A workflow called TELSVirus, or Target-Enriched Long-Read Sequencing of Virus, enables the real-time detection and genomic characterization of multiple viral pathogens from a single sample in a relatively short turnaround time (approximately 24 hours). Researchers Noelle Noyes, Montserrat Torremorell and colleagues at the University of Minnesota applied the TELSVirus as part of a Swine Health Information Center (SHIC)-funded study to apply this workflow to pig oral fluid samples to detect and characterize genomes of target viral pathogens.
“The diagnostic test developed through TELSVirus enabled researchers to detect a high prevalence of co-circulating yet understudied viruses, including porcine bocavirus, porcine sapelovirus 1, and porcine astrovirus 2 and 4, while also allowing for detection of viruses with known production impacts, such as PRRSV, influenza and rotavirus,” SHIC reports. “These viruses were often detected in the same oral fluid sample, and the high sequencing coverage afforded by TELSVirus allowed for robust viral variant analysis. Researchers also demonstrated that TELSVirus’ limit of detection for PRRSV and influenza is comparable to that of qPCR, while providing the benefits of increased genomic information.”
What does this mean for the pork industry? TELSVirus has the potential to support real-time surveillance of endemic and emergent viruses, while also improving understanding of co-circulating viruses, their genetic diversity, and ultimately how they impact swine health and production.
“Viral co-infections on swine farms are common and frequent, contributing to aggravated disease outcomes as well as impairing economic profit and animal well-being. In addition, due to high mutation rates, the co-circulation of viruses within swine herds facilitates the emergence and re-emergence of new variants, potentially impairing disease investigation, control and prevention,” SHIC reports.
Despite significant cost and health relevance, viral co-infections are not studied enough, SHIC adds. Not only are there limitations in sequencing techniques able to generate full-length sequences of multiple viruses from field samples, but the detection and genomic characterization of novel variants are still a challenge. Many questions about the dynamics and interactions of co-circulating viruses in swine herds remain.
Noyes and Torremorell will pursue further funding for additional work and development of best practices for testing field samples using this process. They reported to SHIC their first attempt to incorporate TELSVirus as part of a veterinary diagnostic workflow and showed promising results but agree it is still a work in progress. Researchers are continuing discussions with the veterinary diagnostic laboratory to pursue further application of this testing platform.
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