Whole-Genome Sequencing of Porcine Epidemic Diarrhea Virus by Illumina MiSeq Platform

Leyi Wang; Tod Stuber; Patrick Camp; Suelee Robbe-Austerman; Yan Zhang

doi:10.1007/978-1-4939-3414-0_18

Whole-Genome Sequencing of Porcine Epidemic Diarrhea Virus by Illumina MiSeq Platform

Leyi Wang, Tod Stuber, Patrick Camp, Suelee Robbe-Austerman, Yan Zhang

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Abstract

Porcine epidemic diarrhea virus (PEDV) belongs to the genus Alphacoronavirus of the family Coronaviridae. PEDV was identified as an emerging pathogen in US pig populations in 2013. Since then, this virus has been detected in at least 31 states in the USA and has caused significant economic loss to the swine industry. Active surveillance and characterization of PEDV are essential for monitoring the virus. Obtaining comprehensive information about the PEDV genome can improve our understanding of the evolution of PEDV viruses, and the emergence of new strains, and can enhance vaccine designs. In this chapter, both a targeted amplification method and a random-priming method are described to amplify the complete genome of PEDV for sequencing using the MiSeq platform. Overall, this protocol provides a useful two-pronged approach to complete whole-genome sequences of PEDV depending on the amount of virus in the clinical samples.

Original language	English (US)
Title of host publication	Animal Coronaviruses
Editors	Leyi Wang
Publisher	Humana Press
Chapter	18
Pages	201-208
DOIs	https://doi.org/10.1007/978-1-4939-3414-0_18
State	Published - Mar 16 2016
Externally published	Yes

Publication series

Name	Springer Protocols Handbooks
ISSN (Print)	1949-2448
ISSN (Electronic)	1949-2456

Keywords

Porcine epidemic diarrhea virus
Targeted amplification
SISPA
Whole-genome sequencing
MiSeq

Online availability

10.1007/978-1-4939-3414-0_18

Library availability

Discover UIUC Full Text

1 Book

Animal Coronaviruses
Wang, L. (Editor), 2016, Humana Press. (Springer Protocols Handbooks)
Research output: Book/Report/Conference proceeding › Book

Cite this

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title = "Whole-Genome Sequencing of Porcine Epidemic Diarrhea Virus by Illumina MiSeq Platform",

abstract = "Porcine epidemic diarrhea virus (PEDV) belongs to the genus Alphacoronavirus of the family Coronaviridae. PEDV was identified as an emerging pathogen in US pig populations in 2013. Since then, this virus has been detected in at least 31 states in the USA and has caused significant economic loss to the swine industry. Active surveillance and characterization of PEDV are essential for monitoring the virus. Obtaining comprehensive information about the PEDV genome can improve our understanding of the evolution of PEDV viruses, and the emergence of new strains, and can enhance vaccine designs. In this chapter, both a targeted amplification method and a random-priming method are described to amplify the complete genome of PEDV for sequencing using the MiSeq platform. Overall, this protocol provides a useful two-pronged approach to complete whole-genome sequences of PEDV depending on the amount of virus in the clinical samples.",

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AU - Zhang, Yan

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AB - Porcine epidemic diarrhea virus (PEDV) belongs to the genus Alphacoronavirus of the family Coronaviridae. PEDV was identified as an emerging pathogen in US pig populations in 2013. Since then, this virus has been detected in at least 31 states in the USA and has caused significant economic loss to the swine industry. Active surveillance and characterization of PEDV are essential for monitoring the virus. Obtaining comprehensive information about the PEDV genome can improve our understanding of the evolution of PEDV viruses, and the emergence of new strains, and can enhance vaccine designs. In this chapter, both a targeted amplification method and a random-priming method are described to amplify the complete genome of PEDV for sequencing using the MiSeq platform. Overall, this protocol provides a useful two-pronged approach to complete whole-genome sequences of PEDV depending on the amount of virus in the clinical samples.

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KW - Targeted amplification

KW - SISPA

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Whole-Genome Sequencing of Porcine Epidemic Diarrhea Virus by Illumina MiSeq Platform

Abstract

Publication series

Keywords

Online availability

Library availability

Fingerprint

Research output

Animal Coronaviruses

Cite this