Classical swine fever virus (CSFV) reemerged in naïve pig herds on Jeju Island, South Korea, due to the accidental introduction of the LOM vaccine strain in 2014. Since this reemergence, the previously CSFV-free region has experienced numerous outbreaks, causing the virus to become endemic in provincial herds. In this study, we determined the complete genome sequences and investigated the molecular characteristics of LOM-derived field CSFV strains with unique insertion-deletion (INDEL) mutations in the 3'-untranslated region (UTR) that were responsible for ongoing sporadic outbreaks on Jeju Island in 2019. The Jeju LOM-derived variants that emerged in 2019 had their own INDEL signatures in the 3'-UTR, resulting in changes to the predicted secondary stem-loop structures. The genomes of these strains were 12,297-12,302 nucleotides in length, one nucleotide (nt) shorter or one, two, or four nt longer than the reference LOM strain. The 3'-UTR INDEL variants shared 98.8-99.0% and 98.3-98.6% identity with the LOM strain at the polyprotein and full-genome level, respectively. The total number of genetic variations between the LOM vaccine strain and the 3'-UTR INDEL isolates ranged from 161 to 202 and 37 to 45 at the nucleotide and amino acid level, respectively. These mutations were broadly dispersed throughout the genome and particularly clustered in NS2 and the 3'-UTR, possibly triggering a reversion to low virulence and allowing the virus to adapt to improve its persistence in the field. This study provides important information about the genetic evolution of LOM-derived CSFV circulating in the free region, and suggests that it arose from continuous non-lethal mutations to ensure viral fitness in host animals.

中文翻译：

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韩国济州岛猪的经典猪瘟病毒 LOM 变体与 3'-UTR INDEL 的基因组特征。

由于 2014 年 LOM 疫苗株的意外引入，古典猪瘟病毒 (CSFV) 在韩国济州岛的未接种猪群中重新出现。自此次重新出现以来，以前没有 CSFV 的地区经历了多次疫情爆发，导致该病毒成为省畜群中的地方病。在这项研究中，我们确定了完整的基因组序列，并研究了 LOM 衍生的野外 CSFV 毒株的分子特征，这些毒株在 3'-非翻译区 (UTR) 中具有独特的插入缺失 (INDEL) 突变，这些突变是造成济州岛持续零星爆发的原因2019 年的岛屿。2019 年出现的济州岛 LOM 衍生变体在 3'-UTR 中具有自己的 INDEL 特征，导致预测的二级茎环结构发生变化。这些菌株的基因组长度为 12,297-12,302 个核苷酸，比参考 LOM 菌株短 1 个核苷酸 (nt) 或长 1、2 或 4 个 nt。3'-UTR INDEL 变体在多蛋白和全基因组水平上与 LOM 菌株分别具有 98.8-99.0% 和 98.3-98.6% 的同一性。LOM疫苗株和3'-UTR INDEL分离株之间的遗传变异总数在核苷酸和氨基酸水平上分别为161至202和37至45。这些突变广泛分散在整个基因组中，特别集中在 NS2 和 3'-UTR 中，可能引发低毒力的回复，并使病毒能够适应以提高其在现场的持久性。这项研究提供了有关在游离区域循环的 LOM 衍生 CSFV 遗传进化的重要信息，并表明它源自连续的非致命突变，以确保宿主动物的病毒适应性。