生物学杂志

Journal of Biology ›› 2022, Vol. 39 ›› Issue (3): 12-.doi: 10.3969/j.issn. 2095-1736.2022.03.012

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Isolation and identification of variant strains of porcine epidemic diarrhea virus and analysis of genetic evolution

  

  1. 1. Shandong Agricultural University College of Animal Science and Technology, Taian 271018, China;
    2. Poultry Research Institute, Shandong Academy of Agricultural Sciences, Key Laboratory of Poultry Disease
    Diagnosis and Immunity in Shandong Province, Jinan 250000, China; 3. Institute of Animal Husbandry and Veterinary
    Medicine, Shandong Academy of Agricultural Sciences, Key Laboratory of Animal and Poultry Disease Control
    and Breeding, Shandong Province, Jinan 250000, China
  • Online:2022-06-18 Published:2022-06-17

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Abstract: Porcine epidemic diarrhea (PED) is an acute, highly contact intestinal infectious disease of pigs caused by porcine epidemic diarrhea virus (PEDV). To understand the genetic evolutionary trend of PEDV in Shandong, RT-PCR was performed on clinical material collected from 2020-2021 with suspected epidemic diarrhea. Subsequently, the supernatant of the treated disease material was inoculated into Vero cells for PEDV virus isolation and verified using indirect immunofluorescence (IFA), and a PEDV strain, named QH-202105, was successfully isolated. the isolate was passaged and cultured to the 10th generation, its RNA was extracted, amplified and whole genome was sequenced, and the whole genome and S gene of the isolate were combined with the reference sequence downloaded from NCBI. The results showed that the isolate had the highest nucleotide homology with USA/Colorado/2013 at 99.1% and the lowest homology with CHM2013 at 96.5%. Amino acid sequence analysis of the S gene showed that the isolate QH-202105 had more than 60 mutations in the N terminus of the S gene, two amino acid insertions (including four amino acid insertions in QGVN at amino acids 59-62 and an insertion in amino acid N at position 145) and two amino acid deletions (deletion in amino acids 115-118 and deletion in amino acids 167-168). The results of evolutionary tree analysis showed that the isolated strain QH-202105 was a G2 gene group, which was the closest relative to CH/HNAY/2015 and CH/ZJCX-1/2012 and belonged to the same evolutionary branch. Based on this result, PROVEAN was applied to predict the function of the mutated amino acid in the S protein of QH-202105, and the result showed that the mutation at 1361 (G→C) was determined to be “Deleterious”, and it could be assumed that the mutation here might have an indirect effect on the invasiveness of the virus.The results of the study could provide reference data for the prevalence and prevention and control of PEDV variants in China.

Key words: porcine epidemic diarrhea virus, epidemic strain, isolation and identification, genetic variation

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