[1]彭司华,江守文,孙丹,等.宏基因组学技术在水产动物病毒鉴定中的应用[J].江苏农业学报,2019,(01):229-237.[doi:doi:10.3969/j.issn.1000-4440.2019.01.033]
　PENG Si-hua,JIANG Shou-wen,SUN Dan,et al.Application of metagenomics technology in aquaculture animal virus identification[J].,2019,(01):229-237.[doi:doi:10.3969/j.issn.1000-4440.2019.01.033]
点击复制

宏基因组学技术在水产动物病毒鉴定中的应用()
分享到：

江苏农业学报[ISSN:1006-6977/CN:61-1281/TN]

卷:
期数:
2019年01期
页码:
229-237
栏目:
综述
出版日期:
2019-02-26

文章信息/Info

Title:
Application of metagenomics technology in aquaculture animal virus identification
作者:
彭司华1; 2; 3; 4; 江守文2; 3; 4; 孙丹2; 3; 4; 吴智超2; 3; 4; 陈洁2; 4
（1.上海海洋大学水产与生命学院,上海201306;2.水产种质资源发掘与利用教育部重点实验室/上海海洋大学，上海201306;3.农业部国家水生动物病原库/上海海洋大学，上海201306;4.科学技术部海洋生物科学国际联合研究中心/上海海洋大学，上海201306）
Author(s):
PENG Si-hua1; 2; 3; 4; JIANG Shou-wen2; 3; 4; SUN Dan2; 3; 4; WU Zhi-chao2; 3; 4; CHEN Jie2; 4
(1.College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China;2.Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources/Shanghai Ocean University, Ministry of Education of China, Shanghai 201306, China;3.National Pathogen Collection Center for Aquatic Animals， Ministry of Agriculture of China, Shanghai 201306, China;4.International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology of China, Shanghai 201306, China)
关键词:
水产动物病毒; 宏基因组学; 病毒鉴定; 二代测序
Keywords:
aquatic animal virus; metagenomics; virus identification; next generation sequencing
分类号:
S941.41
DOI:
doi:10.3969/j.issn.1000-4440.2019.01.033
文献标志码:
A
摘要:
近年来水产养殖生产中病毒性疾病的发生越来越严重，所以对水产动物病毒的深入研究成为水产研究者的一个重要课题。随着宏基因组学技术的不断发展，以及测序成本的快速下降，基于宏基因组学技术的水产动物病毒鉴定技术逐渐成为水产动物病毒鉴定的主要技术之一。本文总结了基于宏基因组学的水产动物病毒鉴定技术的主要方法，详细综述了鉴定技术的实现流程，评述了几种基于宏基因组学的水产动物病毒鉴定技术的优缺点，并对基于宏基因组学的水产动物病毒鉴定技术的未来发展方向进行了展望。
Abstract:
In recent years, the occurrence of viral diseases in the production of aquaculture has become more and more serious. Therefore, in-depth research on aquatic virus has become an important issue for aquatic researchers. With the continuous development of metagenomics technology and the rapid decline in sequencing costs, aquatic animal virus identification technology based on metagenomics technology has gradually become one of the main techniques for identification of aquatic animal viruses. This article summarized the main methods for the identification of aquatic animal viruses based on metagenomics, reviews the identification process in detail, and discussed the advantages and disadvantages of the identification techniques. The development of the identification technology of aquatic animal viruses has been forecasted.

参考文献/References:

[1]中国渔业报. 2016年全国渔业经济统计公报[EB/OL]. (2017-04-17)
[2018-02-26].
[2]联合国粮食及农业组织. 世界渔业和水产养殖 [EB/OL]. (2016-09-27)
[2018-02-25]. http://www.fao.org/3/a-i5555c.pdf.
[3]张奇亚,桂建芳. 水生病毒学 [M]. 北京: 中国高等教育出版社, 2008: 3-6.
[4]ZHANG Q, GUI J F. Virus genomes and virus-host interactions in aquaculture animals [J]. Sci China Life Sci, 2015, 58(2):156-169.
[5]ZHANG Q Y, LI Z Q, GUI J F. Isolation of a lethal rhabdovirus from the cultured Chinese sucker Myxocyprinus asiaticus [J]. Diseases of Aquatic Organisms, 2000, 42(1):1-9.
[6]ALAVANDI S V, POORNIMA M. Viral Metagenomics: a tool for virus discovery and diversity in aquaculture [J]. Indian Journal of Virology, 2012, 23(2):88-98.
[7]CRANE M, HYATT A. Viruses of Fish: an overview of significant pathogens [J]. Viruses-Basel, 2011, 3(11):2025-2046.
[8]EDWARDS R A, ROHWER F. Viral metagenomics [J]. Nat Rev Microbiol, 2005, 3(6):504-510.
[9]HANDELSMAN J. Metagenomics: application of genomics to uncultured microorganisms [J]. Microbiol Mol Biol Rev, 2004, 68(4):669-685.
[10]RIESENFELD C S, SCHLOSS P D, HANDELSMAN J. Metagenomics: genomic analysis of microbial communities [J]. Annual Review of Genetics, 2004, 38:525-552.
[11]BEXFIELD N, KELLAM P. Metagenomics and the molecular identification of novel viruses [J]. Veterinary Journal, 2011, 190(2):191-198.
[12]MOKILI J L, ROHWER F, DUTILH B E. Metagenomics and future perspectives in virus discovery [J]. Current Opinion in Virology, 2012, 2(1):63-77.
[13]ROSARIO K, BREITBART M. Exploring the viral world through metagenomics [J]. Current Opinion in Virology, 2011, 1(4):289-297.
[14]TANG P, CHIU C. Metagenomics for the discovery of novel human viruses [J]. Future Microbiology, 2010, 5(2):177-189.
[15]GRENINGER A L. A decade of RNA virus metagenomics is (not) enough [J]. Virus Research, 2018, 244:218-229.
[16]MUNANG′ANDU H M, MUGIMBA K K, BYARUGABA D K, et al. Current advances on virus discovery and diagnostic role of viral metagenomics in aquatic organisms [J]. Frontiers in Microbiology, 2017, 8:406.
[17]何彪,涂长春. 病毒宏基因组学的研究现状及应用 [J]. 畜牧兽医学报, 2012, 43(12):1865-1870.
[18]SHENDURE J, JI H. Next-generation DNA sequencing [J]. Nature Biotechnology, 2008, 26(10):1135-1145.
[19]DAY J M, BALLARD L L, DUKE M V, et al. Metagenomic analysis of the turkey gut RNA virus community [J]. Virology Journal, 2010, 7:313.
[20]EMMENEGGER E J, GLENN J A, WINTON J R, et al. Molecular identification of erythrocytic necrosis virus (ENV) from the blood of Pacific herring (Clupea pallasii) [J]. Veterinary Microbiology, 2014, 174(1/2):16-26.
[21]HONKAVUORI K S, BRIESE T, KRAUSS S, et al. Novel coronavirus and astrovirus in delaware bay shorebirds [J]. PLoS ONE, 2014, 9(4):e93395.
[22]PHAN T G, VO N P, ARONEN M, et al. Novel human gammapapillomavirus species in a nasal swab [J]. Genome Announc, 2013, 1(2):e0002213.
[23]QUAN P-L, FIRTH C, CONTE J M, et al. Bats are a major natural reservoir for hepaciviruses and pegiviruses [J]. Proceedings of the National Academy of Sciences of the United States of America, 2013, 110(20):8194-8199.
[24]YAN L, ZHANG H, MA H, et al. Deep sequencing of hepatitis B virus basal core promoter and precore mutants in HBeAg-positive chronic hepatitis B patients [J]. Scientific Reports, 2015, 5:1-9.
[25]ARCHER J, WEBER J, HENRY K, et al. Use of four next-generation sequencing platforms to determine HIV-1 coreceptor tropism [J]. PLoS ONE, 2012, 7(11):e49602.
[26]GIBSON R M, MEYER A M, WINNER D, et al. Sensitive deep-sequencing-based HIV-1 genotyping assay to simultaneously determine susceptibility to protease, reverse transcriptase, integrase, and maturation inhibitors, as well as HIV-1 coreceptor tropism [J]. Antimicrobial Agents and Chemotherapy, 2014, 58(4):2167-2185.
[27]GASPARETO K V, RIBEIRO R M, MALTA F D M, et al. Resistance-associated variants in HCV subtypes 1a and 1b detected by Ion Torrent sequencing platform [J]. Antiviral Therapy, 2016, 21(8):653-660.
[28]STEYER A, GUTIERREZ-AGUIRE I, KOLENC M, et al. High similarity of novel orthoreovirus detected in a child hospitalized with acute gastroenteritis to mammalian orthoreoviruses found in bats in Europe [J]. Journal of Clinical Microbiology, 2013, 51(11):3818-3825.
[29]KVISGAARD L K, HJULSAGER C K, FAHNOE U, et al. A fast and robust method for full genome sequencing of porcine reproductive and respiratory syndrome virus (PRRSV) Type 1 and Type 2 [J]. Journal of Virological Methods, 2013, 193(2):697-705.
[30]NOUGAIREDE A, BICHAUD L, THIBERVILLE S-D, et al. Isolation of toscana virus from the cerebrospinal fluid of a man with meningitis in Marseille, France, 2010 [J]. Vector-Borne and Zoonotic Diseases, 2013, 13(9):685-688.
[31]LORUSSO A, MARCACCI M, ANCORA M, et al. Complete genome sequence of bluetongue virus serotype 1 circulating in Italy, obtained through a fast next-generation sequencing protocol [J]. Genome Announc, 2014, 2(1):e00093-14.
[32]NYAGA M M, STUCKER K M, ESONA M D, et al. Whole-genome analyses of DS-1-like human G2P 4 and G8P 4 rotavirus strains from Eastern, Western and Southern Africa [J]. Virus Genes, 2014, 49(2):196-207.
[33]VAN DEN HOECKE S, VERHELST J, VUYLSTEKE M, et al. Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing [J]. Bmc Genomics, 2015, 16:79.
[34]KIRCHER M, KELSO J. High-throughput DNA sequencing - concepts and limitations [J]. Bioessays, 2010, 32(6):524-536.
[35]MOROZOVA O, MARRA M A. Applications of next-generation sequencing technologies in functional genomics [J]. Genomics, 2008, 92(5):255-264.
[36]ZHANG P, FERNANDES H. Comparison of two next-generation sequencing systems: assessment of efficiency and quality of results [J]. Journal of Molecular Diagnostics, 2015, 17(6):844.
[37]XU B, LIU L, HUANG X, et al. Metagenomic analysis of fever, thrombocytopenia and leukopenia syndrome (ftls) in henan province, China: discovery of a new bunyavirus [J]. PLoS Pathogens, 2011, 7(11):e1002369.
[38]CHIU C Y, YAGI S, LU X Y, et al. A novel adenovirus species associated with an acute respiratory outbreak in a baboon colony and evidence of coincident human infection [J]. mBio, 2013, 4(2):e00084.
[39]PHAN T G, DRENO B, DA COSTA A C, et al. A new protoparvovirus in human fecal samples and cutaneous T cell lymphomas (mycosis fungoides) [J]. Virology, 2016, 496:299-305.
[40]REUTER J A, SPACEK D V, SNYDER M P. High-throughput sequencing technologies [J]. Mol Cell, 2015, 58(4):586-597.
[41]BULL R A, ELTAHLA A A, RODRIGO C, et al. A method for near full-length amplification and sequencing for six hepatitis C virus genotypes [J]. Bmc Genomics, 2016, 17:247.
[42]HO C K Y, RAGHWANI J, KOEKKOEK S, et al. Characterization of hepatitis C virus (HCV) envelope diversification from acute to chronic infection within a sexually transmitted HCV cluster by using single-molecule, real-time sequencing [J]. Journal of Virology, 2017, 91(6):e02262.
[43]LI J, WANG M, YU D, et al. A comparative study on the characterization of hepatitis B virus quasispecies by clone-based sequencing and third-generation sequencing [J]. Emerging Microbes & Infections, 2017, 6:e100.
[44]MAGI A, SEMERARO R, MINGRINO A, et al. Nanopore sequencing data analysis: state of the art, applications and challenges [J]. Brief Bioinform, 2017,doi: 10.1093/bib/bbx1062.
[45]SCHMIDT M H W, VOGEL A, DENTON A K, et al. De novo assembly of a new solanum pennellii accession using Nanopore sequencing [J]. Plant Cell, 2017, 29(10):2336-2348.
[46]JAIN M, KOREN S, MIGA K H, et al. Nanopore sequencing and assembly of a human genome with ultra-long reads [J]. Nat Biotechnol, 2018, 36(4):338-345.
[47]PALACIOS G, LOVOLL M, TENGS T, et al. Heart and skeletal muscle inflammation of farmed salmon is associated with infection with a novel reovirus [J]. PLoS ONE, 2010, 5(7):e11487.
[48]REUTER G, BOROS A, DELWART E, et al. Novel seadornavirus (family reoviridae) related to Banna virus in Europe [J]. Archives of Virology, 2013, 158(10):2163-2167.
[49]MOR S K, PHELPS N B D. Detection and molecular characterization of a novel piscine-myocarditis-like virus from baitfish in the USA [J]. Archives of Virology, 2016, 161(7):1925-1931.
[50]LORINCZ M, DAN A, LANG M, et al. Novel circovirus in European catfish (silurus glanis) [J]. Archives of Virology, 2012, 157(6):1173-1176.
[51]LANGE J, GROTH M, FICHTNER D, et al. Virus isolate from carp: genetic characterization reveals a novel picornavirus with two aphthovirus 2A-like sequences [J]. Journal of General Virology, 2014, 95:80-90.
[52]PHELPS N B D, MOR S K, ARMIEN A G, et al. Isolation and molecular characterization of a novel picornavirus from baitfish in the USA [J]. PLoS ONE, 2014, 9(2):e87593.
[53]REUTER G, PANKOVICS P, DELWART E, et al. A novel posavirus-related single-stranded RNA virus from fish (cyprinus carpio) [J]. Archives of Virology, 2015, 160(2):565-568.
[54]DILL J A, CAMUS A C, LEARY J H, et al. Distinct viral lineages from fish and amphibians reveal the complex evolutionary history of Hepadnaviruses [J]. Journal of Virology, 2016, 90(17):7920-7933.
[55]HAHN C M, IWANOWICZ L R, CORNMAN R S, et al. Characterization of a novel Hepadnavirus in the white Sucker (catostomus commersonii) from the Great Lakes region of the United States [J]. J Virol, 2015, 89(23):11801-11811.
[56]MOR S K, PHELPS N B D. Molecular detection of a novel totivirus from golden shiner (notemigonus crysoleucas) baitfish in the USA [J]. Archives of Virology, 2016, 161(8):2227-2234.
[57]THOMPSON L R, SANDERS J G, MCDONALD D, et al. A communal catalogue reveals Earth’s multiscale microbial diversity [J]. Nature, 2017, 551(7681):457-463.
[58]PHAM H T, YU Q, BOISVERT M, et al. A circo-like virus isolated from Penaeus monodon shrimps [J]. Genome Announc, 2014, 2(1):e01172.
[59]ZHOU J, ZHANG W, YAN S, et al. Diversity of virophages in metagenomic data sets [J]. Journal of Virology, 2013, 87(8):4225-4236.
[60]DAYARAM A, GOLDSTIEN S, ZAWAR-REZA P, et al. Novel ssDNA virus recovered from estuarine Mollusc (amphibola crenata) whose replication associated protein (Rep) shares similarities with Rep-like sequences of bacterial origin [J]. Journal of General Virology, 2013, 94:1104-1110.
[61]DAYARAM A, GOLDSTIEN S, ZAWAR-REZA P, et al. Identification of Starling Circovirus in an estuarine mollusc (amphibola crenata) in New Zealand using metagenomic approaches [J]. Genome Announc, 2013, 1(3):e00278.
[62]FAHSBENDER E, HEWSON I, ROSARIO K, et al. Discovery of a novel circular DNA virus in the Forbes sea star, Asterias forbesi [J]. Archives of Virology, 2015, 160(9):2349-2351.
[63]HEWSON I, BUTTON J B, GUDENKAUF B M, et al. Densovirus associated with sea-star wasting disease and mass mortality [J]. Proceedings of the National Academy of Sciences of the United States of America, 2014, 111(48):17278-17283.
[64]NG T F F, MANIRE C, BORROWMAN K, et al. Discovery of a novel single-stranded DNA virus from a sea Turtle fibropapilloma by using viral metagenomics [J]. Journal of Virology, 2009, 83(6):2500-2509.
[65]NG T F F, SUEDMEYER W K, WHEELER E, et al. Novel anellovirus discovered from a mortality event of captive California sea lions [J]. Journal of General Virology, 2009, 90:1256-1261.
[66]NG T F F, WHEELER E, GREIG D, et al. Metagenomic identification of a novel anellovirus in Pacific harbor seal (Phoca vitulina richardsii) lung samples and its detection in samples from multiple years [J]. Journal of General Virology, 2011, 92:1318-1323.
[67]SIEGERS J Y, VAN DE BILDT M W G, VAN ELK C E, et al. Genetic relatedness of dolphin rhabdovirus with fish rhabdoviruses [J]. Emerging Infectious Diseases, 2014, 20(6):1081-1082.
[68]KLUGE M, CAMPOS F S, TAVARES M, et al. Metagenomic survey of viral diversity obtained from feces of subantarctic and south American fur Seals [J]. PLoS ONE, 2016, 11(3):e0151921.
[69]LI Y, WANG H, NIE K, et al. VIP: an integrated pipeline for metagenomics of virus identification and discovery [J]. Scientific Reports, 2016, 6:23774.
[70]LIN H-H, LIAO Y C. drVM: a new tool for efficient genome assembly of known eukaryotic viruses from metagenomes [J]. Gigascience, 2017,doi:10.1093/gigascience/gix1003.
[71]TENGS T, RIMSTAD E. Emerging pathogens in the fish farming industry and sequencing based pathogen discovery [J]. Developmental and Comparative Immunology, 2017, 75:109-119.
[72]ZERBINO D R, BIRNEY E. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs [J]. Genome Research, 2008, 18(5):821-829.
[73]LI D, LIU C M, LUO R, et al. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph [J]. Bioinformatics, 2015, 31(10):1674-1676.
[74]LUO R B, LIU B H, XIE Y L, et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler [J]. Gigascience, 2012,doi:10.1186/2047-1217x-1181-1118.
[75]SCHMIEDER R, EDWARDS R. Quality control and preprocessing of metagenomic datasets [J]. Bioinformatics, 2011, 27(6):863-864.
[76]BOLGER A M, LOHSE M, USADEL B. Trimmomatic: a flexible trimmer for Illumina sequence data [J]. Bioinformatics, 2014, 30(15):2114-2120.
[77]PATEL R K, JAIN M. NGS QC Toolkit: A Toolkit for quality control of next generation sequencing data [J]. PLoS ONE, 2012, 7(2):e30619.
[78]BENGTSSON-PALME J, HARTMANN M, ERIKSSON K M, et al. metaxa2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data [J]. Molecular Ecology Resources, 2015, 15(6):1403-1414.
[79]CAPORASO J G, KUCZYNSKI J, STOMBAUGH J, et al. QIIME allows analysis of high-throughput community sequencing data [J]. Nature Methods, 2010, 7(5):335-336.
[80]RAMPELLI S, SOVERINI M, TURRONI S, et al. ViromeScan: a new tool for metagenomic viral community profiling [J]. Bmc Genomics, 2016,doi:10.1186/s12864-12016-12446-12863.
[81]NCBI. TNvg [EB/OL]. (2015-02-12)
[2018-02-25]. http://www.ncbinlmnihgov/genomes/GenomesGroupcgi?opt=virus&taxid=10239.
[82]ROTMISTROVSHY K. BMTagger [EB/OL]. (2012-09-02)
[2018-02-25]. ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/.
[83]REN J, AHLGREN N A, LU Y Y, et al. VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data [J]. Microbiome, 2017,doi:10.1186/s40168-40017-40283-40165.
[84]LIN J, KRAMNA L, AUTIO R, et al. Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples [J]. Bmc Genomics, 2017,doi:10.1186/s12864-12017-13721-12867.
[85]TITHI S S, AYLWARD F O, JENSEN R V, et al. Fast virome explorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data [J]. Peerj, 2018, 6:e4227.
[86]ROSARIO K, NILSSON C, LIM Y W, et al. Metagenomic analysis of viruses in reclaimed water [J]. Environmental Microbiology, 2009, 11(11):2806-2820.
[87]BIBBY K. Metagenomic identification of viral pathogens [J]. Trends Biotechnol, 2013, 31(5):11-15.

备注/Memo

备注/Memo:
收稿日期：2018-03-21基金项目：上海市自然科学基金项目(15ZR1420800)；上海海洋大学博士科研启动项目（A2-0203-00-100313）；上海海洋大学青年基金项目（A2-0203-00-100237）作者简介：彭司华( 1962-)，男，湖南古丈人，博士，副研究员，主要从事生物信息学、基因组学研究。(E-mail)shpeng@shou.edu.cn
更新日期/Last Update: 2019-02-27