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Korean J. Vet. Serv. 2021; 44(2): 73-83

Published online June 30, 2021

https://doi.org/10.7853/kjvs.2021.44.2.73

© The Korean Socitety of Veterinary Service

전북지역 돼지유행성설사 바이러스 Spike 유전자 염기서열 및 계통분석

박미연;문보미;강수진;이종하;박진우;조성우;허철호;

전라북도 동물위생시험소 북부지소;전라북도 동물위생시험소 북부지소;전라북도 동물위생시험소 북부지소;전라북도 동물위생시험소 북부지소;전라북도 동물위생시험소 북부지소;전라북도 동물위생시험소 북부지소;전라북도 동물위생시험소 북부지소;

Received: February 9, 2021; Revised: June 18, 2021; Accepted: June 19, 2021

Genetic sequence and phylogenetic analysis of spike genes of porcine epidemic diarrhea virus (PEDV) in Jeonbuk province

Park, Mi-Yeon;Moon, Bo-Mi;Gang, Su-Jin;Lee, Jong-Ha;Park, Jin-Woo;Cho, Sung-Woo;Her, Cheol-Ho;

North-Branch, Jeonbuk Veterinary Service Laboratory;North-Branch, Jeonbuk Veterinary Service Laboratory;North-Branch, Jeonbuk Veterinary Service Laboratory;North-Branch, Jeonbuk Veterinary Service Laboratory;North-Branch, Jeonbuk Veterinary Service Laboratory;North-Branch, Jeonbuk Veterinary Service Laboratory;North-Branch, Jeonbuk Veterinary Service Laboratory;

Correspondence to : 전라북도 동물위생시험소 북부지소(North-Branch, Jeonbuk Veterinary Service Laboratory)

Received: February 9, 2021; Revised: June 18, 2021; Accepted: June 19, 2021

Although many swine farms continuously vaccinated to sow to prevent Porcine epidemic diarrhea(PED), PED has occurred annually in swine herds in Jeonbuk province, Korea. In the present study, the small intestine and feces samples from 17 farms where severe watery diarrhea and death of newborn piglets occurred in 2019 were collected, amplified by RT-PCR and determined the complete nucleotide sequences of the spike (S) glycoprotein genes of nine Jeonbuk PEDV isolates. The spike (S) glycoprotein is an important determinant for molecular characterization and genetic relationship of PEDV. These nine complete S gene isolates were compared with other PEDV reference strains to identify the molecular diversity, phylogenetic relationships and antigenicity analysis. 9 field strains share 98.5~100% homologies with each other at the nucleotide sequence level and 97.3~100% homologies with each other at the amino acid level. The nine Jeonbuk PEDV isolates were classified into G2b group including a genetic specific signal, S-indels (insertion and deletion of S gene). In addition, comparisons the neutralizing epitopes of S gene between 9 field strains and domestic vaccine strains of Korea mutated 12-15 amino acids with SM-98-1 (G1a group) and mutated 0-3 amino acids with QIAP1401 (G2b group). Therefore, the development of G2b-based live vaccines will have to be expedited to ensure effective prevention of endemic PED in Korea. In addition, we will need to be prepared with periodic updates of preventive vaccines based on the PEDV variants for the re-emergence of a virulent strain.

Keywords PEDV,Spike gene,RT-PCR,Phylogenetic analysis,

  1. Chang SH, Bae JL, Kang TJ. 2002. Identification of the Epitope Region Capable of inducing Neutralizing Antibodies against the Porcine Epidemic Diarrhea Virus. Molecules and Cells 14: 295-299.
  2. Debouck P, Pensaert M. 1980. Experimental infection of pigs with a new porcine enteric coronavirus, CV 777. Am J Vet Res 41: 219-223.
  3. Duarte M, Gelfi J, Lambert P, Rasschaert D, Laude H. 1993. Genome organization of porcine epidemic diarrhoea virus. Adv Exp Med Biol 342: 55-60.
    Pubmed CrossRef
  4. Kumar S, Stecher G, Tamura K. 2016. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol 33: 1870-1874.
    Pubmed KoreaMed CrossRef
  5. Kweon CH, Kwon BJ, Jung TS, Kee YJ, Hur DH, Hwang EK, Rhee JC, An SH. 1993. Isolation of porcine epidemic diarrhea virus (PEDV) in Korea. Korean J Vet Res 33: 249-254.
  6. Langel SN, Paim FC, Lager KM, Vlasova AN, Saif LJ. 2016. Lactogenic immunity and vaccines for porcine epidemic diarrhea virus (PEDV): Historical and current concepts. Virus Res 226: 93-107.
    Pubmed KoreaMed CrossRef
  7. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948.
    Pubmed CrossRef
  8. Lee CH, 2015. Porcine epidemic diarrhea virus: An emerging and re-emerging epizootic swine virus. Virol J 12: 193.
    Pubmed KoreaMed CrossRef
  9. Lee DK, Park CK, Kim SH, Lee C. 2010. Heterogeneity in spike protein genes of porcine epidemic diarrhea viruses isolated in Korea. Virus Res 149: 175-182.
    Pubmed KoreaMed CrossRef
  10. Lee SH, Lee CH. 2014. Outbreak-related porcine epidemic diarrhea virus strains similar to US strains, South Korea, 2013. Emerg Infect Dis 20: 1223-1226.
    Pubmed KoreaMed CrossRef
  11. Lin CM, Saif LJ, Marthaler D, Wang Q. 2016. Evolution, antigenicity and pathogenicity of global porcine epidemic diarrhea virus strains. Virus Res 226: 20-39.
    Pubmed KoreaMed CrossRef
  12. Oh J, Lee KW, Choi HW, Lee CJ. 2014. Immunogenicity and protective efficacy of recombinant S1 domain of the porcine epidemic diarrhea virus spike protein. Arch Virol 159: 2977-2987.
    Pubmed KoreaMed CrossRef
  13. Park HS, Yook SY, Jeon DM, Lee JJ, Shin CH. 2016. Genetic sequence and phylogenetic analysis of spike genes of Porcine epidemic diarrhea virus (PEDV) in Chung-Nam area. Korean Journal of Veterinary Service 39: 259-266.
    CrossRef
  14. Pijpers A, van Nieuwstadt AP, Terpstra C, Verheijden JH. 1993. Porcine epidemic diarrhoea virus as a cause of persistent diarrhoea in a herd of breeding and finishing pigs. Vet Rec 132: 129-131.
    Pubmed CrossRef
  15. Sun RQ, Cai RJ, Chen YQ, Liang PS, Chen DK, Song CX. 2012. Outbreak of Porcine Epidemic Diarrhea in Suckling Piglets, China. Emerging infectious diseases 18: 161- 163.
    Pubmed KoreaMed CrossRef

Article

Research Article

Korean J. Vet. Serv. 2021; 44(2): 73-83

Published online June 30, 2021 https://doi.org/10.7853/kjvs.2021.44.2.73

Copyright © The Korean Socitety of Veterinary Service.

전북지역 돼지유행성설사 바이러스 Spike 유전자 염기서열 및 계통분석

박미연;문보미;강수진;이종하;박진우;조성우;허철호;

전라북도 동물위생시험소 북부지소;전라북도 동물위생시험소 북부지소;전라북도 동물위생시험소 북부지소;전라북도 동물위생시험소 북부지소;전라북도 동물위생시험소 북부지소;전라북도 동물위생시험소 북부지소;전라북도 동물위생시험소 북부지소;

Received: February 9, 2021; Revised: June 18, 2021; Accepted: June 19, 2021

Genetic sequence and phylogenetic analysis of spike genes of porcine epidemic diarrhea virus (PEDV) in Jeonbuk province

Park, Mi-Yeon;Moon, Bo-Mi;Gang, Su-Jin;Lee, Jong-Ha;Park, Jin-Woo;Cho, Sung-Woo;Her, Cheol-Ho;

North-Branch, Jeonbuk Veterinary Service Laboratory;North-Branch, Jeonbuk Veterinary Service Laboratory;North-Branch, Jeonbuk Veterinary Service Laboratory;North-Branch, Jeonbuk Veterinary Service Laboratory;North-Branch, Jeonbuk Veterinary Service Laboratory;North-Branch, Jeonbuk Veterinary Service Laboratory;North-Branch, Jeonbuk Veterinary Service Laboratory;

Correspondence to:전라북도 동물위생시험소 북부지소(North-Branch, Jeonbuk Veterinary Service Laboratory)

Received: February 9, 2021; Revised: June 18, 2021; Accepted: June 19, 2021

Abstract

Although many swine farms continuously vaccinated to sow to prevent Porcine epidemic diarrhea(PED), PED has occurred annually in swine herds in Jeonbuk province, Korea. In the present study, the small intestine and feces samples from 17 farms where severe watery diarrhea and death of newborn piglets occurred in 2019 were collected, amplified by RT-PCR and determined the complete nucleotide sequences of the spike (S) glycoprotein genes of nine Jeonbuk PEDV isolates. The spike (S) glycoprotein is an important determinant for molecular characterization and genetic relationship of PEDV. These nine complete S gene isolates were compared with other PEDV reference strains to identify the molecular diversity, phylogenetic relationships and antigenicity analysis. 9 field strains share 98.5~100% homologies with each other at the nucleotide sequence level and 97.3~100% homologies with each other at the amino acid level. The nine Jeonbuk PEDV isolates were classified into G2b group including a genetic specific signal, S-indels (insertion and deletion of S gene). In addition, comparisons the neutralizing epitopes of S gene between 9 field strains and domestic vaccine strains of Korea mutated 12-15 amino acids with SM-98-1 (G1a group) and mutated 0-3 amino acids with QIAP1401 (G2b group). Therefore, the development of G2b-based live vaccines will have to be expedited to ensure effective prevention of endemic PED in Korea. In addition, we will need to be prepared with periodic updates of preventive vaccines based on the PEDV variants for the re-emergence of a virulent strain.

Keywords: PEDV,Spike gene,RT-PCR,Phylogenetic analysis,

References

  1. Chang SH, Bae JL, Kang TJ. 2002. Identification of the Epitope Region Capable of inducing Neutralizing Antibodies against the Porcine Epidemic Diarrhea Virus. Molecules and Cells 14: 295-299.
  2. Debouck P, Pensaert M. 1980. Experimental infection of pigs with a new porcine enteric coronavirus, CV 777. Am J Vet Res 41: 219-223.
  3. Duarte M, Gelfi J, Lambert P, Rasschaert D, Laude H. 1993. Genome organization of porcine epidemic diarrhoea virus. Adv Exp Med Biol 342: 55-60.
    Pubmed CrossRef
  4. Kumar S, Stecher G, Tamura K. 2016. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol 33: 1870-1874.
    Pubmed KoreaMed CrossRef
  5. Kweon CH, Kwon BJ, Jung TS, Kee YJ, Hur DH, Hwang EK, Rhee JC, An SH. 1993. Isolation of porcine epidemic diarrhea virus (PEDV) in Korea. Korean J Vet Res 33: 249-254.
  6. Langel SN, Paim FC, Lager KM, Vlasova AN, Saif LJ. 2016. Lactogenic immunity and vaccines for porcine epidemic diarrhea virus (PEDV): Historical and current concepts. Virus Res 226: 93-107.
    Pubmed KoreaMed CrossRef
  7. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948.
    Pubmed CrossRef
  8. Lee CH, 2015. Porcine epidemic diarrhea virus: An emerging and re-emerging epizootic swine virus. Virol J 12: 193.
    Pubmed KoreaMed CrossRef
  9. Lee DK, Park CK, Kim SH, Lee C. 2010. Heterogeneity in spike protein genes of porcine epidemic diarrhea viruses isolated in Korea. Virus Res 149: 175-182.
    Pubmed KoreaMed CrossRef
  10. Lee SH, Lee CH. 2014. Outbreak-related porcine epidemic diarrhea virus strains similar to US strains, South Korea, 2013. Emerg Infect Dis 20: 1223-1226.
    Pubmed KoreaMed CrossRef
  11. Lin CM, Saif LJ, Marthaler D, Wang Q. 2016. Evolution, antigenicity and pathogenicity of global porcine epidemic diarrhea virus strains. Virus Res 226: 20-39.
    Pubmed KoreaMed CrossRef
  12. Oh J, Lee KW, Choi HW, Lee CJ. 2014. Immunogenicity and protective efficacy of recombinant S1 domain of the porcine epidemic diarrhea virus spike protein. Arch Virol 159: 2977-2987.
    Pubmed KoreaMed CrossRef
  13. Park HS, Yook SY, Jeon DM, Lee JJ, Shin CH. 2016. Genetic sequence and phylogenetic analysis of spike genes of Porcine epidemic diarrhea virus (PEDV) in Chung-Nam area. Korean Journal of Veterinary Service 39: 259-266.
    CrossRef
  14. Pijpers A, van Nieuwstadt AP, Terpstra C, Verheijden JH. 1993. Porcine epidemic diarrhoea virus as a cause of persistent diarrhoea in a herd of breeding and finishing pigs. Vet Rec 132: 129-131.
    Pubmed CrossRef
  15. Sun RQ, Cai RJ, Chen YQ, Liang PS, Chen DK, Song CX. 2012. Outbreak of Porcine Epidemic Diarrhea in Suckling Piglets, China. Emerging infectious diseases 18: 161- 163.
    Pubmed KoreaMed CrossRef
KJVS
Mar 30, 2024 Vol.47 No.1, pp. 1~7

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