Metagenomic survey of viral diversity obtained from feces of piglets with diarrhea
Lingling Qian,
Zi Zhuang,
Juan Lu,
Huiying Wang,
Xiaochun Wang,
Shixing Yang,
Likai Ji,
Quan Shen,
Wen Zhang,
Tongling Shan
Affiliations
Lingling Qian
Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
Zi Zhuang
Center of Clinical Laboratory, Dushu Lake Hospital Affiliated to Soochow University, Soochow University, Suzhou, Jiangsu, 215000, China
Juan Lu
Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
Huiying Wang
Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 200062, China
Xiaochun Wang
Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
Shixing Yang
Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
Likai Ji
Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
Quan Shen
Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China; Corresponding author.
Wen Zhang
Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China; Corresponding author.
Tongling Shan
Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China; Corresponding author.
Pigs are natural host to various zoonotic pathogens including viruses. In this study, we analyzed the viral communities in the feces of 89 piglets with diarrhea under one month old which were collected from six farms in Jiangsu Province of the Eastern China, using the unbiased virus metagenomic method. A total of 89 libraries were constructed, and 46937894 unique sequence reads were generated by Illumina sequencing. Overall, the family Picornaviridae accounted for the majority of the total reads of putative mammalian viruses. Ten novel virus genomes from different family members were discovered, including Parvoviridae (n = 2), Picobirnaviridae (n = 4) and CRESS DNA viruses (n = 4). A large number of phages were identified, which mainly belonged to the order Caudovirales and the family Microviridae. Moreover, some identified viruses were closely related to viruses found in non-porcine hosts, highlighting the potential for cross-species virus dissemination. This study increased our understanding of the fecal virus communities of diarrhea piglets and provided valuable information for virus monitoring and preventing.
