Spike Gene Analysis and Prevalence of Porcine Epidemic Diarrhea Virus from Pigs in South Korea: 2013-2022

Abstract

From late 2013-2022, 1131 cases of porcine epidemic diarrhea (PED) were reported to the Korean Animal Health Integrated System (KAHIS). There were four major outbreaks from winter to spring (2013-2014, 2017-2018, 2018-2019, and 2021-2022), with the main outbreaks occurring in Chungnam (CN), Jeonbuk (JB), and Jeju (JJ). Analysis of the complete spike (S) gene of 140/1131 KAHIS PEDV cases nationwide confirmed that 139 belonged to the G2b genotype and 1 to the G2a genotype. Among them, two strains (K17GG1 and K17GB3) were similar to an S INDEL isolated in the United States (strain OH851), and 12 strains had deletions (nucleotides (nt) 3-99) or insertions (12 nt) within the S gene. PEDVs in JJ formed a regionally independent cluster. The substitution rates (substitutions/site/year) were as follows: 1.5952 × 10^-3 in CN, 1.8065 × 10^-3 in JB, and 1.5113 × 10^-3 in JJ. A Bayesian skyline plot showed that the effective population size of PEDs in JJ fell from 2013-2022, whereas in CN and JB it was maintained. Genotyping of 340 Korean PEDV strains, including the 140 PEDVs in this study and 200 Korean reference strains from GenBank, revealed that only the highly pathogenic non-INDEL type (G2b) was dominant from 2020 onwards. Therefore, it is predicted that the incidence of PED will be maintained by the G2b (non-INDEL) genotype.

Keywords: PEDV; S INDEL; diarrhea; evolution; piglet; spike.

Figure 1

PED occurrence from 2013–2022, based on information from the KAHIS (Korean Animal Health Investigation System, https://www.kahis.go.kr, accessed on 3 April 2023). The major epidemic PED outbreaks (i–iv) are denoted by year and month (A), and the pig farms involved in the outbreak area are marked on the map (B). GG: Gyeonggi; GW: Gangwon; CN: Chungnam; CB: Chungbuk; GN: Gyeongnam; GB, Gyeongbuk; JN: Jeonnam; JB: Jeonbuk; JJ: Jeju Island.

Figure 2

Phylogenetic tree analysis of the complete spike genes of the 211 PEDVs, comprising the 140 PEDV analyzed in this study and 71 global PEDV reference sequences. Red font (South Korea) denotes PEDVs detected in this study, and black font (South Korea) denotes reference strains obtained from GenBank.

Figure 3

PEDV genotypes detected in South Korea from 1997–2022. ML analysis of 340 Korean PEDVs (the 140 PEDVs used in this study and 200 Korean reference PEDVs registered in GenBank) was conducted. The four genotypes are shown as black (G1), gray (G2a), light brown (G2b, non-INDEL), and peach (G2b, S INDEL) bars.

Figure 4

Deletions and insertions in the spike gene of Korean PEDV strains. Antigenic sites within the spike protein (A), and the 14 Korean PEDV strains harboring insertions and deletions (B). Deletions are marked by dashes (–), and insertions by red letters.

Figure 5

Phylogenetic tree of the complete spike gene sequences of Korean PEDV collected in nine regions. MCC tree analysis of the 140 Korean PEDV strains detected in this study from 2013–2022 was conducted using the BEAST program. Each of the nine regions is marked by a different colored line. Bar = expected year. GG: Gyeonggi; GW: Gangwon; CN: Chungnam; CB: Chungbuk; GN: Gyeongnam; GB, Gyeongbuk; JN: Jeonnam; JB: Jeonbuk; JJ: Jeju Island.

Figure 6

Effective population size of PEDV from 2013–2022, presented as Bayesian skyline plots, in Jeju (A), Chungnam (B), and Jeonbuk (C).