Integrated tools for Influenza genotyping


  • Genotyping and epidemiology of seasonal, pandemic, and exceptional strains
  • Updated reference databases reflect newly described strains
  • Detection of resistance to neuraminidase inhibitors

Influenza viruses cause yearly epidemics with unpredictable spread and pathogenicity. Laboratories need to prepare in advance for rapid testing and analysis of sequence information to cope with outbreak situations. Sequence-based genotyping has become the method of choice to track the epidemics for public health surveillance and therapeutic intervention. Drug resistance determination is being applied in order to optimize the use of available antiviral therapies.

The SmartGene Influenza Module helps laboratories analyze and manage flu sequence data efficiently. It supports the direct uploading and editing of chromatograms for hemagglutinin (HA), neuraminidase (NA), matrix, and other targets. The module automatically assembles and aligns the sequence fragments using representative reference strains embedded in the target-specific IDNS®-ProofReader (Patent No. EP1846853) thus expediting the creation of reliable contigs.

Sample sequences can then be compared to an updated reference database of multiple gene targets in order to determine the most likely subtype. A direct link to the original publication is included with each reference sequence.

Subtype-specific, automated mutation detection reveals mutations which may confer resistance to drugs.

The searchable sample archive allows for easy queries on all samples analyzed, e.g. genotypes over a certain period of time. GPS coordinates in the sample record, inferred from the geographic origin of the sample, can be used for plotting outbreaks on a map. Integrated sequence comparison tools, such as multi-alignments and ad-hoc dendrograms, help to identify case relationships and allow for online surveillance of an epidemic.

Finally, the networking capabilities as described in the IDNS® Networks section enable laboratories to share their data securely online, if they wish.

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