title: 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.
authors.affiliation: Institut Pasteur, Lyssavirus Dynamics and Host Adaptation Unit, Paris, France.
authors.forename: Laurent
authors.initials: L
authors.lastname: Dacheux
authors.forename: Nicolas
authors.initials: N
authors.lastname: Berthet
authors.forename: Gabriel
authors.initials: G
authors.lastname: Dissard
authors.forename: Edward C
authors.initials: EC
authors.lastname: Holmes
authors.forename: Olivier
authors.initials: O
authors.lastname: Delmas
authors.forename: Florence
authors.initials: F
authors.lastname: Larrous
authors.forename: Ghislaine
authors.initials: G
authors.lastname: Guigon
authors.forename: Philip
authors.initials: P
authors.lastname: Dickinson
authors.forename: Ousmane
authors.initials: O
authors.lastname: Faye
authors.forename: Amadou A
authors.initials: AA
authors.lastname: Sall
authors.forename: Iain G
authors.initials: IG
authors.lastname: Old
authors.forename: Katherine
authors.initials: K
authors.lastname: Kong
authors.forename: Giulia C
authors.initials: GC
authors.lastname: Kennedy
authors.forename: Jean-Claude
authors.initials: JC
authors.lastname: Manuguerra
authors.forename: Stewart T
authors.initials: ST
authors.lastname: Cole
authors.forename: Valérie
authors.initials: V
authors.lastname: Caro
authors.forename: Antoine
authors.initials: A
authors.lastname: Gessain
authors.forename: Hervé
authors.initials: H
authors.lastname: Bourhy
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D005838:Genotype; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics*; D012209:Rhabdoviridae / Q000145:classification* / Q000235:genetics*; D018353:Rhabdoviridae Infections / Q000175:diagnosis* / Q000662:veterinary* / Q000821:virology; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods*; D014773:Virology / Q000379:methods*
chemical_list: D012367:RNA, Viral