The Department of Defense (DoD) has a unique marine mammal program maintained by the U.S. Navy that includes the largest forces of bottlenose dolphins (Tursiops truncates) and California sea lions (Zalophus californianus). Marine mammals from this program are deployed worldwide in support of Navy missions and for Fleet exercises. When not on deployment, animals work from netted enclosures in San Diego Bay, California. Sustaining healthy marine mammals is of the utmost importance and the health of these animals is closely related to the environments they are exposed to. Marine mammals may be exposed to a wide variety of environmental stressors such as chemical pollutants, harmful algal blooms and pathogens. In particular, viral diseases of marine mammals have been much more difficult to study and this has led to a limited knowledge on emerging known and unknown viruses which are ongoing threats to the animal health. Therefore, there is a critical need to develop improved and reliable sampling and detection methods for viruses in marine environments in order to generate a comprehensive view of the viral metagenome (virome) for infectious disease surveillance. In the absence of such methods, the development of effective prevention and intervention strategies to address such a problem will likely remain difficult. New instrumentation and technology have increased the ability to understand viruses in the marine environment and in particular viral diseases and dynamics between viruses and their hosts.

The overarching goal of this project is to build the virome data bases in marine waters and bivalve mollusk associated with the corresponding mammals using the nanopore MinION sequencing technology coupled with improved sampling platforms. We have the following objectives to achieve the project goal:

1. Streamline the sample collection protocol for viruses in water using new ultra-filtration system and new nucleic acid extraction technology
2. Develop a protocol for the extraction and concentration of viruses from bivalve mollusks in the context of metagenomic sequencing using the nanopore technology
3. Refine the bioinformatics for the analysis of MinION viral sequencing reads
4. Undertake an environmental surveillance for marine mammal viruses (in water and bivalve mollusks) using the integrated sample processing and sequencing protocol in the laboratory and under field conditions

This unique project is based on the expertise of a multidisciplinary team addressing the health of marine mammals and their associated environments using new technologies to better understand and prevent viral diseases.

This research is in collaboration with the National Marine Mammal Foundation https://www.nmmf.org and the Shedd Aquarium https://www.sheddaquarium.org.