Skip to main content

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

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.

Viruses with single-stranded DNA (ssDNA) genomes infect hosts in all three domains of life and include economically, medically, and environmentally important viral pathogens. Until recently, ssDNA viruses were classified into 10 different taxa—nine families and one genus not assigned to a family [14, 15]. In 2016, the International Committee on Taxonomy of Viruses (ICTV) created two new families for classification of ssDNA viruses, Pleolipoviridae and Genomoviridae [1]. The family Pleolipoviridae includes viruses infecting hyperhalophilic archaea, and it has recently been described elsewhere [25]. Here, we introduce the family Genomoviridae and provide a short overview of the properties of Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1 (SsHADV-1), the only cultivated member of the new family, and putative SsHADV-1-like viruses.

SsHADV-1 is the first—and thus far the only—ssDNA virus known to infect fungi (all other fungal viruses have RNA genomes) [10, 33]. SsHADV-1 was isolated from a plant-pathogenic fungus, Sclerotinia sclerotiorum [34]. Another unique property of SsHADV-1 that has not been described for other fungal viruses is its ability to establish infection when applied extracellularly in the form of purified viral particles [35]. Virions can infect the hyphae of virus-free S. sclerotiorum directly when applied to hyphae or sprayed on leaves of Arabidopsis thaliana and Brassica napus infected with S. sclerotiorum. When applied to S. sclerotiorum-infected leaves, the virus can suppress the development of S. sclerotiorum-induced lesions. SsHADV-1 has a narrow host range and, in addition to S. sclerotiorum, can infect the related species S. minor and S. nivalis, but not other relatively closely related fungi, such as Botrytis cinerea [35]. Furthermore, SsHADV-1 has been identified in New Zealand and the USA in environmental samples and insects; however, this is not surprising given the near global distribution of S. sclerotiorum [6, 11].

SsHADV-1 virions are non-enveloped, isometric, 20-22 nm in diameter, and constructed from one capsid protein (CP) [34]. The genome is a circular ssDNA molecule of 2,166 nucleotides and contains two genes – for CP and replication initiation protein (Rep) (Fig. 1). The prediction of the cp gene has been validated by N-terminal sequencing of the CP purified from the virions. The large intergenic region contains a potential stem-loop structure with a nonanucleotide (TAATATTAT) motif at its apex, which is likely to be important for rolling-circle replication. The CP of SsHADV-1 is not recognizably similar to the corresponding proteins from viruses in other taxa.

Fig. 1
figure1

Genome map of SsHADV-1. Genes encoding the replication-initiation protein (Rep) and capsid protein (CP) are shown with blue and red arrows, respectively. The position of the nonanucleotide (TAATATTAT) at the apex of a potential stem-loop structure is also indicated

Although SsHADV-1 remains the only isolated member of the group, genomes of more than 100 SsHADV-1-like putative viruses have been reported (see Table 1). These genomes have been sequenced from different environmental samples, and many were identified associated with plant material as well as various animal-associated samples, including cerebrospinal fluid and blood of humans (Table 1 and references therein). Even though the hosts of these putative viruses remain unknown, their diversity suggests that SsHADV-1-like viruses are abundant and widespread in the environment.

Table 1 Genome sequences of putative SsHADV-1-like viruses

All putative SsHADV-1-like viruses encode homologous Rep and CP, and in phylogenetic analyses form monophyletic clades with SsHADV-1 (Figures 2 and 3). Their genomes are of similar size, in the range of 2,089-2,290 nucleotides. Structural and genomic features of SsHADV-1 differ considerably from those of all other currently classified viruses. The Rep of SsHADV-1 is most closely related to the corresponding proteins of members of the family Geminiviridae. It shares with geminiviral proteins two conserved domains, namely geminivirus Rep catalytic domain (Gemini_AL1; PF00799) and geminivirus Rep protein central domain (Gemini_AL1_M; PF08283), with conserved motifs for rolling-circle replication. Notably, similar to some geminiviruses [31], certain SsHADV-1-like viruses also contain introns within their Rep-encoding genes [6, 7, 12, 13, 18, 19, 2628, 30]. However, Rep-based phylogenetic analysis shows that SsHADV-1 and other related putative viruses form a well-supported, monophyletic clade, which branches as a sister group to geminiviruses (Fig. 2). Unlike the Rep, the CP of SsHADV-1 (and related viruses) does not display any recognizable sequence similarity to proteins of geminiviruses or any other group of known viruses. Furthermore, all geminiviruses possess distinctive geminate virions constructed from two incomplete T = 1 icosahedra [2, 36], whereas the virion of SsHADV-1 is isometric [34]. Finally, the number of genes and size of the genome differ considerably between SsHADV-1-like viruses and geminiviruses. In particular, all putative SsHADV-1-like viruses lack the movement protein, which is essential for the plant geminiviruses.

Fig. 2
figure2

Phylogenetic analysis of the replication-initiation proteins (Reps) of ssDNA viruses. The type species of the proposed genus Gemycircularvirus within the family Genomoviridae is highlighted in boldface. For phylogenetic analysis, protein sequences were aligned using PROMALS3D [23], and columns containing gaps were removed from the alignment using trimAl (strict mode) [3]. Maximum-likelihood phylogenetic analysis was carried out using PhyML 3.1 [8] with the RtREV +G6 +I +F model, which was selected by PhyML as the best-fitting model. Numbers at the branch points represent aBayes local support values. Branches with lower than 60 % support were collapsed. The scale bar represents the number of substitutions per site. For clarity, the tree was mid-point rooted. All taxa are indicated with the corresponding GenBank accession numbers, followed by abbreviated virus names (full virus names are provided in Table 1)

Fig. 3
figure3

Phylogenetic analysis of the SsHADV-1-like capsid proteins. The type species of the proposed genus Gemycircularvirus within the family Genomoviridae is highlighted in boldface. For phylogenetic analysis, protein sequences were aligned using PROMALS3D [23], and columns containing gaps were removed from the alignment using trimAl (strictplus mode) [3]. Maximum-likelihood phylogenetic analysis was carried out using PhyML 3.1 [8] with the LG +G6 +F model, which was selected by PhyML as the best-fitting model. Numbers at the branch points represent aBayes local support values. Branches with lower than 60 % support were collapsed. The scale bar represents the number of substitutions per site. The tree was rooted with the capsid proteins of geminiviruses. All taxa are indicated with the corresponding GenBank accession numbers, followed by abbreviated virus names (full virus names are provided in Table 1)

In recognition of the unique features described above, SsHADV-1 has been classified into the species Sclerotinia gemycircularvirus 1 within the new genus Gemycircularvirus (Gemini-like myco-infecting circular virus) [26] within the new family Genomoviridae (sigil: Ge- for geminivirus-like, nomo- for no movement protein).

Although Genomoviridae currently includes only a single representative, new members, possibly including uncultivated viruses, are expected to be added to the family in the near future. Based on the available genetic data and phylogenetic analyses (Figures 2 and 3), it is already clear that many new genera will have to be introduced to adequately reflect the diversity of SsHADV-1-like viruses.

References

  1. 1.

    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. 2.

    Böttcher B, Unseld S, Ceulemans H, Russell RB, Jeske H (2004) Geminate structures of African cassava mosaic virus. J Virol 78:6758–6765

    Article  PubMed  PubMed Central  Google Scholar 

  3. 3.

    Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T (2009) trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25:1972–1973

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  4. 4.

    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 12:79

    Article  PubMed  PubMed Central  Google Scholar 

  5. 5.

    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 166:130–135

    CAS  Article  PubMed  Google Scholar 

  6. 6.

    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 30:278–287

    CAS  Article  PubMed  Google Scholar 

  7. 7.

    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 159:1527–1531

    CAS  Article  PubMed  Google Scholar 

  8. 8.

    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 59:307–321

    CAS  Article  PubMed  Google Scholar 

  9. 9.

    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 3:01081-01015

    Article  Google Scholar 

  10. 10.

    Jiang D, Fu Y, Guoqing L, Ghabrial SA (2013) Viruses of the plant pathogenic fungus Sclerotinia sclerotiorum. Adv Virus Res 86:215–248

    CAS  Article  PubMed  Google Scholar 

  11. 11.

    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:e00559-00513

    Article  Google Scholar 

  12. 12.

    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 31:73–86

    CAS  Article  PubMed  Google Scholar 

  13. 13.

    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 160:1303–1311

    CAS  Article  PubMed  Google Scholar 

  14. 14.

    Krupovic M (2013) Networks of evolutionary interactions underlying the polyphyletic origin of ssDNA viruses. Curr Opin Virol 3:578–586

    CAS  Article  PubMed  Google Scholar 

  15. 15.

    Krupovic M, Forterre P (2015) Single-stranded DNA viruses employ a variety of mechanisms for integration into host genomes. Ann N Y Acad Sci 1341:41–53

    CAS  Article  PubMed  Google Scholar 

  16. 16.

    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:e00848-00814

    Article  Google Scholar 

  17. 17.

    Li W, Gu Y, Shen Q, Yang S, Wang X, Wan Y, Zhang W (2015) A novel gemycircularvirus from experimental rats. Virus Genes 51:302–305

    Article  PubMed  Google Scholar 

  18. 18.

    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:e01144-01115

    Article  Google Scholar 

  19. 19.

    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 39:279–292

    CAS  Article  PubMed  Google Scholar 

  20. 20.

    Marzano SL, Domier L (2016) Novel mycoviruses discovered from metatranscriptomics survey of soybean phyllosphere phytobiomes. Virus Res 213:332–342

    CAS  Article  PubMed  Google Scholar 

  21. 21.

    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 111:16842–16847

    Article  PubMed  PubMed Central  Google Scholar 

  22. 22.

    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:e20579

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  23. 23.

    Pei J, Grishin NV (2014) PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information. Methods Mol Biol 1079:263–271

    Article  PubMed  PubMed Central  Google Scholar 

  24. 24.

    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 482:98–104

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  25. 25.

    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 161:249–256

    Article  PubMed  Google Scholar 

  26. 26.

    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 93:2668–2681

    CAS  Article  PubMed  Google Scholar 

  27. 27.

    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 177:209–216

    CAS  Article  PubMed  Google Scholar 

  28. 28.

    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 43:151–164

    CAS  Article  PubMed  Google Scholar 

  29. 29.

    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 21:2096–2098

    Article  PubMed  PubMed Central  Google Scholar 

  30. 30.

    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 86:2360–2365

    Article  PubMed  PubMed Central  Google Scholar 

  31. 31.

    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 159:2193–2203

    CAS  Article  PubMed  Google Scholar 

  32. 32.

    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

    Google Scholar 

  33. 33.

    Xie J, Jiang D (2014) New insights into mycoviruses and exploration for the biological control of crop fungal diseases. Annu Rev Phytopathol 52:45–68

    CAS  Article  PubMed  Google Scholar 

  34. 34.

    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 107:8387–8392

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  35. 35.

    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 110:1452–1457

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  36. 36.

    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 279:471–477

    CAS  Article  PubMed  Google Scholar 

Download references

Author information

Affiliations

Authors

Corresponding authors

Correspondence to Mart Krupovic or Arvind Varsani.

Ethics declarations

The authors declare that no competing interests exist. This article does not contain any studies with human participants or animals performed by any of the authors.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Krupovic, M., Ghabrial, S.A., Jiang, D. et al. Genomoviridae: a new family of widespread single-stranded DNA viruses. Arch Virol 161, 2633–2643 (2016). https://doi.org/10.1007/s00705-016-2943-3

Download citation

Keywords

  • Capsid Protein
  • Monophyletic Clade
  • Fungal Virus
  • Replication Initiation Protein
  • ssDNA Virus