Dr. Ganwu Li, assistant professor of veterinary diagnostic and production animal medicine in Iowa State University’s College of Veterinary Medicine, believes he is at the forefront of a revolution.
“Next Generation Sequencing (NGS) is a potentially game-changing opportunity in veterinary diagnostic and clinical medicine,” Dr. Li says. “Not only is Next Generation Sequencing very fast and very powerful, but is much more economical.”
NGS is a generic term used to describe a number of different modern sequencing technologies and enables researchers such as Dr. Li to study biological systems at a level never before possible. Traditional DNA sequencing technologies just don’t have the capacity to provide the level of information as quickly or at a lower cost.
The hypothesis-free metagenomics strategy enables NGS to simultaneously detect mixed infections of different microorganisms and identify novel and/or uncharacterized pathogens directly from the clinical samples requiring no prior knowledge of the pathogen(s). These are obvious advantages over traditional diagnostic technologies.
The Veterinary Diagnostic Laboratory at Iowa State is one of the few VDLs in the country to have a section dedicated to NGS. That investment has paid off in recent years when porcine epidemic diarrhea, infections of deltacoronavirus and Senecavirus A hit the nation’s animal agriculture industry.
“We tested samples from these cases here with Next Generation Sequencing and were able to quickly and accurately find answers,” Dr. Li said. He reports that analysis based on the whole genome sequences helped determine the genetic relationship of the identified strains to historical strains of the diseases.
“Through this method we were able to track where the virus came from and where it might be going,” he said.
Compared to traditional epidemiology, genomic epidemiology based on whole genome sequences is the ultimate source of information and may never be superseded. In addition, NGS can also be used for the microbiome and dynamics studies associated with special pathogens during the course of infection.
Currently however, NGS is rarely used in veterinary diagnostic medicine despite its advantages.
“In the short term this won’t replace traditional DNA sequencing,” Dr. Li said. “Right now it is very complimentary to traditional diagnostic sequencing but I believe in the near future more and more labs will start using Next Generation Sequencing because there are just too many things that the more traditional diagnostic tools simply can’t do.”