大庆地区犊牛肠道病毒种群的宏基因组学分析

doi:10.16431/j.cnki.1671-7236.2024.12.005

摘要/Abstract

摘要： 【目的】了解大庆地区奶牛群体犊牛肠道病毒的种群组成及遗传变异情况，为犊牛腹泻病毒性病原的检测与防控技术研究提供理论依据。【方法】于大庆周边奶牛场，采集155份犊牛粪便样品，随机分为6个腹泻样品池和3个临床无腹泻症状样品池。提取总核酸，基于Illumina测序平台进行高通量测序，利用SPAdes和SOAPdenovo进行序列拼接和组装，根据获得的序列分析病毒种群组成和遗传变异情况。【结果】成功注释到21个病毒科的6 517 147条病毒相关序列，除噬菌体外，冠状病毒科丰度最高，小RNA病毒科次之。将腹泻样本的注释结果与临床无腹泻样本进行比较发现，无腹泻样本中的病毒种群多样性明显高于腹泻样本，细小病毒科、小RNA病毒科及呼肠孤病毒科在腹泻样本中的相对丰度高于无腹泻样本。本研究还注释到牛环曲病毒(BToV)、牛嵴病毒(BKV)和牛诺如病毒(BNoV)等多种新发犊牛腹泻病毒序列，且首次在黑龙江地区犊牛粪便中注释到牛纽布病毒(BNeV)。对组装到的牛轮状病毒(BRV)、牛冠状病毒(BCoV)和牛星状病毒(BoAstV)基因组进行遗传进化分析，结果表明，BRV流行基因型为G6、G10、P[5]和P[11]；组装到的1条BCoV全长基因组与中国流行毒株Coronavirus/Bo/BCoV6/2021/CHN亲缘关系最近；组装到的5条BoAstV均聚集在肠道组织嗜性毒株分支。【结论】大庆地区犊牛肠道病毒种群中冠状病毒科丰度最高，腹泻组样本病毒种群多样性低于无腹泻组。粪便样本中注释到BToV、BKV和BNoV等多种致犊牛腹泻的病毒，首次在黑龙江犊牛粪便中注释到BNeV，分析了当地流行BRV、BCoV和BoAstV遗传进化特点，为当地犊牛腹泻病毒性病原检测提供理论依据。

关键词: 犊牛肠道病毒; 病毒宏基因组学; 高通量测序

Abstract: 【Objective】 The experiment was aimed to comprehend the composition and genetic variability of calf intestinal viruses within the dairy cattle population in the Daqing region,and furnish a theoretical framework for the detection of viral pathogens responsible for diarrhea in local calves.【Method】 A total of 155 fecal samples of calves were collected from dairy farms surrounding Daqing,which were divided into six diarrhea sample pools and three clinically asymptomatic sample pools.Total nucleic acid was extracted,high-throughput sequencing was performed based on Illumina sequencing platform,SPAdes and SOAPdenovo were used for sequence splicing and assembly,and viral population composition and genetic variation were analyzed according to the obtained sequences.【Result】 A total of 6 517 147 viral-related sequences from 21 viral families were successfully annotated.In the calf intestinal viral community,except for bacteriophaes,Coronaviridae exhibited the highest abundance,followed by Picornaviridae.Comparison of annotation results of the diarrhea samples with asymptomatic samples,the diversity of the virus population in the asymptomatic samples was significantly higher than that in the diarrhea samples,and it was found that the relative abundance of Parvoviridae, Picornaviridae and Reoviridae was higher in the diarrhea group samples compared to the non-diarrhea group.This study annotated multiple novel sequences of calf diarrhea viruses such as Bovine torovirus (BToV),Bovine kobuvirus (BKV) and Bovine norovirus (BNoV).In addition,for the first time,Bovine nebovirus was identified in calf feces in Heilongjiang region.Genetic evolution analysis on the assembled genomes of BRV,BCoV and BoAstV was conducted,and it showed that the predominant genotypes of BRV were identified as G6,G10,P[5] and P[11].The assembled full-length genome of BCoV showed the closest phylogenetic relationship with Coronavirus/Bo/BCoV6/2021/CHN,a prevalent strain in China.BoAstV sequences clustered consistently within the branch of enteric tissue tropism strains.【Conclusion】 The abundance of Coronaviraceae was the highest in the calf enterovirus population in Daqing area.The abundance of viral population in the diarrhea group samples was lower than that in the non-diarrhea group samples.Several calf diarrhea viruses,such as BToV,BKV and BNoV were annotated in the fecal samples.Additionally,BNeV was first annotated in calf feces from Heilongjiang province.Genetic evolution characteristics of local prevalent viruses such as BRV,BCoV and BoAstV were analyzed.These findings provided a theoretical basis for the detection of viral pathogens causing diarrhea in local calves.

Key words: calf intestinal virus; viral metagenomics; high-throughput sequencing

中图分类号:

S852.65⁺3

陈天杰, 李玉铎, 周华亮, 肇慧君, 赵建军. 大庆地区犊牛肠道病毒种群的宏基因组学分析[J]. 中国畜牧兽医, 2024, 51(12): 5162-5173.

CHEN Tianjie, LI Yuduo, ZHOU Hualiang, ZHAO Huijun, ZHAO Jianjun. Metagenomic Analysis of Calf Intestinal Viral Population in Daqing Region[J]. China Animal Husbandry and Veterinary Medicine, 2024, 51(12): 5162-5173.

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