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Next Generation Sequencing

Exploratory sequencing and targeted whole-genome sequencing

The Virology Laboratory at the Animal Health Diagnostic Center is now offering NGS services for viral diagnostics and whole genome sequencing. Clients can request exploratory metagenomic sequencing to detect viruses in a wide variety of species and sample types, including swabs, fluids, and tissues. We also perform targeted whole genome sequencing of SARS-CoV-2, influenza A (IAV), porcine reproductive and respiratory syndrome virus (PRRSV), senecavirus A (SVA) porcine circovirus 3 (PCV-3), equine parvovirus (EqPV) and equine hepacivirus (EqHV).

Sequencing Process Overview

Sequencing Process Overview

Sequencing can be performed on the MinION (Oxford Nanopore Technologies) or MiSeq (Illumina) platforms. Our NGS procedures have been validated on both platforms and are effective for the detection of viral co-infectious in multiple animal species and sample types. Our viral metagenomic workflow includes the addition of a spike-in virus as an internal control, which provides effective quality control assessment of the sequencing run and increased data reliability.

Validation on the viral metagenomic sequencing on MinION and MiSeq platforms using SVA-positive samples

Targeted Whole-genome Sequencing

Our targeted whole-genome sequencing approaches have been used to sequence complete or near complete genomes of SARS-CoV-2, IAV (all segments), PRRSV, SVA PCV-3, EqPV and EqHV. These standardized procedures can be quickly adapted to obtain high quality whole genome sequences for other viruses of interest.

Options of viruses for targeted whole-genome sequencing and the animals that we have sequenced

Sequencing Reports

The reports include a comprehensive summary of sequencing results, including the number of reads for each virus, the best Blast hit of the consensus sequence, a genome coverage plot and a phylogenetic tree demonstrating the genetic relationship of the virus detected in the clinical sample with other sequences. Genotyping can also be included if applicable.

Other Information

Information about sample submission please refer to our ESEQ test and fee catalog. If you need assistance or would like to discuss your project or sequencing needs please, contact Virology Management at