Application of broad-spectrum resequencing microarray for genotyping rhabdoviruses.

Abstract:

: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.

journal_name

J Virol

journal_title

Journal of virology

authors

Dacheux L,Berthet N,Dissard G,Holmes EC,Delmas O,Larrous F,Guigon G,Dickinson P,Faye O,Sall AA,Old IG,Kong K,Kennedy GC,Manuguerra JC,Cole ST,Caro V,Gessain A,Bourhy H

doi

10.1128/JVI.00771-10

subject

Has Abstract

pub_date

2010-09-01 00:00:00

pages

9557-74

issue

18

eissn

0022-538X

issn

1098-5514

pii

JVI.00771-10

journal_volume

84

pub_type

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