Evolutionary dynamics of classical swine fever virus in South Korea: 1987–2017

•From 2000, Korean CSFV changed from genotype 3 to 2 (subgenotypes 2.1b and 2.1d).•Subgenotype 2.1d(prevalent in Korea) was detected in wild boar and breeding pigs.•The mean substitution rate for circulating Korean CSFVs is 2.2114(×10−3 s/s/y). The 5′ UTR (n=102) and full-length E2 (n=37) genes of classical swine fever viruses (CSFVs) circulating in South Korea over the past 30 years (1987–2017) were examined to determine the evolutionary rate and estimated time of the most recent common ancestor (tMRCA). From 2000, the Korean classical swine fever (CSF) antigen changed from genotype 3 to 2, which comprises subgenotypes 2.1b (2002–2013) and 2.1d (2011–2017). There are genotypic variations in the full-length E2 gene of Korean CSFV genotypes 2.1b and 2.1d (seven separate amino acid substitutions); these are useful distinguishing markers. The mean substitution rate (×103 substitutions/site/year) for Korean CSFV was estimated to be 2.2088 (95% highest posterior density (HPD): lower, 1.7045; upper, 2.7574) and the mean tMRCA was estimated to be 1901 (95% HPD: lower, 1865; upper, 1933). The effective population size of Korean CSFV genotype 2 increased rapidly from 2002 to 2003, after which it remained constant. The occurrence of CSF in Korea is expected to decline in the future; however, it will likely be more prevalent in wild boar than in domestic pigs. Thus, there is a risk of transmission from wild boar to breeding pigs.