In the face of concerns over an influenza pandemic, identification of virulent influenza isolates must be obtained quickly for effective responses. Knowledge of the exact strain, origin of the strain and probable characteristics of the virus are critical for surveillance of a disease outbreak and preventing the spread of the disease. Rapid subtype identification of flu is not always straightforward. Simple serological tests on infected individuals are awkward to administer and are an ineffective tool for monitoring viruses undergoing a high rate of mutation or rapid recombination. RT-PCR assays have better sensitivity but are problematic in scenarios where new strains of virus emerge or mixtures of viruses exist.

In many situations the identification of the circulating subtype is not sufficient and specific knowledge of the genetic makeup of the virus is required. For example, the avian H5N1 virus ("Bird Flu") has significant potential for further recombination with common human strains (such as H3N2) or other non-human strains common in avian populations (H7 and H9 strains).The H5N1 subtype is also difficult to identify because of the lack of sensitivity and specificity of many of the commercial tests. In addition, genotype Z, the dominant H5N1 virus genotype currently circulating in Vietnam and Thailand, contains a mutation that is associated with resistance to amantadine and rimantadine. Also, because of the high susceptibility in humans and resistance to antibiotics of this isolate, neuraminidase inhibitors must be given within 48 hours of onset of illness to be effective. Thus rapid and specific identification of this subtype and accurate sequence information is crucial for proper treatment.

CombiMatrix has also developed a semiconductor-based DNA chip, the CombiMatrix Influenza A Research Microarray, that can detect and accurately type flu strains with hemagglutinin subtypes 1 through 15 and neuraminidase subtypes 1 through 9 using a protocol that requires less than four hours start to finish. In addition to providing very high resolution information on genotype of any given flu strain, it can also provide information on novel strains of flu produced by rapid mutation or recombination between multiple strains of flu.

This system is available to the flu researcher as a tool or as a service from CombiMatrix (for research use only at this time). This system is also being developed as a field deployable biodetector using electrochemical techniques for analysis. This chip can be employed as an adjunct to existing technology: to type difficult or ambiguous samples of flu, provide greatly increased confidence in RT-PCR assays or study genetic drift in a flu virus as it moves through a population.

The CombiMatrix Influenza A Research Microarray is based on CustomArray® 12K array format. The specific oligonucleotide probe sets are designed for all known subtypes of hemagglutinin and neuraminidase from the influenza A viruses. The virus genetic material is amplified by PCR, and the resultant target nucleic acid mixture is hybridized to a CombiMatrix Influenza A Research Microarray chip. The enzymatic reactions that are performed on the chip as steps of CombiMatrix Hyb & Seq® procedure allow for short hybridization times and rapid detection. The whole assay may be performed in less than 4 hours.

The CombiMatrix Influenza A Research Microarrays were hybridized with genetic material from two of influenza A subtypes: subtype 1, H2N2, and subtype 2, H15N9, respectively. The detected hybridization signals resulted in unambiguous determination of influenza subtypes.

If you would like more information on the CombiMatrix Influenza A Research Microarray, please contact us at 1-800-985-CBMX or email for more information.