Singapore And US Scientists First To Develop A Publicly Available And Fully Automated System To Detect Dangerous Genetic Changes In Influenza Virus

Singapore And US Scientists First To Develop A Publicly Available And Fully Automated System To Detect Dangerous Genetic Changes In Influenza Virus
Main Category: Infectious Diseases / Bacteria / Viruses
Also Included In: Genetics; Biology / Biochemistry; Flu / Cold / SARS
Article Date: 03 Jan 2011 - 1:00 PST

Scientists from the Genome Institute of Singapore (GIS), a biomedical research institute of the Agency for Science, Technology and Research (A*STAR), and the University of Maryland, USA, have designed an automated approach to identify dangerous changes in the genome of the influenza virus with high accuracy and sensitivity. Available freely as a software package called GiRaF (Graph-incompatibility based Reassortment Finder), the method can analyze large databases of influenza genomes and all eight segments of the viral genome to detect reassortments.

This approach, published this month in Nucleic Acids Research, is the result of a three-year collaboration between Dr Niranjan Nagarajan, Senior Research Scientist, Computational and Mathematical Biology at the GIS and Prof Carl Kingsford, Assistant Professor of Computer Science at the University of Maryland.

Viruses typically evolve by a gradual accumulation of mutations, but in some cases new Influenza strains can emerge as a hybrid of two different strains. This process is termed "reassortment" and represents a jump in the evolution of the virus. Influenza strains emerging from this process can acquire new skills such as the ability to replicate faster or better evade the human immune system, making it particularly important to detect such viruses from a public health perspective. In fact, reassortments have been implicated in two out of three pandemics of the 20th century as well as in the 2009 H1N1 outbreak. "Besides its utility for influenza surveillance, GiRaf also enables more systematic studies of the reassortment process, as we search for clues on how and when novel flu strains emerge." said Dr Nagarajan. Professor Steven Salzberg, Director of the Center for the Bioinformatics and Computational Biology at the University of Maryland added, "This system represents the first truly sophisticated computational method for finding reassortments in the influenza virus genome. Reassortment is the driving force behind all of the major pandemics of the past century, and until very recently, we were unable to detect these important evolutionary events. "Today, with the growing amount of influenza genome sequence data and with the GiRaF algorithm, we can finally begin to track these major genetic shifts in the composition of the virus." said Professor Salzberg.

Notes

Research publication:

The research findings described in the press release can be found in the 21 December 2010 online issue of Nucleic Acids Research under the title "GiRaF: robust, computational identification of influenza reassortments via graph mining".

Authors:

Niranjan Nagarajan1,* and Carl Kingsford2,3

1. Computational and Mathematical Biology, Genome Institute of Singapore, Singapore-127726
2. Center for Bioinformatics and Computational Biology
3. Department of Computer Science, University of Maryland, College Park, MD 20742, USA

Source:
Genome Institute of Singapore
Agency for Science, Technology and Research (A*STAR)
Singapore And US Scientists First To Develop A Publicly Available And Fully Automated System To Detect Dangerous Genetic Changes In Influenza Virus