Advertisement

Molecular characteristics of a novel recombinant of porcine epidemic diarrhea virus

  • Mariia Nefedeva
  • Ilya Titov
  • Alexander MalogolovkinEmail author
Annotated Sequence Record

Abstract

Porcine epidemic diarrhea (PED) is a contagious viral disease in pigs, caused by the coronavirus porcine epidemic diarrhea virus (PEDV). PEDV infection results in significant mortality in piglets in unvaccinated herds. Like many others RNA viruses, PEDV has high evolutionary rate and is prone to genetic mutations. In this study, we analyzed the complete genome sequence of the recently sequenced isolate PEDV/Belgorod/dom/2008. A recombination event in S gene of PEDV/Belgorod/dom/2008 was detected. Pairwise identity analysis of the whole genome sequences revealed that PEDV/Belgorod/dom/2008 is an intermediate between PEDV and transmissible gastroenteritis virus (TGEV) strains. These results can be used for further analysis of the evolutionary variability, prevalence, and epidemiology of the porcine epidemic diarrhea virus.

Notes

Acknowledgements

We thank Olga Strizhakova for providing PEDV/Belgorod/dom/2008. We also acknowledge Yegor Bazykin and Alexey Neverov for fruitful discussions of virus evolution and recombination analysis. We appreciate Sandra Blome and Dennis Hanke for PEDV/Belgorod/dom/2008 complete genome sequencing.

Compliance with ethical standards

Funding

Our work was supported by the Ministry of Science and Higher Education of the Russian Federation.

Conflict of interest

The authors declare no competing interests.

References

  1. 1.
    Pensaert M (2006) Porcine epidemic diarrhea. In: Straw BE et al (eds) Diseases of swine, 9th edn. Blackwell, Ames, pp 367–372Google Scholar
  2. 2.
    Pan Y, Tian X, Li W, Zhou Q, Wang D, Bi Y, Chen F, Song Y (2012) Isolation and characterization of a variant porcine epidemic diarrhea virus in China. Virol J 9:195.  https://doi.org/10.1186/1743-422X-9-195 CrossRefGoogle Scholar
  3. 3.
    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.  https://doi.org/10.3201/eid1808.120002 CrossRefGoogle Scholar
  4. 4.
    Stevenson GW, Hoang H, Schwartz KJ, Burrough ER, Sun D, Madson D, Cooper VL, Pillatzki A, Gauger P, Schmitt BJ, Koster LG, Killian ML, Yoon KJ (2013) Emergence of Porcine epidemic diarrhea virus in the United States: clinical signs, lesions, and viral genomic sequences. J Vet Diagn Investig 25:649–654.  https://doi.org/10.1177/1040638713501675 CrossRefGoogle Scholar
  5. 5.
    Chen JF, Sun DB, Wang CB, Shi HY, Cui XC, Liu SW, Qiu HJ, Feng L (2008) Molecular characterization and phylogenetic analysis of membrane protein genes of porcine epidemic diarrhea virus isolates in China. Virus Genes 36:355–364.  https://doi.org/10.1007/s11262-007-0196-7 CrossRefGoogle Scholar
  6. 6.
    Sun M, Ma J, Wang Y, Wang M, Song W, Zhang W, Lu C, Yao H (2015) Genomic and epidemiological characteristics provide new insights into the phylogeographical and spatiotemporal spread of porcine epidemic diarrhea virus in Asia. J Clin Microbiol 53:1484–1492.  https://doi.org/10.1128/JCM.02898-14 CrossRefGoogle Scholar
  7. 7.
    Park SJ, Moon HJ, Yang JS, Lee CS, Song DS, Kang BK, Park BK (2007) Sequence analysis of the partial spike glycoprotein gene of porcine epidemic diarrhea viruses isolated in Korea. Virus Genes 35:321–332CrossRefGoogle Scholar
  8. 8.
    Kubota S, Sasaki O, Animoto K, Okada N, Kitazima T, Yasuhara H (1999) Detection of porcine epidemic diarrhea virus using polymerase chain reaction and comparison of the nucleocapsid protein genes among strains of the virus. J Vet Med Sci 61:827–830CrossRefGoogle Scholar
  9. 9.
    Jung K, Saif LJ (2015) Porcine epidemic diarrhea virus infection: Etiology, epidemiology, pathogenesis and immunoprophylaxis. Vet J 204:134–143.  https://doi.org/10.1016/j.tvjl.2015.02.017 CrossRefGoogle Scholar
  10. 10.
    Oka T, Saif LJ, Marthaler D, Esseili MA, Meulia T, Lin CM, Vlasova AN, Jung K, Zhang Y, Wang Q (2014) Cell culture isolation and sequence analysis of genetically diverse US porcine epidemic diarrhea virus strains including a novel strain with a large deletion in the spike gene. Vet Microbiol 173:258–269.  https://doi.org/10.1016/j.vetmic.2014.08.012 CrossRefGoogle Scholar
  11. 11.
    Wang L, Byrum B, Zhang Y (2014) New variant of porcine epidemic diarrhea virus, United States, 2014. Emerg Infect Dis 20:917–919.  https://doi.org/10.3201/eid2005.140195 CrossRefGoogle Scholar
  12. 12.
    Hanke D, Jenckel M, Petrov A, Ritzmann M, Stadler J, Akimkin V, Blome S, Pohlmann A, Schirrmeier H, Beer M, Hoper D (2015) Comparison of porcine epidemic diarrhea viruses from Germany and the United States, 2014. Emerg Infect Dis 21:493–496.  https://doi.org/10.3201/eid2103.141165 CrossRefGoogle Scholar
  13. 13.
    Jarvis MC, Lam HC, Zhang Y, Wang L, Hesse RA, Hause BM, Vlasova A, Wang Q, Zhang J, Nelson MI, Murtaugh MP, Marthaler D (2015) Genomic and evolutionary inferences between American and global strains of porcine epidemic diarrhea virus. Prev Vet Med 123:175–184.  https://doi.org/10.1016/j.prevetmed.2015.10.020 CrossRefGoogle Scholar
  14. 14.
    Vlasova AN, Marthaler D, Wang Q, Culhane MR, Rossow KD, Rovira A, Collins J, Jung K (2014) Distinct characteristics and complex evolution of PEDV strains, North America, May 2013–February 2014. Emerg Infect Dis 20:1620–1628.  https://doi.org/10.3201/eid2010.140491 CrossRefGoogle Scholar
  15. 15.
    Strizhakova O, Hanke D, Titov I, Blome S, Malogolovkin A (2017) Complete genome sequence of a porcine epidemic diarrhea virus isolated in Belgorod, Russia, in 2008. Genome Announc 5:e01026–17.  https://doi.org/10.1128/genomeA.01026-17 CrossRefGoogle Scholar
  16. 16.
    Martin DP, Murrell B, Golden M, Khoosal A, Muhire B (2015) RDP4: Detection and analysis of recombination patterns in virus genomes. Virus Evol 1:vev003.  https://doi.org/10.1093/ve/vev003 CrossRefGoogle Scholar
  17. 17.
    Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, Novak NG, Ingersoll R, Sheppard HW, Ray SC (1999) Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol 73:152–160Google Scholar
  18. 18.
    Muhire BM, Varsani A, Martin DP (2014) SDT: a virus classification tool based on pairwise sequence alignment and identity calculation. PLoS One 9:e108277CrossRefGoogle Scholar
  19. 19.
    Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797.  https://doi.org/10.1093/nar/gkh340 CrossRefGoogle Scholar
  20. 20.
    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.  https://doi.org/10.1093/molbev/mst197 CrossRefGoogle Scholar
  21. 21.
    Strizhakova O (2013) Isolation and identification of porcine epidemic diarrhea virus in pigs under the outbreak at a large farm. Sel’skokhozyaistvennaya Biologia 4:65–69.  https://doi.org/10.15389/agrobiology.2013.4.65eng Google Scholar
  22. 22.
    Strizhakova OM, Malogolovkin AS, Titov IA, Zhivoderov SP, Kurinnov VV, Strizhakov AA (2017) Biological characteristics of an epizootic isolate BS-08 of porcine epidemic diarrhea virus. Veterinariya 3:31–34Google Scholar
  23. 23.
    Boniotti MB, Papetti A, Lavazza A, Alborali G, Sozzi E, Chiapponi C, Faccini S, Bonilauri P, Cordioli P, Marthaler D (2016) Porcine epidemic diarrhea virus and discovery of a recombinant swine enteric coronavirus, Italy. Emerg Infect Dis 22:83–87.  https://doi.org/10.3201/eid2201.150544 CrossRefGoogle Scholar
  24. 24.
    Akimkin V, Beer M, Blome S, Hanke D, Hoper D, Jenckel M, Pohlmann A (2016) New chimeric porcine coronavirus in swine feces, Germany, 2012. Emerg Infect Dis 22:1314–1315.  https://doi.org/10.3201/eid2207.160179 CrossRefGoogle Scholar
  25. 25.
    Belsham GJ, Rasmussen TB, Normann P, Vaclavek P, Strandbygaard B, Botner A (2016) Characterization of a novel chimeric swine enteric coronavirus from diseased pigs in Central Eastern Europe in 2016. Transbound Emerg Dis 63:595–601.  https://doi.org/10.1111/tbed.12579 CrossRefGoogle Scholar
  26. 26.
    Li R, Qiao S, Yang Y, Guo J, Xie S, Zhou E, Zhang G (2016) Genome sequencing and analysis of a novel recombinant porcine epidemic diarrhea virus strain from Henan, China. Virus Genes 52:91–98.  https://doi.org/10.1007/s11262-015-1254-1 CrossRefGoogle Scholar

Copyright information

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

Authors and Affiliations

  1. 1.Molecular Virology LaboratoryFederal Research Center for Virology and MicrobiologyVolginskyRussia

Personalised recommendations