Virus Genes

, Volume 54, Issue 2, pp 323–327 | Cite as

Identification of porcine epidemic diarrhea virus variant with a large spike gene deletion from a clinical swine sample in the United States

  • Jianqiang Zhang
  • Wannarat Yim-Im
  • Qi Chen
  • Ying Zheng
  • Loni Schumacher
  • Haiyan Huang
  • Phillip Gauger
  • Karen Harmon
  • Ganwu Li


Two genetically different porcine epidemic diarrhea virus (PEDV) strains have been identified in the USA: US prototype (also called non-S INDEL) and S INDEL PEDVs. In February 2017, a PEDV variant (USA/OK10240-8/2017) was identified in a rectal swab from a sow farm in Oklahoma, USA. Complete genome sequence analyses indicated this PEDV variant was genetically similar to US non-S INDEL strain but had a continuous 600-nt (200-aa) deletion in the N-terminal domain of the spike gene compared to non-S INDEL PEDVs. This is the first report of detecting PEDV bearing large spike gene deletion in clinical swine samples in the USA.


PEDV Variant Large S gene deletion Clinical swine sample 



This study was supported by the Iowa State University Veterinary Diagnostic Laboratory.

Author contributions

JZ supervised the work, conducted data analyses, and composed the manuscript. WYI performed RT-PCR testing. QC, YZ, and GL performed next-generation sequencing. HH attempted virus isolation. LS, WYI, and QC performed pig inoculation study. PG and KH collected clinical information of the case. WYI, QC, YZ, LS, HH, PG, KH, and GL edited the manuscript.

Compliance with ethical standards

Conflict of interest

All authors declare that they have no conflict of interest.

Human participants and/or animals

No human subjects were used in this study. Pigs were used in this study and the animal study protocol was approved by the Iowa State University Institutional Animal Care and Use Committee (approved number 5-17-8515-S; approved on May 12, 2017).


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Jianqiang Zhang
    • 1
  • Wannarat Yim-Im
    • 1
  • Qi Chen
    • 1
  • Ying Zheng
    • 1
  • Loni Schumacher
    • 1
  • Haiyan Huang
    • 1
  • Phillip Gauger
    • 1
  • Karen Harmon
    • 1
  • Ganwu Li
    • 1
  1. 1.Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary MedicineIowa State UniversityAmesUSA

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