1887

Abstract

Over the past couple of years highly diverse novel ssDNA viruses have been discovered. Here, we present the first ssDNA virus, Gastropod-associated circular ssDNA virus (GaCSV), recovered from a mollusc Martyn 1784, which is a deposit feeder that grazes micro-organisms and organic detritus on the surface of tidal mudflats. The GaCSV (2351 nt) genome contains two large bidirectionally transcribed ORFs. The smaller ORF (874 nt) has similarities to viral replication-associated protein (Rep) sequences of some bacteria and circoviruses, whereas the larger ORF (955 nt) does not relate to any sequences in public databases and we presume it potentially encodes the capsid protein. Phylogenetic analysis shows that the GaCSV Rep clusters with Rep-like sequences of bacterial origin, highlighting the role of ssDNA viruses in horizontal gene transfer. The occurrence of previously unknown viruses in organisms associated with human pollution is a relatively unexplored field.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/vir.0.050088-0
2013-05-01
2019-12-13
Loading full text...

Full text loading...

/deliver/fulltext/jgv/94/5/1104.html?itemId=/content/journal/jgv/10.1099/vir.0.050088-0&mimeType=html&fmt=ahah

References

  1. Allan G. M. , Ellis J. A. . ( 2000; ). Porcine circoviruses: a review. . J Vet Diagn Invest 12:, 3–14. [CrossRef] [PubMed]
    [Google Scholar]
  2. Altschul S. F. , Gish W. , Miller W. , Myers E. W. , Lipman D. J. . ( 1990; ). Basic local alignment search tool. . J Mol Biol 215:, 403–410.[PubMed] [CrossRef]
    [Google Scholar]
  3. Anisimova M. , Gascuel O. . ( 2006; ). Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative. . Syst Biol 55:, 539–552. [CrossRef] [PubMed]
    [Google Scholar]
  4. Blinkova O. , Victoria J. , Li Y. , Keele B. F. , Sanz C. , Ndjango J. B. N. , Peeters M. , Travis D. , Lonsdorf E. V. . & other authors ( 2010; ). Novel circular DNA viruses in stool samples of wild-living chimpanzees. . J Gen Virol 91:, 74–86. [CrossRef] [PubMed]
    [Google Scholar]
  5. Cheng P. K. C. , Wong D. K. K. , Chung T. W. H. , Lim W. W. L. . ( 2005; ). Norovirus contamination found in oysters worldwide. . J Med Virol 76:, 593–597. [CrossRef] [PubMed]
    [Google Scholar]
  6. Comps M. . ( 1980; ). Fluorescence study of the branchiae disease virus of Portuguese oyster Crassotrea angulata Lmk. Science et Peche;. 301, 17–18.
    [Google Scholar]
  7. Comps M. . ( 1988; ). Epizootic diseases of oysters associated with viral infections. . American Fisheries Society Special Publication 18:, 23–37.
    [Google Scholar]
  8. Cutrin J. M. , Olveira J. G. , Barja J. L. , Dopazo C. P. . ( 2000; ). Diversity of infectious pancreatic necrosis virus strains isolated from fish, shellfish, and other reservoirs in Northwestern Spain. . Appl Environ Microbiol 66:, 839–843. [CrossRef] [PubMed]
    [Google Scholar]
  9. Dayaram A. , Opong A. , Jäschke A. , Hadfield J. , Baschiera M. , Dobson R. C. J. , Offei S. K. , Shepherd D. N. , Martin D. P. , Varsani A. . ( 2012; ). Molecular characterisation of a novel cassava associated circular ssDNA virus. . Virus Res 166:, 130–135. [CrossRef] [PubMed]
    [Google Scholar]
  10. Delwart E. , Li L. . ( 2012; ). Rapidly expanding genetic diversity and host range of the Circoviridae viral family and other Rep encoding small circular ssDNA genomes. . Virus Res 164:, 114–121. [CrossRef] [PubMed]
    [Google Scholar]
  11. Edgar R. C. . ( 2004; ). muscle: multiple sequence alignment with high accuracy and high throughput. . Nucleic Acids Res 32:, 1792–1797. [CrossRef] [PubMed]
    [Google Scholar]
  12. Elston R. . ( 1997; ). Bivalve mollusc viruses. . World J Microbiol Biotechnol 13:, 393–403. [CrossRef]
    [Google Scholar]
  13. Elston R. , Wilkinson M. . ( 1985; ). Pathology, management and diagnosis of oyster velar virus disease (OVVD). . Aquaculture 48:, 189–210. [CrossRef]
    [Google Scholar]
  14. Farley C. A. . ( 1969; ). Probable neoplastic disease of the hematopoietic system in oysters, Crassostrea virginica and Crassostrea gigas. . Natl Cancer Inst Monogr 31:, 541–555.[PubMed]
    [Google Scholar]
  15. Farley C. A. . ( 1976; ). Ultrastructural observations on epizootic neoplasia and lytic virus infection in bivalve mollusks. . Prog Exp Tumor Res 20:, 283–294.[PubMed]
    [Google Scholar]
  16. Farley C. A. , Banfield W. G. , Kasnic G. Jr , Foster W. S. . ( 1972; ). Oyster herpes-type virus. . Science 178:, 759–760. [CrossRef] [PubMed]
    [Google Scholar]
  17. Gibbs M. J. , Smeianov V. V. , Steele J. L. , Upcroft P. , Efimov B. A. . ( 2006; ). Two families of rep-like genes that probably originated by interspecies recombination are represented in viral, plasmid, bacterial, and parasitic protozoan genomes. . Mol Biol Evol 23:, 1097–1100. [CrossRef] [PubMed]
    [Google Scholar]
  18. 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. . Syst Biol 59:, 307–321. [CrossRef] [PubMed]
    [Google Scholar]
  19. Haible D. , Kober S. , Jeske H. . ( 2006; ). Rolling circle amplification revolutionizes diagnosis and genomics of geminiviruses. . J Virol Methods 135:, 9–16. [CrossRef] [PubMed]
    [Google Scholar]
  20. Ilyina T. V. , Koonin E. V. . ( 1992; ). Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria. . Nucleic Acids Res 20:, 3279–3285. [CrossRef] [PubMed]
    [Google Scholar]
  21. Inoue-Nagata A. K. , Albuquerque L. C. , Rocha W. B. , Nagata T. . ( 2004; ). A simple method for cloning the complete begomovirus genome using the bacteriophage phi29 DNA polymerase. . J Virol Methods 116:, 209–211. [CrossRef] [PubMed]
    [Google Scholar]
  22. Jones J. , Scotti P. , Dearing S. , Wesney B. . ( 1996; ). Virus-like particles associated with marine mussel mortalities in New Zealand. . Dis Aquat Organ 25:, 143–149. [CrossRef]
    [Google Scholar]
  23. Juniper K. . ( 1986; ). Deposit feeding strategy of Amphibola crenata: feeding behaviour, selective feeding and digestion. . Mauri ora 13:, 103–115.
    [Google Scholar]
  24. Kapoor A. , Dubovi E. J. , Henriquez-Rivera J. A. , Lipkin W. I. . ( 2012; ). Complete genome sequence of the first canine circovirus. . J Virol 86:, 7018–7018. [CrossRef] [PubMed]
    [Google Scholar]
  25. Kim H. K. , Park S. J. , Nguyen V. G. , Song D. S. , Moon H. J. , Kang B. K. , Park B. K. . ( 2012; ). Identification of a novel single stranded circular DNA virus from bovine stool. . J Gen Virol 93:, 635–639. [CrossRef] [PubMed]
    [Google Scholar]
  26. Koonin E. V. , Ilyina T. V. . ( 1992; ). Geminivirus replication proteins are related to prokaryotic plasmid rolling circle DNA replication initiator proteins. . J Gen Virol 73:, 2763–2766. [CrossRef] [PubMed]
    [Google Scholar]
  27. Krupovic M. , Ravantti J. J. , Bamford D. H. . ( 2009; ). Geminiviruses: a tale of a plasmid becoming a virus. . BMC Evol Biol 9:, 112. [CrossRef] [PubMed]
    [Google Scholar]
  28. Li L. , Kapoor A. , Slikas B. , Bamidele O. S. , Wang C. , Shaukat S. , Masroor M. A. , Wilson M. L. , Ndjango J. B. N. . & other authors ( 2010; ). Multiple diverse circoviruses infect farm animals and are commonly found in human and chimpanzee feces. . J Virol 84:, 1674–1682. [CrossRef] [PubMed]
    [Google Scholar]
  29. Liu H. , Fu Y. , Li B. , Yu X. , Xie J. , Cheng J. , Ghabrial S. A. , Li G. , Yi X. , Jiang D. . ( 2011; ). Widespread horizontal gene transfer from circular single-stranded DNA viruses to eukaryotic genomes. . BMC Evol Biol 11:, 276. [CrossRef] [PubMed]
    [Google Scholar]
  30. Martin D. P. , Biagini P. , Lefeuvre P. , Golden M. , Roumagnac P. , Varsani A. . ( 2011; ). Recombination in eukaryotic single stranded DNA viruses. . Viruses 3:, 1699–1738. [CrossRef] [PubMed]
    [Google Scholar]
  31. Meyers T. R. , Burton T. , Evans W. , Starkey N. . ( 2009; ). Detection of viruses and virus-like particles in four species of wild and farmed bivalve molluscs in Alaska, U.S.A., from 1987 to 2009. . Dis Aquat Organ 88:, 1–12. [CrossRef] [PubMed]
    [Google Scholar]
  32. Morley N. J. . ( 2010; ). Interactive effects of infectious diseases and pollution in aquatic molluscs. . Aquat Toxicol 96:, 27–36. [CrossRef] [PubMed]
    [Google Scholar]
  33. Munn C. B. . ( 2006; ). Viruses as pathogens of marine organisms - from bacteria to whales. . J Mar Biol Assoc U K 86:, 453–467. [CrossRef]
    [Google Scholar]
  34. Ng T. F. F. , Willner D. L. , Lim Y. W. , 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.[CrossRef]
    [Google Scholar]
  35. Oprandy J. J. , Chang P. W. , Pronovost A. D. , Cooper K. R. , Brown R. S. , Yates V. J. . ( 1981; ). Isolation of a viral agent causing hematopoietic neoplasia in the soft-shell clam, Mya arenaria . . J Invertebr Pathol 38:, 45–51. [CrossRef]
    [Google Scholar]
  36. Oshima K. , Kakizawa S. , Nishigawa H. , Kuboyama T. , Miyata S. , Ugaki M. , Namba S. . ( 2001; ). A plasmid of phytoplasma encodes a unique replication protein having both plasmid- and virus-like domains: clue to viral ancestry or result of virus/plasmid recombination?. Virology 285:, 270–277. [CrossRef] [PubMed]
    [Google Scholar]
  37. Phan T. G. , Kapusinszky B. , Wang C. , Rose R. K. , Lipton H. L. , Delwart E. L. . ( 2011; ). The fecal viral flora of wild rodents. . PLoS Pathog 7:, e1002218. [CrossRef] [PubMed]
    [Google Scholar]
  38. Renault T. , Novoa B. . ( 2004; ). Viruses infecting bivalve molluscs. . Aquat Living Resour 17:, 397–409. [CrossRef]
    [Google Scholar]
  39. Romalde J. L. , Area E. , Sánchez G. , Ribao C. , Torrado I. , Abad X. , Pintó R. M. , Barja J. L. , Bosch A. . ( 2002; ). Prevalence of enterovirus and hepatitis A virus in bivalve molluscs from Galicia (NW Spain): inadequacy of the EU standards of microbiological quality. . Int J Food Microbiol 74:, 119–130. [CrossRef] [PubMed]
    [Google Scholar]
  40. Rosario K. , Marinov M. , Stainton D. , Kraberger S. , Wiltshire E. J. , Collings D. A. , Walters M. , Martin D. P. , Breitbart M. , Varsani A. . ( 2011; ). Dragonfly cyclovirus, a novel single-stranded DNA virus discovered in dragonflies (Odonata: Anisoptera). . J Gen Virol 92:, 1302–1308. [CrossRef] [PubMed]
    [Google Scholar]
  41. Rosario K. , Dayaram A. , Marinov M. , Ware J. , Kraberger S. , Stainton D. , Breitbart M. , Varsani A. . ( 2012a; ). Diverse circular ssDNA viruses discovered in dragonflies (Odonata: Epiprocta). . J Gen Virol 93:, 2668–2681. [CrossRef] [PubMed]
    [Google Scholar]
  42. Rosario K. , Duffy S. , Breitbart M. . ( 2012b; ). A field guide to eukaryotic circular single-stranded DNA viruses: insights gained from metagenomics. . Arch Virol 157:, 1851–1871. [CrossRef] [PubMed]
    [Google Scholar]
  43. Rosario K. , Padilla-Rodriguez M. , Kraberger S. , Stainton D. , Martin D. P. , Breitbart M. , Varsani A. . ( 2013; ). Discovery of a novel mastrevirus and alphasatellite-like circular DNA in dragonflies (Epiprocta) from Puerto Rico. . Virus Res 171:, 231–237. [CrossRef] [PubMed]
    [Google Scholar]
  44. Savin K. W. , Cocks B. G. , Wong F. , Sawbridge T. , Cogan N. , Savage D. , Warner S. . ( 2010; ). A neurotropic herpesvirus infecting the gastropod, abalone, shares ancestry with oyster herpesvirus and a herpesvirus associated with the amphioxus genome. . Virol J 7:, 308. [CrossRef] [PubMed]
    [Google Scholar]
  45. Shan T. , Li L. , Simmonds P. , Wang C. , Moeser A. , Delwart E. . ( 2011; ). The fecal virome of pigs on a high-density farm. . J Virol 85:, 11697–11708. [CrossRef] [PubMed]
    [Google Scholar]
  46. Shepherd D. N. , Martin D. P. , Lefeuvre P. , Monjane A. L. , Owor B. E. , Rybicki E. P. , Varsani A. . ( 2008; ). A protocol for the rapid isolation of full geminivirus genomes from dried plant tissue. . J Virol Methods 149:, 97–102. [CrossRef] [PubMed]
    [Google Scholar]
  47. Sikorski A. , Argüello-Astorga G. R. , Dayaram A. , Dobson R. C. J. , Varsani A. . ( 2013; ). Discovery of a novel circular single-stranded DNA virus from porcine faeces. . Arch Virol 158:, 283–289. [CrossRef] [PubMed]
    [Google Scholar]
  48. van den Brand J. M. A. , van Leeuwen M. , Schapendonk C. M. , Simon J. H. , Haagmans B. L. , Osterhaus A. D. M. E. , Smits S. L. . ( 2012; ). Metagenomic analysis of the viral flora of pine marten and European badger feces. . J Virol 86:, 2360–2365. [CrossRef] [PubMed]
    [Google Scholar]
  49. Varsani A. , Regnard G. L. , Bragg R. , Hitzeroth I. I. , Rybicki E. P. . ( 2011; ). Global genetic diversity and geographical and host-species distribution of beak and feather disease virus isolates. . J Gen Virol 92:, 752–767. [CrossRef] [PubMed]
    [Google Scholar]
  50. Yoon H. S. , Price D. C. , Stepanauskas R. , Rajah V. D. , Sieracki M. E. , Wilson W. H. , Yang E. C. , Duffy S. , Bhattacharya D. . ( 2011; ). Single-cell genomics reveals organismal interactions in uncultivated marine protists. . Science 332:, 714–717. [CrossRef] [PubMed]
    [Google Scholar]
  51. Yu X. , Li B. , Fu Y. P. , Jiang D. H. , Ghabrial S. A. , Li G. Q. , Peng Y. L. , Xie J. T. , Cheng J. S. . & other authors ( 2010; ). A geminivirus-related DNA mycovirus that confers hypovirulence to a plant pathogenic fungus. . Proc Natl Acad Sci U S A 107:, 8387–8392. [CrossRef] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/vir.0.050088-0
Loading
/content/journal/jgv/10.1099/vir.0.050088-0
Loading

Data & Media loading...

Supplements

Supplementary tables 

PDF

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error