Nimblegen tracks evolutionary path of H1N1 virus

A team at the Genome Institute of Singapore has developed a 'generic' PCR approach that can amplify the full genome of any influenza A virus.

This is followed by Nimblegen microarray-based hybridisation sequencing, allowing a rapid turnaround for entire genomes (as many as 36 a day with one chip-reader device) in about 24 hours.

This method can use the same RNA material that is left over from traditional PCR-based diagnostics and can recognise any novel strain of influenza in the first pass.

This will enable a faster development of diagnostics for any possible new variant.

It also can rapidly determine if the strain of DNA changed to become even more dangerous, for example, in terms of drug resistance.

Working in close collaboration with scientists from Roche Nimblegen, and utilising the flexibility that the Nimblegen platform offers, the first arrays were designed, manufactured, and shipped to Singapore four days after the project was started.

The custom-developed high-density microarray contains probes that can reveal the complete sequence of the flu virus from patient samples (nasal swabs/nasal pharyngeal wash).

This will enable detection of any single base mutations in the regions of the genome, which is important for drug susceptibility.

Where virus re-assortment has occurred, it will be able to identify which strain of influenza A it has recombined with, as well as the genomic location of the re-assortment to better understand and track the evolutionary path and variants of the virus.

A similar approach using Nimblegen arrays was used during the Sars outbreak in 2003 to understand the infectious source and to globally monitor the Sars virus.

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