宏基因组测序揭示一例荷斯坦犊牛腹泻粪便的病毒组成与分子特征OA

Diarrhea is one of the most common and difficult-to-prevent-and-control diseases in cattle herds,among which viral diarrhea causes particularly serious economic losses to the cattle in-dustry.To investigate the viral composition and molecular characteristics of a calf with refractory diarrhea,three fresh fecal samples from the affected calf were collected,mixed,and subjected to high-throughput metagenomic sequencing on the Illumina NovaSeq platform.After quality control,assem-bly with SPAdes,and bioinformatic alignment analyses,the viral composition and molecular evolution-ary characteristics in the samples were determined.The results showed that after quality control,host removal,and assembly,a total of 14 369 775 DNA clean reads and 11 653 867 RNA clean reads were obtained.Viral composition analysis revealed 73 viral families(38 DNA virus families and 35 RNA virus families).Among DNA viruses,Straboviridae was the most abundant(57％),while among RNA viruses,Picornaviridae had the highest proportion(63％).At the species level,321 viral species were identified:among DNA viruses,Goslarvirus goslar phage was the most abundant(47％),among RNA viruses,bovine kobuvirus(Aichi B type)accounted for the highest proportion(32％).Further sequence alignment identified ten major viral contigs,including bovine rotavirus(BRV),bovine nebovirus(BoNoV),Boosepivirus(BooV),bovine hunnivirus(BoHuV),bovine kobuvirus(BKV),and bovine nebovirus(BoNeV).Phylogenetic analysis deter-mined:BRV as group A G6P[5]type,BoNoV as GⅢ group,BoNeV as genotype 2(RdRp-based typing:SC-Yak type),BooV as B1 type,BoHuV as A1 type,and BKV as Aichi B type and Aichi D type.Using metagenomic sequencing,this study comprehensively revealed the viral population and genetic evolutionary characteristics of a calf with refractory diarrhea.Notably,the BoNeV/SC-Yak genotype was detected in a non-yak host,and two genotypes of BKV were identified.We speculate that the refractory diarrhea in this calf might be associated with co-infection by multiple RNA viruses.These findings enrich our knowledge of the viral community and genetic evolution associated with bovine diarrhea and provide important etiological evidence for the effective prevention and control of calf diarrhea.