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Detection of Long-Distance Transmission Events During the CSF Epidemic in Japan Using Whole-Genome-Sequence Data.
Takehisa Yamamoto1, Tatsuya Nishi2, Katsuhiko Fukai2
1Epidemiology and Arbovirus Group, Division of Transboundary Animal Disease Research, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan.
Long-distance transmission of Classical swine fever virus (CSFV) in Japan, primarily from wild boars, drove the 2018 epidemic. Identifying these routes is crucial for preventing future farm outbreaks and spread.
Area of Science:
- Veterinary Virology
- Epidemiology
- Genomics
Background:
- Classical swine fever (CSF) is a highly contagious viral disease threatening the global swine industry.
- CSF re-emerged in Japan in 2018, spreading from domestic pigs to wild boars and causing subsequent farm outbreaks.
- Long-distance transmission is a key factor in the spatial expansion and persistence of epidemics.
Purpose of the Study:
- To identify and quantify long-distance transmission events of the Classical swine fever virus (CSFV) during the 2018-2024 Japanese epidemic.
- To determine the sources and routes of CSFV spread, differentiating between farm and wild boar populations.
- To provide data for targeted control measures against CSFV.
Main Methods:
- Whole-genome sequencing of 100 farm and 585 wild boar CSFV isolates.
- Inference of putative ancestral strains using single-nucleotide variants (SNVs).
- Calculation of transmission distances and classification of long-distance events (>182.2 km).
Main Results:
- Six long-distance transmission events (exceeding the 99th percentile) were identified: three affecting farms and three affecting wild boars.
- All identified long-distance transmission events originated from infected wild boars.
- One farm outbreak was linked to illegal feeding of contaminated food waste; others and wild boar introductions were associated with anthropogenic activities.
Conclusions:
- Wild boars are significant sources of long-distance CSFV transmission in Japan.
- Anthropogenic activities, including illegal food waste feeding and movement of people/vehicles, facilitate CSFV spread.
- Understanding these transmission dynamics is essential for effective CSF control and prevention strategies.
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