H1N1 Microarray: Universal Oligonucleotide Microarray For Influenza A Virus Sub-Types Developed

Recent outbreak of H1N1 swine influenza virus was a serious public health problem. A group of scientists from the US FDA and Russia now report the development of a universal microchip for identifying Influenza A viruses. The test using this microarray chip is expected to classify new isolates of influenza A viruses by sub-typing specific viral proteins.

3D graphical representation of the biology and structure of a generic influenza virus, (not specific to the 2009 H1N1 virus): Courtesy: CDC.gov

The Influenza A virus is a single stranded RNA virus. Wild aquatic birds are the natural hosts for different strains of influenza A. However, humans can get infected occasionally.

The Influenza A microchip contains two sets of oligonucleotide probes allowing viruses to be classified by the subtypes of hemagglutinin (H1-H13, H15, H16) and neuraminidase (N1-N9). Hemaglutinin (HA) and neurominidase (NA) form the outer coat of the viral particles with the core of the particle formed with genomic RNA and other proteins. There are 16 subtypes of HA proteins (H1-H16) and 9 subtypes of NA proteins (N1-N9).

The paper was published in the April 29, 2011 issue of PLOS ONE, an open access peer-reviewed journal. The authors were: Vladimir A. Ryabinin, Elena V. Kostina, Galiya A. Maksakova, Alexander N. Sinyakov of the Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia and Alexander A. Neverov and Konstantin M. Chumakov of the Food and Drug Administration, Maryland, USA.

The usual method of sub-typing influenza viruses involves virus isolation, analysis using standard immunochemical techniques or real-time polymerase chain reaction (PCR) amplification, and nucleotide sequencing of HA and NA genes. In this study they developed a microchip for specific identification of Influenza A subtype. Amino acid sequences typical of the sub-type of interest, but absent from other sub-types, were identified and oligonucleotide probes were derived from these conserved peptides and their properties optimized. The probes generated were chemically attached on to glass slides to create the microarray. For sub-typing the virus, microarrays were hybridized with fluorescent color-labeled nucleotide fragments prepared from the complementary DNA (cDNA) of Influenza A virus.

In the process of selecting probes they found that none of the probes selected based on GenBank sequences deposited prior to March of 2008 matched the DNA of H1N1 swine influenza. This is because there can be substantial mutations occurring in the subtypes of H and N proteins. It is reported that H1 protein of H1N1 2009 strain was 29% different from H1N1 virus that circulated in 2008; and 18% different at the N1 protein. Therefore, they designed a set of probes for selective determination of H1 hemagglutinin of swine H1N1 influenza virus.

In a previous study, the authors had developed a microchip of 3D gel-based elements containing immobilized probes and validated using a panel of 21 known reference strains of influenza virus. In that study, 41 clinical samples isolated during the poultry fall in Novosibirsk (Russia, 2005) were successfully identified using the proposed technique.

The presently reported microarray contained two sub-arrays; one for the NA-specific probes and the other for HA-specific probes. According to the authors, this new study describes a different method for the development of oligonucleotide hybridization probes that enables the creation of universal microchips for sub-typing HA and NA genes of Influenza A viruses. In this study, out of 40 samples tested, 36 unambiguously identified HA and NA subtypes of Influenza A virus.

Source paper: Ryabinin VA, Kostina EV, Maksakova GA, Neverov AA, Chumakov KM, Sinyakov AN.
Universal Oligonucleotide Microarray for Sub-Typing of Influenza A Virus. PLoS ONE 2011;6(4): e17529. doi:10.1371/journal.pone.0017529
 

References used:

Gallaher WR.Towards a sane and rational approach to management of Influenza H1N1 2009. Virol J. 2009;6:51. PMID:19422701.

Fesenko EE, Kireyev DE, Gryadunov DA, Mikhailovich VM, Grebennikova TV, L'vov DK, Zasedatelev AS. Oligonucleotide microchip for subtyping of influenza A virus. Influenza Other Respi Viruses. 2007;1(3):121-9. PMID:19453417.

Influenza or Flu Part II: How flu spreads?
What is avian flu? What is H1N1 or swine flu?