Detection of Long-Distance Transmission Events During the CSF Epidemic in Japan Using Whole-Genome-Sequence Data

Classical swine fever (CSF) is a highly contagious disease affecting domestic pigs and wild boars, posing a serious threat to the global swine industry. In Japan, CSF re-emerged on a pig farm in Gifu Prefecture in 2018, just 3 years after the country was declared CSF-free. The CSF virus (CSFV) was soon detected in neighboring wild boars and subsequently spread to adjacent areas, leading to further farm outbreaks. Given that long-distance transmission accelerates both spatial expansion and epidemic persistence, we aimed to identify such events during the current Japanese epidemic. Whole-genome sequences were generated for 100 farm isolates and 585 wild boar isolates collected through national surveillance. Putative ancestral strains were inferred for each isolate by comparing single-nucleotide variants (SNVs), and the great-circle distance to the nearest ancestral strain was considered the transmission distance. Six routes exceeding the 99th percentile of the distance distribution (182.2 km) were classified as long-distance transmission events: three involving farms and three involving wild boars. The sources of all these transmission events were identified as infected wild boars. The route to a farm in Okinawa Prefecture (January 2020) was linked to the illegal feeding of unheated food waste containing meat products. No specific sources were identified in the remaining two farm outbreaks. The three introductions into wild boar populations were most plausibly associated with anthropogenic activities, such as the movement of people or vehicles through infected habitats. To the best of our knowledge, this is the first study to comprehensively quantify long-distance CSFV spread across the entire course of the Japanese epidemic (2018-2024). Our findings will inform targeted control measures to prevent farm infections and the inadvertent spread of contaminated material to remote areas.