基于宏病毒组学技术挖掘猪腹泻粪便的病毒群落组成  

Viral metagenome analysis of the viral community composition of the porcine diarrhea feaces

作　　者：陶洁[1,2,3] 李本强 程靖华[1,2,3] 石迎 刘佩红[1] 何桂霞 徐伟杰 刘惠莉[1,2,3] Jie Tao;Benqiang Li;Jinghua Cheng;Ying Shi;Peihong Liu;Guixia He;Weijie Xu;Huili Liu(Shanghai Academy of Agricultural Sciences,Shanghai 201106;Shanghai Key Laboratory of Agricultural Genetic Breeding,Shanghai 201106;Key Laboratory of Disease Prevention and Control of Livestock and Poultry Varieties with Regional Characteristics,Ministry of Agriculture and Rural Affairs,Shanghai 201106;Guangming Agriculture and Animal Husbandry Technology Co.Ltd,Shanghai 202150)

机构地区：[1]上海市农业科学院,上海201106 [2]上海市农业遗传育种重点实验室,上海201106 [3]农业农村部区域特色畜禽品种疾病防控重点实验室,上海201106 [4]光明农牧科技有限公司,上海202150

出　　处：《生物多样性》2023年第11期131-139,共9页Biodiversity Science

基　　金：上海市科技兴农项目(2022-02-08-00-12-F01167);动物疾病防控团队(沪农科卓[2022]012)。

摘　　要：为系统鉴定现阶段上海地区仔猪腹泻样品中的病毒群落组成,本研究利用宏病毒组学技术对临床采集的猪腹泻粪便进行了宏病毒高通量测序。结果显示,测序获得了1,676,726个RNAcontig和95,111个DNAcontig,RNA病毒和DNA病毒序列分别占比38.58%和3.10%。其中星状病毒科、杯状病毒科和小RNA病毒科是病毒总群落中占比最高的前3个科。虽然DNA病毒在病毒总群落中的占比较低,但其单组分环状DNA(CRESS-DNA)病毒种类丰富多样,包含有18种CRESS-DNA病毒。经基因组序列深度拼接,共获得了46条病毒全基因组序列,包括2株猪星状病毒和3株类似星状病毒、2株札幌病毒、16株小双节RNA病毒和23株CRESS-DNA病毒。其中1株札幌病毒归属于GII/3亚型,与人札幌病毒亲缘性较近。16株小双节RNA病毒中有4株归属于GGI亚型,其余12株归属于GGII亚型。23株CRESS-DNA病毒中有1株归属于类双生病毒科、12株CRESS-DNA病毒归属于小环状DNA病毒科,另外10株CRESS-DNA病毒未分类。本研究揭示现阶段猪腹泻粪便中以RNA病毒为主导,且存在宿主多样性,提示可能存在种间基因重组,病原潜在危害性需进一步挖掘和验证。研究数据将为临床猪腹泻病防控提供参考和借鉴。Aims:Porcine diarrhea disease is still an intractable problem with complicated infection mode.The aim of this study was to identify the viral community composition in porcine diarrhea stools systematically,and excavating the potential risk agents.Methods:Viral metagenomics technology was used to analyze the viral community composition of the diarrhea stools in piglets via high-throughput sequencing.Then the complete viral sequences were spliced and their genetic characteristics were further analyzed by constructing the phylogenetic trees.Results:A total of 1,676,726 RNA contigs and 95,111 DNA contigs were obtained,with RNA and DNA virus sequences accounting for 38.58%and 3.10%,respectively.Astroviridae,Caliciviridae and Picornaviridae were the top three in the total community.Although DNA viruses occupied a relatively low proportion,there was a wide variety of CRESS-DNA viruses,including 18 kinds of CRESS-DNA viruses.Forty-six whole genome sequences were obtained by depth sequence splicing,including 2 porcine astrovirus(PAstV)isolates,3 bastrovirus(BAstV)isolates,2 sapporo isolates,16 picobirnaviridae(PBV)isolates and 23 CRESS-DNA isolates.One of the Sapporo isolates belonged to GII/3 subtype,which was closely related to human Sapporo virus.Four of the 16 PBVs were classified as GGI subtype,and the other 12 isolates were classified as GGII subtype.Besides,one of the 23 CRESS-DNA viruses was the member of Genomoviridae,12 were Smacoviridae members,and the others were unclassified CRESS-DNA viruses.Conclusion:RNA viruses play dominate role in pig diarrhea feces with high host diversity,suggesting that there may be interspecific gene recombination.However,the potential pathogenicity needs to be further explored and verified.These data would provide database for the prevention and control of clinical porcine diarrhea disease.

关 键 词：仔猪腹泻病 宏病毒组学 病毒群落 全基因组序列 

分 类 号：S858.28[农业科学—临床兽医学]