Literature DB >> 28134265

Consensus statement: Virus taxonomy in the age of metagenomics.

Peter Simmonds1, Mike J Adams, Mária Benkő2, Mya Breitbart3, J Rodney Brister4, Eric B Carstens5, Andrew J Davison6, Eric Delwart7,8, Alexander E Gorbalenya9,10, Balázs Harrach2, Roger Hull11, Andrew M Q King12, Eugene V Koonin4, Mart Krupovic13, Jens H Kuhn14, Elliot J Lefkowitz15, Max L Nibert16, Richard Orton6, Marilyn J Roossinck17, Sead Sabanadzovic18, Matthew B Sullivan19, Curtis A Suttle20,21, Robert B Tesh22, René A van der Vlugt23, Arvind Varsani24, F Murilo Zerbini25.   

Abstract

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.

Mesh:

Year:  2017        PMID: 28134265     DOI: 10.1038/nrmicro.2016.177

Source DB:  PubMed          Journal:  Nat Rev Microbiol        ISSN: 1740-1526            Impact factor:   60.633


  69 in total

1.  Partitioning the genetic diversity of a virus family: approach and evaluation through a case study of picornaviruses.

Authors:  Chris Lauber; Alexander E Gorbalenya
Journal:  J Virol       Date:  2012-01-25       Impact factor: 5.103

Review 2.  Single-stranded DNA phages: from early molecular biology tools to recent revolutions in environmental microbiology.

Authors:  Anna J Székely; Mya Breitbart
Journal:  FEMS Microbiol Lett       Date:  2016-02-05       Impact factor: 2.742

3.  Previously unknown and highly divergent ssDNA viruses populate the oceans.

Authors:  Jessica M Labonté; Curtis A Suttle
Journal:  ISME J       Date:  2013-07-11       Impact factor: 10.302

4.  Virophage control of antarctic algal host-virus dynamics.

Authors:  Sheree Yau; Federico M Lauro; Matthew Z DeMaere; Mark V Brown; Torsten Thomas; Mark J Raftery; Cynthia Andrews-Pfannkoch; Matthew Lewis; Jeffrey M Hoffman; John A Gibson; Ricardo Cavicchioli
Journal:  Proc Natl Acad Sci U S A       Date:  2011-03-28       Impact factor: 11.205

5.  FastTree 2--approximately maximum-likelihood trees for large alignments.

Authors:  Morgan N Price; Paramvir S Dehal; Adam P Arkin
Journal:  PLoS One       Date:  2010-03-10       Impact factor: 3.240

6.  Uncovering Earth's virome.

Authors:  David Paez-Espino; Emiley A Eloe-Fadrosh; Georgios A Pavlopoulos; Alex D Thomas; Marcel Huntemann; Natalia Mikhailova; Edward Rubin; Natalia N Ivanova; Nikos C Kyrpides
Journal:  Nature       Date:  2016-08-17       Impact factor: 49.962

7.  Circular replication-associated protein encoding DNA viruses identified in the faecal matter of various animals in New Zealand.

Authors:  Olivia Steel; Simona Kraberger; Alyssa Sikorski; Laura M Young; Ryan J Catchpole; Aaron J Stevens; Jenny J Ladley; Dorien S Coray; Daisy Stainton; Anisha Dayaram; Laurel Julian; Katherine van Bysterveldt; Arvind Varsani
Journal:  Infect Genet Evol       Date:  2016-05-20       Impact factor: 3.342

8.  Genomoviridae: a new family of widespread single-stranded DNA viruses.

Authors:  Mart Krupovic; Said A Ghabrial; Daohong Jiang; Arvind Varsani
Journal:  Arch Virol       Date:  2016-06-24       Impact factor: 2.574

9.  Nonhuman transferrin receptor 1 is an efficient cell entry receptor for Ocozocoautla de Espinosa virus.

Authors:  Yíngyún Caì; Shuiqìng Yú; Steven Mazur; Lián Dong; Krisztina Janosko; Téngfei Zhang; Marcel A Müller; Lisa E Hensley; Sina Bavari; Peter B Jahrling; Sheli R Radoshitzky; Jens H Kuhn
Journal:  J Virol       Date:  2013-10-09       Impact factor: 5.103

10.  Divergent Viruses Discovered in Arthropods and Vertebrates Revise the Evolutionary History of the Flaviviridae and Related Viruses.

Authors:  Mang Shi; Xian-Dan Lin; Nikos Vasilakis; Jun-Hua Tian; Ci-Xiu Li; Liang-Jun Chen; Gillian Eastwood; Xiu-Nian Diao; Ming-Hui Chen; Xiao Chen; Xin-Cheng Qin; Steven G Widen; Thomas G Wood; Robert B Tesh; Jianguo Xu; Edward C Holmes; Yong-Zhen Zhang
Journal:  J Virol       Date:  2015-10-21       Impact factor: 5.103

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  209 in total

1.  New virus isolates from Italian hydrothermal environments underscore the biogeographic pattern in archaeal virus communities.

Authors:  Diana P Baquero; Patrizia Contursi; Monica Piochi; Simonetta Bartolucci; Ying Liu; Virginija Cvirkaite-Krupovic; David Prangishvili; Mart Krupovic
Journal:  ISME J       Date:  2020-04-22       Impact factor: 10.302

2.  The 13th International Double-Stranded RNA Virus Symposium, Houffalize, Belgium, 24 to 28 September 2018.

Authors:  Ulrich Desselberger
Journal:  J Virol       Date:  2019-02-05       Impact factor: 5.103

Review 3.  ssDNA viruses: key players in global virome.

Authors:  V G Malathi; P Renuka Devi
Journal:  Virusdisease       Date:  2019-04-19

Review 4.  Metaviromics coupled with phage-host identification to open the viral 'black box'.

Authors:  Kira Moon; Jang-Cheon Cho
Journal:  J Microbiol       Date:  2021-02-23       Impact factor: 3.422

5.  Multiple origins of viral capsid proteins from cellular ancestors.

Authors:  Mart Krupovic; Eugene V Koonin
Journal:  Proc Natl Acad Sci U S A       Date:  2017-03-06       Impact factor: 11.205

6.  Biological species in the viral world.

Authors:  Louis-Marie Bobay; Howard Ochman
Journal:  Proc Natl Acad Sci U S A       Date:  2018-05-21       Impact factor: 11.205

7.  Diversity of Active Viral Infections within the Sphagnum Microbiome.

Authors:  Joshua M A Stough; Max Kolton; Joel E Kostka; David J Weston; Dale A Pelletier; Steven W Wilhelm
Journal:  Appl Environ Microbiol       Date:  2018-11-15       Impact factor: 4.792

8.  Genomes of viral isolates derived from different mosquitos species.

Authors:  Mohammadreza Sadeghi; Vsevolod Popov; Hilda Guzman; Tung Gia Phan; Nikos Vasilakis; Robert Tesh; Eric Delwart
Journal:  Virus Res       Date:  2017-09-21       Impact factor: 3.303

9.  A Needle in A Haystack: Tracing Bivalve-Associated Viruses in High-Throughput Transcriptomic Data.

Authors:  Umberto Rosani; Maxwell Shapiro; Paola Venier; Bassem Allam
Journal:  Viruses       Date:  2019-03-01       Impact factor: 5.048

10.  Problems of classification in the family Paramyxoviridae.

Authors:  Bert Rima; Peter Collins; Andrew Easton; Ron Fouchier; Gael Kurath; Robert A Lamb; Benhur Lee; Andrea Maisner; Paul Rota; Lin-Fa Wang
Journal:  Arch Virol       Date:  2018-01-25       Impact factor: 2.574

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