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research article

Application of broad-spectrum resequencing microarray for genotyping rhabdoviruses

Dacheux, Laurent
•
Berthet, Nicolas
•
Dissard, Gabriel
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2010
Journal of virology

The rapid and accurate identification of pathogens is critical in the control of infectious disease. To this end, we analyzed 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, 12 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 suggest 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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Type
research article
DOI
10.1128/JVI.00771-10
PubMed ID

20610710

Author(s)
Dacheux, Laurent
Berthet, Nicolas
Dissard, Gabriel
Holmes, Edward C
Delmas, Olivier
Larrous, Florence
Guigon, Ghislaine
Dickinson, Philip
Faye, Ousmane
Sall, Amadou A
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Date Issued

2010

Published in
Journal of virology
Volume

84

Issue

18

Start page

9557

End page

74

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
UPCOL  
Available on Infoscience
September 7, 2010
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/53076
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