1887

Abstract

The use of metagenomics for virus discovery in clinical samples has opened new opportunities for understanding the aetiology of unexplained illness. This study explores the potential of this sequence-independent approach in a public-health setting, by systematic analysis of samples cultured from patients with unexplained illness through a combination of PCR-based assays and viral metagenomics. In total, 1834 cell-culture isolates were collected between 1994 and 2007 through the Enterovirus Surveillance programme in the Netherlands. During the 13 year period, seven samples that exhibited reproducible cytopathogenic effects in cell culture tested negative in standard PCR assays for a range of viruses. In order to fill the diagnostic gap, viral metagenomics was applied to these culture supernatants, resulting in the rapid identification of viruses in all of the samples. The unexplained samples contained BK polyomavirus, herpes simplex virus, Newcastle disease virus and the recently discovered Saffold viruses (SAFV) (which dominated the unexplained samples; =4). The full genomic sequences of four SAFV genotype 3 (SAFV-3) viruses, which share 88–93 % nucleotide identity with known SAFV-3 viruses, are reported. Further screening for SAFV in additional cultured, unidentified clinical isolates from 2008 and 2009 resulted in identification of another SAFV-positive sample. Although the pathogenicity of the identified viruses has not been established, this study demonstrates that viral metagenomics is a powerful tool that can be integrated into public-health monitoring efforts to investigate unidentified viruses in cell cultures from clinical isolates where standard PCR assays fail to detect viruses.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/vir.0.024612-0
2010-11-01
2019-11-21
Loading full text...

Full text loading...

/deliver/fulltext/jgv/91/11/2846.html?itemId=/content/journal/jgv/10.1099/vir.0.024612-0&mimeType=html&fmt=ahah

References

  1. Abed, Y. & Boivin, G. ( 2008; ). New Saffold cardioviruses in 3 children, Canada. Emerg Infect Dis 14, 834–836.[CrossRef]
    [Google Scholar]
  2. Allander, T., Tammi, M. T., Eriksson, M., Bjerkner, A., Tiveljung-Lindell, A. & Andersson, B. ( 2005; ). Cloning of a human parvovirus by molecular screening of respiratory tract samples. Proc Natl Acad Sci U S A 102, 12891–12896.[CrossRef]
    [Google Scholar]
  3. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. ( 1997; ). Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25, 3389–3402.[CrossRef]
    [Google Scholar]
  4. Angly, F. E., Felts, B., Breitbart, M., Salamon, P., Edwards, R. A., Carlson, C., Chan, A. M., Haynes, M., Kelley, S. & other authors ( 2006; ). The marine viromes of four oceanic regions. PLoS Biol 4, e368.[CrossRef]
    [Google Scholar]
  5. 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]
  6. Blinkova, O., Victoria, J., Li, Y., Keele, B. F., Sanz, C., Ndjango, J. B., 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]
    [Google Scholar]
  7. Breitbart, M. & Rohwer, F. ( 2005; ). Method for discovering novel DNA viruses in blood using viral particle selection and shotgun sequencing. Biotechniques 39, 729–736.[CrossRef]
    [Google Scholar]
  8. 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]
  9. Breitbart, M., Felts, B., Kelley, S., Mahaffy, J. M., Nulton, J., Salamon, P. & Rohwer, F. ( 2004; ). Diversity and population structure of a near-shore marine-sediment viral community. Proc Biol Sci 271, 565–574.[CrossRef]
    [Google Scholar]
  10. 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]
  11. Cann, A. J., Fandrich, S. E. & Heaphy, S. ( 2005; ). Analysis of the virus population present in equine faeces indicates the presence of hundreds of uncharacterized virus genomes. Virus Genes 30, 151–156.[CrossRef]
    [Google Scholar]
  12. 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]
  13. Chiu, C. Y., Greninger, A., Chen, E., Haggerty, T. D., Parsonnet, J., Delwart, E., DeRisi, J. L. & Ganem, D. ( 2010; ). Cultivation and serological characterization of a human Theiler's-like cardiovirus associated with diarrheal disease. J Virol 84, 4407–4414.[CrossRef]
    [Google Scholar]
  14. Conyn-van Spaendonck, M. A., Oostvogel, P. M., van Loon, A. M., van Wijngaarden, J. K. & Kromhout, D. ( 1996; ). Circulation of poliovirus during the poliomyelitis outbreak in the Netherlands in 1992–1993. Am J Epidemiol 143, 929–935.[CrossRef]
    [Google Scholar]
  15. Cox-Foster, D. L., Conlan, S., Holmes, E. C., Palacios, G., Evans, J. D., Moran, N. A., Quan, P. L., Briese, T., Hornig, M. & other authors ( 2007; ). A metagenomic survey of microbes in honey bee colony collapse disorder. Science 318, 283–287.[CrossRef]
    [Google Scholar]
  16. Delwart, E. L. ( 2007; ). Viral metagenomics. Rev Med Virol 17, 115–131.[CrossRef]
    [Google Scholar]
  17. Dinsdale, E. A., Edwards, R. A., Hall, D., Angly, F., Breitbart, M., Brulc, J. M., Furlan, M., Desnues, C., Haynes, M. & other authors ( 2008; ). Functional metagenomic profiling of nine biomes. Nature 452, 629–632.[CrossRef]
    [Google Scholar]
  18. Djikeng, A., Kuzmickas, R., Anderson, N. G. & Spiro, D. J. ( 2009; ). Metagenomic analysis of RNA viruses in a fresh water lake. PLoS One 4, e7264.[CrossRef]
    [Google Scholar]
  19. Drexler, J. F., Luna, L. K., Stocker, A., Almeida, P. S., Ribeiro, T. C., Petersen, N., Herzog, P., Pedroso, C., Huppertz, H. I. & other authors ( 2008; ). Circulation of 3 lineages of a novel Saffold cardiovirus in humans. Emerg Infect Dis 14, 1398–1405.[CrossRef]
    [Google Scholar]
  20. Drexler, J. F., Baumgarte, S., de Souza Luna, L. K., Stocker, A., Almeida, P. S., Ribeiro, T. C., Petersen, N., Herzog, P., Pedroso, C. & other authors ( 2010; ). Genomic features and evolutionary constraints in Saffold-like cardioviruses. J Gen Virol 91, 1418–1427.[CrossRef]
    [Google Scholar]
  21. Edwards, R. A. & Rohwer, F. ( 2005; ). Viral metagenomics. Nat Rev Microbiol 3, 504–510.[CrossRef]
    [Google Scholar]
  22. Hall, T. A. ( 1999; ). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41, 95–98.
    [Google Scholar]
  23. Jones, M. S., Kapoor, A., Lukashov, V. V., Simmonds, P., Hecht, F. & Delwart, E. ( 2005; ). New DNA viruses identified in patients with acute viral infection syndrome. J Virol 79, 8230–8236.[CrossRef]
    [Google Scholar]
  24. Jones, M. S., II, Harrach, B., Ganac, R. D., Gozum, M. M., Dela Cruz, W. P., Riedel, B., Pan, C., Delwart, E. L. & Schnurr, D. P. ( 2007; ). New adenovirus species found in a patient presenting with gastroenteritis. J Virol 81, 5978–5984.[CrossRef]
    [Google Scholar]
  25. Kapoor, A., Victoria, J., Simmonds, P., Wang, C., Shafer, R. W., Nims, R., Nielsen, O. & Delwart, E. ( 2008; ). A highly divergent picornavirus in a marine mammal. J Virol 82, 311–320.[CrossRef]
    [Google Scholar]
  26. Leland, D. S. & Ginocchio, C. C. ( 2007; ). Role of cell culture for virus detection in the age of technology. Clin Microbiol Rev 20, 49–78.[CrossRef]
    [Google Scholar]
  27. Li, L., Kapoor, A., Slikas, B., Bamidele, O. S., Wang, C., Shaukat, S., Masroor, M. A., Wilson, M. L., Ndjango, J. B. & other authors ( 2010; ). Multiple diverse circoviruses infect farm animals and are commonly found in human and chimpanzee feces. J Virol 84, 1674–1682.[CrossRef]
    [Google Scholar]
  28. Liang, Z., Kumar, A. S., Jones, M. S., Knowles, N. J. & Lipton, H. L. ( 2008; ). Phylogenetic analysis of the species Theilovirus: emerging murine and human pathogens. J Virol 82, 11545–11554.[CrossRef]
    [Google Scholar]
  29. 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]
  30. Ng, T. F., Manire, C., Borrowman, K., Langer, T., Ehrhart, L. & Breitbart, M. ( 2009a; ). 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]
  31. Ng, T. F., Suedmeyer, W. K., Wheeler, E., Gulland, F. & Breitbart, M. ( 2009b; ). Novel anellovirus discovered from a mortality event of captive California sea lions. J Gen Virol 90, 1256–1261.[CrossRef]
    [Google Scholar]
  32. Nix, W. A., Oberste, M. S. & Pallansch, M. A. ( 2006; ). Sensitive, seminested PCR amplification of VP1 sequences for direct identification of all enterovirus serotypes from original clinical specimens. J Clin Microbiol 44, 2698–2704.[CrossRef]
    [Google Scholar]
  33. Oberste, M. S., Maher, K., Kilpatrick, D. R., Flemister, M. R., Brown, B. A. & Pallansch, M. A. ( 1999; ). Typing of human enteroviruses by partial sequencing of VP1. J Clin Microbiol 37, 1288–1293.
    [Google Scholar]
  34. Oostvogel, P. M., van Wijngaarden, J. K., van der Avoort, H. G., Mulders, M. N., Conyn-van Spaendonck, M. A., Rumke, H. C., van Steenis, G. & van Loon, A. M. ( 1994; ). Poliomyelitis outbreak in an unvaccinated community in the Netherlands, 1992–93. Lancet 344, 665–670.[CrossRef]
    [Google Scholar]
  35. Ren, L., Gonzalez, R., Xiao, Y., Xu, X., Chen, L., Vernet, G., Paranhos-Baccala, G., Jin, Q. & Wang, J. ( 2009; ). Saffold cardiovirus in children with acute gastroenteritis, Beijing, China. Emerg Infect Dis 15, 1509–1511.[CrossRef]
    [Google Scholar]
  36. Rohwer, F. & Edwards, R. ( 2002; ). The phage proteomic tree: a genome-based taxonomy for phage. J Bacteriol 184, 4529–4535.[CrossRef]
    [Google Scholar]
  37. Svraka, S., Duizer, E., Vennema, H., de Bruin, E., van der Veer, B., Dorresteijn, B. & Koopmans, M. ( 2007; ). Etiological role of viruses in outbreaks of acute gastroenteritis in the Netherlands from 1994 through 2005. J Clin Microbiol 45, 1389–1394.[CrossRef]
    [Google Scholar]
  38. Svraka, S., Duizer, E., Egberink, H., Dekkers, J., Vennema, H. & Koopmans, M. ( 2009a; ). A new generic real-time reverse transcription polymerase chain reaction assay for vesiviruses; vesiviruses were not detected in human samples. J Virol Methods 157, 1–7.[CrossRef]
    [Google Scholar]
  39. Svraka, S., van der Veer, B., Duizer, E., Dekkers, J., Koopmans, M. & Vennema, H. ( 2009b; ). Novel approach for detection of enteric viruses to enable syndrome surveillance of acute viral gastroenteritis. J Clin Microbiol 47, 1674–1679.[CrossRef]
    [Google Scholar]
  40. Tamura, K., Dudley, J., Nei, M. & Kumar, S. ( 2007; ). mega4: molecular evolutionary genetics analysis (mega) software version 4.0. Mol Biol Evol 24, 1596–1599.[CrossRef]
    [Google Scholar]
  41. Thompson, J. D., Higgins, D. G. & Gibson, T. J. ( 1994; ). clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673–4680.[CrossRef]
    [Google Scholar]
  42. Thurber, R. V., Haynes, M., Breitbart, M., Wegley, L. & Rohwer, F. ( 2009; ). Laboratory procedures to generate viral metagenomes. Nat Protoc 4, 470–483.[CrossRef]
    [Google Scholar]
  43. van der Hoek, L., Pyrc, K., Jebbink, M. F., Vermeulen-Oost, W., Berkhout, R. J., Wolthers, K. C., Wertheim-van Dillen, P. M., Kaandorp, J., Spaargaren, J. & Berkhout, B. ( 2004; ). Identification of a new human coronavirus. Nat Med 10, 368–373.[CrossRef]
    [Google Scholar]
  44. van der Sanden, S., de Bruin, E., Vennema, H., Swanink, C., Koopmans, M. & van der Avoort, H. ( 2008; ). Prevalence of human parechovirus in the Netherlands in 2000 to 2007. J Clin Microbiol 46, 2884–2889.[CrossRef]
    [Google Scholar]
  45. van der Sanden, S., Koopmans, M., Uslu, G. & van der Avoort, H. ( 2009; ). Epidemiology of enterovirus 71 in the Netherlands, 1963 to 2008. J Clin Microbiol 47, 2826–2833.[CrossRef]
    [Google Scholar]
  46. van Gageldonk-Lafeber, A. B., Heijnen, M. L., Bartelds, A. I., Peters, M. F., van der Plas, S. M. & Wilbrink, B. ( 2005; ). A case–control study of acute respiratory tract infection in general practice patients in the Netherlands. Clin Infect Dis 41, 490–497.[CrossRef]
    [Google Scholar]
  47. 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]
  48. Willner, D., Furlan, M., Haynes, M., Schmieder, R., Angly, F. E., Silva, J., Tammadoni, S., Nosrat, B., Conrad, D. & Rohwer, F. ( 2009; ). Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals. PLoS One 4, e7370.[CrossRef]
    [Google Scholar]
  49. Xu, Z. Q., Cheng, W. X., Qi, H. M., Cui, S. X., Jin, Y. & Duan, Z. J. ( 2009; ). New Saffold cardiovirus in children, China. Emerg Infect Dis 15, 993–994.[CrossRef]
    [Google Scholar]
  50. Zaoutis, T. & Klein, J. D. ( 1998; ). Enterovirus infections. Pediatr Rev 19, 183–191.[CrossRef]
    [Google Scholar]
  51. 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]
  52. Zoll, J., Erkens Hulshof, S., Lanke, K., Verduyn Lunel, F., Melchers, W. J., Schoondermark-van de Ven, E., Roivainen, M., Galama, J. M. & van Kuppeveld, F. J. ( 2009; ). Saffold virus, a human Theiler's-like cardiovirus, is ubiquitous and causes infection early in life. PLoS Pathog 5, e1000416.[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/vir.0.024612-0
Loading
/content/journal/jgv/10.1099/vir.0.024612-0
Loading

Data & Media loading...

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