A Microarray Based Approach for the Identification of Common Foodborne Viruses
Mobolanle Ayodeji, Michael Kulka, Scott A Jackson, Isha Patel, Mark Mammel, Thomas A Cebula§, Biswendu B Goswami*
Division of Molecular Biology, Office of Applied Research and Safety Assessment (OARSA), Food And Drug Administration, 8301 Muirkirk Road, Laurel, Maryland, 20708, USA
An oligonucleotide array (microarray) incorporating 13,000 elements representing selected strains of hepatitis A virus (HAV), human coxsackieviruses A and B (CVA and CVB), genogroups I and II of Norovirus (NV), and human rotavirus (RV) gene segments 3,4,10, and 11 was designed based on the principle of tiling. Each oligonucleotide was 29 bases long, starting at every 5th base of every sequence, resulting in an overlap of 24 bases in two consecutive oligonucleotides. The applicability of the array for virus identification was examined using PCR amplified products from multiple HAV and CV strains. PCR products labeled with biotin were hybridized to the array, and the biotin was detected using a brief reaction with Cy3-labeled streptavidin, the array subjected to laser scanning, and the hybridization data plotted as fluorescence intensity against each oligonucleotide in the array. The combined signal intensities of all probes representing a particular strain of virus were calculated and plotted against all virus strains identified on a linear representation of the array. The profile of the total signal intensity identified the strain that is most likely represented in the amplified cDNA target. The results obtained with HAV and CV indicated that the hybridization profile thus generated can be used to identify closely related viral strains. This represents a significant improvement over current methods for virus identification using PCR amplification and amplicon sequencing.
open-access license: This is an open access article licensed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/) which permits unrestricted, non-commercial use, distribution and reproduction in any medium, provided the work is properly cited.
* Address correspondence to this author at the Division of Molecular Biology, Office of Applied Research and Safety Assessment (OARSA), Food and Drug Administration, 8301 Muirkirk Road, HFS-025, Laurel, MD, 20708, USA; Tel: +1-301-210-7812; E-mail: firstname.lastname@example.org§Present Address: Visiting Professor, Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA