- Boid Inclusion Body Disease is a disease that affects snakes worldwide.
- A team of researchers has sequenced the genome of viruses found in sample snakes.
- The researchers made use of software and computing resources provided by Finland’s CSC - IT Center for Science and EGI in their work.
- They have discovered that that the viruses previously linked to this disease are actually only the tip of the iceberg.
Boid Inclusion Body Disease is a threat to boas and pythons in homes and zoos around the world. The disease starts with lack of appetite and poor digestion, but the main tell-tale sign is the many protein inclusions that appear in all cell types. The disease is often fatal.
Besides the trouble it brings to conservation projects, the disease is also an economic burden — imposing strict quarantine rules for the transport of 200,000 snakes a year does not come cheap.
So far, scientists know that the disease is somehow related to viruses from the arenavirus family, which are usually carried by mice and may cause hemorrhagic fever or meningitis if transmitted to humans.
Jussi Hepojoki, a virologist based at the University of Helsinki in Finland, and his team set out to sequence the genome of the viruses found in the samples of six snakes. The first step was to isolate the RNA of the viruses — their genetic information — and sequence the samples using modern ‘next-generation sequencing’ (NGS) techniques.
Chipster: NGS in the EGI Federated Cloud
Hepojoki used the Chipster platform to handle the millions of sequences generated by the NGS analysis. Chipster is a user-friendly analysis software for high-throughput data developed by Finland’s CSC - IT Center for Science and ELIXIR, a distributed infrastructure for life-science information.
Chipster contains over 340 analysis tools for NGS, microarray, proteomics, and sequence data. Users can save and share automatic analysis workflows, and visualize data interactively using a built-in genome browser and many other visualizations.
Chipster's client software uses Java Web Start to install itself automatically and it connects to computing servers for the actual analysis. Chipster is open source and the server environment is available as a virtual machine image.
Computational resources support genome assembly
“I think that without CSC and Chipster, I would not have been able to carry out the sequence assembly,” said Hepojoki. “The power of ‘normal’ computers is just not enough for this type of work, or it takes a ridiculous lot of time.”
The surprising conclusion is that all samples had more than one arenavirus, some of them from entirely new species. It seems that the viruses previously linked to this disease are only the tip of the iceberg.
The research, which was published in the Journal of Virology, doesn’t point to a cure just yet, but “it brings us perhaps a bit closer to understanding the mechanisms of the disease,” concludes Hepojoki.