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

As members of the positive-stranded RNA virus family Picornaviridae, Hepatitis A virus and coxsackievirus belong to the genera Hepatovirus and Enterovirus, respectively. At the nucleotide level there is substantial genetic diversity between these two groups with a greater within group diversity observed for coxsackieviruses than for hepatitis virus strains. Indeed, the coxsackievirus genomes are much less conserved and mutations are distributed throughout the genome [23] . Sequence analyses of small segments of different strains of HAV have led to the recognition of six genotypes (I to VI) of this virus [24] . Genotypes I, II and III have been further subdivided into two subgenotypes, a and b [24, 25] . Within each genotype the strains have greater than 85% sequence homology, whereas subgenotypes may differ from each other in up to 7.5% of nucleotide positions. Genotype I is the most prevalent HAV genotype world wide [25] . For the present investigation, complete HAV genome sequences available at the time of chip design and construction belonging to genotypes I and II were clustered into five groups (Fig. 1) . Two of these groups contain subgenotype Ia (groups 4 and 5) while sequences belonging to subgenotype Ib were clustered into two groups (1 and 2) and a single sequence of genotype II was designated group 3 ( Fig. 1) .