BACKGROUND
In 1999 a Nipah virus outbreak became a major cause for concern when it led to 265 cases of encephalitis among farmers in the region of Sungai Nipah, a previously little-known district in Perak, Malaysia. Forty percent of these cases were fatal.1

It is believed that some species of fruit bat are natural hosts of the Nipah virus. Studies have shown that animal to animal transmission occurs via close contact with the contaminated tissue or bodily fluids of the infected animal. In the local viral outbreak above, humans were infected with the Nipah virus through close contact with infected pigs.

The need to provide diagnostic methods to rapidly identify this virus is vital in preventing another epidemic. One well known method of rapidly identifying viruses is through the design of viral microarray probes. The added ability of the probes to pick up several variants is an advantage in identifying new isolates of the Nipah virus. A rapid, low-cost system for identifying this virus would enable fast and effective treatment to be administered to the patient at an earlier time-point in disease progression.
SOLUTION
Develop a viral-specific probe that targets the Nipah virus, as well as potentially identify new strains or isolates.
BENEFIT
SynaProbe™ is able to rapidly design a set of 10 possible probes for the Nipah virus. It can also be used to design probes for other organisms. The specificity of the probes for different serotypes and even different viruses can be determined using SynaHybridise™. In this case the probe selected binds to different types of Nipah virus isolates.
WHAT ARE SynaProbe AND SynaHybridise?
SynaProbe is a tool used to design probes for genes or mRNA transcripts. It helps design oligomer probes on microarrays rapidly. SynaProbe enables users to find the best probe sequence by weighting the following parameters: specificity, sensitivity and homogeneity, as well as the probe sequence's position within the transcript or gene.

SynaHybridise is a web-based application for finding potential binding sites of a microarray probe. SynaHybridise uses a weight matrix search approach. Hence it offers a more sensitive and selective search for potential hybridisation sites compared to traditional tools.
To conduct this simple probe design and hybridisation test:
  1. Go to www.mgrc.com.my.
  2. Click on SynaPROBE.
  3. Click on the Test Sequence and select "Nipah virus genome".
  4. Click PROBE button.
  5. On the results page, select Probe 1 and click the button.
  6. Click on HYBRIDISE button.
Figure 1: The result above shows the top 10 probes. Click the button highlighted in red (on the bottom right) to test the selected probe (Probe 1) for specificity with SynaHybridise.
Figure 2: The result from SynaHybridise shows that the probe is able to hybridise with multiple local Nipah viral isolates.
1. Lam, S. K., and K. B. Chua. 2002. Nipah virus encephalitis outbreak in Malaysia. Clin. Infect. Dis. 34:S48-51.

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