Mixed Strain Identification of Porcine Reproductive and Respiratory Syndrome Virus in Multiplexed Samples using Nanopore Sequencing

For over thirty years, Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) has been a major contributor to morbidity and mortality in the commercial swine industry across the globe. This highly mutagenic RNA virus causes significant economic losses wherever it is prevalent, leading to $664 million in annual losses in the United States. Unfortunately, the current prevention and diagnostic techniques available have proven to be insufficient in controlling the spread of this disease. We describe an alternative diagnostic method exploiting the rapid turnaround time and long-read capacity of Oxford Nanopore Technology's MinION next-generation sequencer. We have developed a novel primer set designed to span Open Reading Frames 3 through 7 of the PRRSV genome, which has allowed for multiplexing of samples, thus reducing individual cost of testing, while yielding significantly more information than previously available. This novel primer pair and sequencing technique have distinguished mixed infections within individual animals and may be used to determine vaccination status. This new approach will help producers and veterinarians make better-informed decisions about co-mingling of animals and vaccination strategies, thus reducing the emergence of new, pathogenic strains of PRRSV.

Name thesis:degree_name

Master of Science

Level thesis:degree_level

masters

Discipline thesis:degree_discipline

Biomedical and Veterinary Sciences

Department dc:contributor.department

Biomedical and Veterinary Sciences

Grantor dc:publisher

Virginia Tech

Year dc:date.issued

2024

Author dc:creator

• Buman Ruiz Diaz, Maria Paz

Chair dc:contributor.committeechair

• Lahmers, Kevin K.

Committee members dc:contributor.committeemember

• Slade, Daniel Joseph
• LeRoith, Tanya

• porcine reproductive and respiratory syndrome virus
• nanopore
• sequencing
• multiplex
• next-generation sequencing

Statement dc:rights

• In Copyright

Licence dc:rights.uri

• http://rightsstatements.org/vocab/InC/1.0/

Language dc:language.iso

en

Dc Identifier Other

vt_gsexam:39020

OAI identifier oai:identifier

oai:vtechworks.lib.vt.edu:10919/117321