1887

Abstract

Novel circular ssDNA genomes have recently been detected in animals and in the environment using metagenomic and high-throughput sequencing approaches. In this study, five full-length circular ssDNA genomes were recovered from bat faecal samples using inverse PCR with sequences designed based on circovirus-related sequences obtained from Solexa sequencing data derived from a random amplification method. These five sequences shared a similar genomic organization to circovirus or the recently proposed cyclovirus of the family . The newly obtained circovirus/cyclovirus-like genomes ranged from 1741 to 2177 bp, and each consisted of two major ORFs, ORF1 and ORF2, encoding putative replicase (Rep) and capsid (Cap) proteins, respectively. The potential stem–loop region was predicted in all five genomes, and three of them had the typical conserved nonanucleotide motif of cycloviruses. A set of primers targeting the conserved Rep region was designed and used to detect the prevalence of circovirus/cyclovirus sequences in individual bats. Among 199 samples tested, 47 were positive (23.6 %) for the circovirus genome and two (1.0 %) were positive for the cyclovirus genome. In total, 48 partial Rep sequences plus the five full-length genomes were obtained in this study. Detailed analysis indicated that these sequences are distantly related to known circovirus/cyclovirus genomes and may represent 22 novel species that belong to the family .

Loading

Article metrics loading...

/content/journal/jgv/10.1099/vir.0.034108-0
2011-11-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/jgv/92/11/2646.html?itemId=/content/journal/jgv/10.1099/vir.0.034108-0&mimeType=html&fmt=ahah

References

  1. Bassami M. R., Berryman D., Wilcox G. E., Raidal S. R. 1998; Psittacine beak and feather disease virus nucleotide sequence analysis and its relationship to porcine circovirus, plant circoviruses, and chicken anaemia virus. Virology 249:453–459 [View Article][PubMed]
    [Google Scholar]
  2. Blinkova O., Victoria J., Li Y., Keele B. F., Sanz C., Ndjango J.-B. N., Peeters M., Travis D., Lonsdorf E. V. et al. 2010; Novel circular DNA viruses in stool samples of wild-living chimpanzees. J Gen Virol 91:74–86 [View Article][PubMed]
    [Google Scholar]
  3. Chae C. 2005; A review of porcine circovirus 2-associated syndromes and diseases. Vet J 169:326–336 [View Article][PubMed]
    [Google Scholar]
  4. Cheung A. K. 2006; Rolling-circle replication of an animal circovirus genome in a theta-replicating bacterial plasmid in Escherichia coli . J Virol 80:8686–8694 [View Article][PubMed]
    [Google Scholar]
  5. Darwich L., Segalés J., Mateu E. 2004; Pathogenesis of postweaning multisystemic wasting syndrome caused by Porcine circovirus 2: an immune riddle. Arch Virol 149:857–874 [View Article][PubMed]
    [Google Scholar]
  6. Donaldson E. F., Haskew A. N., Gates J. E., Huynh J., Moore C. J., Frieman M. B. 2010; Metagenomic analysis of the viromes of three North American bat species: viral diversity among different bat species that share a common habitat. J Virol 84:13004–13018 [View Article][PubMed]
    [Google Scholar]
  7. Ellis J., Hassard L., Clark E., Harding J., Allan G., Willson P., Strokappe J., Martin K., McNeilly F. et al. 1998; Isolation of circovirus from lesions of pigs with postweaning multisystemic wasting syndrome. Can Vet J 39:44–51[PubMed]
    [Google Scholar]
  8. Ellis J., Clark E., Haines D., West K., Krakowka S., Kennedy S., Allan G. M. 2004; Porcine circovirus-2 and concurrent infections in the field. Vet Microbiol 98:159–163 [View Article][PubMed]
    [Google Scholar]
  9. Fauquet C. M., Fargette D. 2005; International Committee on Taxonomy of Viruses and the 3,142 unassigned species. Virol J 2:64 [View Article][PubMed]
    [Google Scholar]
  10. Firth C., Charleston M. A., Duffy S., Shapiro B., Holmes E. C. 2009; Insights into the evolutionary history of an emerging livestock pathogen: porcine circovirus 2. J Virol 83:12813–12821 [View Article][PubMed]
    [Google Scholar]
  11. Hattermann K., Schmitt C., Soike D., Mankertz A. 2003; Cloning and sequencing of Duck circovirus (DuCV). Arch Virol 148:2471–2480 [View Article][PubMed]
    [Google Scholar]
  12. Hino S., Prasetyo A. A. 2009; Relationship of Torque teno virus to chicken anemia virus. Curr Top Microbiol Immunol 331:117–130 [View Article][PubMed]
    [Google Scholar]
  13. Kappe E. C., Halami M., Schade B., Bauer J., Dekant W., Buitkamp J., Boettcher J., Mueller H. 2009; Fatal aplastic anaemia with haemorrhagic disease in calves in Germany. J Comp Pathol 141:293 [View Article]
    [Google Scholar]
  14. Kumar S., Nei M., Dudley J., Tamura K. 2008; mega: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform 9:299–306 [View Article][PubMed]
    [Google Scholar]
  15. Li W., Shi Z., Yu M., Ren W., Smith C., Epstein J. H., Wang H., Crameri G., Hu Z. et al. 2005; Bats are natural reservoirs of SARS-like coronaviruses. Science 310:676–679 [View Article][PubMed]
    [Google Scholar]
  16. Li L., Kapoor A., Slikas B., Bamidele O. S., Wang C., Shaukat S., Masroor M. A., Wilson M. L., Ndjango J.-B. N. et al. 2010a; Multiple diverse circoviruses infect farm animals and are commonly found in human and chimpanzee feces. J Virol 84:1674–1682 [View Article][PubMed]
    [Google Scholar]
  17. Li L., Victoria J. G., Wang C., Jones M., Fellers G. M., Kunz T. H., Delwart E. 2010b; Bat guano virome: predominance of dietary viruses from insects and plants plus novel mammalian viruses. J Virol 84:6955–6965 [View Article][PubMed]
    [Google Scholar]
  18. Li L., Shan T., Soji O. B., Alam M. M., Kunz T. H., Zaidi S. Z., Delwart E. 2011; Possible cross-species transmission of circoviruses and cycloviruses among farm animals. J Gen Virol 92:768–772 [View Article][PubMed]
    [Google Scholar]
  19. Li Y., Ge X., Zhang H., Zhou P., Zhu Y., Zhang Y., Yuan J., Wang L.-F., Shi Z. 2010; Host range, prevalence, and genetic diversity of adenoviruses in bats. J Virol 84:3889–3897 [View Article][PubMed]
    [Google Scholar]
  20. Lőrincz M., Cságola A., Biksi I., Szeredi L., Dán A., Tuboly T. 2010; Detection of porcine circovirus in rodents – short communication. Acta Vet Hung 58:265–268 [View Article][PubMed]
    [Google Scholar]
  21. Rosario K., Duffy S., Breitbart M. 2009a; Diverse circovirus-like genome architectures revealed by environmental metagenomics. J Gen Virol 90:2418–2424 [View Article][PubMed]
    [Google Scholar]
  22. Rosario K., Nilsson C., Lim Y. W., Ruan Y. J., Breitbart M. 2009b; Metagenomic analysis of viruses in reclaimed water. Environ Microbiol 11:2806–2820 [View Article][PubMed]
    [Google Scholar]
  23. 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 [View Article][PubMed]
    [Google Scholar]
  24. Schat K. A. 2009; Chicken anemia virus. In TT Viruses – the Still Elusive Human Pathogens pp. 151–183 Edited by de Villiers E. M., zur Hausen H. Berlin: Springer-Verlag Berlin;
    [Google Scholar]
  25. Smyth J. A., Moffett D. A., Connor T. J., McNulty M. S. 2006; Chicken anaemia virus inoculated by the oral route causes lymphocyte depletion in the thymus in 3-week-old and 6-week-old chickens. Avian Pathol 35:254–259 [View Article][PubMed]
    [Google Scholar]
  26. Stewart M. E., Perry R., Raidal S. R. 2006; Identification of a novel circovirus in Australian ravens (Corvus coronoides) with feather disease. Avian Pathol 35:86–92 [View Article][PubMed]
    [Google Scholar]
  27. Todd D. 2000; Circoviruses: immunosuppressive threats to avian species: a review. Avian Pathol 29:373–394 [View Article][PubMed]
    [Google Scholar]
  28. Todd D., Weston J., Ball N. W., Borghmans B. J., Smyth J. A., Gelmini L., Lavazza A. 2001a; Nucleotide sequence-based identification of a novel circovirus of canaries. Avian Pathol 30:321–325 [View Article][PubMed]
    [Google Scholar]
  29. Todd D., Weston J. H., Soike D., Smyth J. A. 2001b; Genome sequence determinations and analyses of novel circoviruses from goose and pigeon. Virology 286:354–362 [View Article][PubMed]
    [Google Scholar]
  30. Todd D., Scott A. N. J., Fringuelli E., Shivraprasad H. L., Gavier-Widen D., Smyth J. A. 2007; Molecular characterization of novel circoviruses from finch and gull. Avian Pathol 36:75–81 [View Article][PubMed]
    [Google Scholar]
  31. Zuker M. 2003; Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406–3415 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/vir.0.034108-0
Loading
/content/journal/jgv/10.1099/vir.0.034108-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
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