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

PCR Primers. Two primers, 3399 -3423 (forward) and 7084 -7105 (reverse), were used to amplify an approximately 3.7 kb region of the HAV genome [4, 6, 20] . Tables 1 and 2 show the sequences around the primer binding sites of selected HAV strains represented on the array. Tables 3 and 4 contain the sequence alignments at the forward and reverse Dendrogram showing the grouping of CV serotype strains based on their genetic relatedness for developing viral probe sequences to be used for oligonucleotide design. CV strains are identified by their GenBank accession number and their respective complete sequences were used to generate the dendrogram. CV serotypes are given in parenthesis following the accession numbers. Brackets encompass strain sequences selected to derive a group consensus sequence while arrows identify group individual (i.e. non-consensus) strain sequences for probe set development. Group sequences are designated by the numbers 1-8 followed by the probe set identifier (within parentheses). Brackets (outer right) indicate which human enterovirus species (HEA, HEB and HEC) are represented by the CV serotype strains used to develop the dendrogram.