Application of Broad-Spectrum Resequencing Microarray for Genotyping Rhabdoviruses. - Institut Pasteur Access content directly
Journal Articles Journal of Virology Year : 2010

Application of Broad-Spectrum Resequencing Microarray for Genotyping Rhabdoviruses.

Philip Dickinson
  • Function : Author
Katherine Kong
  • Function : Author
Giulia C Kennedy
  • Function : Author

Abstract

The rapid and accurate identification of pathogens is critical in the control of infectious disease. To this end we analysed the capacity for viral detection and identification of a newly described high density resequencing microarray (RMA), termed PathogenID, which was designed for multiple pathogen detection using database similarity searching. We focused on one of the largest and most diverse viral families described to date, the family Rhabdoviridae. We demonstrate that this approach has the potential to identify both known and related viruses for which precise sequence information is unavailable. In particular, we demonstrate that a strategy based on consensus sequence determination for analysis of RMA output data enabled successful detection of viruses exhibiting up to 26% nucleotide divergence with the closest sequence tiled on the array. Using clinical specimens obtained from rabid patients and animals, this method also shows a high species-level concordance with standard reference assays, indicating that it is amenable for the development of diagnostic assays. Finally, twelve animal rhabdoviruses which were currently unclassified, unassigned, or assigned as tentative species within the family Rhabdoviridae were successfully detected. These new data allowed an unprecedented phylogenetic analysis of 106 rhabdoviruses, and further suggests that the principles and methodology developed here may be used for the broad-spectrum surveillance and the broader-scale investigation of biodiversity in the viral world.
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Dates and versions

pasteur-00507428 , version 1 (30-01-2011)

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Laurent Dacheux, Nicolas Berthet, Gabriel Dissard, Edward C Holmes, Olivier Delmas, et al.. Application of Broad-Spectrum Resequencing Microarray for Genotyping Rhabdoviruses.. Journal of Virology, 2010, epub ahead of print. ⟨10.1128/JVI.00771-10⟩. ⟨pasteur-00507428⟩
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