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  

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

作　　者：张家祺 甲呷格西 周群 宋鑫[1] 张斌[1] ZHANG Jiaqi;JIA GA Gexi;ZHOU Qun;SONG Xin;ZHANG Bin(College of Animal Husbandry and Veterinary Medicine,Southwest Minzu University,Chengdu 610041,China;Ganzi County Agriculture,Animal Husbandry,Rural and Technology Bureau,Ganzi Tibetan Autonomous Prefecture,Sichuan Ganzi 626700,China)

机构地区：[1]西南民族大学畜牧兽医学院,成都610041 [2]甘孜县农牧农村和科技局,甘孜626700

出　　处：《畜牧兽医学报》2023年第6期2478-2486,共9页ACTA VETERINARIA ET ZOOTECHNICA SINICA

基　　金：西南民族大学2023年中央高校优秀学生培养工程项目(2023NYXXS110)

摘　　要：旨在了解四川省集约化猪场腹泻仔猪粪便中病毒种群的变化。于2019年从四川省15个猪场采集腹泻仔猪粪便样本共156份,每个猪场挑取3份样本混合成1个pool样,提取其总RNA并进行高通量测序,利用SOAP denovo软件进行序列组装,并对病毒的种类和分子特征进行研究。分析结果显示,腹泻仔猪粪便样本中的病毒种群包括12个科的20种病毒,以冠状病毒科(Coronaviridae)成员为主,与腹泻相关的主要病原有猪流行性腹泻病毒(porcine pidemic diarrhea virus,PEDV)、猪传染性胃肠炎病毒(porcine infectious gastroenteritis virus,TGEV)和猪轮状病毒(porcine rotavirus,PoRV)。获得PEDV N基因的完整基因组和TGEV、猪星状病毒2型(porcine astrovirus,PAstV-2)、posavirus 1和猪细小病毒4型(porcine parvovirus,PPV-4)的部分基因组。系统发育结果显示,PEDV、TGEV、PAstV-2、posavirus 1和PPV-4均与参考毒株有较近的遗传进化关系。研究结果表明,2019年四川地区仔猪腹泻粪便中病毒种类复杂多样,冠状病毒丰度有所上升,为四川省仔猪腹泻的防控提供了一定的数据支撑。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.(Conclusion)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.

关 键 词：仔猪病毒性腹泻 宏基因组学 分子特征 

分 类 号：S852.651[农业科学—基础兽医学]