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Archives of Virology

, Volume 164, Issue 10, pp 2621–2625 | Cite as

Complete genome sequences of novel S-deletion variants of porcine epidemic diarrhea virus identified from a recurrent outbreak on Jeju Island, South Korea

  • Guehwan Jang
  • Jonghyun Park
  • Changhee LeeEmail author
Annotated Sequence Record

Abstract

Porcine epidemic diarrhea virus (PEDV) is a deadly epizootic swine coronavirus that is of importance to the world pork industry. Since the re-emergence of the virulent genotype 2b (G2b) in 2014, Jeju Island in South Korea has faced periodic outbreaks, leading to the occurrence of endemics in provincial herds. In this study, we examined the complete genome sequences and molecular characteristics of novel G2b PEDV variants with a two-amino-acid deletion in the neutralizing epitope of the spike (S) gene, which were concurrently identified on a re-infected farm and its neighboring farm on Jeju Island. Whole-genome sequencing of the Jeju S-DEL isolates KNU-1829 and KNU-1830 revealed the presence of a continuous 9-nucleotide deletion within the nonstructural protein coding region. Their genomes were 28,023 nucleotides in length, 15 nucleotides shorter than those of the classical G2b PEDV strains. The two S-DEL isolates had 96.4–99.2% and 98.3–99.7% identity at the S-gene and full-genome level, respectively, to other global G2b PEDV strains. Genetic and antigenic analyses indicated that the S-DEL isolates are most closely related to the primary strain identified from the initial exposure at the same farm, but the virus appears to undergo continuous evolution, possibly leading to antigenic drift under recurrent or endemic pressure. This study provides important information about the antigenic diversity of PEDV circulating in the endemic areas, which arises from continuous non-lethal mutations to ensure viral fitness in the host environment.

Notes

Acknowledgements

We gratefully thank Hyong-Seok Yang and Hyekyung Yoo for providing clinical samples and critical information about the current status of PEDV on the farms.

Compliance with ethical standards

Funding

This research was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (NRF-2018R1D1A1B07040334).

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with animals performed by any of the authors.

Supplementary material

705_2019_4360_MOESM1_ESM.pdf (9.7 mb)
Supplementary material 1 (PDF 9938 kb)

References

  1. 1.
    Andersen PH, Nielsen M, Lund O (2006) Prediction of residues in discontinuous B-cell epitopes using protein 3D structures. Protein Sci 15:2558–2567CrossRefGoogle Scholar
  2. 2.
    Fan B, Jiao D, Zhao X, Pang F, Xiao Q, Yu Z, Mao A, Guo R, Yuan W, Zhao P, He K, Li B (2017) Characterization of Chinese porcine epidemic diarrhea virus with novel insertions and deletions in genome. Sci Rep 7:44209CrossRefGoogle Scholar
  3. 3.
    Hou Y, Lin CM, Yokoyama M, Yount BL, Marthaler D, Douglas AL, Ghimire S, Qin Y, Baric RS, Saif LJ, Wang Q (2017) Deletion of a 197-amino-acid region in the N-terminal domain of spike protein attenuates porcine epidemic diarrhea virus in piglets. J Virol 91:e00227–e00227-17Google Scholar
  4. 4.
    Hulswit RJ, de Haan CA, Bosch BJ (2016) Coronavirus spike protein and tropism changes. Adv Virus Res 96:29–57CrossRefGoogle Scholar
  5. 5.
    Kuo L, Godeke GJ, Raamsman MJ, Masters PS, Rottier PJ (2000) Retargeting of coronavirus by substitution of the spike glycoprotein ectodomain: crossing the host cell species barrier. J Virol 74:1393–1406CrossRefGoogle Scholar
  6. 6.
    Lee C (2015) Porcine epidemic diarrhea virus: An emerging and re-emerging epizootic swine virus. Virol J 12:193CrossRefGoogle Scholar
  7. 7.
    Lee DK, Cha SY, Lee C (2011) The N-terminal region of the porcine epidemic diarrhea virus spike protein is important for the receptor binding. Korean J Microbiol Biotechnol 39:140–145Google Scholar
  8. 8.
    Lee DK, Park CK, Kim SH, Lee C (2010) Heterogeneity in spike protein genes of porcine epidemic diarrhea viruses isolated in Korea. Virus Res 149:175–182CrossRefGoogle Scholar
  9. 9.
    Lee S, Ko DH, Kwak WK, Lim CH, Moon SU, Lee DS, Lee C (2014) Reemergence of porcine epidemic diarrhea virus on Jeju Island. Korean J Vet Res 54:185–188CrossRefGoogle Scholar
  10. 10.
    Lee S, Lee C (2014) Outbreak-related porcine epidemic diarrhea virus strains similar to US strains, South Korea, 2013. Emerg Infect Dis 20:1223–1226CrossRefGoogle Scholar
  11. 11.
    Lee S, Lee C (2017) Complete genome sequence of a novel S-insertion variant of porcine epidemic diarrhea virus from South Korea. Arch Virol 162:2919–2922CrossRefGoogle Scholar
  12. 12.
    Lee S, Lee DU, Noh YH, Lee SC, Choi HW, Yang HS, Seol JH, Mun SH, Kang WM, Yoo H, Lee C (2019) Molecular characteristics and pathogenic assessment of porcine epidemic diarrhea virus isolates from the 2018 endemic outbreaks on Jeju Island, South Korea. Transb Emerg Dis.  https://doi.org/10.1111/tbed.13219 Google Scholar
  13. 13.
    Li C, Li W, de Esesarte EL, Guo H, van den Elzen P, Aarts E, van den Born E, Rottier PJ, Bosch BJ (2017) Cell attachment domains of the porcine epidemic diarrhea virus spike protein are key targets of neutralizing antibodies. J Virol 12:e00273–e00275Google Scholar
  14. 14.
    Lin CM, Annamalai T, Liu X, Gao X, Lu Z, El-Tholoth M, Hu H, Saif LJ, Wang Q (2015) Experimental infection of a US spike-insertion deletion porcine epidemic diarrhea virus in conventional nursing piglets and cross-protection to the original US PEDV infection. Vet Res 46:134CrossRefGoogle Scholar
  15. 15.
    Okda FA, Lawson S, Singrey A, Nelson J, Hain KS, Joshi LR, Christopher-Hennings J, Nelson EA, Diel DG (2017) The S2 glycoprotein subunit of porcine epidemic diarrhea virus contains immunodominant neutralizing epitopes. Virology 509:185–194CrossRefGoogle Scholar
  16. 16.
    Suzuki T, Shibahara T, Yamaguchi R, Nakade K, Yamamoto T, Miyazaki A, Ohashi S (2016) Pig epidemic diarrhoea virus S gene variant with a large deletion non-lethal to colostrum-deprived newborn piglets. J Gen Virol 97:1823–1828CrossRefGoogle Scholar
  17. 17.
    Van Diep N, Norimine J, Sueyoshi M, Lan NT, Yamaguchi R (2017) Novel porcine epidemic diarrhea virus (PEDV) variants with large deletions in the spike (S) gene coexist with PEDV strains possessing an intact S Gene in domestic pigs in Japan: a new disease situation. PLoS One 12:e0170126CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Austria, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Animal Virology Laboratory, School of Life Sciences, BK21 Plus KNU Creative BioResearch GroupKyungpook National UniversityDaeguRepublic of Korea

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