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Phylogenetic analysis of porcine epidemic diarrhea virus field strains prevailing recently in China

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Abstract

Porcine epidemic diarrhea virus (PEDV) is the causative agent of porcine epidemic diarrhea (PED), which is characterized by severe diarrhea, dehydration and high mortality in the affected pigs. Recently, clinical outbreaks of diarrhea in suckling piglets emerged in pig-producing areas of China. In this study, molecular detection of PEDV was conducted using RT-PCR (targeting the M gene) on samples collected from piglets with watery diarrhea from 15 pig farms, and phylogenetic analysis of PEDV field strains was carried out based on their M and S genes. In addition, the complete genome sequence of a PEDV field strain was determined. PEDV was detected in 92.7 % of the samples (267/288). The 15 M genes that were amplified shared 99.6-100 % nucleotide identity and 99.1-100 % amino acid similarity with each other. The 15 S genes exhibited 98.6-99.9 % homology, both at the nucleotide level and at the deduced amino acid level. Phylogenetic analysis showed that all of the amplified M genes grouped in cluster 3, together with some Chinese, Korean and Thai strains, while all of the amplified S genes were in cluster 3 and were closely related to Korean strains. Compared with previous PEDV strains, all of the S genes have common characteristics, namely, a 4-aa (GENQ) insertion between positions 55 and 56, a 1-aa (N) insertion between positions 135 and 136, and a 2-aa (DG) deletion between positions 155 and 156, similar or identical to Korean KNU-serial strains reported in recent years. The genome of the sequenced PEDV field strain is 28,038 nucleotides in length, excluding the poly (A) tail. Our findings suggest that a novel PEDV with a characteristic variant S gene is responsible for recent outbreaks of clinical diarrhea in piglets in China.

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Acknowledgments

This work was supported by China Agriculture Research System of China (CARS-36).

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Authors and Affiliations

  1. Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, College of Veterinary Medicine and State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, People’s Republic of China

    Yueyi Gao, Qiuwen Kou, Xinna Ge, Lei Zhou & Xin Guo

  2. College of Veterinary Medicine, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, People’s Republic of China

    Hanchun Yang

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  1. Yueyi Gao
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  2. Qiuwen Kou
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  3. Xinna Ge
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  4. Lei Zhou
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  5. Xin Guo
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  6. Hanchun Yang
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Correspondence to Hanchun Yang.

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Gao, Y., Kou, Q., Ge, X. et al. Phylogenetic analysis of porcine epidemic diarrhea virus field strains prevailing recently in China. Arch Virol 158, 711–715 (2013). https://doi.org/10.1007/s00705-012-1541-2

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