Abstract
The genomes of a large number of highly diverse novel circular DNA viruses from a wide range of sources have been characterised in recent years, including circular single-stranded DNA (ssDNA) viruses that share similarities with plant-infecting ssDNA viruses of the family Geminiviridae. Here, we describe six novel circular DNA viral genomes that encode replication-associated (Rep) proteins that are most closely related to those of either geminiviruses or gemycircularviruses (a new group of ssDNA viruses that are closely related to geminiviruses). Four possible viral genomes were recovered from Bromus hordeaceus sampled in New Zealand, and two were recovered from B. hordeaceus and Trifolium resupinatum sampled in France. Two of the viral genomes from New Zealand (one from the North Island and one from the South Island each) share >99 % sequence identity, and two genomes recovered from B. hordeaceus and T. resupinatum sampled in France share 74 % identity. All of the viral genomes that were recovered were found to have a major open reading frame on both their complementary and virion-sense strands, one of which likely encodes a Rep and the other a capsid protein. Although future infectivity studies are needed to identify the host range of these viruses, this is the first report of circular DNA viruses associated with grasses in New Zealand.
References
Anisimova M, Gascuel O (2006) Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative. System Biol 55:539–552
Barker NP, Clark LG, Davis JI, Duvall MR, Guala GF, Hsiao C, Kellogg EA, Linder HP (2001) Phylogeny and subfamilial classification of the grasses (Poaceae). Ann Mo Bot Gard 88:373–457
Bernardo P, Golden M, Akram M, Naimuddin, Nadarajan N, Fernandez E, Granier M, Rebelo AG, Peterschmitt M, Martin DP, Roumagnac P (2013) Identification and characterisation of a highly divergent geminivirus: evolutionary and taxonomic implications. Virus Res 177:35–45
Candresse T, Filloux D, Muhire B, Julian C, Galzi S, Fort G, Bernardo P, Daugrois JH, Fernandez E, Martin DP, Varsani A, Roumagnac P (2014) Appearances can be deceptive: revealing a hidden viral infection with deep sequencing in a plant quarantine context. PLoS One 9:e102945
Darriba D, Taboada GL, Doallo R, Posada D (2011) ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 27:1164–1165
Dayaram A, Opong A, Jäschke A, Hadfield J, Baschiera M, Dobson RCJ, Offei SK, Shepherd DN, Martin DP, Varsani A (2012) Molecular characterisation of a novel cassava associated circular ssDNA virus. Virus Res 166:130–135
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. Infection, Genetics and Evolution (In press)
Dekker EL, Woolston CJ, Xue Y, Cox B, Mullineaux PM (1991) Transcript mapping reveals different expression strategies for the bicistronic RNAs of the geminivirus wheat dwarf virus. Nucleic Acids Res 19:4075–4081
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
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797
Ge X, Li J, Peng C, Wu L, Yang X, Wu Y, Zhang Y, Shi Z (2011) Genetic diversity of novel circular ssDNA viruses in bats in China. J General Virol 92:2646–2653
Guindon S, Dufayard J-F, 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. System Biol 59:307–321
Heydarnejad J, Keyvani N, Razavinejad S, Massumi H, Varsani A (2013) Fulfilling Koch’s postulates for beet curly top Iran virus and proposal for consideration of new genus in the family Geminiviridae. Arch Virol 158:435–443
Ilyina TV, Koonin EV (1992) Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria. Nucleic Acids Research 20:3279–3285
Koonin EV, Ilyina TV (1992) Geminivirus replication proteins are related to prokaryotic plasmid rolling circle DNA replication initiator proteins. Journal of General Virology 73:2763–2766
Koonin EV (1993) A common set of conserved motifs in a vast variety of putative nucleic acid-dependent ATPases including MCM proteins involved in the initiation of eukaryotic DNA replication. Nucleic Acids Res 21:2541–2547
Kraberger S, Thomas JE, Geering ADW, Dayaram A, Stainton D, Hadfield J, Walters M, Parmenter KS, van Brunschot S, Collings DA, Martin DP, Varsani A (2012) Australian monocot-infecting mastrevirus diversity rivals that in Africa. Virus Res 169:127–136
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:e00559-13
Kreuze JF, Perez A, Untiveros M, Quispe D, Fuentes S, Barker I, Simon R (2009) Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: A generic method for diagnosis, discovery and sequencing of viruses. Virology 388:1–7
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:e00848-14
Liu H, Fu Y, Li B, Yu X, Xie J, Cheng J, Ghabrial SA, Li G, Yi X, Jiang D (2011) Widespread horizontal gene transfer from circular single-stranded DNA viruses to eukaryotic genomes. BMC Evol Biol 11:e276
Loconsole G, Saldarelli P, Doddapaneni H, Savino V, Martelli GP, Saponari M (2012) Identification of a single-stranded DNA virus associated with citrus chlorotic dwarf disease, a new member in the family Geminiviridae. Virology 432:162–172
Martin D, Willment J, Rybicki E (1999) Evaluation of Maize streak virus pathogenicity in differentially resistant Zea mays genotypes. Phytopathology 89:695–700
Martin DP, Linderme D, Lefeuvre P, Shepherd DN, Varsani A (2011) Eragrostis minor streak virus: an Asian streak virus in Africa. Arch Virol 156:1299–1303
Monjane AL, Harkins GW, Martin DP, Lemey P, Lefeuvre P, Shepherd DN, Oluwafemi S, Simuyandi M, Zinga I, Komba EK, Lakoutene DP, Mandakombo N, Mboukoulida J, Semballa S, Tagne A, Tiendrebeogo F, Erdmann JB, van Antwerpen T, Owor BE, Flett B, Ramusi M, Windram OP, Syed R, Lett JM, Briddon RW, Markham PG, Rybicki EP, Varsani A (2011) Reconstructing the history of Maize streak virus strain a dispersal to reveal diversification hot spots and its origin in southern Africa. J Virol 85:9623–9636
Muhire BM, Varsani A, Martin DP (2014) SDT: A virus classification tool based on pairwise sequence alignment and identity calculation. PLoS One 9:e108277
Nash TE, Dallas MB, Reyes MI, Buhrman GK, Ascencio-Ibañez JT, Hanley-Bowdoin L (2011) Functional analysis of a novel motif conserved across geminivirus Rep proteins. J Virol 85:1182–1192
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. Proceedings of the National Academy of Sciences of the United States of America 111:16842–16847
Ng TFF, Willner DL, Lim YW, Schmieder R, Chau B, Nilsson C, Anthony S, Ruan Y, Rohwer F, Breitbart M (2011) Broad surveys of DNA viral diversity obtained through viral metagenomics of mosquitoes. PLoS One 6:e20579
Ng TFF, Marine R, Wang C, Simmonds P, Kapusinszky B, Bodhidatta L, Oderinde BS, Wommack KE, Delwart E (2012) High variety of known and new RNA and DNA viruses of diverse origins in nntreated sewage. J Virol 86:12161–12175
Oluwafemi S, Varsani A, Monjane AL, Shepherd DN, Owor BE, Rybicki EP, Martin DP (2008) A new African streak virus species from Nigeria. Arch Virol 153:1407–1410
Oluwafemi S, Kraberger S, Shepherd DN, Martin DP, Varsani A (2014) A high degree of African streak virus diversity within Nigerian maize fields includes a new mastrevirus from Axonopus compressus. Arch Virol 159:2765–2770
Phan TG, Kapusinszky B, Wang C, Rose RK, Lipton HL, Delwart EL (2011) The fecal viral flora of wild rodents. PLoS Pathog 7:e1002218
Poojari S, Alabi OJ, Fofanov VY, Naidu RA (2013) A leafhopper-transmissible DNA virus with novel evolutionary lineage in the family Geminiviridae implicated in grapevine redleaf disease by next-generation sequencing. PLoS One 8:e64194
Rosario K, Duffy S, Breitbart M (2009) Diverse circovirus-like genome architectures revealed by environmental metagenomics. J Gen Virol 90:2418–2424
Rosario K, Dayaram A, Marinov M, Ware J, Kraberger S, Stainton D, Breitbart M, Varsani A (2011) Diverse circular single-stranded DNA viruses discovered in dragonflies (Odonata: Epiprocta). J Gen Virol 93:2668–2681
Rosario K, Duffy S, Breitbart M (2012) A field guide to eukaryotic circular single-stranded DNA viruses: insights gained from metagenomics. Arch Virol 157:1851–1871
Shepherd DN, Varsani A, Windram OP, Lefeuvre P, Monjane AL, Owor BE, Martin DP (2008) Novel sugarcane streak and Sugarcane streak Reunion mastreviruses from southern Africa and La Reunion. Arch Virol 153:605–609
Shepherd DN, Martin DP, Van Der Walt E, Dent K, Varsani A, Rybicki EP (2010) Maize streak virus: An old and complex ‘emerging’ pathogen. Mol Plant Pathol 11:1–12
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
Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJM, Birol İ (2009) ABySS: A parallel assembler for short read sequence data. Genome Res 19:1117–1123
van den Brand JMA, van Leeuwen M, Schapendonk CM, Simon JH, Haagmans BL, Osterhaus ADME, Smits SL (2012) Metagenomic analysis of the viral flora of pine marten and European badger feces. J Virol 86:2360–2365
Varsani A, Shepherd DN, Monjane AL, Owor BE, Erdmann JB, Rybicki EP, Peterschmitt M, Briddon RW, Markham PG, Oluwafemi S, Windram OP, Lefeuvre P, Lett JM, Martin DP (2008) Recombination, decreased host specificity and increased mobility may have driven the emergence of Maize streak virus as an agricultural pathogen. J Gen Virol 89:2063–2074
Varsani A, Monjane AL, Donaldson L, Oluwafemi S, Zinga I, Komba EK, Plakoutene D, Mandakombo N, Mboukoulida J, Semballa S, Briddon RW, Markham PG, Lett JM, Lefeuvre P, Rybicki EP, Martin DP (2009) Comparative analysis of Panicum streak virus and Maize streak virus diversity, recombination patterns and phylogeography. Virol J 6:e194
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 107:8387–8392
Zawar-Reza P, Arguello-Astorga GR, Kraberger S, Julian L, Stainton D, Broady PA, Varsani A (2014) Diverse small circular single-stranded DNA viruses identified in a freshwater pond on the McMurdo Ice Shelf (Antarctica). Infect Genet Evol 26:132–138
Acknowledgements
SK is supported by a scholarship from the School of Biological Sciences (University of Canterbury, New Zealand). We thank Captain Milen Marinov for assistance with grass sampling. This work was supported by the Marsden Fund Council from Government funding, administered by the Royal Society of New Zealand (grant UOC0903). AV and DPM are supported by the National Research Foundation of South Africa. PB was supported by a fellowship funded by the MEM-INRA Metaprogram and the DGA (Département Général des Armées, France).
GenBank accession numbers
BasCV-1 [NZ-NZG01-Sef-2012] KM510189, BasCV-1 [NZ-NZG03-Wel-2012] KM510190, BasCV-2 [NZ-NZG03-Wel-2012] KM510191, BasCV-3 [NZ-NZG01-Sef-2012] KM510192, BasCV-4 [FR- FR38-38-Cam-2010] KP005454, TasCV-1 [FR- FR34-34-Cam-2010] KP0054543
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705_2015_2358_MOESM2_ESM.doc
Supplementary Table 2 Details for bromus-associated circular DNA viral isolates and back-to-back primers used to recover full genomes (DOC 32 kb)
705_2015_2358_MOESM3_ESM.pdf
Supplementary Figure 1 Comparisons of the replication origin regions of BasCV-3 and SsHADV-1, illustrating the resemblance between their putative Rep-binding sites (iterons). Note that the nick site (the conserved nonanucleotide) of BasCV-3 differs from that of SsHADV-1 at position N5 (PDF 406 kb)
705_2015_2358_MOESM4_ESM.pdf
Supplementary Figure 2 Correlations between iteron core sequences and potential Rep DNA-binding SPDs of BasCV-3 and selected gemycircularviruses. Amino acid residues identified as putative SPDs in the beta-1 strand (r1) are shaded in yellow, whereas SPDs in the beta-strand (r-2) associated with motif II are shaded in blue. The conserved RCR motifs I and II are indicated at the top of the alignments. The N-terminus of the Rep of BasCV-1 is also aligned to show the similarity of its RCR motifs with those of gemycircularviruses (PDF 431 kb)
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Kraberger, S., Farkas, K., Bernardo, P. et al. Identification of novel Bromus- and Trifolium-associated circular DNA viruses. Arch Virol 160, 1303–1311 (2015). https://doi.org/10.1007/s00705-015-2358-6
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DOI: https://doi.org/10.1007/s00705-015-2358-6