Influenza and other influenza like illnesses significantly influence modern society. Global surveillance of influenza is critical for improvements in disease management and is especially important for early detection, rapid intervention and a possible reduction of the impact of an influenza pandemic. Enhanced surveillance requires rapid, robust and inexpensive analytical techniques capable of providing a detailed strain analysis of influenza viruses. Low-density oligonucleotide microarrays, with highly multiplexed "signatures" for influenza, offer many of the desired characteristics. However, the high mutability of the influenza virus represents a design challenge that needs to be addressed.

For this purpose, an algorithm was created to allow efficient examining large databases of influenza virus genomes. This approach was unique in that it incorporated use of a phylogenetic grouping of similar influenza genomes; thus minimizing the number of microarray sequences necessary for detection of a wide range of influenza viruses. Using this approach, conserved regions were identified, and capture and label sequences chosen that discriminate between different influenza types and subtypes. A small set of sequences was initially selected for development of the FluChip™, a diagnostic microarray for relatively rapid identification of influenza viruses. Specifically, the FluChip-55 was designed and characterized for subtyping of H1N1, H3N2 and H5N1 influenza viruses. An assay for isolation and amplification of viral RNA, followed by hybridization and detection on the FluChip was developed and tested. In a series of blind studies, over 150 influenza virus isolates were processed and identified. These results are presented here and discussed.

Additionally, using a modified version the sequence selection algorithm, capture and label pairs were chosen to demonstrate proof-of-principle detection of influenza antiviral resistance on a microarray. The use of the antiviral drugs will be one of the main defenses against the potential devastation caused by an influenza pandemic. The detection of single nucleotide changes responsible for resistance to the adamantane ion channel inhibitors is presented. Influenza H3N2 and H1N1 viruses with the mutations V27A and S31N in the M2 protein were tested in a series of studies. The successful identification of many of these viruses is presented here as well.