Genomic characterization of classical swine fever virus LOM variants with 3′-UTR INDELs from pigs on Jeju Island, South Korea

Abstract

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.