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.

in the genome by synthesizing four different oligonucleotides containing each base (N=A,T,G,C) at the central position [20] . The alternative and simpler array, called a tiling array, can cover an entire viral genome using overlapping oligonucleotides at two base intervals requiring one eighth the number of oligoprobes necessary to identify a change in the genome. In both cases oligonucleotides are synthesized in situ and immobilized on a solid support by a process called photolithography, whereby hundreds of thousands to millions of probes can be arrayed in a short time [19] . In the tiling array, a nucleotide change in the genome is identified by comparing the hybridization profile of a test virus to that of a reference strain matching the probe sequences. By avoiding PCR based target synthesis, the process is made independent of the sequence of the virus present in the sample (Fig. 1) .