Epidemiology Unit, Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan.
Foot and Mouth Disease Unit, Division of Transboundary Animal Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, Kodaira, Japan.
Transbound Emerg Dis. 2022 May;69(3):1166-1177. doi: 10.1111/tbed.14076. Epub 2021 Mar 30.
Classical swine fever (CSF) is a worldwide devastating disease of the pig industry caused by classical swine fever virus (CSFV). In September 2018, an outbreak of CSF occurred in Japan where the disease had been eradicated and was officially designated a CSF-free country since 2015. Following the detection of the first 2018 case on a farm in Gifu Prefecture, the disease spread among both farm pigs and wild boars and still continues. Epigenome analysis using whole-genome information is helpful in identifying the infection route, but the current approaches provide an insufficient resolution. In this study, a novel method of using single-nucleotide variants (SNVs) was employed to identify the associations among 158 isolates (65 from farms and 93 from wild boars). The identified groups of CSFV strains were plotted in different colours on a map, identifying the location where each strain was collected. The lack of an SNV set shared between the index case and the other strains suggested the first infection in Japan during the outbreak occurred in wild boars, not at the index farm. For the Atsumi Peninsula outbreaks, where nine farms were found infected within a 10-km radius area, the farm strains were assembled into three groups, suggesting these outbreaks resulted from at least three different infection events in this area. For the infections in the area around Saitama Prefecture, an area remote from the epicentre, strains from both the farms and wild boars were identified as being in the same group, suggesting they resulted from one viral introduction. Likewise, seven infected farms in Okinawa Prefecture, almost 1,500 km from Gifu Prefecture, were identified as being in a common, but separate group. By demonstrating the variety of transmission routes and possibility of long-distance infection, these results will help improve disease control measures.
古典猪瘟（Classical swine fever，CSF）是一种对养猪业具有全球破坏性的疾病，由古典猪瘟病毒（Classical swine fever virus，CSFV）引起。2018 年 9 月，日本爆发了 CSF，该疾病在 2015 年已被根除，日本被正式指定为 CSF 无疫区。在岐阜县的一个农场发现首例 2018 年病例后，该疾病在农场猪和野猪中传播，并仍在继续传播。使用全基因组信息进行表观基因组分析有助于识别感染途径，但目前的方法分辨率不足。在这项研究中，采用了一种新的方法，使用单核苷酸变异（Single-nucleotide variants，SNVs）来识别 158 个分离株（农场 65 株，野猪 93 株）之间的关联。确定的 CSFV 株系被绘制成不同颜色的地图，以标识每个株系的采集地点。在日本暴发期间，首例感染病例与其他株系之间缺乏共享的 SNV 集，这表明在日本的首次感染发生在野猪中，而不是在首例感染的农场。对于发生在距震中约 10 公里半径范围内的九个农场的敦贺半岛暴发，将农场株系组装成三个组，表明这些暴发是由该地区至少三个不同的感染事件引起的。对于埼玉县周边地区的感染，由于该地区远离震中，来自农场和野猪的株系被鉴定为同一组，表明它们是由一次病毒传入引起的。同样，在距岐阜县约 1500 公里的冲绳县的七个受感染农场也被鉴定为属于同一组，但属于不同的组。这些结果表明了多种传播途径和远距离感染的可能性，将有助于改善疾病控制措施。
