Using MinION for Rapid Detection of Viral Pathogens of Marine Mammals
Abstract
Marine mammals are susceptible to a wide variety of viral pathogens, among which morbillivirus, parapoxvirus, calicivirus, herpesvirus is listed in the ten highest priority pathogens among small cetaceans by the Working Group of Marine Mammal Unusual Mortality Events (Venn-Watson et al., 2010). It is thus critical to establish a real-time genomic surveillance of these high-priority viral pathogens for routine monitoring, and more importantly, time-sensitive clinical applications including outbreak investigation and detection of infection. Technically, the real-time genomic surveillance system relies on direct sequencing of viral genomic materials without isolation or culture of individual virus. A primary challenge lies in the low viral copy numbers and interference of host DNA. Quantitative real-time PCR (qPCR) has been applied to provide simultaneous amplification and quantification of a targeted DNA sequence in a certain sample. The technique has successfully detected adenovirus in bottlenose dolphins (RubioGuerri et al., 2015), Influenza A virus in seals (Krog et al., 2015; Puryear et al., 2016), and morbilliviruses in dolphin and porpoise (Grant et al., 2009). However, qPCR is neither capable of genotyping nor time-efficient in simultaneous detection of multiple viruses within the same sample. An alternative approach is metagenomics, where high-throughput next-generation sequencing technologies have been applied to probe the viral community and potential viral pathogens to marine mammals including California sea lions (Li et al., 2011) and South American fur seals (Kluge et al., 2016). However, the slow turnaround, short sequence reads impede its application as a routine monitoring procedure. A recently developed portable sequencer- the Nanopore MinION device, enables long sequence reads and real-time data output. Here we propose a proof-of-concept workflow using the MinION for rapid detection of viral pathogens for marine mammals. Archived clinical samples from Dr. Eric Jensen of the Navy s Marine Mammal Program will be used for this study.
Document Details
- Document Type
- DoD Grant Award
- Publication Date
- Jul 27, 2018
- Source ID
- N000141812648
Entities
People
- Joan B. Rose
Organizations
- Michigan State University
- Office of Naval Research
- United States Navy