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The United States Swine Pathogen Database: integrating veterinary diagnostic laboratory sequence data to monitor emerging pathogens of swine

View ORCID ProfileTavis K. Anderson, Blake Inderski, View ORCID ProfileDiego G. Diel, Benjamin M. Hause, Elizabeth G. Porter, View ORCID ProfileTravis Clement, View ORCID ProfileEric A. Nelson, View ORCID ProfileJianfa Bai, Jane Christopher-Hennings, View ORCID ProfilePhillip C. Gauger, Jianqiang Zhang, Karen M. Harmon, Rodger Main, View ORCID ProfileKelly M. Lager, View ORCID ProfileKay S. Faaberg
doi: https://doi.org/10.1101/2021.04.16.439882
Tavis K. Anderson
1Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa, USA
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  • For correspondence: tavis.anderson@usda.gov kay.faaberg@usda.gov
Blake Inderski
1Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa, USA
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Diego G. Diel
2Department of Veterinary & Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA
3South Dakota Animal Disease Research & Diagnostic Laboratory, South Dakota State University, Brookings, South Dakota, USA
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Benjamin M. Hause
2Department of Veterinary & Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA
3South Dakota Animal Disease Research & Diagnostic Laboratory, South Dakota State University, Brookings, South Dakota, USA
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Elizabeth G. Porter
4Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
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Travis Clement
2Department of Veterinary & Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA
3South Dakota Animal Disease Research & Diagnostic Laboratory, South Dakota State University, Brookings, South Dakota, USA
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Eric A. Nelson
2Department of Veterinary & Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA
3South Dakota Animal Disease Research & Diagnostic Laboratory, South Dakota State University, Brookings, South Dakota, USA
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Jianfa Bai
4Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
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Jane Christopher-Hennings
2Department of Veterinary & Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA
3South Dakota Animal Disease Research & Diagnostic Laboratory, South Dakota State University, Brookings, South Dakota, USA
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Phillip C. Gauger
6Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, Iowa, USA
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  • ORCID record for Phillip C. Gauger
Jianqiang Zhang
6Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, Iowa, USA
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Karen M. Harmon
6Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, Iowa, USA
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Rodger Main
6Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, Iowa, USA
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Kelly M. Lager
1Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa, USA
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Kay S. Faaberg
1Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa, USA
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  • ORCID record for Kay S. Faaberg
  • For correspondence: tavis.anderson@usda.gov kay.faaberg@usda.gov
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ABSTRACT

Veterinary diagnostic laboratories annually derive thousands of nucleotide sequences from clinical samples of swine pathogens such as porcine reproductive and respiratory syndrome virus (PRRSV), Senecavirus A, and swine enteric coronaviruses. In addition, next generation sequencing has resulted in the rapid production of full-length genomes. Presently, sequence data are released to diagnostic clients for the purposes of informing control measures, but are not publicly available as data may be associated with sensitive information. However, public sequence data can be used to objectively design field-relevant vaccines; determine when and how pathogens are spreading across the landscape; identify virus transmission hotspots; and are a critical component in genomic surveillance for pandemic preparedness. We have developed a centralized sequence database that integrates a selected set of previously private clinical data, using PRRSV data as an exemplar, alongside publicly available genomic information. We implemented the Tripal toolkit, using the open source Drupal content management system and the Chado database schema. Tripal consists of a collection of Drupal modules that are used to manage, visualize, and disseminate biological data stored within Chado. Hosting is provided by Amazon Web Services (AWS) EC2 cloud instance with resource scaling. New sequences sourced from diagnostic labs contain at a minimum four data items: genomic information; date of collection; collection location (state or province level); and a unique identifier. Users can download annotated genomic sequences from the database using a customized search interface that incorporates data mined from published literature; search for similar sequences using BLAST-based tools; and explore annotated reference genomes. Additionally, because the bulk of data presently are PRRSV sequences, custom curation and annotation pipelines have determined PRRSV genotype (Type 1 or 2), the location of open reading frames and nonstructural proteins, generated amino acid sequences, the occurrence of putative frame shifts, and restriction fragment length polymorphism (RFLP) classification of GP5 genes. Genomic data from seven major swine pathogens have been curated and annotated. The resource provides researchers timely access to sequences discovered by veterinary diagnosticians, allowing for epidemiological and comparative virology studies. The result will be a better understanding on the emergence of novel swine viruses in the United States (US), and how these novel strains are disseminated in the US and abroad.

Database URL https://swinepathogendb.org

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://swinepathogendb.org/

  • https://github.com/us-spd

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted April 19, 2021.
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The United States Swine Pathogen Database: integrating veterinary diagnostic laboratory sequence data to monitor emerging pathogens of swine
Tavis K. Anderson, Blake Inderski, Diego G. Diel, Benjamin M. Hause, Elizabeth G. Porter, Travis Clement, Eric A. Nelson, Jianfa Bai, Jane Christopher-Hennings, Phillip C. Gauger, Jianqiang Zhang, Karen M. Harmon, Rodger Main, Kelly M. Lager, Kay S. Faaberg
bioRxiv 2021.04.16.439882; doi: https://doi.org/10.1101/2021.04.16.439882
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The United States Swine Pathogen Database: integrating veterinary diagnostic laboratory sequence data to monitor emerging pathogens of swine
Tavis K. Anderson, Blake Inderski, Diego G. Diel, Benjamin M. Hause, Elizabeth G. Porter, Travis Clement, Eric A. Nelson, Jianfa Bai, Jane Christopher-Hennings, Phillip C. Gauger, Jianqiang Zhang, Karen M. Harmon, Rodger Main, Kelly M. Lager, Kay S. Faaberg
bioRxiv 2021.04.16.439882; doi: https://doi.org/10.1101/2021.04.16.439882

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