On the front lines of biodefense
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WHEN a sudden outbreak of a strange virus called Severe Acute Respiratory Syndrome (SARS) occurred last year, the Centers for Disease Control and Prevention (CDC
On the front lines of biodefense
Click here for additional images.
WHEN a sudden outbreak of a strange virus called Severe Acute Respiratory Syndrome (SARS) occurred last year, the Centers for Disease Control and Prevention (CDC) sought help from a team of Lawrence Livermore biologists, mathematicians, and computer scientists. Within three hours of receiving the first sequenced genome (genetic blueprint) of the virus from the CDC, the Livermore team produced several candidate signatures of the pathogen (disease-causing microbe). Signatures are specific regions of DNA or RNA that uniquely identify a pathogen. The SARS case was one of many in which the group has developed signatures using a novel whole-genome analysis approach that is changing pathogen diagnostic design.
The team, part of the Laboratory's Biology and Biotechnology Research Program (BBRP), has been on the front lines of the nation's biodefense effort since 2001. Eleven computer scientists, biologists, and mathematicians led by computer scientist Tom Slezak comprise one of the largest pathogen bioinformatics groups. Their work spans the full spectrum of effort, from identifying signature candidates to developing DNA-based signatures and deploying validated assays in the field. Team members have traveled throughout the nation, often with only a few hours' notice, to support the national effort to defend against bioterrorism.
Biological weapons could include bacteria (anthrax, plague), DNA viruses (smallpox), RNA viruses (ebola, SARS, foot-and-mouth disease), fungi (soybean rust, corn rust), protozoa (giardiasis), and toxins (ricin). Pathogens such as these and many others could be used to sicken or kill urban populations, livestock, or crops. Early detection and unmistakable identification are crucial to limiting the potentially catastrophic human and economic costs of a bioattack.
Many types of signature requests are received by the team. One request may be for all strains of a normally pathogenic species, including its nonpathogenic and vaccine strains. Another request may be for all of the pathogenic strains of a particular species. Fulfilling these requests can be difficult because while there may be hundreds of strains of a particular species, genomic sequences may exist for only a few. Strains may also vary in pathogenicity, and their genetic near-neighbors may or may not be virulent or may affect hosts other than humans. In addition, RNA viruses have extremely high mutation rates, so it may be difficult or impossible to find adequate stable regions suitable for use as a signature.
The Livermore bioinformatics team has developed DNA-based signatures of virtually every biothreat pathogen (the organisms identified by the CDC as high-priority threat agents) for which adequate genomic sequences are available as well as for several other human and livestock pathogens. Signature requests come from agencies such as the Department of Energy (DOE), the CDC's Laboratory Response Network and BioWatch Program, the Department of Agriculture, the Food and Drug Administration, and the Department of Defense. Livermore signatures are part of the nation's public health system and have been in use for homeland defense since fall 2001.
Pipeline Called KPATH
Livermore's signature pipeline, called KPATH, is used to develop the signatures of bacterial and viral pathogens. This Livermore-designed system is a fully automated DNA-based signature "pipeline," able to deliver signature candidates (spanning 200–300 base pairs of DNA) in minutes to hours. In simplest terms, KPATH works by comparing the genome of the target pathogen to a library of microbial genomes, searching for those areas that are unique to the target organism.
KPATH uses the software programs Multiple Genome Aligner (MGA) and Vmatch, which were developed by collaborators in Germany. MGA aligns the multiple genomes of a target pathogen, and Vmatch uses efficient algorithms to quickly compare the genome of interest with all other sequenced microbial genomes. "These software tools allow the pathogen genomes themselves to show us w