Viral particles in stool samples from wild-living chimpanzees were analysed using random PCR amplification and sequencing. Sequences encoding proteins distantly related to the replicase protein of single-stranded circular DNA viruses were identified. Inverse PCR was used to amplify and sequence multiple small circular DNA viral genomes. The viral genomes were related in size and genome organization to vertebrate circoviruses and plant geminiviruses but with a different location for the stem–loop structure involved in rolling circle DNA replication. The replicase genes of these viruses were most closely related to those of the much smaller (∼1 kb) plant nanovirus circular DNA chromosomes. Because the viruses have characteristics of both animal and plant viruses, we named them chimpanzee stool-associated circular viruses (ChiSCV). Further metagenomic studies of animal samples will greatly increase our knowledge of viral diversity and evolution.


Article metrics loading...

Loading full text...

Full text loading...



  1. Allander, T., Emerson, S. U., Engle, R. E., Purcell, R. H. & Bukh, J.(2001). A virus discovery method incorporating DNase treatment and its application to the identification of two bovine parvovirus species. Proc Natl Acad Sci U S A 98, 11609–11614.[CrossRef] [Google Scholar]
  2. 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.[CrossRef] [Google Scholar]
  3. Benson, G.(1999). Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27, 573–580.[CrossRef] [Google Scholar]
  4. Blinkova, O., Kapoor, A., Victoria, J., Jones, M., Wolfe, N., Naeem, A., Shaukat, S., Sharif, S., Alam, M. M. & other authors(2009). Cardioviruses are genetically diverse and cause common enteric infections in South Asian children. J Virol 83, 4631–4641.[CrossRef] [Google Scholar]
  5. Breitbart, M., Salamon, P., Andresen, B., Mahaffy, J. M., Segall, A. M., Mead, D., Azam, F. & Rohwer, F.(2002). Genomic analysis of uncultured marine viral communities. Proc Natl Acad Sci U S A 99, 14250–14255.[CrossRef] [Google Scholar]
  6. Breitbart, M., Hewson, I., Felts, B., Mahaffy, J. M., Nulton, J., Salamon, P. & Rohwer, F.(2003). Metagenomic analyses of an uncultured viral community from human feces. J Bacteriol 185, 6220–6223.[CrossRef] [Google Scholar]
  7. Breitbart, M., Haynes, M., Kelley, S., Angly, F., Edwards, R. A., Felts, B., Mahaffy, J. M., Mueller, J., Nulton, J. & other authors(2008). Viral diversity and dynamics in an infant gut. Res Microbiol 159, 367–373.[CrossRef] [Google Scholar]
  8. Cai, C. Z., Han, L. Y., Ji, Z. L., Chen, X. & Chen, Y. Z.(2003a). SVM-Prot: web-based support vector machine software for functional classification of a protein from its primary sequence. Nucleic Acids Res 31, 3692–3697.[CrossRef] [Google Scholar]
  9. Cai, C. Z., Wang, W. L., Sun, L. Z. & Chen, Y. Z.(2003b). Protein function classification via support vector machine approach. Math Biosci 185, 111–122.[CrossRef] [Google Scholar]
  10. 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.[CrossRef] [Google Scholar]
  11. Chiu, C. Y., Greninger, A. L., Kanada, K., Kwok, T., Fischer, K. F., Runckel, C., Louie, J. K., Glaser, C. A., Yagi, S. & other authors(2008). Identification of cardioviruses related to Theiler's murine encephalomyelitis virus in human infections. Proc Natl Acad Sci U S A 105, 14124–14129.[CrossRef] [Google Scholar]
  12. Chu, P. W. & Helms, K.(1988). Novel virus-like particles containing circular single-stranded DNAs associated with subterranean clover stunt disease. Virology 167, 38–49.[CrossRef] [Google Scholar]
  13. Delwart, E. L.(2007). Viral metagenomics. Rev Med Virol 17, 115–131.[CrossRef] [Google Scholar]
  14. Edwards, R. A. & Rohwer, F.(2005). Viral metagenomics. Nat Rev Microbiol 3, 504–510.[CrossRef] [Google Scholar]
  15. Fauquet, C. M., Mayo, M. A., Maniloff, J., Desselberger, U. & Ball, L. A.(2005).Virus Taxonomy. Eighth Report of the International Committee on Taxonomy of Viruses. Amsterdam: Academic Press.
  16. Finkbeiner, S. R., Allred, A. F., Tarr, P. I., Klein, E. J., Kirkwood, C. D. & Wang, D.(2008). Metagenomic analysis of human diarrhea: viral detection and discovery. PLoS Pathog 4, e1000011[CrossRef] [Google Scholar]
  17. Gibbs, M. J. & Weiller, G. F.(1999). Evidence that a plant virus switched hosts to infect a vertebrate and then recombined with a vertebrate-infecting virus. Proc Natl Acad Sci U S A 96, 8022–8027.[CrossRef] [Google Scholar]
  18. 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] [Google Scholar]
  19. Harding, R. M., Burns, T. M. & Dale, J. L.(1991). Virus-like particles associated with banana bunchy top disease contain small single-stranded DNA. J Gen Virol 72, 225–230.[CrossRef] [Google Scholar]
  20. Hattermann, K., Schmitt, C., Soike, D. & Mankertz, A.(2003). Cloning and sequencing of Duck circovirus (DuCV). Arch Virol 148, 2471–2480.[CrossRef] [Google Scholar]
  21. Heath, L., Martin, D. P., Warburton, L., Perrin, M., Horsfield, W., Kingsley, C., Rybicki, E. P. & Williamson, A. L.(2004). Evidence of unique genotypes of beak and feather disease virus in southern Africa. J Virol 78, 9277–9284.[CrossRef] [Google Scholar]
  22. Kapoor, A., Victoria, J., Simmonds, P., Slikas, E., Chieochansin, T., Naeem, A., Shaukat, S., Sharif, S., Alam, M. M. & other authors(2008a). A highly prevalent and genetically diversified Picornaviridae genus in South Asian children. Proc Natl Acad Sci U S A 105, 20482–20487.[CrossRef] [Google Scholar]
  23. Kapoor, A., Victoria, J., Simmonds, P., Wang, C., Shafer, R. W., Nims, R., Nielsen, O. & Delwart, E.(2008b). A highly divergent picornavirus in a marine mammal. J Virol 82, 311–320.[CrossRef] [Google Scholar]
  24. Kapoor, A., Slikas, E., Simmonds, P., Chieochansin, T., Naeem, A., Shaukat, S., Alam, M. M., Sharif, S., Angez, M. & other authors(2009). A newly identified bocavirus species in human stool. J Infect Dis 199, 196–200.[CrossRef] [Google Scholar]
  25. Katul, L., Maiss, E., Morozov, S. Y. & Vetten, H. J.(1997). Analysis of six DNA components of the faba bean necrotic yellows virus genome and their structural affinity to related plant virus genomes. Virology 233, 247–259.[CrossRef] [Google Scholar]
  26. Keele, B. F., Van Heuverswyn, F., Li, Y., Bailes, E., Takehisa, J., Santiago, M. L., Bibollet-Ruche, F., Chen, Y., Wain, L. V. & other authors(2006). Chimpanzee reservoirs of pandemic and nonpandemic HIV-1. Science 313, 523–526.[CrossRef] [Google Scholar]
  27. Keele, B. F., Jones, J. H., Terio, K. A., Estes, J. D., Rudicell, R. S., Wilson, M. L., Learn, G. H., Beasley, T. M., Schumacher-Stankey, J. & other authors(2009). Increased mortality and AIDS-like immmunopathology in wild chimpanzees infected with SIVcpz. Nature 460, 515–519.[CrossRef] [Google Scholar]
  28. Klute, K. A., Nadler, S. A. & Stenger, D. C.(1996). Horseradish curly top virus is a distinct subgroup II geminivirus species with rep and C4 genes derived from a subgroup III ancestor. J Gen Virol 77, 1369–1378.[CrossRef] [Google Scholar]
  29. Lefeuvre, P., Lett, J. M., Varsani, A. & Martin, D. P.(2009). Widely conserved recombination patterns among single-stranded DNA viruses. J Virol 83, 2697–2707.[CrossRef] [Google Scholar]
  30. Li, L., Victoria, J., Kapoor, A., Naeem, A., Shaukat, S., Sharif, S., Alam, M. M., Angez, M., Zaidi, S. Z. & Delwart, E.(2009). Genomic characterization of novel human parechovirus type. Emerg Infect Dis 15, 288–291.[CrossRef] [Google Scholar]
  31. Liu, W., Worobey, M., Li, Y., Keele, B. F., Bibollet-Ruche, F., Guo, Y., Goepfert, P. A., Santiago, M. L., Ndjango, J. B. & other authors(2008). Molecular ecology and natural history of simian foamy virus infection in wild-living chimpanzees. PLoS Pathog 4, e1000097[CrossRef] [Google Scholar]
  32. Lole, K. S., Bollinger, R. C., Paranjape, R. S., Gadkari, D., Kulkarni, S. S., Novak, N. G., Ingersoll, R., Sheppard, H. W. & Ray, S. C.(1999). Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol 73, 152–160. [Google Scholar]
  33. Ma, C. M., Hon, C. C., Lam, T. Y., Li, V. Y., Wong, C. K., de Oliveira, T. & Leung, F. C.(2007). Evidence for recombination in natural populations of porcine circovirus type 2 in Hong Kong and mainland China. J Gen Virol 88, 1733–1737.[CrossRef] [Google Scholar]
  34. Morilla, G., Janssen, D., García-Andrés, S., Moriones, E., Cuadrado, I. M. & Bejarano, E. R.(2005). Pepper (Capsicum annuum) is a dead-end host for Tomato yellow leaf curl virus. Phytopathology 95, 1089–1097.[CrossRef] [Google Scholar]
  35. Nakamura, S., Yang, C. S., Sakon, N., Ueda, M., Tougan, T., Yamashita, A., Goto, N., Takahashi, K., Yasunaga, T. & other authors(2009). Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach. PLoS One 4, e4219[CrossRef] [Google Scholar]
  36. Nawaz-ul-Rehman, M. S. & Fauquet, C. M.(2009). Evolution of geminiviruses and their satellites. FEBS Lett 583, 1825–1832.[CrossRef] [Google Scholar]
  37. Neumann, E. J., Dobbinson, S. S., Welch, E. B. & Morris, R. S.(2007). Descriptive summary of an outbreak of porcine post-weaning multisystemic wasting syndrome (PMWS) in New Zealand. N Z Vet J 55, 346–352.[CrossRef] [Google Scholar]
  38. Ng, T. F., Manire, C., Borrowman, K., Langer, T., Ehrhart, L. & Breitbart, M.(2009). Discovery of a novel single-stranded DNA virus from a sea turtle fibropapilloma by using viral metagenomics. J Virol 83, 2500–2509.[CrossRef] [Google Scholar]
  39. Niagro, F. D., Forsthoefel, A. N., Lawther, R. P., Kamalanathan, L., Ritchie, B. W., Latimer, K. S. & Lukert, P. D.(1998). Beak and feather disease virus and porcine circovirus genomes: intermediates between the geminiviruses and plant circoviruses. Arch Virol 143, 1723–1744.[CrossRef] [Google Scholar]
  40. Okamoto, H.(2009). History of discoveries and pathogenicity of TT viruses. Curr Top Microbiol Immunol 331, 1–20. [Google Scholar]
  41. Padidam, M., Beachy, R. N. & Fauquet, C. M.(1995). Classification and identification of geminiviruses using sequence comparisons. J Gen Virol 76, 249–263.[CrossRef] [Google Scholar]
  42. Padidam, M., Sawyer, S. & Fauquet, C. M.(1999). Possible emergence of new geminiviruses by frequent recombination. Virology 265, 218–225.[CrossRef] [Google Scholar]
  43. Phenix, K. V., Weston, J. H., Ypelaar, I., Lavazza, A., Smyth, J. A., Todd, D., Wilcox, G. E. & Raidal, S. R.(2001). Nucleotide sequence analysis of a novel circovirus of canaries and its relationship to other members of the genus circovirus of the family Circoviridae. J Gen Virol 82, 2805–2809. [Google Scholar]
  44. Rohde, W., Randles, J. W., Langridge, P. & Hanold, D.(1990). Nucleotide sequence of a circular single-stranded DNA associated with coconut foliar decay virus. Virology 176, 648–651.[CrossRef] [Google Scholar]
  45. Santiago, M. L., Lukasik, M., Kamenya, S., Li, Y., Bibollet-Ruche, F., Bailes, E., Muller, M. N., Emery, M., Goldenberg, D. A. & other authors(2003). Foci of endemic simian immunodeficiency virus infection in wild-living eastern chimpanzees (Pan troglodytes schweinfurthii). J Virol 77, 7545–7562.[CrossRef] [Google Scholar]
  46. Segales, J. & Domingo, M.(2002). Postweaning multisystemic wasting syndrome (PMWS) in pigs. A review. Vet Q 24, 109–124.[CrossRef] [Google Scholar]
  47. Steinfeldt, T., Finsterbusch, T. & Mankertz, A.(2001). Rep and Rep′ protein of porcine circovirus type 1 bind to the origin of replication in vitro. Virology 291, 152–160.[CrossRef] [Google Scholar]
  48. Todd, D.(2004). Avian circovirus diseases: lessons for the study of PMWS. Vet Microbiol 98, 169–174.[CrossRef] [Google Scholar]
  49. Todd, D., McNulty, M. S., Adair, B. M. & Allan, G. M.(2001a). Animal circoviruses. Adv Virus Res 57, 1–70. [Google Scholar]
  50. 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.[CrossRef] [Google Scholar]
  51. Varsani, A., Shepherd, D. N., Monjane, A. L., Owor, B. E., Erdmann, J. B., Rybicki, E. P., Peterschmitt, M., Briddon, R. W., Markham, P. G. & other authors(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.[CrossRef] [Google Scholar]
  52. Vega-Rocha, S., Byeon, I. J., Gronenborn, B., Gronenborn, A. M. & Campos-Olivas, R.(2007a). Solution structure, divalent metal and DNA binding of the endonuclease domain from the replication initiation protein from porcine circovirus 2. J Mol Biol 367, 473–487.[CrossRef] [Google Scholar]
  53. Vega-Rocha, S., Gronenborn, B., Gronenborn, A. M. & Campos-Olivas, R.(2007b). Solution structure of the endonuclease domain from the master replication initiator protein of the nanovirus faba bean necrotic yellows virus and comparison with the corresponding geminivirus and circovirus structures. Biochemistry 46, 6201–6212.[CrossRef] [Google Scholar]
  54. Victoria, J. G., Kapoor, A., Dupuis, K., Schnurr, D. P. & Delwart, E. L.(2008). Rapid identification of known and new RNA viruses from animal tissues. PLoS Pathog 4, e1000163[CrossRef] [Google Scholar]
  55. Victoria, J. G., Kapoor, A., Li, L., Blinkova, O., Slikas, B., Wang, C., Naeem, A., Zaidi, S. & Delwart, E.(2009). Metagenomic analyses of viruses in stool samples from children with acute flaccid paralysis. J Virol 83, 4642–4651.[CrossRef] [Google Scholar]
  56. Wilson, M. E., Mainprize, T. H., Friesen, P. D. & Miller, L. K.(1987). Location, transcription, and sequence of a baculovirus gene encoding a small arginine-rich polypeptide. J Virol 61, 661–666. [Google Scholar]
  57. Worobey, M., Santiago, M. L., Keele, B. F., Ndjango, J. B., Joy, J. B., Labama, B. L., Dhed'A, B. D., Rambaut, A., Sharp, P. M. & other authors(2004). Origin of AIDS: contaminated polio vaccine theory refuted. Nature 428, 820[CrossRef] [Google Scholar]
  58. Zhang, T., Breitbart, M., Lee, W. H., Run, J. Q., Wei, C. L., Soh, S. W., Hibberd, M. L., Liu, E. T., Rohwer, F. & Ruan, Y.(2006). RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS Biol 4, e3[CrossRef] [Google Scholar]
  59. Zuker, M.(2003). Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31, 3406–3415.[CrossRef] [Google Scholar]

Data & Media loading...

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