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Article

Characterization of Emerging Swine Viral Diseases through Oxford Nanopore Sequencing Using Senecavirus A as a Model

Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA
*
Author to whom correspondence should be addressed.
Deceased.
Received: 14 September 2020 / Revised: 30 September 2020 / Accepted: 2 October 2020 / Published: 7 October 2020
(This article belongs to the Special Issue Endemic and Emerging Swine Viruses)
Emerging viral infectious diseases present a major threat to the global swine industry. Since 2015, Senecavirus A (SVA) has been identified as a cause of vesicular disease in different countries and is considered an emerging disease. Despite the growing concern about SVA, there is a lack of preventive and diagnostic strategies, which is also a problem for all emerging infectious diseases. Using SVA as a model, we demonstrated that Oxford Nanopore MinION sequencing could be used as a robust tool for the investigation and surveillance of emerging viral diseases. Our results identified that MinION sequencing allowed for rapid, unbiased pathogen detection at the species and strain level for clinical cases. SVA whole genome sequences were generated using both direct RNA sequencing and PCR-cDNA sequencing methods, with an optimized consensus accuracy of 94% and 99%, respectively. The advantages of direct RNA sequencing lie in its shorter turnaround time, higher analytical sensitivity and its quantitative relationship between input RNA and output sequencing reads, while PCR-cDNA sequencing excelled at creating highly accurate sequences. This study developed whole genome sequencing methods to facilitate the control of SVA and provide a reference for the timely detection and prevention of other emerging infectious diseases. View Full-Text
Keywords: emerging infectious diseases; molecular diagnostic techniques; Oxford Nanopore sequencing; Senecavirus A; bioinformatics; swine viral diseases emerging infectious diseases; molecular diagnostic techniques; Oxford Nanopore sequencing; Senecavirus A; bioinformatics; swine viral diseases
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MDPI and ACS Style

Tan, S.; Dvorak, C.M.T.; Murtaugh, M.P. Characterization of Emerging Swine Viral Diseases through Oxford Nanopore Sequencing Using Senecavirus A as a Model. Viruses 2020, 12, 1136. https://0-doi-org.brum.beds.ac.uk/10.3390/v12101136

AMA Style

Tan S, Dvorak CMT, Murtaugh MP. Characterization of Emerging Swine Viral Diseases through Oxford Nanopore Sequencing Using Senecavirus A as a Model. Viruses. 2020; 12(10):1136. https://0-doi-org.brum.beds.ac.uk/10.3390/v12101136

Chicago/Turabian Style

Tan, Shaoyuan, Cheryl M.T. Dvorak, and Michael P. Murtaugh. 2020. "Characterization of Emerging Swine Viral Diseases through Oxford Nanopore Sequencing Using Senecavirus A as a Model" Viruses 12, no. 10: 1136. https://0-doi-org.brum.beds.ac.uk/10.3390/v12101136

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