基于宏病毒组学技术挖掘猪腹泻粪便的病毒群落组成

doi:10.17520/biods.2023170

生物多样性 ›› 2023, Vol. 31 ›› Issue (11): 23170. DOI: 10.17520/biods.2023170

• 研究报告: 微生物多样性 • 上一篇下一篇

基于宏病毒组学技术挖掘猪腹泻粪便的病毒群落组成

陶洁¹^,²^,³, 李本强¹^,²^,³, 程靖华¹^,²^,³, 石迎¹^,²^,³, 刘佩红¹, 何桂霞⁴, 徐伟杰⁴, 刘惠莉¹^,²^,³^,^*()

1.上海市农业科学院, 上海 201106
2.上海市农业遗传育种重点实验室, 上海 201106
3.农业农村部区域特色畜禽品种疾病防控重点实验室, 上海 201106
4.光明农牧科技有限公司, 上海 202150

收稿日期:2023-05-26 接受日期:2023-09-05 出版日期:2023-11-20 发布日期:2023-09-20
通讯作者: * E-mail: huilil@163.com
作者简介:^# 共同第一作者
基金资助:
上海市科技兴农项目(2022-02-08-00-12-F01167);动物疾病防控团队(沪农科卓[2022]012)

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 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: huilil@163.com
About author:^# Co-first authors

1. 附录1 星状病毒、小RNA病毒、小双节RNA和轮状病毒组成.pdf(248KB)

摘要/Abstract

摘要：

为系统鉴定现阶段上海地区仔猪腹泻样品中的病毒群落组成, 本研究利用宏病毒组学技术对临床采集的猪腹泻粪便进行了宏病毒高通量测序。结果显示, 测序获得了1,676,726个RNA contig和95,111个DNA contig, RNA病毒和DNA病毒序列分别占比38.58%和3.10%。其中星状病毒科、杯状病毒科和小RNA病毒科是病毒总群落中占比最高的前3个科。虽然DNA病毒在病毒总群落中的占比较低, 但其单组分环状DNA (CRESS-DNA)病毒种类丰富多样, 包含有18种CRESS-DNA病毒。经基因组序列深度拼接, 共获得了46条病毒全基因组序列, 包括2株猪星状病毒和3株类似星状病毒、2株札幌病毒、16株小双节RNA病毒和23株CRESS-DNA病毒。其中1株札幌病毒归属于GII/3亚型, 与人札幌病毒亲缘性较近。16株小双节RNA病毒中有4株归属于GGI亚型, 其余12株归属于GGII亚型。23株CRESS-DNA病毒中有1株归属于类双生病毒科、12株CRESS-DNA病毒归属于小环状DNA病毒科, 另外10株CRESS-DNA病毒未分类。本研究揭示现阶段猪腹泻粪便中以RNA病毒为主导, 且存在宿主多样性, 提示可能存在种间基因重组, 病原潜在危害性需进一步挖掘和验证。研究数据将为临床猪腹泻病防控提供参考和借鉴。

关键词: 仔猪腹泻病, 宏病毒组学, 病毒群落, 全基因组序列

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

陶洁, 李本强, 程靖华, 石迎, 刘佩红, 何桂霞, 徐伟杰, 刘惠莉 (2023) 基于宏病毒组学技术挖掘猪腹泻粪便的病毒群落组成. 生物多样性, 31, 23170. DOI: 10.17520/biods.2023170.

Jie Tao, Benqiang Li, Jinghua Cheng, Ying Shi, Peihong Liu, Guixia He, Weijie Xu, Huili Liu (2023) Viral metagenome analysis of the viral community composition of the porcine diarrhea feaces. Biodiversity Science, 31, 23170. DOI: 10.17520/biods.2023170.

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链接本文: https://www.biodiversity-science.net/CN/10.17520/biods.2023170

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

图/表 6

表1 猪腹泻粪便中微生物序列组成分析

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

图1 不同种属RNA病毒序列组成

Fig. 1 Composition of different RNA virus sequence

图2 星状病毒全基因组系统发育进化树分析。进化树中包含4个不同亚型猪星状病毒(猪星状病毒1型、猪星状病毒2型、猪星状病毒3型、猪星状病毒4型和猪星状病毒5型)和星状病毒样病毒。红色圆点表示本研究中拼接获得病毒序列。0.05表示进化树的比例尺; 树枝上数值为自展值, 表示可信度。

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.

图3 札幌病毒全基因组系统发育进化树分析。进化树中包括4个亚型: GI (GI/1和GI/2)、GII (GII/3)、GIII和GIV。标尺表示进化树的比例尺; 分枝上数值表示可信度。

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.

图4 小双节RNA病毒全基因组系统发育进化树分析。进化树中包含GGI和GGII两个亚型。标尺表示进化树的比例尺; 分枝上数值表示可信度。

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.

图5 DNA病毒群落组成和系统进化发育分析。A: DNA病毒序列组成分析; B: 单组分环状DNA病毒进化分析。0.05表示距离标尺(进化树的比例尺); 树枝上数值表示自展值。

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.

参考文献 29

[1]	Bai GH, Lin SC, Hsu YH, Chen SY (2022) The human virome: Viral metagenomics, relations with human diseases, and therapeutic applications. Viruses, 14, 278. DOI URL
[2]	Bauermann FV, Hause B, Buysse AR, Joshi LR, Diel DG (2019) Identification and genetic characterization of a porcine hepe-astrovirus (bastrovirus) in the United States. Archives of Virology, 164, 2321-2326. DOI PMID
[3]	Bhella D, Goodfellow IG (2011) The cryo-electron microscopy structure of feline calicivirus bound to junctional adhesion molecule A at 9-angstrom resolution reveals receptor- induced flexibility and two distinct conformational changes in the capsid protein VP1. Journal of Virology, 85, 11381-11390. DOI PMID
[4]	Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics, 30, 2114-2120. DOI PMID
[5]	Chen CY, Zhou YY, Fu H, Xiong XW, Fang SM, Jiang H, Wu JY, Yang H, Gao J, Huang LS (2021) Expanded catalog of microbial genes and metagenome-assembled genomes from the pig gut microbiome. Nature Communications, 12, 1106. DOI PMID
[6]	Ganesh B, Bányai K, Martella V, Jakab F, Masachessi G, Kobayashi N (2012) Picobirnavirus infections: Viral persistence and zoonotic potential. Reviews in Medical Virology, 22, 245-256. DOI PMID
[7]	Guo JR, Bolduc B, Zayed AA, Varsani A, Dominguez-Huerta G, Delmont TO, Pratama AA, Gazitúa MC, Vik D, Sullivan MB, Roux S (2021) VirSorter2: A multi-classifier, expert- guided approach to detect diverse DNA and RNA viruses. Microbiome, 9, 37. DOI URL
[8]	Hameed M, Liu K, Anwar MN, Wahaab A, Li CX, Di D, Wang X, Khan S, Xu JP, Li BB, Nawaz M, Shao DH, Qiu YF, Wei JC, Ma ZY (2020) A viral metagenomic analysis reveals rich viral abundance and diversity in mosquitoes from pig farms. Transboundary and Emerging Diseases, 67, 328-343. DOI PMID
[9]	Knox MA, Gedye KR, Hayman DS (2018) The challenges of analysing highly diverse Picobirnavirus sequence data. Viruses, 10, 685. DOI URL
[10]	Li DH, Luo RB, Liu CM, Leung CM, Ting HF, Sadakane K, Yamashita H, Lam TW (2016) MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods, 102, 3-11. DOI PMID
[11]	Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760. DOI PMID
[12]	Liu TN, Liu CX, Liao JY, Xiong WJ, Xia JY, Xiao CT (2022) Identification and genomic characterization of a novel porcine CRESS DNA virus from a pig suffering from diarrhea in China. Archives of Virology, 167, 1355-1359. DOI
[13]	Liu X, Song CL, Liu YH, Qu KX, Bi JY, Bi JL, Wang YH, Yang Y, Sun JH, Guo ZG, Li GW, Liu JP, Yin GF (2022) High genetic diversity of porcine sapovirus from diarrheic piglets in Yunnan Province, China. Frontiers in Veterinary Science, 9, 854905. DOI URL
[14]	Martínez LC, Masachessi G, Carruyo G, Ferreyra LJ, Barril PA, Isa MB, Giordano MO, Ludert JE, Nates SV (2010) Picobirnavirus causes persistent infection in pigs. Infection, Genetics and Evolution, 10, 984-988. DOI PMID
[15]	Nayfach S, Camargo AP, Schulz F, Eloe-Fadrosh E, Roux S, Kyrpides NC (2021) CheckV assesses the quality and completeness of metagenome-assembled viral genomes. Nature Biotechnology, 39, 578-585. DOI PMID
[16]	Park YS, Kim S, Park DG, Kim DH, Yoon KW, Shin W, Han K (2019) Comparison of library construction kits for mRNA sequencing in the Illumina platform. Genes & Genomics, 41, 1233-1240.
[17]	Pons JC, Paez-Espino D, Riera G, Ivanova N, Kyrpides NC, Llabrés M (2021) VPF-Class: Taxonomic assignment and host prediction of uncultivated viruses based on viral protein families. Bioinformatics, 37, 1805-1813. DOI PMID
[18]	Qiu M, Li SB, Xiao YZ, Li JX, Zhang YW, Li XS, Feng BH, Li C, Lin H, Zhu JZ, Chen NH (2022) Pathogenic and metagenomic evaluations reveal the correlations of porcine epidemic diarrhea virus, porcine kobuvirus and porcine astroviruses with neonatal piglet diarrhea. Microbial Pathogenesis, 170, 105703. DOI URL
[19]	Shen XJ, Li JJ, Bian J, Zhao TT, Hua XG, Cui L (2019) Metagenomics analysis of feces from diarrhea piglets reveals the viral composition and epidemic characteristics of Coronavirus. Acta Veterinaria et Zootechnica Sinica, 50, 611-619. (in Chinese with English abstract)
	[沈小娟, 李晶娇, 边疆, 赵婷婷, 华修国, 崔立 (2019) 腹泻仔猪肠道病毒组学分析. 畜牧兽医学报, 50, 611-619.]
[20]	Shi Y, Tao J, Li BQ, Shen XH, Cheng JH, Liu HL (2021) The gut viral metagenome analysis of domestic dogs captures snapshot of viral diversity and potential risk of coronavirus. Frontiers in Veterinary Science, 8, 695088. DOI URL
[21]	Shu X, Han F, Hu Y, Hao CL, Li ZY, Wei ZY, Zhang HL (2022) Co-infection of porcine deltacoronavirus and porcine epidemic diarrhoea virus alters gut microbiota diversity and composition in the colon of piglets. Virus Research, 322, 198954. DOI URL
[22]	Slavov SN (2022) Viral metagenomics for identification of emerging viruses in transfusion medicine. Viruses, 14, 2448. DOI URL
[23]	Su MJ, Qi SS, Yang D, Guo DH, Yin BS, Sun DB (2020) Coinfection and genetic characterization of porcine astrovirus in diarrheic piglets in China from 2015 to 2018. Frontiers in Veterinary Science, 7, 462.
[24]	Villanova F, Milagres FAP, Brustulin R, Araújo ELL, Pandey RP, Raj VS, Deng XT, Delwart E, Luchs A, da Costa AC, Leal É (2022) A new circular single-stranded DNA virus related with howler monkey associated Porpris macovirus 1 detected in children with acute gastroenteritis. Viruses, 14, 1472.
[25]	Wang LY, Marthaler D, Fredrickson R, Gauger PC, Zhang JQ, Burrough ER, Petznick T, Li GW (2020) Genetically divergent porcine sapovirus identified in pigs, United States. Transboundary and Emerging Diseases, 67, 18-28. DOI PMID
[26]	Wang QH, Han MG, Funk JA, Bowman G, Janies DA, Saif LJ (2005) Genetic diversity and recombination of porcine sapoviruses. Journal of Clinical Microbiology, 43, 5963-5972. DOI URL
[27]	Wang QH, Vlasova AN, Kenney SP, Saif LJ (2019) Emerging and re-emerging coronaviruses in pigs. Current Opinion in Virology, 34, 39-49. DOI PMID
[28]	Wu Q, Zhang Y, Zheng HX, Yin H (2011) The research progress of sapovirus. Acta Veterinaria et Zootechnica Sinica, 42, 754-758. (in Chinese with English abstract)
	[吴琼, 张艳, 郑海学, 殷宏 (2011) 札幌病毒研究进展. 畜牧兽医学报, 42, 754-758.]
[29]	Zhang FF, Luo SX, Gu J, Li ZQ, Li K, Yuan WF, Ye Y, Li H, Ding Z, Song DP, Tang YX (2019) Prevalence and phylogenetic analysis of porcine diarrhea associated viruses in Southern China from 2012 to 2018. BMC Veterinary Research, 15, 470. DOI PMID

基于宏病毒组学技术挖掘猪腹泻粪便的病毒群落组成

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

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