利用宏基因组学鉴定藏猪腹泻粪便病毒种群

doi:10.11843/j.issn.0366-6964.2019.12.012

Abstract

Abstract: This study was conducted to further understand the viral community in diarrheal feces of Tibetan pig. The 146 diarrheal fecal samples were collected from 16 Tibetan pig farms in Qinghai-Tibet Plateau. The samples were mixed into a pool sample, then RNAs were purified and synthesized into cDNAs. TruSeq Illumina sequencing was used to analyze the sequences and molecular characteristics of the diarrhea-associated viruses. The results showed that the virus species in the fecal samples of diarrheal Tibetan pigs included 19 viruses from 11 families. They were mainly linear and cyclic small DNA viruses, such as porcine stool-associated circular virus type 7, porcine adenovirus and porcine bocavirus(PBoV). There are three diarrheal viral pathogens, such as porcine epidemic diarrhea virus (PEDV), porcine circovirus type 2 (PCV-2) and bovine viral diarrhea virus type 1 (BVDV-1), as well as three new pathogens, such as porcine bufavirus, rabovirus and pasivirus. The complete or nearly full-length genome of porcine parvovirus type 6(PPV-6), PCV-2, PBoV-2 and complete ORF2 gene sequence of hepatitis E virus (HEV) were assembled by SOAP software. The phylogenetic results showed that PPV-6 and PCV-2 had a relatively close genetic and evolutionary relationship with the reference strain, while PBoV-2 had a relatively distant genetic and evolutionary relationship with the reference strain, which were gathered into a single cluster, and may be a completely new genotype. In order to further investigate the detection rate of PCV-2 in diarrheal feces of Tibetan pigs, 146 samples were collected and the detection rate was 10.96% (16/146, 95% CI:6.4%-17.2%), and it was closely related to the epidemic strain of PCV-2 in Sichuan region. In this study, it was found that the viruses in diarrheal feces of Tibetan pigs are complex and varied, and may be cross-infected with other animals and humans, which has important public health significance, and also provides theoretical basis for prevention and control of diarrhea in Tibetan pigs.

Key words: Tibetan pig, diarrheal feces, metagenomics, molecular characteristics, porcine circovirus type 2 (PCV-2)

CLC Number:

S852.65

HU Chengzhe, ZHOU Qun, LI Yu, ZHANG Min, TANG Cheng, ZHANG Bin. Identification of Viral Community in Diarrheal Feces of Tibetan Pig by Metagenomics[J]. Acta Veterinaria et Zootechnica Sinica, 2019, 50(12): 2479-2487.

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Identification of Viral Community in Diarrheal Feces of Tibetan Pig by Metagenomics

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