A Microarray Based Approach for the Identification of Common Foodborne Viruses

Ayodeji, Mobolanle; Kulka, Michael; Jackson, Scott A; Patel, Isha; Mammel, Mark; Cebula, Thomas A; Goswami, Biswendu B

differences. For example, differences in signal height could be attributed to differing hybridization efficiencies between two different experiments. Indeed, a target derived from in vitro synthesized RNA from pHAV/7 (representing in vitro replication of the viral genome) was indistinguishable from plasmid derived target, or the virus following several rounds of replication in culture except for the peak height (data not shown). We pursued, therefore, an alternative method of analysis because the tiling array design offers the potential to distinguish between these closely related strains following hybridization by i) determining the normalized probe intensities for each target, and ii) plotting the change in signal intensity of hybridization by each target to the same probe set as the ratio (fold-change in probe intensity) vs the individual probes. As discussed by Jackson et al. [15] , this method of analysis can reveal distinct peaks with defined slopes (above background/signal noise) where changes in signal strength would occur with probes tiled further up or down stream of the nucleotide change. The presence of a mutation in the genome causes a destabilization of a number of probes around the mutation, which can be identified by the appearance of well defined peaks. Therefore, this method of analysis offers the potential to differentiate closely related strains of virus belonging to subgenotype Ib at the level of individual nucleotide differences, thereby producing data that can be used to tell them apart.