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Erschienen in: Archives of Virology 9/2016

24.06.2016 | Virology Division News

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

verfasst von: Mart Krupovic, Said A. Ghabrial, Daohong Jiang, Arvind Varsani

Erschienen in: Archives of Virology | Ausgabe 9/2016

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Abstract

Here, we introduce a new family of eukaryote-infecting single-stranded (ss) DNA viruses that was created recently by the International Committee on Taxonomy of Viruses (ICTV). The family, named Genomoviridae, contains a single genus, Gemycircularvirus, which currently has one recognized virus species, Sclerotinia gemycircularvirus 1. Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1 (SsHADV-1) is currently the sole representative isolate of the family; however, a great number of SsHADV-1-like ssDNA virus genomes has been sequenced from various environmental, plant- and animal-associated samples, indicating that members of family Genomoviridae are widespread and abundant in the environment.
Literatur
1.
Zurück zum Zitat Adams MJ, Lefkowitz EJ, King AMQ, Harrach B, Harrison RL, Knowles NJ, Kropinski AM, Krupovic M, Kuhn JH, Mushegian AR, Nibert M, Sabanadzovic S, Sanfaçon H, Siddell SG, Simmonds P, Varsani A, Zerbini FM, Gorbalenya AE, Davison AJ (2016) Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2016). Arch Virol (submitted) Adams MJ, Lefkowitz EJ, King AMQ, Harrach B, Harrison RL, Knowles NJ, Kropinski AM, Krupovic M, Kuhn JH, Mushegian AR, Nibert M, Sabanadzovic S, Sanfaçon H, Siddell SG, Simmonds P, Varsani A, Zerbini FM, Gorbalenya AE, Davison AJ (2016) Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2016). Arch Virol (submitted)
2.
3.
Zurück zum Zitat Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T (2009) trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25:1972–1973CrossRefPubMedPubMedCentral Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T (2009) trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25:1972–1973CrossRefPubMedPubMedCentral
4.
Zurück zum Zitat Conceicao-Neto N, Zeller M, Heylen E, Lefrere H, Mesquita JR, Matthijnssens J (2015) Fecal virome analysis of three carnivores reveals a novel nodavirus and multiple gemycircularviruses. Virol J 12:79CrossRefPubMedPubMedCentral Conceicao-Neto N, Zeller M, Heylen E, Lefrere H, Mesquita JR, Matthijnssens J (2015) Fecal virome analysis of three carnivores reveals a novel nodavirus and multiple gemycircularviruses. Virol J 12:79CrossRefPubMedPubMedCentral
5.
Zurück zum Zitat Dayaram A, Opong A, Jaschke A, Hadfield J, Baschiera M, Dobson RC, Offei SK, Shepherd DN, Martin DP, Varsani A (2012) Molecular characterisation of a novel cassava associated circular ssDNA virus. Virus Res 166:130–135CrossRefPubMed Dayaram A, Opong A, Jaschke A, Hadfield J, Baschiera M, Dobson RC, Offei SK, Shepherd DN, Martin DP, Varsani A (2012) Molecular characterisation of a novel cassava associated circular ssDNA virus. Virus Res 166:130–135CrossRefPubMed
6.
Zurück zum Zitat Dayaram A, Potter KA, Pailes R, Marinov M, Rosenstein DD, Varsani A (2015) Identification of diverse circular single-stranded DNA viruses in adult dragonflies and damselflies (Insecta: Odonata) of Arizona and Oklahoma, USA. Infect Genet Evol 30:278–287CrossRefPubMed Dayaram A, Potter KA, Pailes R, Marinov M, Rosenstein DD, Varsani A (2015) Identification of diverse circular single-stranded DNA viruses in adult dragonflies and damselflies (Insecta: Odonata) of Arizona and Oklahoma, USA. Infect Genet Evol 30:278–287CrossRefPubMed
7.
Zurück zum Zitat Du Z, Tang Y, Zhang S, She X, Lan G, Varsani A, He Z (2014) Identification and molecular characterization of a single-stranded circular DNA virus with similarities to Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1. Arch Virol 159:1527–1531CrossRefPubMed Du Z, Tang Y, Zhang S, She X, Lan G, Varsani A, He Z (2014) Identification and molecular characterization of a single-stranded circular DNA virus with similarities to Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1. Arch Virol 159:1527–1531CrossRefPubMed
8.
Zurück zum Zitat Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59:307–321CrossRefPubMed Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59:307–321CrossRefPubMed
9.
Zurück zum Zitat Hanna ZR, Runckel C, Fuchs J, DeRisi JL, Mindell DP, Van Hemert C, Handel CM, Dumbacher JP (2015) Isolation of a complete circular virus genome sequence from an Alaskan black-capped chickadee (Poecile atricapillus) gastrointestinal tract sample. Genome Announc 3:01081-01015CrossRef Hanna ZR, Runckel C, Fuchs J, DeRisi JL, Mindell DP, Van Hemert C, Handel CM, Dumbacher JP (2015) Isolation of a complete circular virus genome sequence from an Alaskan black-capped chickadee (Poecile atricapillus) gastrointestinal tract sample. Genome Announc 3:01081-01015CrossRef
10.
Zurück zum Zitat Jiang D, Fu Y, Guoqing L, Ghabrial SA (2013) Viruses of the plant pathogenic fungus Sclerotinia sclerotiorum. Adv Virus Res 86:215–248CrossRefPubMed Jiang D, Fu Y, Guoqing L, Ghabrial SA (2013) Viruses of the plant pathogenic fungus Sclerotinia sclerotiorum. Adv Virus Res 86:215–248CrossRefPubMed
11.
Zurück zum Zitat Kraberger S, Stainton D, Dayaram A, Zawar-Reza P, Gomez C, Harding JS, Varsani A (2013) Discovery of Sclerotinia sclerotiorum hypovirulence-associated virus-1 in urban river sediments of Heathcote and Styx Rivers in Christchurch City, New Zealand. Genome Announc 1:e00559-00513CrossRef Kraberger S, Stainton D, Dayaram A, Zawar-Reza P, Gomez C, Harding JS, Varsani A (2013) Discovery of Sclerotinia sclerotiorum hypovirulence-associated virus-1 in urban river sediments of Heathcote and Styx Rivers in Christchurch City, New Zealand. Genome Announc 1:e00559-00513CrossRef
12.
Zurück zum Zitat Kraberger S, Arguello-Astorga GR, Greenfield LG, Galilee C, Law D, Martin DP, Varsani A (2015) Characterisation of a diverse range of circular replication-associated protein encoding DNA viruses recovered from a sewage treatment oxidation pond. Infect Genet Evol 31:73–86CrossRefPubMed Kraberger S, Arguello-Astorga GR, Greenfield LG, Galilee C, Law D, Martin DP, Varsani A (2015) Characterisation of a diverse range of circular replication-associated protein encoding DNA viruses recovered from a sewage treatment oxidation pond. Infect Genet Evol 31:73–86CrossRefPubMed
13.
Zurück zum Zitat Kraberger S, Farkas K, Bernardo P, Booker C, Arguello-Astorga GR, Mesleard F, Martin DP, Roumagnac P, Varsani A (2015) Identification of novel Bromus- and Trifolium-associated circular DNA viruses. Arch Virol 160:1303–1311CrossRefPubMed Kraberger S, Farkas K, Bernardo P, Booker C, Arguello-Astorga GR, Mesleard F, Martin DP, Roumagnac P, Varsani A (2015) Identification of novel Bromus- and Trifolium-associated circular DNA viruses. Arch Virol 160:1303–1311CrossRefPubMed
14.
Zurück zum Zitat Krupovic M (2013) Networks of evolutionary interactions underlying the polyphyletic origin of ssDNA viruses. Curr Opin Virol 3:578–586CrossRefPubMed Krupovic M (2013) Networks of evolutionary interactions underlying the polyphyletic origin of ssDNA viruses. Curr Opin Virol 3:578–586CrossRefPubMed
15.
Zurück zum Zitat Krupovic M, Forterre P (2015) Single-stranded DNA viruses employ a variety of mechanisms for integration into host genomes. Ann N Y Acad Sci 1341:41–53CrossRefPubMed Krupovic M, Forterre P (2015) Single-stranded DNA viruses employ a variety of mechanisms for integration into host genomes. Ann N Y Acad Sci 1341:41–53CrossRefPubMed
16.
Zurück zum Zitat Lamberto I, Gunst K, Muller H, Zur Hausen H, de Villiers EM (2014) Mycovirus-like DNA virus sequences from cattle serum and human brain and serum samples from multiple sclerosis patients. Genome Announc 2:e00848-00814CrossRef Lamberto I, Gunst K, Muller H, Zur Hausen H, de Villiers EM (2014) Mycovirus-like DNA virus sequences from cattle serum and human brain and serum samples from multiple sclerosis patients. Genome Announc 2:e00848-00814CrossRef
17.
Zurück zum Zitat Li W, Gu Y, Shen Q, Yang S, Wang X, Wan Y, Zhang W (2015) A novel gemycircularvirus from experimental rats. Virus Genes 51:302–305CrossRefPubMed Li W, Gu Y, Shen Q, Yang S, Wang X, Wan Y, Zhang W (2015) A novel gemycircularvirus from experimental rats. Virus Genes 51:302–305CrossRefPubMed
18.
Zurück zum Zitat Male MF, Kami V, Kraberger S, Varsani A (2015) Genome sequences of Poaceae-associated Gemycircularviruses from the Pacific Ocean Island of Tonga. Genome Announc 3:e01144-01115CrossRef Male MF, Kami V, Kraberger S, Varsani A (2015) Genome sequences of Poaceae-associated Gemycircularviruses from the Pacific Ocean Island of Tonga. Genome Announc 3:e01144-01115CrossRef
19.
Zurück zum Zitat Male MF, Kraberger S, Stainton D, Kami V, Varsani A (2016) Cycloviruses, gemycircularviruses and other novel replication-associated protein encoding circular viruses in Pacific flying fox (Pteropus tonganus) faeces. Infect Genet Evol 39:279–292CrossRefPubMed Male MF, Kraberger S, Stainton D, Kami V, Varsani A (2016) Cycloviruses, gemycircularviruses and other novel replication-associated protein encoding circular viruses in Pacific flying fox (Pteropus tonganus) faeces. Infect Genet Evol 39:279–292CrossRefPubMed
20.
Zurück zum Zitat Marzano SL, Domier L (2016) Novel mycoviruses discovered from metatranscriptomics survey of soybean phyllosphere phytobiomes. Virus Res 213:332–342CrossRefPubMed Marzano SL, Domier L (2016) Novel mycoviruses discovered from metatranscriptomics survey of soybean phyllosphere phytobiomes. Virus Res 213:332–342CrossRefPubMed
21.
Zurück zum Zitat Ng TF, Chen LF, Zhou Y, Shapiro B, Stiller M, Heintzman PD, Varsani A, Kondov NO, Wong W, Deng X, Andrews TD, Moorman BJ, Meulendyk T, MacKay G, Gilbertson RL, Delwart E (2014) Preservation of viral genomes in 700-y-old caribou feces from a subarctic ice patch. Proc Natl Acad Sci USA 111:16842–16847CrossRefPubMedPubMedCentral Ng TF, Chen LF, Zhou Y, Shapiro B, Stiller M, Heintzman PD, Varsani A, Kondov NO, Wong W, Deng X, Andrews TD, Moorman BJ, Meulendyk T, MacKay G, Gilbertson RL, Delwart E (2014) Preservation of viral genomes in 700-y-old caribou feces from a subarctic ice patch. Proc Natl Acad Sci USA 111:16842–16847CrossRefPubMedPubMedCentral
22.
Zurück zum Zitat Ng TFF, Willner DL, Lim YW, Schmieder R, Chau B, Nilsson C, Anthony S, Ruan YJ, Rohwer F, Breitbart M (2011) Broad surveys of DNA viral diversity obtained through viral metagenomics of mosquitoes. PLoS One 6:e20579CrossRefPubMedPubMedCentral Ng TFF, Willner DL, Lim YW, Schmieder R, Chau B, Nilsson C, Anthony S, Ruan YJ, Rohwer F, Breitbart M (2011) Broad surveys of DNA viral diversity obtained through viral metagenomics of mosquitoes. PLoS One 6:e20579CrossRefPubMedPubMedCentral
23.
Zurück zum Zitat Pei J, Grishin NV (2014) PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information. Methods Mol Biol 1079:263–271CrossRefPubMedPubMedCentral Pei J, Grishin NV (2014) PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information. Methods Mol Biol 1079:263–271CrossRefPubMedPubMedCentral
24.
Zurück zum Zitat Phan TG, Mori D, Deng X, Rajindrajith S, Ranawaka U, Fan Ng TF, Bucardo-Rivera F, Orlandi P, Ahmed K, Delwart E (2015) Small circular single stranded DNA viral genomes in unexplained cases of human encephalitis, diarrhea, and in untreated sewage. Virology 482:98–104CrossRefPubMedPubMedCentral Phan TG, Mori D, Deng X, Rajindrajith S, Ranawaka U, Fan Ng TF, Bucardo-Rivera F, Orlandi P, Ahmed K, Delwart E (2015) Small circular single stranded DNA viral genomes in unexplained cases of human encephalitis, diarrhea, and in untreated sewage. Virology 482:98–104CrossRefPubMedPubMedCentral
25.
Zurück zum Zitat Pietilä MK, Roine E, Sencilo A, Bamford DH, Oksanen HM (2016) Pleolipoviridae, a newly proposed family comprising archaeal pleomorphic viruses with single-stranded or double-stranded DNA genomes. Arch Virol 161:249–256CrossRefPubMed Pietilä MK, Roine E, Sencilo A, Bamford DH, Oksanen HM (2016) Pleolipoviridae, a newly proposed family comprising archaeal pleomorphic viruses with single-stranded or double-stranded DNA genomes. Arch Virol 161:249–256CrossRefPubMed
26.
Zurück zum Zitat Rosario K, Dayaram A, Marinov M, Ware J, Kraberger S, Stainton D, Breitbart M, Varsani A (2012) Diverse circular ssDNA viruses discovered in dragonflies (Odonata: Epiprocta). J Gen Virol 93:2668–2681CrossRefPubMed Rosario K, Dayaram A, Marinov M, Ware J, Kraberger S, Stainton D, Breitbart M, Varsani A (2012) Diverse circular ssDNA viruses discovered in dragonflies (Odonata: Epiprocta). J Gen Virol 93:2668–2681CrossRefPubMed
27.
Zurück zum Zitat Sikorski A, Massaro M, Kraberger S, Young LM, Smalley D, Martin DP, Varsani A (2013) Novel myco-like DNA viruses discovered in the faecal matter of various animals. Virus Res 177:209–216CrossRefPubMed Sikorski A, Massaro M, Kraberger S, Young LM, Smalley D, Martin DP, Varsani A (2013) Novel myco-like DNA viruses discovered in the faecal matter of various animals. Virus Res 177:209–216CrossRefPubMed
28.
Zurück zum Zitat Steel O, Kraberger S, Sikorski A, Young LM, Catchpole RJ, Steven AJ, Ladley JJ, Coray DS, Stainton D, Dayaram A, Julian L, van Bysterveldt K, Varsani A (2016) Circular replication-associated protein encoding DNA viruses identified in the faecal matter of various animals in New Zealand. Infect Genet Evol 43:151–164CrossRefPubMed Steel O, Kraberger S, Sikorski A, Young LM, Catchpole RJ, Steven AJ, Ladley JJ, Coray DS, Stainton D, Dayaram A, Julian L, van Bysterveldt K, Varsani A (2016) Circular replication-associated protein encoding DNA viruses identified in the faecal matter of various animals in New Zealand. Infect Genet Evol 43:151–164CrossRefPubMed
29.
Zurück zum Zitat Uch R, Fournier PE, Robert C, Blanc-Tailleur C, Galicher V, Barre R, Jordier F, de Micco P, Raoult D, Biagini P (2015) Divergent Gemycircularvirus in HIV-positive blood, France. Emerg Infect Dis 21:2096–2098CrossRefPubMedPubMedCentral Uch R, Fournier PE, Robert C, Blanc-Tailleur C, Galicher V, Barre R, Jordier F, de Micco P, Raoult D, Biagini P (2015) Divergent Gemycircularvirus in HIV-positive blood, France. Emerg Infect Dis 21:2096–2098CrossRefPubMedPubMedCentral
30.
Zurück zum Zitat van den Brand JM, van Leeuwen M, Schapendonk CM, Simon JH, Haagmans BL, Osterhaus AD, Smits SL (2012) Metagenomic analysis of the viral flora of pine marten and European badger feces. J Virol 86:2360–2365CrossRefPubMedPubMedCentral van den Brand JM, van Leeuwen M, Schapendonk CM, Simon JH, Haagmans BL, Osterhaus AD, Smits SL (2012) Metagenomic analysis of the viral flora of pine marten and European badger feces. J Virol 86:2360–2365CrossRefPubMedPubMedCentral
31.
Zurück zum Zitat Varsani A, Navas-Castillo J, Moriones E, Hernandez-Zepeda C, Idris A, Brown JK, Murilo Zerbini F, Martin DP (2014) Establishment of three new genera in the family Geminiviridae: Becurtovirus, Eragrovirus and Turncurtovirus. Arch Virol 159:2193–2203CrossRefPubMed Varsani A, Navas-Castillo J, Moriones E, Hernandez-Zepeda C, Idris A, Brown JK, Murilo Zerbini F, Martin DP (2014) Establishment of three new genera in the family Geminiviridae: Becurtovirus, Eragrovirus and Turncurtovirus. Arch Virol 159:2193–2203CrossRefPubMed
32.
Zurück zum Zitat Wu Z, Yang L, Ren X, He G, Zhang J, Yang J, Qian Z, Dong J, Sun L, Zhu Y, Du J, Yang F, Zhang S, Jin Q (2015) Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases. ISME J. doi:10.1038/ismej.2015.1138 Wu Z, Yang L, Ren X, He G, Zhang J, Yang J, Qian Z, Dong J, Sun L, Zhu Y, Du J, Yang F, Zhang S, Jin Q (2015) Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases. ISME J. doi:10.​1038/​ismej.​2015.​1138
33.
Zurück zum Zitat Xie J, Jiang D (2014) New insights into mycoviruses and exploration for the biological control of crop fungal diseases. Annu Rev Phytopathol 52:45–68CrossRefPubMed Xie J, Jiang D (2014) New insights into mycoviruses and exploration for the biological control of crop fungal diseases. Annu Rev Phytopathol 52:45–68CrossRefPubMed
34.
Zurück zum Zitat Yu X, Li B, Fu Y, Jiang D, Ghabrial SA, Li G, Peng Y, Xie J, Cheng J, Huang J, Yi X (2010) A geminivirus-related DNA mycovirus that confers hypovirulence to a plant pathogenic fungus. Proc Natl Acad Sci USA 107:8387–8392CrossRefPubMedPubMedCentral Yu X, Li B, Fu Y, Jiang D, Ghabrial SA, Li G, Peng Y, Xie J, Cheng J, Huang J, Yi X (2010) A geminivirus-related DNA mycovirus that confers hypovirulence to a plant pathogenic fungus. Proc Natl Acad Sci USA 107:8387–8392CrossRefPubMedPubMedCentral
35.
Zurück zum Zitat Yu X, Li B, Fu Y, Xie J, Cheng J, Ghabrial SA, Li G, Yi X, Jiang D (2013) Extracellular transmission of a DNA mycovirus and its use as a natural fungicide. Proc Natl Acad Sci USA 110:1452–1457CrossRefPubMedPubMedCentral Yu X, Li B, Fu Y, Xie J, Cheng J, Ghabrial SA, Li G, Yi X, Jiang D (2013) Extracellular transmission of a DNA mycovirus and its use as a natural fungicide. Proc Natl Acad Sci USA 110:1452–1457CrossRefPubMedPubMedCentral
36.
Zurück zum Zitat Zhang W, Olson NH, Baker TS, Faulkner L, Agbandje-McKenna M, Boulton MI, Davies JW, McKenna R (2001) Structure of the Maize streak virus geminate particle. Virology 279:471–477CrossRefPubMed Zhang W, Olson NH, Baker TS, Faulkner L, Agbandje-McKenna M, Boulton MI, Davies JW, McKenna R (2001) Structure of the Maize streak virus geminate particle. Virology 279:471–477CrossRefPubMed
Metadaten
Titel
Genomoviridae: a new family of widespread single-stranded DNA viruses
verfasst von
Mart Krupovic
Said A. Ghabrial
Daohong Jiang
Arvind Varsani
Publikationsdatum
24.06.2016
Verlag
Springer Vienna
Erschienen in
Archives of Virology / Ausgabe 9/2016
Print ISSN: 0304-8608
Elektronische ISSN: 1432-8798
DOI
https://doi.org/10.1007/s00705-016-2943-3

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