畜牧兽医学报2024，Vol.55Issue(8)：3579-3589,11.DOI:10.11843/j.issn.0366-6964.2024.08.029
宏转录组测序技术在一起仔猪病毒性腹泻疾病诊断中的运用及分析
Application and Analysis of Meta-transcriptomics Sequencing Technology in the Diagnosis of Viral Diarrhea Diseases in Piglets
摘要
Abstract
The purpose of this research is to determine the pathogen of piglet diarrhea in pig farms in Hezhou area of Guangxi in the spring of 2023 by using the Meta-transcriptomics sequencing technology to screen the incidence and infection of pigs in this area,so as to provide theoretical basis for the prevention and control of piglet diarrhea diseases in local pig farms.In March 2023,swabs and feces of six adjacent pig farms with simultaneous outbreak of diarrhea within a range of 10 kilometers were collected in Hezhou,Guangxi,and Meta-transcriptomics sequencing was per-formed by MGISEQ 200 sequencing platform for porcine pathogenic infectomes research.The pathogenic spectrum of piglet diarrhea in this area was systematically screened and the abundance of each pathogen was quantitatively analyzed.The most important viruses were confirmed by Re-al-time PCR,after which the identified viral gene sequences were selected for phylogenetic analy-sis.Pearson analysis was used to analyze the correlation of pathogenic co-infection.The results showed that a total of 17 pathogenic bacteria,12 viruses,and 3 parasites were detected in these samples by Meta-transcriptomics sequencing.The predominant viruses were diarrhea-associated viruses represented by the porcine epidemic diarrhea virus(PEDV),including porcine sapovirus(SaV),porcine kobuvirus(PKV),porcine astrovirus(PAstV),porcine sapelovirus(PSV),and rotavirus A(RVA).The bacteria mainly consisted of three kinds of Enterobacteriaceae,three kinds of Lactobacillaceae,and two kinds of Bacillaceae.The parasites included two kinds of Trichomonads and Iodamoeba.The phylogenetic analysis of spike gene(S gene)of PEDV from five farms showed that the strains all belonged to the G2c cluster group,that the nucleotide simi-larity between the strains was 99.99％,and that S gene was recombined.Additionally,partial VP4 gene of rotavirus A,of the P[6]genotype,was detected in one of the farms,which had the highest nucleotide similarity with human rotavirus.In addition,more than 2 piglet diarrhea-re-lated viral infections were detected in 4 pig farms.Phylogenetic analysis showed that there was a multi-lineage co-epidemic of diarrheal pathogens in this region,and even different lineages of the same virus were circulating in the same farm.Pathogen correlation analysis showed that there was a significant negative correlation between PEDV/PSV(P＜0.001),PEDV/porcine torovirus(PToV)(P＜0.001)and PEDV/PAstV(P＜0.05),while PEDV/PKV had a significant posi-tive correlation(P＜0.05).The above findings indicate a diverse pathogenic spectrum of piglet diarrhea in adjacent breeding regions of this area,with PEDV identified as the primary pathogen.Furthermore,a correlation between PEDV and other diarrhea-related viruses was observed in the samples.This study offers a comprehensive overview of the infection spectrum of diarrhea patho-gens in piglets in this region,pinpointing the most direct causes of diarrhea.Additionally,it ena-bles the analysis of the relationship between diarrhea-associated pathogens in small-scale breeding areas,providing precise guidance and reference for the prevention and control of piglet diarrhea in this region.关键词
宏转录组测序技术/仔猪腹泻疾病/病原识别/PEDV/遗传进化分析/相关性分析Key words
meta-transcriptomics/piglet diarrhea disease/pathogen identification/PEDV/genet-ic evolution analysis/correlation analysis分类
农业科技引用本文复制引用
李跃,高校鹏,王衡,龚浪,张桂红,孙彦阔,张长春,刘光裕,高梦源,符超俊,邢家宝,徐思佳,邝麒元,刘静..宏转录组测序技术在一起仔猪病毒性腹泻疾病诊断中的运用及分析[J].畜牧兽医学报,2024,55(8):3579-3589,11.基金项目
"十四五"国家重点研发计划项目(2022YFD1800804) （2022YFD1800804）
国家自然科学基金项目(32102704) （32102704）
茂名实验室科研启动项目(2021TDQD002) （2021TDQD002）
财政部和农业农村部:国家现代农业产业技术体系资助(CARS-35) （CARS-35）
