Discovery of a novel circular single-stranded DNA virus from porcine faeces

Archives of Virology

Volumn 158, Issue 1, 2013, Pages 283-289

  Sikorski, Alyssa ^a   Argüello Astorga, Gerardo R ^b   Dayaram, Anisha ^a   Dobson, Renwick C J ^a   Varsani, Arvind ^a,c  

^a UNIVERSITY OF CANTERBURY   (New Zealand)

^b INSTITUTO POTOSINO DE INVESTIGACIÓN CIENTÍFICA Y TECNOLÓGICA   (Mexico)

^c UNIVERSITY OF CAPE TOWN   (South Africa)

Author keywords

[No Author keywords available]

Indexed keywords

BOVINAE; DNA VIRUSES; MIRIDAE; PAN; SSDNA VIRUSES; SUIDAE; SUS;

EID: 84872269812     PISSN: 03048608     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00705-012-1470-0     Document Type: Article

References (33)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
2. Anisimova M, Gascuel O (2006) Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative. Syst Biol 55: 539-552.
3. Arnold K, Bordoli L, Kopp J, Schwede T (2006) The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22: 195-201.
4. Asahina AY, Lu Y, Wu C, Fujioka RS, Loh PC (2009) Potential biosentinels of human waste in marine coastal waters: bioaccumulation of human noroviruses and enteroviruses from sewage-polluted waters by indigenous mollusks. J Virol Methods 158: 46-50.
5. Bitton G (2002) Entamoeba Histolytica/Entamoeba Dispar. Wiley, New York, pp 1136-1146.
6. Blinkova O, Victoria J, Li Y, Keele BF, Sanz C, Ndjango JB, Peeters M, Travis D, Lonsdorf EV, Wilson ML, Pusey AE, Hahn BH, Delwart EL (2010) Novel circular DNA viruses in stool samples of wild-living chimpanzees. J Gen Virol 91: 74-86.
7. Bordoli L, Kiefer F, Arnold K, Benkert P, Battey J, Schwede T (2009) Protein structure homology modeling using SWISS-MODEL workspace. Nat Protoc 4: 1-13.
8. 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.
9. 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.
10. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
11. Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U, Sali A (2006) Comparative protein structure modeling using Modeller. Current protocols in bioinformatics/editoral board, Andreas D Baxevanis [et al.] Chapter 5: Unit 5 6.
12. Fiser A, Sali A (2003) Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol 374: 461-491.
13. 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 Gen Virol 92: 2646-2653.
14. 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.
15. 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 Res 20: 3279.
16. Kiefer F, Arnold K, Kunzli M, Bordoli L, Schwede T (2009) The SWISS-MODEL repository and associated resources. Nucleic Acids Res 37: D387-D392.
17. Kim HK, Park SJ, Nguyen VG, Song DS, Moon HJ, Kang BK, Park BK (2012) Identification of a novel single-stranded, circular DNA virus from bovine stool. J Gen Virol 93: 635-639.
18. Koonin EV, Ilyina TV (1992) Geminivirus replication proteins are related to prokaryotic plasmid rolling circle DNA replication initiator proteins. J Gen Virol 73: 2763.
19. Li L, Kapoor A, Slikas B, Bamidele OS, Wang C, Shaukat S, Masroor MA, Wilson ML, Ndjango JB, Peeters M, Gross-Camp ND, Muller MN, Hahn BH, Wolfe ND, Triki H, Bartkus J, Zaidi SZ, Delwart E (2010) Multiple diverse circoviruses infect farm animals and are commonly found in human and chimpanzee feces. J Virol 84: 1674-1682.
20. Li L, Shan T, Soji OB, Alam MM, Kunz TH, Zaidi SZ, Delwart E (2011) Possible cross-species transmission of circoviruses and cycloviruses among farm animals. J Gen Virol 92: 768-772.
21. 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.
22. Phan TG, Kapusinszky B, Wang C, Rose RK, Lipton HL, Delwart EL (2011) The fecal viral flora of wild rodents. PLoS Pathog 7: e1002218.
23. Piasecki T, Kurenbach B, Chrzastek K, Bednarek K, Kraberger S, Martin DP, Varsani A (2012) Molecular characterisation of an avihepadnavirus isolated from Psittacula krameri (ring-necked parrot). Arch Virol 157: 585-590.
24. Rosario K, Breitbart M (2011) Exploring the viral world through metagenomics. Curr Opin Virol 1: 289-297.
25. Rosario K, Marinov M, Stainton D, Kraberger S, Wiltshire EJ, Collings DA, Walters M, Martin DP, Breitbart M, Varsani A (2011) Dragonfly cyclovirus, a novel single-stranded DNA virus discovered in dragonflies (Odonata: Anisoptera). J Gen Virol 92: 1302-1308.
26. Rosario K, Duffy S, Breitbart M (2012) A field guide to eukaryotic circular single-stranded DNA viruses: insights gained from metagenomics. Arch Virol. doi: 10. 1007/s00705-012-1391-y.
27. Sachsenröder J, Twardziok S, Hammerl JA, Janczyk P, Wrede P, Hertwig S, Johne R (2012) Simultaneous identification of DNA and RNA viruses present in pig faeces using process-controlled deep sequencing. PLoS ONE 7: e34631.
28. 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.
29. Shepherd DN, Martin DP, Lefeuvre P, Monjane AL, Owor BE, Rybicki EP, Varsani A (2008) A protocol for the rapid isolation of full geminivirus genomes from dried plant tissue. J Virol Methods 149: 97-102.
30. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
31. 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.
32. Varsani A, Regnard GL, Bragg R, Hitzeroth II, Rybicki EP (2011) Global genetic diversity and geographical and host-species distribution of beak and feather disease virus isolates. J Gen Virol 92: 752-767.
33. Woolhouse M, Gaunt E (2007) Ecological origins of novel human pathogens. Crit Rev Microbiol 33: 231-242.