Consensus statement: Virus taxonomy in the age of metagenomics

[1]  George M Garrity,et al.  International Code of Nomenclature of Prokaryotes. , 2015, International journal of systematic and evolutionary microbiology.

[2]  Ken Youens-Clark,et al.  iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure , 2016, The ISME Journal.

[3]  M. H. Regenmortel.  Classes, taxa and categories in hierarchical virus classification: a review of current debates on definitions and names of virus species , 2016 .

[4]  Peer Bork,et al.  Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses , 2016, Nature.

[5]  D. Coray,et al.  Circular replication-associated protein encoding DNA viruses identified in the faecal matter of various animals in New Zealand. , 2016, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[6]  Georgios A. Pavlopoulos,et al.  Uncovering Earth’s virome , 2016, Nature.

[7]  R. L. Harrison,et al.  Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2016) , 2016, Archives of Virology.

[8]  M. Krupovic,et al.  Genomoviridae: a new family of widespread single-stranded DNA viruses , 2016, Archives of Virology.

[9]  M. Krupovic,et al.  Genomoviridae: a new family of widespread single-stranded DNA viruses , 2016, Archives of Virology.

[10]  P. Roumagnac,et al.  Diverse circular replication-associated protein encoding viruses circulating in invertebrates within a lake ecosystem. , 2016, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[11]  M. Breitbart,et al.  Single-stranded DNA phages: from early molecular biology tools to recent revolutions in environmental microbiology. , 2016, FEMS microbiology letters.

[12]  Joshua S Weitz,et al.  Re-examination of the relationship between marine virus and microbial cell abundances , 2016, Nature Microbiology.

[13]  E. Koonin,et al.  A novel group of diverse Polinton-like viruses discovered by metagenome analysis , 2015, BMC Biology.

[14]  C. Suttle,et al.  Biogeography of Viruses in the Sea. , 2015, Annual review of virology.

[15]  Nikos Vasilakis,et al.  Divergent Viruses Discovered in Arthropods and Vertebrates Revise the Evolutionary History of the Flaviviridae and Related Viruses , 2015, Journal of Virology.

[16]  Taigang Liu,et al.  Four novel algal virus genomes discovered from Yellowstone Lake metagenomes , 2015, Scientific Reports.

[17]  Tanja Woyke,et al.  Viral dark matter and virus–host interactions resolved from publicly available microbial genomes , 2015, eLife.

[18]  Mya Breitbart,et al.  Novel circular single-stranded DNA viruses identified in marine invertebrates reveal high sequence diversity and consistent predicted intrinsic disorder patterns within putative structural proteins , 2015, Front. Microbiol..

[19]  P. Simmonds,et al.  Methods for virus classification and the challenge of incorporating metagenomic sequence data. , 2015, The Journal of general virology.

[20]  J. T. Staley,et al.  The changing landscape of microbial biodiversity exploration and its implications for systematics. , 2015, Systematic and applied microbiology.

[21]  Ramon Rosselló-Móra,et al.  Classifying the uncultivated microbial majority: A place for metagenomic data in the Candidatus proposal. , 2015, Systematic and applied microbiology.

[22]  P. Bork,et al.  Patterns and ecological drivers of ocean viral communities , 2015, Science.

[23]  M. Roossinck.  Plants, viruses and the environment: Ecology and mutualism. , 2015, Virology.

[24]  E. Koonin,et al.  A new family of hybrid virophages from an animal gut metagenome , 2015, Biology Direct.

[25]  M. Roossinck.  Move Over, Bacteria! Viruses Make Their Mark as Mutualistic Microbial Symbionts , 2015, Journal of Virology.

[26]  S. Hallam,et al.  Previously unknown evolutionary groups dominate the ssDNA gokushoviruses in oxic and anoxic waters of a coastal marine environment , 2015, Front. Microbiol..

[27]  A. Varsani,et al.  Characterisation of a diverse range of circular replication-associated protein encoding DNA viruses recovered from a sewage treatment oxidation pond. , 2015, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[28]  Peyman Zawar-Reza,et al.  Diverse small circular DNA viruses circulating amongst estuarine molluscs. , 2015, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[29]  M. Shi,et al.  Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses , 2015, eLife.

[30]  N. J. Knowles,et al.  Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2015) , 2009, Archives of Virology.

[31]  Evelien M. Adriaenssens,et al.  High-Level Diversity of Tailed Phages, Eukaryote-Associated Viruses, and Virophage-Like Elements in the Metaviromes of Antarctic Soils , 2014, Applied and Environmental Microbiology.

[32]  R. Edwards,et al.  A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes , 2014, Nature Communications.

[33]  G. Steward,et al.  The Characterization of RNA Viruses in Tropical Seawater Using Targeted PCR and Metagenomics , 2014, mBio.

[34]  R. Andino,et al.  Library preparation for highly accurate population sequencing of RNA viruses , 2014, Nature Protocols.

[35]  M. Breitbart,et al.  Diversity of environmental single-stranded DNA phages revealed by PCR amplification of the partial major capsid protein , 2014, The ISME Journal.

[36]  C. Suttle.  Viruses: unlocking the greatest biodiversity on Earth. , 2013, Genome.

[37]  J. Kuhn,et al.  Nonhuman Transferrin Receptor 1 Is an Efficient Cell Entry Receptor for Ocozocoautla de Espinosa Virus , 2013, Journal of Virology.

[38]  E. Koonin,et al.  A virocentric perspective on the evolution of life , 2013, Current Opinion in Virology.

[39]  Curtis A Suttle,et al.  Previously unknown and highly divergent ssDNA viruses populate the oceans , 2013, The ISME Journal.

[40]  E. Koonin,et al.  “Megavirales”, a proposed new order for eukaryotic nucleocytoplasmic large DNA viruses , 2013, Archives of Virology.

[41]  Matthew B. Sullivan,et al.  The Pacific Ocean Virome (POV): A Marine Viral Metagenomic Dataset and Associated Protein Clusters for Quantitative Viral Ecology , 2013, PloS one.

[42]  Ying-jie Pan,et al.  Diversity of Virophages in Metagenomic Data Sets , 2013, Journal of Virology.

[43]  David S. Hibbett,et al.  Fungal systematics: is a new age of enlightenment at hand? , 2013, Nature Reviews Microbiology.

[44]  G. Steward,et al.  Are we missing half of the viruses in the ocean? , 2012, The ISME Journal.

[45]  M. Roossinck,et al.  Plant virus metagenomics: biodiversity and ecology. , 2012, Annual review of genetics.

[46]  Axel Poulet,et al.  Evolution and Diversity of the Microviridae Viral Family through a Collection of 81 New Complete Genomes Assembled from Virome Reads , 2012, PloS one.

[47]  M. Breitbart,et al.  A field guide to eukaryotic circular single-stranded DNA viruses: insights gained from metagenomics , 2012, Archives of Virology.

[48]  John L. Spouge,et al.  Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi , 2012, Proceedings of the National Academy of Sciences.

[49]  A. Gorbalenya,et al.  Partitioning the Genetic Diversity of a Virus Family: Approach and Evaluation through a Case Study of Picornaviruses , 2012, Journal of Virology.

[50]  F. Rohwer,et al.  Metagenomics and future perspectives in virus discovery , 2012, Current Opinion in Virology.

[51]  N. Pace,et al.  Phylogeny and beyond: Scientific, historical, and conceptual significance of the first tree of life , 2012, Proceedings of the National Academy of Sciences.

[52]  Graham F Hatfull,et al.  Bacteriophages and their genomes. , 2011, Current opinion in virology.

[53]  M. Breitbart,et al.  Exploring the viral world through metagenomics. , 2011, Current opinion in virology.

[54]  Maureen A. O’Malley,et al.  How stands the Tree of Life a century and a half after The Origin? , 2011, Biology Direct.

[55]  Seung-Beom Hong,et al.  The Amsterdam Declaration on Fungal Nomenclature , 2011, IMA fungus.

[56]  E. Holmes.  What Does Virus Evolution Tell Us about Virus Origins? , 2011, Journal of Virology.

[57]  Matthew Z. DeMaere,et al.  Virophage control of antarctic algal host–virus dynamics , 2011, Proceedings of the National Academy of Sciences.

[58]  P. Simmonds,et al.  Use of Nucleotide Composition Analysis To Infer Hosts for Three Novel Picorna-Like Viruses , 2010, Journal of Virology.

[59]  Paramvir S. Dehal,et al.  FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.

[60]  N. Gross-Camp,et al.  Multiple Diverse Circoviruses Infect Farm Animals and Are Commonly Found in Human and Chimpanzee Feces , 2009, Journal of Virology.

[61]  E. Koonin,et al.  The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups , 2008, Nature Reviews Microbiology.

[62]  Gipsi Lima-Mendez,et al.  Reticulate representation of evolutionary and functional relationships between phage genomes. , 2008, Molecular biology and evolution.

[63]  Florent E. Angly,et al.  The Marine Viromes of Four Oceanic Regions , 2006, PLoS biology.

[64]  E. Koonin,et al.  The ancient Virus World and evolution of cells , 2006, Biology Direct.

[65]  R. Edwards,et al.  Viral metagenomics , 2005, Nature Reviews Microbiology.

[66]  P. Salamon,et al.  Diversity and population structure of a near–shore marine–sediment viral community , 2004, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[67]  R. Edwards,et al.  The Phage Proteomic Tree: a Genome-Based Taxonomy for Phage , 2002, Journal of bacteriology.

[68]  K. Katoh,et al.  MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. , 2002, Nucleic acids research.

[69]  David H. L. Bishop,et al.  The International Committee on Taxonomy of Viruses , 1995 .

[70]  E. Stackebrandt,et al.  Taxonomic note: implementation of the provisional status Candidatus for incompletely described procaryotes. , 1995, International journal of systematic bacteriology.

[71]  J. Maniloff,et al.  Virus taxonomy : eighth report of the International Committee on Taxonomy of Viruses , 2005 .

[72]  H J Alter,et al.  An assay for circulating antibodies to a major etiologic virus of human non-A, non-B hepatitis. , 1990, Science.

[73]  M. Houghton,et al.  Isolation of a cDNA clone derived from a blood-borne non-A, non-B viral hepatitis genome. , 1989, Science.

[74]  C. Woese,et al.  Bacterial evolution , 1987, Microbiological reviews.