Zoonotic Agents

Bait Capture and Enrichment Followed by Long-Read Whole-Genome Sequencing and Viral Variant Discrimination Through TELSVirus Workflow Using Influenza a Virus as a Model

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Abstract

Viral co-infections are a frequent health challenge in swine worldwide, contributing to aggravated disease outcomes. Whole-genome sequence (WGS) of viral genomes can improve our understanding of viral co-circulation dynamics, ecology, evolution, and pathogenesis in swine herds. However, low viral titers and high levels of host genomic material are some of the technical challenges when applying sequencing to field samples. Furthermore, methods such as PCR amplicon sequencing usually target only single viruses, which limits the ability to understand viral co-infection and co-circulation dynamics. Finally, viral culture is often needed to enrich genomic material prior to sequencing, which can introduce bias into the resulting genomic sequences. To overcome these limitations, we have developed a workflow called “TELSVirus”, or “Target-Enriched Long-read Sequencing of Virus”. The workflow combines a “capture & enrichment” method with long-read, real-time sequencing technology (by Oxford Nanopore), followed by an ensemble bioinformatics pipeline for data analysis.

How to Cite:

Meneguzzi, M., Torremorell, M. & Noyes, N., (2023) “Bait Capture and Enrichment Followed by Long-Read Whole-Genome Sequencing and Viral Variant Discrimination Through TELSVirus Workflow Using Influenza a Virus as a Model”, SafePork 14(1).