At the request of the California Department of Public Health, a Lawrence Livermore team is mutation prospecting—developing computational tools that can analyze viruses to identify trends and potentially important mutations. The team is using the Laboratory's computational resources and expertise in bioinformatics and virology, including techniques such as ultradeep sequencing and long-fragment analysis, to better understand the evolution of rabies and other ribonucleic acid (RNA) viruses in samples from a 2009 Humboldt County rabies breakout among skunks and foxes.
RNA viruses, which mutate a thousand times faster than bacteria and DNA-based viruses, sometimes jump from one host species to another. Such diseases are a homeland security concern, and the U.S. Department of Defense considers viral infections a significant threat to soldiers worldwide. The team will use the information gleaned by mutation prospecting to build a database that, when combined with viral studies, can help them spot rare variants and predict which viruses are most likely to jump from host to host. The Defense Threat Reduction Agency currently funds this work.
The ultradeep sequencing and long-fragment analysis methods will yield huge amounts of data, which will require high-performance computing resources to analyze and strong information technology expertise to manage. In the future, this work will contribute to the understanding of how viruses mutate and thus aid in the development and testing of therapeutics and vaccines.
For more details, see the Science and Technology Review article A New Method to Track Viral Evolution.