Biodiv Sci ›› 2023, Vol. 31 ›› Issue (11): 23170.  DOI: 10.17520/biods.2023170

• Original Papers: Microbial Diversity • Previous Articles     Next Articles

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

Jie Tao1,2,3, Benqiang Li1,2,3, Jinghua Cheng1,2,3, Ying Shi1,2,3, Peihong Liu1, Guixia He4, Weijie Xu4, Huili Liu1,2,3,*()   

  1. 1 Shanghai Academy of Agricultural Sciences, Shanghai 201106
    2 Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai 201106
    3 Key Laboratory of Disease Prevention and Control of Livestock and Poultry Varieties with Regional Characteristics, Ministry of Agriculture and Rural Affairs, Shanghai 201106
    4 Guangming Agriculture and Animal Husbandry Technology Co. Ltd, Shanghai 202150
  • Received:2023-05-26 Accepted:2023-09-05 Online:2023-11-20 Published:2023-09-20
  • Contact: * E-mail:
  • About author:# Co-first authors


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.

Key words: porcine diarrheal disease, metagenome, viral community, whole genome sequence