Biopolym. Cell. 2019; 35(6):486-494.
Viruses and Cell
Molecular characteristics of the Porcine Epidemic Diarrhea Virus strains isolated in different regions of Ukraine
1Masiuk D. N., 1Hlebeniuk V. V., 1Kokariev A. V., 1Vasylenko T. A.
  1. Dnipro State Agrarianand Economic University
    25, Sergei Efremov Str., Dnipro, Ukraine, 49600

Abstract

Aim. Research on the molecular characteristics of the PEDV strains isolated in different regions of Ukraine. Methods. PEDV was detected and differentiated in biological material by PCR using the EZ-RED / TGE / PDCoV MPX 1.0 Realtime RT-PCR test system from Tetracore (USA). For comparative genotyping of the PEDV strains using PCR, the complete S gene was sequenced. Results. The diagnosis of PED was confirmed in the pig farms under investigation. As a result of sequencing, it was found that the PED strains isolated in different regions of Ukraine have a high identity (99 %) with the strains from North America 2013-2014 and China 2011-2012 and a lower similarity (90 %) with the strains circulating in Europe until 1995. The strain PEDV_Cherkasy_UA_17 was clustered into group 2 (cognate to the Chinese strain BJ-2011-1) in the North American clade II of the PEDV. It was shown that the Ukrainian PEDV strain was phylogenetically clustered together with the highly virulent North American PEDV strains, but differed from the strains circulating in European countries. Conclusions. The PEDV strains isolated in various regions of Ukraine have a high (>99.5 %) degree of homology and are phylogenetically clustered with the highly virulent North American PEDV strains.
Keywords: diagnostics, PCR, S gene, phylogenetic analysis, virulence

References

[1] Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403-10.
[2] Brnić D, Šimić I, Lojkić I, Krešić N, Jungić A, Balić D, Lolić M, Knežević D, Hengl B. The emergence of porcine epidemic diarrhoea in Croatia: molecular characterization and serology. BMC Vet Res. 2019; 15:249
[3] Dastjerdi A, Carr J, Ellis RJ, Steinbach F, Williamson S. Porcine Epidemic Diarrhea Virus among Farmed Pigs, Ukraine. Emerg Infect Dis. 2015;21(12):2235-7.
[4] Hanke D, Jenckel M, Petrov A, Ritzmann M, Stadler J, Akimkin V, Blome S, Pohlmann A, Schirrmeier H, Beer M, Höper D. Comparison of porcine epidemic diarrhea viruses from Germany and the United States, 2014. Emerg Infect Dis. 2015;21(3):493-6.
[5] Huang YW, Dickerman AW, Piñeyro P, Li L, Fang L, Kiehne R, Opriessnig T, Meng XJ. Origin, evolution, and genotyping of emergent porcine epidemic diarrhea virus strains in the United States. MBio. 2013;4(5):e00737-13.
[6] Lee DK, Park CK, Kim SH, Lee C. Heterogeneity in spike protein genes of porcine epidemic diarrhea viruses isolated in Korea. Virus Res. 2010;149(2):175-82.
[7] Li W, Li H, Liu Y, Pan Y, Deng F, Song Y, Tang X, He Q. New variants of porcine epidemic diarrhea virus, China, 2011. Emerg Infect Dis. 2012;18(8):1350-3.
[8] Masiuk DM, Sosnitsky OI, Nedzvetsky VS, Kokarev AV, Koliada SG. Epidemiology, etiology and gene analysis of spike S protein of porcine epidemic diarrhea virus infection in Ukraine during 2016–2017. Reg Mech Biosyst. 2017; 8(4): 602–10.
[9] Okonechnikov K, Golosova O, Fursov M; UGENE team. Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics. 2012;28(8):1166-7.
[10] Paarlberg P. Updated estimated economic welfare impacts of porcine epidemic diarrhea virus (PEDV). Dept. Of Agricultural Economics. 2014;10(14):2038.
[11] Park SJ, Song DS, Ha GW, Park BK. Cloning and further sequence analysis of the spike gene of attenuated porcine epidemic diarrhea virus DR13. Virus Genes. 2007;35(1):55-64.
[12] Puranaveja S, Poolperm P, Lertwatcharasarakul P, Kesdaengsakonwut S, Boonsoongnern A, Urairong K, Kitikoon P, Choojai P, Kedkovid R, Teankum K, Thanawongnuwech R. Chinese-like strain of porcine epidemic diarrhea virus, Thailand. Emerg Infect Dis. 2009;15(7):1112-5.
[13] Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32(5):1792-7.
[14] Steinrigl A, Fernández SR, Stoiber F, Pikalo J, Sattler T, Schmoll F. First detection, clinical presentation and phylogenetic characterization of Porcine epidemic diarrhea virus in Austria. BMC Vet Res. 2015;11:310.
[15] 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. Emergence of Porcine epidemic diarrhea virus in the United States: clinical signs, lesions, and viral genomic sequences. J Vet Diagn Invest. 2013;25(5):649-54.
[16] Valkó A, Biksi I, Cságola A, Tuboly T, Kiss K, Ursu K, Dán Á. Porcine epidemic diarrhoea virus with a recombinant S gene detected in Hungary, 2016. Acta Vet Hung. 2017;65(2):253-261.