Virologica Sinica

, Volume 32, Issue 4, pp 298–306 | Cite as

Coexistence of multiple genotypes of porcine epidemic diarrhea virus with novel mutant S genes in the Hubei Province of China in 2016

  • Zhe Zeng
  • Ting-Ting Li
  • Xin Jin
  • Fu-Hu Peng
  • Nian-Hua Song
  • Gui-Qing PengEmail author
  • Xing-Yi GeEmail author
Research Article


The emergence of highly virulent porcine epidemic diarrhea virus (PEDV) variants in China caused huge economic losses in 2010. Since then, large-scale sporadic outbreaks of PED caused by PEDV variants have occasionally occurred in China. However, the molecular diversity and epidemiology of PEDV in different provinces has not been completely understood. To determine the molecular diversity of PEDV in the Hubei Province of China, we collected 172 PED samples from 34 farms across the province in 2016 and performed reverse transcription polymerase chain reaction (RT-PCR) by targeting the nucleocapsid (N) gene. Seventy-four samples were found to be PEDV-positive. We further characterized the complete spike (S) glycoprotein genes from the positive samples and found 21 different S genes with amino acid mutations. The PEDV isolates here presented most of the genotypes which were found previously in field isolates in East and South-East Asia, North America, and Europe. Besides the typical Genotypes I and II, the INDEX groups were also found. Importantly, 58 new amino acids mutant sites in the S genes, including 44 sites in S1 and 14 sites in S2, were first described. Our results revealed that the S genes of PEDV showed variation and that diverse genotypes of PEDV coexisted and were responsible for the PED outbreaks in Hubei in 2016. This work highlighted the complexity of the epidemiology of PEDV and emphasized the need for reassessing the efficacy of classic PEDV vaccines against emerging variant strains and developing new vaccines to facilitate the prevention and control of PEDV in fields.


porcine epidemic diarrhea virus (PEDV) coronavirus spike genetic variation 


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This work funded by the National Natural Science Foundation of China (31470260 and 81401672) and the "Fundamental Research Funds for the Central Universities" (531107040975).

Supplementary material

12250_2017_4021_MOESM1_ESM.pdf (1.3 mb)
Coexistence of multiple genotypes of porcine epidemic diarrhea virus with novel mutant S genes in the Hubei Province of China in 2016


  1. Belouzard S, Millet JK, Licitra BN, Whittaker GR. 2012. Mechanisms of coronavirus cell entry mediated by the viral spike protein. Viruses, 4: 1011–1033.CrossRefPubMedPubMedCentralGoogle Scholar
  2. Brnic D, Jemersic L, Keros T, Prpic J. 2014. High prevalence and genetic heterogeneity of porcine astroviruses in domestic pigs. Vet J, 202: 390–392.CrossRefPubMedGoogle Scholar
  3. Cai Y, Yin W, Zhou Y, Li B, Ai L, Pan M, Guo W. 2016. Molecular detection of Porcine astrovirus in Sichuan Province, China. Virol J, 13: 6.CrossRefPubMedPubMedCentralGoogle Scholar
  4. Chen J, Liu X, Shi D, Shi H, Zhang X, Li C, Chi Y, Feng L. 2013. Detection and molecular diversity of spike gene of porcine epidemic diarrhea virus in China. Viruses, 5: 2601–2613.CrossRefPubMedPubMedCentralGoogle Scholar
  5. Criscuolo A. 2011. morePhyML: improving the phylogenetic tree space exploration with PhyML 3. Mol Phylogenet Evol, 61: 944–948.CrossRefPubMedGoogle Scholar
  6. Cruz DJ, Kim CJ, Shin HJ. 2008. The GPRLQPY motif located at the carboxy-terminal of the spike protein induces antibodies that neutralize Porcine epidemic diarrhea virus. Virus Res, 132: 192–196.CrossRefPubMedGoogle Scholar
  7. Deng F, Ye G, Liu QQ, Navid MT, Zhong XL, Li YW, Wan CY, Xiao SB, He QG, Fu ZF, Peng GQ. 2016. Identification and Comparison of Receptor Binding Characteristics of the Spike Protein of Two Porcine Epidemic Diarrhea Virus Strains. Viruses, 8: 55.CrossRefPubMedPubMedCentralGoogle Scholar
  8. Graham RL, Donaldson EF, Baric RS. 2013. A decade after SARS: strategies for controlling emerging coronaviruses. Nat Rev Microbiol, 11: 836–848.CrossRefPubMedPubMedCentralGoogle Scholar
  9. Huan CC, Wang Y, Ni B, Wang R, Huang L, Ren XF, Tong GZ, Ding C, Fan HJ, Mao X. 2015. Porcine epidemic diarrhea virus uses cell-surface heparan sulfate as an attachment factor. Arch Virol, 160: 1621–1628.CrossRefPubMedGoogle Scholar
  10. Jung K, Saif LJ. 2015. Porcine epidemic diarrhea virus infection: Etiology, epidemiology, pathogenesis and immunoprophylaxis. Vet J, 204: 134–143.CrossRefPubMedGoogle Scholar
  11. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A. 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics, 28: 1647–1649.CrossRefPubMedPubMedCentralGoogle Scholar
  12. Kim SH, Kim IJ, Pyo HM, Tark DS, Song JY, Hyun BH. 2007. Multiplex real-time RT-PCR for the simultaneous detection and quantification of transmissible gastroenteritis virus and porcine epidemic diarrhea virus. J Virol Methods, 146: 172–177.CrossRefPubMedGoogle Scholar
  13. Lee C. 2015. Porcine epidemic diarrhea virus: An emerging and re-emerging epizootic swine virus. Virol J, 12: 193.CrossRefPubMedPubMedCentralGoogle Scholar
  14. Li F. 2015. Receptor recognition mechanisms of coronaviruses: a decade of structural studies. J Virol, 89: 1954–1964.CrossRefPubMedGoogle Scholar
  15. Li R, Qiao S, Yang Y, Guo J, Xie S, Zhou E, Zhang G. 2016a. Genome sequencing and analysis of a novel recombinant porcine epidemic diarrhea virus strain from Henan, China. Virus Genes, 52: 91–98.CrossRefPubMedGoogle Scholar
  16. Li RF, Tian XQ, Liu Y, Xu J, Liu DY. 2016b. Isolation and genetic analysis of a variant porcine epidemic diarrhea virus in China. Pol J Vet Sci, 19: 65–73.PubMedGoogle Scholar
  17. Li W, Li H, Liu Y, Pan Y, Deng F, Song Y, Tang X, He Q. 2012. New variants of porcine epidemic diarrhea virus, China, 2011. Emerg Infect Dis, 18: 1350–1353.CrossRefPubMedPubMedCentralGoogle Scholar
  18. Liu C, Tang J, Ma Y, Liang X, Yang Y, Peng G, Qi Q, Jiang S, Li J, Du L, Li F. 2015. Receptor usage and cell entry of porcine epidemic diarrhea coronavirus. J Virol, 89: 6121–6125.CrossRefPubMedPubMedCentralGoogle Scholar
  19. Masters, PS, Perlman, S. 2013. Fields Virology. Philadelphia: Lippincott Williams & Wilkins. pp. 825–858.Google Scholar
  20. Molinari BL, Possatti F, Lorenzetti E, Alfieri AF, Alfieri AA. 2016. Unusual outbreak of post-weaning porcine diarrhea caused by single and mixed infections of rotavirus groups A, B, C, and H. Vet Microbiol, 193: 125–132.CrossRefPubMedGoogle Scholar
  21. Pensaert MB, de Bouck P. 1978. A new coronavirus-like particle associated with diarrhea in swine. Arch Virol, 58: 243–247.CrossRefPubMedGoogle Scholar
  22. Perlman S, Netland J. 2009. Coronaviruses post-SARS: update on replication and pathogenesis. Nat Rev Microbiol, 7: 439–450.CrossRefPubMedPubMedCentralGoogle Scholar
  23. Sun D, Feng L, Shi H, Chen J, Cui X, Chen H, Liu S, Tong Y, Wang Y, Tong G. 2008. Identification of two novel B cell epitopes on porcine epidemic diarrhea virus spike protein. Vet Microbiol, 131: 73–81.CrossRefPubMedGoogle Scholar
  24. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol, 30: 2725–2729.CrossRefPubMedPubMedCentralGoogle Scholar
  25. Tian PF, Jin YL, Xing G, Qv LL, Huang YW, Zhou JY. 2014. Evidence of recombinant strains of porcine epidemic diarrhea virus, United States, 2013. Emerg Infect Dis, 20: 1735–1738.CrossRefPubMedPubMedCentralGoogle Scholar
  26. Vlasova AN, Marthaler D, Wang Q, Culhane MR, Rossow KD, Rovira A, Collins J, Saif LJ. 2014. Distinct characteristics and complex evolution of PEDV strains, North America, May 2013-February 2014. Emerg Infect Dis, 20: 1620–1628.CrossRefPubMedPubMedCentralGoogle Scholar
  27. Wang D, Fang L, Xiao S. 2016. Porcine epidemic diarrhea in China. Virus Res, 226: 7–13.CrossRefPubMedGoogle Scholar
  28. Wang L, Byrum B, Zhang Y. 2014. New variant of porcine epidemic diarrhea virus, United States, 2014. Emerg Infect Dis, 20: 917–919.CrossRefPubMedPubMedCentralGoogle Scholar
  29. Woo PC, Lau SK, Lam CS, Lau CC, Tsang AK, Lau JH, Bai R, Teng JL, Tsang CC, Wang M, et al., 2012. Discovery of seven novel Mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus. J Virol, 86: 3995–4008.CrossRefPubMedPubMedCentralGoogle Scholar
  30. Xuan H, Xing DK, Wang DY, Zhu WZ, Zhao FY, Gong HJ, Fei SG. 1984. Study on the culture of porcine epidemic diarrhea virus adapted to fetalporcine intestine primary cell monolayer. Chin J Vet Sci, 4: 202–208.Google Scholar
  31. Zhang Q, Hu R, Tang X, Wu C, He Q, Zhao Z, Chen H, Wu B. 2013. Occurrence and investigation of enteric viral infections in pigs with diarrhea in China. Arch Virol, 158: 1631–1636.CrossRefPubMedGoogle Scholar

Copyright information

© Wuhan Institute of Virology, CAS and Springer Nature Singapore Pte Ltd. 2017

Authors and Affiliations

  1. 1.State Key Laboratory of Agricultural Microbiology, College of Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
  2. 2.Hubei Animal Disease Prevention and Control CenterWuhanChina
  3. 3.College of BiologyHunan UniversityChangshaChina

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