Integrating a rapid nanopore sequencing platform for building the virome of marine mammals associated environments
Abstract
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 new project is to build the virome data bases in marine waters and bivalve mollusk housing marine mammals using a nanopore MinION sequencing technology coupled with improved sampling platforms. Project objectives are to: (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; and (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 novel onsite viral screening and quantification approach will provide to the Navy with an initial surveillance of the virome in marine mammals~ habitat. It will also provide a rapid protocol for viral screening and quantification in the field. This will ultimately improve the surveillance of marine mammal infectious diseases and allow for early detection of viral pathogens.
Document Details
- Document Type
- DoD Grant Award
- Publication Date
- Mar 11, 2020
- Source ID
- N000142012117
Entities
People
- Tiong Aw
Organizations
- Office of Naval Research
- Tulane University of Louisiana
- United States Navy