Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field strains in south China

A total of 127 porcine samples were collected from 48 farms in six provinces in south China. The positive rate of porcine epidemic diarrhea virus (PEDV) was 43.0 % (55/127), and the co-infection rate of PEDV and transmissible gastroenteritis virus (TGEV) was 12.0 % (15/127). The partial S gene and c...

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Bibliographic Details
Published in:Virus genes 2012-08, Vol.45 (1), p.181-185
Main Authors: Li, Zhi-Li, Zhu, Ling, Ma, Jing-Yun, Zhou, Qing-Feng, Song, Yan-Hua, Sun, Bao-Li, Chen, Rui-Ai, Xie, Qing-Mei, Bee, Ying-Zuo
Format: Article
Language:English
Subjects:
Amino acid sequence
Animals
Biomedical and Life Sciences
Biomedicine
China - epidemiology
Coronavirus Infections - epidemiology
Coronavirus Infections - veterinary
Coronavirus Infections - virology
Farms
genes
Homology
M gene
Medical Microbiology
Membrane Glycoproteins - genetics
Nucleotide sequence
Phylogeny
Plant Sciences
Polymerase chain reaction
Porcine epidemic diarrhea virus
Porcine epidemic diarrhea virus - classification
Porcine epidemic diarrhea virus - genetics
Porcine epidemic diarrhea virus - isolation & purification
Reverse Transcriptase Polymerase Chain Reaction
S gene
Sequence Analysis, DNA
sequence homology
Spike Glycoprotein, Coronavirus
swine
Swine - virology
Swine Diseases - epidemiology
Swine Diseases - virology
Transmissible gastroenteritis
Transmissible gastroenteritis virus
Vaccines
Viral Envelope Proteins - genetics
Viral Matrix Proteins - genetics
Virology
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Summary:A total of 127 porcine samples were collected from 48 farms in six provinces in south China. The positive rate of porcine epidemic diarrhea virus (PEDV) was 43.0 % (55/127), and the co-infection rate of PEDV and transmissible gastroenteritis virus (TGEV) was 12.0 % (15/127). The partial S gene and complete M gene were amplified from PEDV-positive strains by RT-PCR, cloned, sequenced and compared with each other, as well as with the reference strains in GenBank. Sequence homology results of the partial S gene and complete M gene showed that all south China field PEDV strains had nucleotide (deduced amino acid) sequence identities of 86.7–98.7 % (83.2–99.3 %) and 96.1–100 % (95.0–100%), respectively, with the foreign reference strains reported in GenBank. Phylogenetic analysis of the partial S gene showed that all the south China PEDV strains and two Thailand strains (08UB01 and 08RB07) belong to the same group and differ genetically from European strains and early domestic strains. Phylogenetic analysis of the complete M gene showed that all south China PEDV strains have a close relationship with most of the strains in Korea and Thailand, but differ genetically from the vaccine strain (CV777).
ISSN:0920-8569
1572-994X
DOI:10.1007/s11262-012-0735-8