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

probe hybridization (normalized) intensities for CVA3 and CVA5 derived targets compared to those values obtained following hybridization with a CVB1 target (data not shown). As shown in Fig. (7, panels B and C) , this is also observed following conversion to average probe intensity. The peak average probe intensity for these hybridizations is approximately 2750 units and 900 units with CVA3 and CVA5 targets, respectively. The results indicate that in the absence of matching probe sets on the array the sequence heterogeneity between these CV targets and the existing probe sets precludes the establishment of any strong or efficient hybridization to a single probe set. It is important to note, however, that neither of these targets hybridizes with any significance to non-CV probe sets suggesting that the genetic diversity between CV targets and probe sets does not prevent or obscure virus target group (i.e. CV) identification. In addition, these hybridization profiles are not only distinct from B1 (Fig. 7) but also from one another suggesting the possibility that unique hybridization profile patterns (calculated as normalized and/or averaged probe intensity) could be used for CV serotype target identification. The results from Fig. (7) also suggest that in a single experiment it is possible to identify whether a virus belongs to group A or group B. Indeed, identification of coxsackieviruses at the level of serotype strain may be possible without single nucleotide polymorphism (SNP) analysis and limited only by the number of probe sequences/sets present on the array.