宏基因组学技术分析四川省集约化猪场中仔猪腹泻粪便的病毒种群

doi:10.11843/j.issn.0366-6964.2023.06.026

Abstract

Abstract: The purpose of this study is to investigate the changes of virus populations in the diarrheal feces of piglets in intensive pig farms in Sichuan Province. In 2019, 156 pig diarrheal fecal samples were collected from 15 pig farms in Sichuan Province. Three samples from each farm were mixed into a pool sample, and their total RNA was extracted and subjected to high-throughput sequencing. Sequence assembly was performed using SOAP denovo software, and the virus species and molecular characteristics were studied. The results revealed that the virus population in the fecal samples of diarrheal piglets included 20 viruses from 12 families, mainly Coronaviridae. The main pathogens associated with diarrhea are porcine epidemic diarrhea virus (PEDV), porcine infectious gastroenteritis virus (TGEV) and porcine rotavirus (PoRV). By SOAP denovo software, we assembled and obtained the complete sequences of the PEDV N gene and the partial genomes of TGEV, porcine astrovirus (PAstV-2), Posavirus 1 and PPV-4. The phylogenetic analysis results revealed that PEDV, TGEV, PAstV-2, Posavirus 1 and PPV-4 were more closely related to the reference strains. The above results indicated that the virus species in the feces of piglet diarrhea in Sichuan Province in 2019 were complex and diverse, and that the abundance of Coronaviridae increased, which provided a foundation for the prevention and control of piglet diarrhea in Sichuan Province.

Key words: piglet viral diarrhea, metagenomics, molecular characterization

CLC Number:

S852.651

ZHANG Jiaqi, JIA GA Gexi, ZHOU Qun, SONG Xin, ZHANG Bin. Metagenomics Analysis of Virus Populations in Piglet Diarrheal Feces from Intensive Pig Farms in Sichuan Province[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(6): 2478-2486.

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Metagenomics Analysis of Virus Populations in Piglet Diarrheal Feces from Intensive Pig Farms in Sichuan Province

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