Rapid dengue classification using SynaTree phylogenetic tree application

Dengue fever has long been a menace in tropical and equatorial countries, including Africa, Malaysia, Thailand, India and Brazil. It remains one of the deadliest infectious diseases to date, having first struck as an epidemic in the 1950s. The World Health Organization reports that up to 2.5 billion people, constituting two fifths of the world's population, are at risk from dengue. This staggering statistic is made even worse by current estimates that some 50 million people throughout the world are affected by dengue every year.

What is known of this lethal disease? For starters, dengue fever is caused by viruses transmitted by the Aedes mosquito, predominantly Aedes aegypti. These dengue viruses contain single stranded, positive sense RNA and belong to the genus Flavivirus, family Flaviviridae. There are four types of dengue viruses (classified as DEN-1 to DEN-4) which are immunologically related, yet different enough to not be affected by cross-protection. To date, there is no vaccine that offers protection against dengue viruses, and any vaccine developed must be able to immunise patients against all four serotypes effectively. This makes the early screening and identification of viral isolates even more vital.

One effective approach is to rapidly identify all the major and minor dengue serotypes using phylogenetics applications. This approach then makes it possible to design multivalent vaccines which could offer cross-protection against all dengue virus sub-types.

This process can be laborious and slow, as the genomes to be compared need to fetched and collated, after which pair-wise distance matrices need to be derived. In contrast, SynaTree™ provides an easy interface for collating the genomes to be compared, then rapidly generates distance measures from multi-comparisons, and provides an output file suitable for drawing phylogenetic trees. The collation and analysis of viral and bacterial genomes can be completed in a matter of minutes.

To generate a phylogenetic tree of new dengue viral strains using SynaTree, please follow the instructions below:

Stage 1: Generating a distance matrix using SynaTree
  1. Click HERE.
  2. Select the ‘Dengue Viral Genome’ database.
  3. Under the sequence expression box, type ‘dengue' and select ‘List Sequence’. A list of all dengue viruses will appear in a box below.
  4. Click the ‘Add All’ button under the Sequence List header. All the sequences will be transferred to the box below, under the header ‘Selected Sequence’.
  5. Click ‘TREE’ to run the programme and wait for the data file to be generated.
  6. Once the results window appears, click ‘SAVE’ to save the results file on your computer.
Stage 2: Drawing a phylogenetic tree from the SynaTree data file
  1. If you do not already have SplitsTree on your computer, download and install the SplitsTree software from HERE.
  2. Open the SynaTree data file from the SplitsTree “Open” command.


Figure 1: The SplitsTree graph of the dengue phylogenetic tree using SynaTree





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