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

doi:10.17520/biods.2023170

Abstract

Abstract:

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

Jie Tao, Benqiang Li, Jinghua Cheng, Ying Shi, Peihong Liu, Guixia He, Weijie Xu, Huili Liu. Viral metagenome analysis of the viral community composition of the porcine diarrhea feaces[J]. Biodiv Sci, 2023, 31(11): 23170.

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URL: https://www.biodiversity-science.net/EN/10.17520/biods.2023170

https://www.biodiversity-science.net/EN/Y2023/V31/I11/23170

Figures/Tables 6

Table 1 Metagenomic analysis of porcine diarrhea feces

微生物名称 Microbial name		百分比 Percentage (%)
噬菌体 Phages		31.55
未分类病毒 Unclassified viruses		26.77
DNA病毒 DNA viruses	小环状DNA病毒科 Smacoviridae	1.96	3.10
	圆环病毒 Circoviridae	0.63
	类双生病毒科 Genomoviridae	0.50
	其他DNA病毒 Other DNA viruses	0.01
RNA病毒 RNA viruses	星状病毒科 Astroviridae	19.15	38.58
	杯状病毒科 Caliciviridae	15.15
	小RNA病毒科 Picornaviridae	2.78
	小双节RNA病毒科 Picobirnaviridae	1.35
	呼肠孤病毒 Reoviridae	0.07
	其他RNA病毒 Other RNA viruses	0.08

Fig. 1 Composition of different RNA virus sequence

Fig. 2 Phylogenetic analysis of astrovirus based on the whole genome. Four PAstV genotypes (PAstV-1, PAstV-2, PAstV-3, PAstV-4 and PAstV-5) and bastrovirus were included in the phylogenetic tree. The red dots represent the viral sequences obtained in this study. 0.05 represents the scale of the phylogenetic tree; The values on the branches represent the Bootstrap value, indicating the confidence level.

Fig. 3 Phylogenetic analysis of sapovirus based on the whole genome. Four genotypes of GI (GI/1 and GI/2), GII (GII/3), GIII and GIV were included in this phylogenetic tree. The ruler represents the scale of the phylogenetic tree; The values on the branches represent the confidence level.

Fig. 4 Phylogenetic analysis of picobirnavirus based on the whole genome. Two genotypes of GGI and GGII were included in this phylogenetic tree. The ruler represents the scale of the phylogenetic tree; The values on the branches represent the confidence level.

Fig. 5 Composition and phylogenetic analysis of DNA viruses. A, Composition analysis of DNA virus sequences; B, Phylogenetic analysis of CRESS-DNA viruses. 0.05 represents the distance scale (the scale of the phylogenetic tree); The values on the branches represent the bootstrap value.

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