Joint genome-sequencing service established to head off future pandemics

Hand washing is advised to prevent infection with the pathogens S. aureus and E. coli, which are behind a huge numbers of deaths every year – Copyright AFP/File JENS SCHLUETER

To slow down or halt a disease outbreak in humans the first step is identifying the cause. In many cases, a pathogen is involved.

If existing tests cannot pinpoint the pathogen this is probably because it is a previously unknown agent or one that is known but has mutated so much that existing tests cannot recognise it.

To counter this,  examining the entire sample genetically to discover any pathogen within it can be the best path forward. 

The Virginia Tech Animal Laboratory Services (ViTALS) has helped to found a genomics-based pathogen identification service to assist animal and plant disease diagnosticians in identifying pathogens and enhance biosecurity and pandemic prevention. 

According to 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. 

Yet traditional diagnostic techniques sometimes fail to provide clear answers. This is where metagenomics can be particularly valuable. Metagenomics refers to the study of the entire genetic sequence of organisms in a sample without having to individually culture a particular organism.

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. From its incepti0n, Lahmers and Vinatzer have headed up the creation of the lab,

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.  The new centres capabilities in rapid pathogen identification and characterisation using metagenomics contribute to effective and sustainable disease management.