Genomic Epidemiology of African Swine Fever Virus Identified in Domestic Pig Farms in South Korea during 2019–2021

Abstract

African swine fever (ASF), a contagious viral disease, poses a significant threat to the global swine industry. In South Korea, ASF outbreaks have occurred since 2019, highlighting the need for a comprehensive understanding of the epidemiology and genetic characterization of the circulating African swine fever viruses (ASFVs). We obtained 21 ASFV isolates from domestic pig farms and analyzed their whole-genome sequences using the Illumina MiniSeq. Phylogenetic analysis was conducted using the maximum likelihood and time-scaled approaches to determine the genetic relationships and evolutionary dynamics of the Korean ASFV isolates. Comparative analysis of the 21 ASFV genomes with the reference strain Georgia 2007/1 revealed that while Korean isolates shared 11 mutations, they also had 22 discrete mutations, including single nucleotide polymorphisms and insertion/deletion polymorphisms (Indels). Phylogenetic analysis indicated that all Korean isolates were within the Asian subgroup of ASFV genotype II but were further divided into at least three distinct subclusters. Spatiotemporal analysis indicated multiple introductions of ASFVs into South Korea, crossing the national border with North Korea. In addition, we observed putative self-recombination between MGF 505-9R and MGF 505-10R genes in the ASFV/Korea/Pig/Inje2/2021 strain. Our findings provide insights into the genetic variations and evolution of ASFVs on South Korean pig farms from 2019 to 2021, uncovering multiple introductions of ASFVs across the national border, and highlighting the need for enhanced disease control strategies.