Virus taxonomy in the age of metagenomics

被引：506

作者：

Simmonds, Peter ^{[2
]}

Adams, Mike J. ^{[3
]}

Benko, Maria ^{[4
]}

Breitbart, Mya ^{[5
]}

Brister, J. Rodney ^{[6
]}

Carstens, Eric B. ^{[7
]}

Davison, Andrew J. ^{[8
]}

Delwart, Eric ^{[9
,10
]}

Gorbalenya, Alexander E. ^{[11
,12
]}

Harrach, Balazs ^{[4
]}

Hull, Roger ^{[1
,13
]}

King, Andrew M. Q. ^{[14
]}

Koonin, Eugene V. ^{[6
]}

Krupovic, Mart ^{[15
]}

Kuhn, Jens H. ^{[16
]}

Lefkowitz, Elliot J. ^{[17
]}

Nibert, Max L. ^{[18
]}

Orton, Richard ^{[8
]}

Roossinck, Marilyn J. ^{[19
]}

Sabanadzovic, Sead ^{[20
]}

Sullivan, Matthew B. ^{[21
,22
]}

Suttle, Curtis A. ^{[23
,24
,25
,26
]}

Tesh, Robert B. ^{[27
,28
]}

van der Vlugt, Rene A. ^{[29
]}

Varsani, Arvind ^{[30
,31
]}

Zerbini, Murilo ^{[32
]}

机构：

[1] John Innes Ctr, Norwich, Norfolk, England

[2] Univ Oxford, Nuffield Dept Med, South Parks Rd, Oxford OX1 3SY, England

[3] 24 Woodland Way, Stevenage SG2 8BT, Herts, England

[4] Hungarian Acad Sci, Agr Res Ctr, Inst Vet Med Res, 21 Hungaria Krt, H-1143 Budapest, Hungary

[5] Univ S Florida, Coll Marine Sci, 140 7th Ave South, St Petersburg, FL 33701 USA

[6] NIH, Natl Ctr Biotechnol Informat, Natl Lib Med, Bethesda, MD 20894 USA

[7] Queens Univ, Dept Biomed & Mol Sci, 18 Stuart St, Kingston, ON K7L 3N6, Canada

[8] Univ Glasgow, Ctr Virus Res, UK Med Res Council MRC, Sir Michael Stoker Bldg,464 Bearsden Rd, Glasgow G61 1QH, Lanark, Scotland

[9] Blood Syst Res Inst, 270 Mason Ave, San Francisco, CA 94118 USA

[10] Univ Calif San Francisco, Dept Lab Med, 521 Parnassus Ave, San Francisco, CA 94118 USA

[11] Leiden Univ, Dept Med Microbiol, Med Ctr, POB 9600,E4-P,Room E4-72, NL-2300 RC Leiden, Netherlands

[12] Lomonosov Moscow State Univ, Fac Bioengn & Bioinformat, Moscow 119899, Russia

[13] 3 Portman Dr, Blandford Forum DT11 8HU, Dorset, England

[14] Pirbright Inst, Ash Rd, Woking GU24 0NF, Surrey, England

[15] Inst Pasteur, Dept Microbiol, 25 Rue Dr Roux, F-75015 Paris, France

[16] NIAID, Integrated Res Facil Ft Detrick IRF Frederick, B-8200 Res Plaza, Frederick, MD 21702 USA

[17] Univ Alabama Birmingham, Dept Microbiol, Bevill Biomed Res Bldg BBRB Suite 276, Birmingham, AL 35294 USA

[18] Harvard Med Sch, Dept Microbiol & Immunobiol, 77 Ave Louis Pasteur, Boston, MA 02115 USA

[19] Penn State Univ, Ctr Infect Dis Dynam, Dept Plant Pathol & Environm Microbiol, University Pk, PA 16802 USA

[20] Mississippi State Univ, Dept Biochem Mol Biol Entomol & Plant Pathol, 100 Old Highway 12 Mail Stop 9775, Mississippi State, MS 39762 USA

[21] Ohio State Univ, Dept Microbiol, Columbus, OH 43210 USA

[22] Ohio State Univ, Dept Civil Environm & Geodet Engn, Columbus, OH 43210 USA

[23] Univ British Columbia, Dept Earth Ocean & Atmospher Sci, Vancouver, BC V6T 1Z4, Canada

[24] Univ British Columbia, Dept Microbiol & Immunol, Vancouver, BC V6T 1Z4, Canada

[25] Univ British Columbia, Dept Bot, Vancouver, BC V6T 1Z4, Canada

[26] CIFAR, 180 Dundas St West, Toronto, ON M5G 1Z8, Canada

[27] Univ Texas Med Branch, Dept Pathol, 301 Univ Blvd, Galveston, TX 77555 USA

[28] Univ Texas Med Branch, Ctr Biodef & Emerging Infect Dis, 301 Univ Blvd, Galveston, TX 77555 USA

[29] Wageningen Univ & Res Ctr WUR PRI, Wageningen Plant Res, Droevendaalsesteeg 1, NL-6708 PB Wageningen, Netherlands

[30] Arizona State Univ, Biodesign Inst, Ctr Fundamental & Appl Microbiom, 1001 South McAllister Ave, Tempe, AZ 85281 USA

[31] Arizona State Univ, Sch Life Sci, 1001 South McAllister Ave, Tempe, AZ 85281 USA

[32] Univ Fed Vicosa, Dept Fitopatol BIOAGRO, BR-36570900 Vicosa, MG, Brazil

来源：

NATURE REVIEWS MICROBIOLOGY | 2017年 / 15卷 / 03期

基金：

美国国家卫生研究院; 匈牙利科学研究基金会; 美国国家科学基金会; 英国惠康基金;

关键词：

NON-A; DIVERSITY; EVOLUTION; BIODIVERSITY; FAMILY; TREE; INVERTEBRATES; VIROPHAGES; CANDIDATUS; ANIMALS;

D O I：

10.1038/nrmicro.2016.177

中图分类号：

Q93 [微生物学];

学科分类号：

071005 ; 100705 ;

摘要：

The number and diversity of viral sequences that are identified in metagenomic data far exceeds that of experimentally characterized virus isolates. In a recent workshop, a panel of experts discussed the proposal that, with appropriate quality control, viruses that are known only from metagenomic data can, and should be, incorporated into the official classification scheme of the International Committee on Taxonomy of Viruses (ICTV). Although a taxonomy that is based on metagenomic sequence data alone represents a substantial departure from the traditional reliance on phenotypic properties, the development of a robust framework for sequence-based virus taxonomy is indispensable for the comprehensive characterization of the global virome. In this Consensus Statement article, we consider the rationale for why metagenomic sequence data should, and how it can, be incorporated into the ICTV taxonomy, and present proposals that have been endorsed by the Executive Committee of the ICTV.

引用

页码：161 / 168

页数：8

共 71 条

[11] The Characterization of RNA Viruses in Tropical Seawater Using Targeted PCR and Metagenomics [J].

Culley, Alexander I. ;

Mueller, Jaclyn A. ;

Belcaid, Madhi ;

Wood-Charlson, Elisha M. ;

Poisson, Guylaine ;

Steward, Grieg F. .

MBIO, 2014, 5 (03)

[12] Diverse circular replication-associated protein encoding viruses circulating in invertebrates within a lake ecosystem [J].

Dayaram, Anisha ;

Galatowitsch, Mark L. ;

Argueello-Astorga, Gerardo R. ;

van Bysterveldt, Katherine ;

Kraberger, Simona ;

Stainton, Daisy ;

Harding, Jon S. ;

Roumagnac, Philippe ;

Martin, Darren P. ;

Lefeuvre, Pierre ;

Varsani, Arvind .

INFECTION GENETICS AND EVOLUTION, 2016, 39 :304-316

[13] Diverse small circular DNA viruses circulating amongst estuarine molluscs [J].

Dayaram, Anisha ;

Goldstien, Sharyn ;

Argueello-Astorga, Gerardo R. ;

Zawar-Reza, Peyman ;

Gomez, Christopher ;

Harding, Jon S. ;

Varsani, Arvind .

INFECTION GENETICS AND EVOLUTION, 2015, 31 :284-295

[14] A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes [J].

Dutilh, Bas E. ;

Cassman, Noriko ;

McNair, Katelyn ;

Sanchez, Savannah E. ;

Silva, Genivaldo G. Z. ;

Boling, Lance ;

Barr, Jeremy J. ;

Speth, Daan R. ;

Seguritan, Victor ;

Aziz, Ramy K. ;

Felts, Ben ;

Dinsdale, Elizabeth A. ;

Mokili, John L. ;

Edwards, Robert A. .

NATURE COMMUNICATIONS, 2014, 5

[15] Viral metagenomics [J].

Edwards, RA ;

Rohwer, F .

NATURE REVIEWS MICROBIOLOGY, 2005, 3 (06) :504-510

[16] Bacteriophages and their genomes [J].

Hatfull, Graham F. ;

Hendrix, Roger W. .

CURRENT OPINION IN VIROLOGY, 2011, 1 (04) :298-303

[17] The Amsterdam Declaration on Fungal Nomenclature [J].

Hawksworth, David L. ;

Crous, Pedro W. ;

Redhead, Scott A. ;

Reynolds, Don R. ;

Samson, Robert A. ;

Seifert, Keith A. ;

Taylor, John W. ;

Wingfield, Michael J. ;

Abaci, Ozlem ;

Aime, Catherine ;

Asan, Ahmet ;

Bai, Feng-Yan ;

de Beer, Z. Wilhelm ;

Begerow, Dominik ;

Berikten, Derya ;

Boekhout, Teun ;

Buchanan, Peter K. ;

Burgess, Treena ;

Buzina, Walter ;

Cai, Lei ;

Cannon, Paul F. ;

Crane, J. Leland ;

Damm, Ulrike ;

Daniel, Heide-Marie ;

van Diepeningen, Anne D. ;

Druzhinina, Irina ;

Dyer, Paul S. ;

Eberhardt, Ursula ;

Fell, Jack W. ;

Frisvad, Jens C. ;

Geiser, David M. ;

Geml, Jozsef ;

Glienke, Chirlei ;

Grafenhan, Tom ;

Groenewald, Johannes Z. ;

Groenewald, Marizeth ;

de Gruyter, Johannes ;

Gueho-Kellermann, Eveline ;

Guo, Liang-Dong ;

Hibbett, David S. ;

Hong, Seung-Beom ;

de Hoog, G. Sybren ;

Houbraken, Jos ;

Huhndorf, Sabine M. ;

Hyde, Kevin D. ;

Ismail, Ahmed ;

Johnston, Peter R. ;

Kadaifciler, Duygu G. ;

Kirk, Paul M. ;

Koljalg, Urmas .

IMA FUNGUS, 2011, 2 (01) :105-112

[18] The changing landscape of microbial biodiversity exploration and its implications for systematics [J].

Hedlund, Brian P. ;

Dodsworth, Jeremy A. ;

Staley, James T. .

SYSTEMATIC AND APPLIED MICROBIOLOGY, 2015, 38 (04) :231-236

[19] Fungal systematics: is a new age of enlightenment at hand? [J].

Hibbett, David S. ;

Taylor, John W. .

NATURE REVIEWS MICROBIOLOGY, 2013, 11 (02) :129-133

[20] What Does Virus Evolution Tell Us about Virus Origins? [J].

Holmes, Edward C. .

JOURNAL OF VIROLOGY, 2011, 85 (11) :5247-5251

← 1 2 3 4 5 6 7 8 →