Department of Homeland Security Fellowship Internship Experience at Lawrence Livermore National Laboratory

As a DHS intern at Lawrence Livermore National Laboratory (LLNL), I was a member of the Agricultural Domestic Demonstration and Application Program (AgDDAP) under the mentorship of Benjamin Hindson. This group is focused on developing assays for the rapid detection of animal diseases that threaten agriculture in the United States. The introduction of a foreign animal disease to the US could potentially result in devastating economic losses. The 2001 Foot-and-Mouth Disease (FMD) outbreak in the UK cost over 20 billion dollars and resulted in the death of over 6 million animals. FMD virus is considered to be one of greatest threats to agriculture due to its high infectivity, robustness, and broad species range. Thus, export of meat and animal products from FMD endemic countries is strictly regulated. Although the disease is rarely fatal in adult animals, morbidity is close to 100%. FMD also causes overall production (i.e. milk, mass) to decrease dramatically and can reduce it permanently. The rapid and accurate diagnosis of FMD and other foreign animal diseases is essential to prevent these diseases from spreading and becoming endemic to the country. Every hour delay in the detection of FMD is estimated to cost up to 3 million dollars. Diagnosis of FMD is often complicated by other diseases manifesting similar symptoms in the animal, such as vesicular stomatitis, bluetongue, etc. Typically, diagnosis cannot be made by clinical signs alone and samples must be sent away for testing. Depending on the test, such as in virus isolation, this can take several days. AgDDAP had previously developed a high-throughput multiplexed polymerase chain reaction (PCR) assay for the rule-out of Foot-and-Mouth Disease and six other look-alike diseases. This assay is intended for use in FMD surveillance, differential diagnosis in an outbreak scenario, and to establish an FMD-clean state after an outbreak. PCR based assays are favorable for multiple reasons. Viral nucleic acids can be detected in samples several days before clinical signs appear. PCR is quick with results available in a few hours. The ability to multiplex PCR allows many different diseases to be detected. Also multiple signatures can be detected for each disease, decreasing the likelihood of a false negative result due to viral mutation. The virus would have to obtain multiple mutations in the correct areas in the genome to escape detection. PCR can also be easily automated with robotics and made high-throughput, allowing close to a hundred samples to be processed at a time with minimal chance of cross over contamination. This assay panel will be expanded in the future to screen for more diseases and also be separated into specific panels targeted at bovine, ovine, and porcine diseases. The assay is designed to be deeply multiplexed and could potentially screen for as many as 96 different diseases. The assay will also be modified to accept different types of sample matrices, including blood, milk, and tissues. This is necessary because the presence of viral nucleic acids in a particular sample matrix can be dependent on the virus, the stage of infection, and the species infected