Before there is any hope of slowing or halting a disease outbreak in humans, animals, or plants, the first step is identifying the cause. In many cases, a pathogen is involved. 

If existing tests cannot pinpoint the pathogen because it is a previously unknown agent or one that is known but has mutated so much that existing tests cannot recognize it, examining the entire sample genetically to discover any pathogen within it can be the best path forward. 

The Virginia Tech Animal Laboratory Services (ViTALS), within the Virginia-Maryland College of Veterinary Medicine, and the Virginia Tech Plant Disease Clinic, within the College of Agriculture and Life Sciences, have jointly established a genomics-based pathogen identification service to assist animal and plant disease diagnosticians in identifying pathogens and enhance biosecurity and pandemic prevention. 

"It's a concept, but it's also a service," said Kevin Lahmers, clinical professor of anatomic pathology at the veterinary college. "The concept that we have been working on, rather than developing PCR tests for individual pathogens, is to sequence everything that's in the sample, figuring out all of the nucleic acids that are in a sample, and then using bioinformatics to figure out the composition of that sample. Are any of the things that are in that sample of concern?" 

Limits of PCR testing

Known pathogens, such as COVID-19, are identified using polymerase chain reaction (PCR) tests, which amplify small sections of RNA to find genetic material matching that of the pathogen. 

"Traditional diagnostic techniques sometimes fail to provide clear answers, especially when it comes to detecting hard-to-recover, new or emerging pathogens," said Lina Rodriguez Salamanca, Plant Disease Clinic manager and diagnostician. "This is where metagenomics can be particularly valuable."  

The term "metagenomics" refers to the study of the entire genetic sequence of organisms in a sample without having to individually culture a particular organism.

Lahmers said the genome-sequencing method is potentially much faster in animal pathology because it does not require growing a pathogen in a laboratory or injecting it into an animal. 

"The long-established method for proving the existence of an infectious pathogen in animals follows Koch's postulates, which requires isolating the potential pathogen, describing the syndrome, then growing the pathogen and infecting another animal to prove it as the cause of a disease," Lahmers said.  

Collaboration opportunity 

The genomics-sequencing service, part of the grant-supported Virginia Tech Integration Incubator for Plant and Animal Health Sciences, began when Lahmers and Boris Vinatzer, professor in the School of Plant and Environmental Sciences, discovered they were applying similar methods in their research. 

"We realized that we are doing very similar things, that Lahmers is using the same sequencing approaches to identify animal pathogens as I do in my group to identify plant pathogens," Vinatzer said. "It just seemed obvious that the two of us should collaborate." 

Vinatzer said the goal is to make the service available to anyone in the U.S. and around the world. "The goal is that within the next two years we can provide results to users within a couple of days of receiving their samples," Vinatzer said. "The benefits will be that we can identify new plant and animal pathogens faster and help contain outbreaks more effectively to the benefit of farmers and consumers."  

Both Lahmers and Vinatzer pointed to the COVID-19 pandemic as a situation in which an unknown pathogen was discovered through metagenomics and only after that occurred could proper tests and vaccines be developed.  

"In December 2019, there were people who had unusual cases of pneumonia, and the doctors didn't know what it was they had," Vinatzer said. "They tested for the flu, it was negative. They tested for other known pathogens, all tests came back negative. Then they took samples from the lungs of those patients and sequenced everything in these samples, compared all sequences to a database of known sequences, and they found that there was a new pathogen that was similar to the known SARS virus, but a little different, and SARS-CoV2 was discovered." 

Some animal diseases can become human diseases if not detected and mitigated in a timely manner. While plants do not typically carry pathogens that evolve into human pathogens, the genome-sequencing process can help identify viruses, bacteria, or fungi that either cause devastating disease of plants threatening food security or that cause foodborne illnesses in animals or people, Vinatzer said. 

Multiple-level benefits 

While Lahmers and Vinatzer have headed up the creation of the lab, they are both quick to direct much credit to those who do much of the hands-on work — Sahar Abdelrazek, research assistant professor of microbial pathogen metagenomics who is project manager for the joint genomics lab, and Lina Rodriguez Salamanca, Plant Disease Clinic manager and diagnostician. 

"The service is all well and good, but there's got to be somebody who actually can do this," Lahmers said. 

Abdelrazek, who Lahmers said handles much of the communication with clients, sequences the samples, and collects and interprets the data, described the value of the genomics-sequencing service on multiple levels. 

"At the university level, it provides significant opportunities for advancing pathogen detection, identification, and infectious disease research," Abdelrazek said. “It fosters interdisciplinary collaboration across departments and establishes valuable partnerships with external entities, including regional and national plant and animal disease clinics and government agencies. 

"Regionally, the center's capabilities in rapid pathogen identification and characterization using metagenomics contribute to effective and sustainable disease management. Globally, the center will aid in tracking the spread of infectious diseases, facilitate pathogen discovery, and lower the risk of local outbreaks escalating into epidemics or pandemics."

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