腹泻仔猪肠道病毒组学分析

doi:10.11843/j.issn.0366-6964.2019.03.016

Abstract

Abstract:

To clarify the epidemiological characteristics of diarrhea in pigs around Shanghai, especially the prevalence of coronavirus, we used viral metagenomic method to detect viruses in stools from 90 diarrhea piglets from 6 swine farms in parts of Shanghai. And then a multiple sequence alignment was carried out using Clustal W and Geneious, and the phylogenetic trees were generated by the distance-based maximum likelihood method using MEGA 7.0. The data showed that the intestinal virus community of diarrhea piglets was mainly composed of Picornaviridae (63.67%), Astroviridae (12.68%), Caliciviridae (4.07%), and Parvoviridae (2.51%). We found that the farm C was the only farm where PEDV is the main cause of piglet diarrhea, and the positive rate of PEDV infection in farm C was as high as 43.33%(13/30). The genetic evolution analysis showed that one of the three PEDV ORF3 gene sequences obtained in this study belonged to the G2 genotype, and the homology with other reference PEDV strains was higher (96.44%-99.70%), which was relatively conservative; the other two ORF3 gene sequences belong to the G1 genotype, and the homology was relatively lower (95.11%-99.41%). In the comparison analysis of protein sequence with the traditional strain CV777, we found that in addition to the piglet91 strain showed a mutation of F2S, three ORF3 sequences both showed consistent mutations, namely:V21A, I70M, V79I, F80V, L85I, L92F. This characteristic may be regarded as the basis for identification of PEDV traditional strains and the popular strain genotype. The enterovirus of diarrhea piglets from surrounding areas of Shanghai were rich in composition. The infection status in the different pigs were significantly different. Apart from PEDV, astrovirus and calicivirus are also the main pathogens of diarrhea piglets. As one of the main pathogens of piglet diarrhea in this particular region, the ORF3 gene of PEDV has unique molecular characteristics compared with traditional isolates. The relationship between mutation site and viral virulence of the newly detected virus needs further experimental research.

CLC Number:

S851.21

SHEN Xiaojuan, LI Jingjiao, BIAN Jiang, ZHAO Tingting, HUA Xiuguo, CUI Li. Metagenomics Analysis of Feces from Diarrhea Piglets Reveals the Viral Composition and Epidemic Characteristics of Coronavirus[J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2019, 50(3): 611-619.

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Metagenomics Analysis of Feces from Diarrhea Piglets Reveals the Viral Composition and Epidemic Characteristics of Coronavirus

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