1887

Abstract

This paper reports significant improvements in the efficacy of sequence-independent amplification and quality of sequencing of viruses with segmented double-stranded RNA (dsRNA) genomes. We demonstrate that most remaining bottlenecks in dsRNA virus genome characterization have now been eliminated. Both the amplification and sequencing technologies used require no previous sequence knowledge of the viral dsRNA, there is no longer a need to separate genome segments or amplicons and the sequence-determined bias observed in cloning has been overcome. Combining very efficient genome amplification with pyrophosphate-based 454 (GS20/FLX) sequencing enabled sequencing of complete segmented dsRNA genomes and accelerated the sequence analysis of the amplified viral genomes. We report the complete consensus sequence of seven viruses from four different dsRNA virus groups, which include the first complete sequence of the genome of equine encephalosis virus (EEV), the first complete sequence of an African horsesickness virus (AHSV) genome determined directly from a blood sample and a complete human rotavirus genome determined from faeces. We also present the first comparison between the complete consensus sequence of a virulent and an attenuated strain of AHSV1. Ultra-deep sequencing (>400-fold coverage) of the AHSV1 reference and attenuated strains revealed different ratios of reassortants in the reference strain and allowed quasispecies detection in the plaque-purified attenuated strain of AHSV1. This approach amounts to a paradigm shift in dsRNA virus research, since it is sensitive and specific enough for comprehensive investigations of the evolution and genetic diversity in dsRNA virus populations.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/vir.0.009381-0
2009-06-01
2019-09-18
Loading full text...

Full text loading...

/deliver/fulltext/jgv/90/6/1423.html?itemId=/content/journal/jgv/10.1099/vir.0.009381-0&mimeType=html&fmt=ahah

References

  1. Attoui, H., Billoir, F., Cantaloube, J. F., Biagini, P., de Micco, P. & de Lamballerie, X. ( 2000; ). Strategies for the sequence determination of viral dsRNA genomes. J Virol Methods 89, 147–158.[CrossRef]
    [Google Scholar]
  2. Bhattacharya, B., Noad, R. & Roy, P. ( 2007; ). Interaction between Bluetongue virus outer capsid protein VP2 and vimentin is necessary for virus egress. Virol J 4, 7 [CrossRef]
    [Google Scholar]
  3. Bigot, Y., Drezen, J. M., Sizaret, P. Y., Rabouille, A., Hamelin, M. H. & Periquet, G. ( 1995; ). The genome segments of DpRV, a commensal reovirus of the wasp Diadromus pulchellus (Hymenoptera). Virology 210, 109–119.[CrossRef]
    [Google Scholar]
  4. Bonfield, J. K., Smith, K. F. & Staden, R. ( 1995; ). A new DNA sequence assembly program. Nucleic Acids Res 23, 4992–4999.[CrossRef]
    [Google Scholar]
  5. Bonneau, K. R., Mullens, B. A. & MacLachlan, N. J. ( 2001; ). Occurrence of genetic drift and founder effect during quasispecies evolution of the VP2 and NS3/NS3A genes of Bluetongue virus upon passage between sheep, cattle, and Culicoides sonorensis. J Virol 75, 8298–8305.[CrossRef]
    [Google Scholar]
  6. Cashdollar, L. W., Esparza, J., Hudson, G. R., Chmelo, R., Lee, P. W. & Joklik, W. K. ( 1982; ). Cloning the double-stranded RNA genes of reovirus: sequence of the cloned S2 gene. Proc Natl Acad Sci U S A 79, 7644–7648.[CrossRef]
    [Google Scholar]
  7. Erasmus, B. J. ( 1973; ). The pathogenesis of African horsesickness. In Proceedings of the Third International Conference on Equine Infectious Diseases. Basel, Switzerland: Karger.
  8. Fasina, F., Potgieter, A. C., Ibironke, A., Bakod, B., Bwala, D. & Kumbish, P. ( 2008; ). First report of an outbreak of African horsesickness virus serotype 2 in the Northern hemisphere. J Equine Vet Sci 28, 167–170.[CrossRef]
    [Google Scholar]
  9. Harrison, B. & Zimmerman, S. B. ( 1984; ). Polymer-stimulated ligation: enhanced ligation of oligo- and polynucleotides by T4 RNA ligase in polymer solutions. Nucleic Acids Res 12, 8235–8251.[CrossRef]
    [Google Scholar]
  10. Laemmli, U. K. ( 1970; ). Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227, 680–685.[CrossRef]
    [Google Scholar]
  11. Lambden, P. R., Cooke, S. J., Caul, E. O. & Clarke, I. N. ( 1992; ). Cloning of noncultivatable human rotavirus by single primer amplification. J Virol 66, 1817–1822.
    [Google Scholar]
  12. Maan, S., Rao, S., Maan, N. S., Anthony, S. J., Attoui, H., Samuel, A. R. & Mertens, P. P. ( 2007; ). Rapid cDNA synthesis and sequencing techniques for the genetic study of bluetongue and other dsRNA viruses. J Virol Methods 143, 132–139.[CrossRef]
    [Google Scholar]
  13. Margulies, M., Egholm, M., Altman, W. E., Attiya, S., Bader, J. S., Bemben, L. A., Berka, J., Braverman, M. S., Chen, Y. J. & other authors ( 2005; ). Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376–380.
    [Google Scholar]
  14. Matthijnssens, J., Ciarlet, M., Heiman, E., Arijs, I., Delbeke, T., McDonald, S. M., Palombo, E. A., Iturriza-Gómara, M., Maes, P. & other authors ( 2008; ). Full genome-based classification of rotaviruses reveals a common origin between human Wa-like and porcine rotavirus strains and human DS-1-like and bovine rotavirus strains. J Virol 82, 3204–3219.[CrossRef]
    [Google Scholar]
  15. Mertens, P. ( 2004; ). The dsRNA viruses. Virus Res 101, 3–13.[CrossRef]
    [Google Scholar]
  16. Mertens, P. P. C., Duncan, R., Attoui, H. & Dermody, T. S. ( 2005; ). Reoviridae. In Virus Taxonomy, VIIIth Report of the ICTV, pp. 447–454. Edited by C. M. Fauquet, M. A. Mayo, J. Maniloff, U. Desselberger & L. A. Ball. London: Elsevier.
  17. Meyer, M., Stenzel, U., Myles, S., Prufer, K. & Hofreiter, M. ( 2007; ). Targeted high-throughput sequencing of tagged nucleic acid samples. Nucleic Acids Res 35, e97 [CrossRef]
    [Google Scholar]
  18. Mortola, E., Noad, R. & Roy, P. ( 2004; ). Bluetongue virus outer capsid proteins are sufficient to trigger apoptosis in mammalian cells. J Virol 78, 2875–2883.[CrossRef]
    [Google Scholar]
  19. Potgieter, A. C., Steele, A. D. & van Dijk, A. A. ( 2002; ). Cloning of complete genome sets of six dsRNA viruses using an improved cloning method for large dsRNA genes. J Gen Virol 83, 2215–2223.
    [Google Scholar]
  20. Rao, C. D., Kiuchi, A. & Roy, P. ( 1983; ). Homologous terminal sequences of the genome double-stranded RNAs of bluetongue virus. J Virol 46, 378–383.
    [Google Scholar]
  21. Roy, P., Mertens, P. P. & Casal, I. ( 1994; ). African horse sickness virus structure. Comp Immunol Microbiol Infect Dis 17, 243–273.[CrossRef]
    [Google Scholar]
  22. Vreede, F. T., Cloete, M., Napier, G. B., van Dijk, A. A. & Viljoen, G. J. ( 1998; ). Sequence-independent amplification and cloning of large dsRNA virus genome segments by poly(dA)-oligonucleotide ligation. J Virol Methods 72, 243–247.[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/vir.0.009381-0
Loading
/content/journal/jgv/10.1099/vir.0.009381-0
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