Scientists conducting research in the area of pathogen discovery, especially virus discovery met for a 4 day workshop on 5-8 Nov 2012. Held at the International Livestock Research Institute (ILRI) Nairobi, the aim of the workshop was to enable ILRI to make informed decisions about which technologies to be investing in to support the pathogen activities in the CGIAR Research Program on Agriculture for Improved Nutrition and Health (A4NH).
Why virus discovery?
Viruses contribute the highest burden of emerging and re-emerging infectious diseases in livestock and humans. To detect, prevent and control outbreaks of zoonotic diseases, virus discovery is one key research area at ILRI that helps scientists to understand diseases and come up with disease prevention measures. This area makes a huge contribution to the control of livestock diseases.
Though a lot of research has been done on characterization of viruses, the world still faces the threat of viral emerging infectious diseases (EID) such as severe acute respiratory syndrome (SARS), bird flu, Rift Valley fever and blue tongue disease. These diseases pose serious threats to many poor livestock keepers and necessitate the need for more investments in this research. In this rapidly changing research field, a review of the state of the art technology that supports virus discovery is important to enable research organizations to be informed and keep up with the changing technology.
The workshop brought together a rich mix of participants who were drawn from institutions such as: the Commonwealth Scientific and Industrial Research Organisation (CSIRO); Australian Animal Health Laboratory; Roche; Natural History Museum of Denmark; Los Alamos National Laboratory; University of Chicago; Onderstepoort Veterinary Institute and the Defence Threat Reduction Agency (DTRA).
Among the participants were Andreas Wilke from the University of Chicago who is one of the MGRAST software developers and Tony Walters from the University of Colorado who is among the developers of QIIME software. MGRAST and QIIME pipelines are used by the ILRI genomics group in analysis of meta genomics data obtained from the high throughput sequencing platform. These developers shared first hand experiences in designing the pipelines and also received first hand feedback from the users on usability issues and possible areas of improvement on the software.
Topics discussed included field sampling strategies, virus samples handling/shipment and preservation, viral genome detection, sequencing, isolation or enrichment from mixed samples and metagenomic data analysis.
A key output from the workshop was a set of consolidated tools, techniques and strategies appropriate for pathogen discovery. Second, new opportunities for potential collaboration were identified including an outline of CSIRO collaboration for the A4NH research work. Last, a funding opportunity from DTRA was identified.
The workshop was supported by the CGIAR Research Program on Agriculture for Improved Nutrition and Health (A4NH) and Roche.