximize the likelihood of daily new cases and cumulative number of recovered farms modelled given the actual numbers during the first 40 days of the epidemic using data provided by the Kagoshima Prefectural government. The incubation period was set at two days, and the first case of each farm was assumed to be reported on the next day to the authority. The basic reproduction number Rsub0 was calculated using the next generation matrix. As results, the infectious period and Rsub0 were estimated to be 54.4 days and 5.39, respectively. In conclusion, inter-farm infectiousness was very high during the initial phase, and the long infectious period at the farm level, in addition to the common source infections already reported, contributed to the rapid spread of the disease.