Sui Hoa Janet S. H Lorv
School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, U.S.A.
Blacksburg, Virginia, United States
Sahar Abdelrazek
Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, U.S.A.
Blacksburg, Virginia, United States
Reza Mazloom
Graduate Researcher
Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, U.S.A.
Blacksburg, Virginia, United States
Rituraj Sharma
Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, U.S.A.
Blacksburg, Virginia, United States
Kassaye Belay (he/him/his)
School of Plant and Environmental Sciences and Graduate Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA 24061, U.S.A
Blacksburg, VA, USA
Sehgeet Kaur
School of Plant and Environmental Sciences and Graduate Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA 24061, U.S.A
Blacksburg, Virginia, United States
Mitchell Gercken
School of Plant and Environmental Sciences and Graduate Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA 24061, U.S.A
Blacksburg, VA, USA
Lenwood S. Heath
Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, U.S.A.
Blacksburg, Virginia, United States
Lina Rodriguez Salamanca
School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, U.S.A.
Blacksburg, Virginia, United States
Kevin Lahmers
Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, U.S.A.
Blacksburg, Virginia, United States
Boris A. Vinatzer
Professor
School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061
Blacksburg, Virginia, United States
The sooner an emerging disease is detected and its pathogen identified, the higher the chances to contain the initial outbreak before it turns into an epidemic or pandemic. The challenge with newly emerging pathogens is that pathogen-specific detection assays are not yet available. Therefore, a pathogen agnostic approach is necessary. Metagenomics, i.e., sequencing all DNA or RNA in a sample followed by sequence-based identification of all microbes that are present, has the potential to quickly and precisely identify any emerging pathogen. However, there are still many challenges to implementing this approach, including the possibly high abundance of host sequences reducing the number of available pathogen sequences and the presence of non-pathogenic microbes that are difficult to distinguish from the pathogen itself. Since metagenomics-based identification of plant and animal pathogens uses the same workflow, the Virginia Tech Plant Disease Clinic and the Virginia Tech Animal Laboratory Services have joined forces to streamline the process as part of a combined metagenomics-based pathogen identification service. To overcome the challenges listed above and to implement metagenomics on a routine basis, we are improving experimental workflows. Simultaneously, we are developing comprehensive genome databases, computational pipelines, and a relational database for entering, tracking, and retrieving metadata, sequencing results, and reports for customers. We will give an overview of the current service provided and examples of pathogen identified so far.