Detection and Identification of Common Food-Borne Viruses with a Tiling Microarray

Chen, Haifeng; Mammel, Mark; Kulka, Mike; Patel, Isha; Jackson, Scott; Goswami, Biswendu B.

Despite recent findings that suggest the growth phenotype of some food-borne virus strains is linked to the activation of the interferon controlled RNase L system [13] most food-borne viral pathogens remain refractory to growth in cultured cells [5, 14] . Indeed, any existing methods are currently impractical for rapid virus detection and identification, particularly when there is a need to applied detection methods for foods that are highly perishable and can contain cell culture inhibitory substances [5, 14] . For these reasons, there is an urgent need for the development of viral genome based rapid detection and identification methods for food-borne viruses with discriminatory power at the level of species and strain/genotype (or genogroup). Based on our previous results using a lower density array [15] as well as the work of others on non-food-borne viral pathogens [16] [17] [18] , microarray based methods offer one such methodological approach. Initial attempts at virus detection and typing by microarray hybridization were limited to detection of known mutations in the viral genome based on hybridization to a "handful" of oligonucleotide probes immobilized on a solid support. In the current investigation, we have successfully developed and applied a high density microarray to detection and identification of multiple viral species as well as virus strains within the same species. In addition, our results indicate the capacity of this methodology to discriminate between multiple virus species contained within the same sample.