PMID- 35165687 OWN - NLM STAT- MEDLINE DCOM- 20220429 LR - 20220429 IS - 1758-0463 (Electronic) IS - 1758-0463 (Linking) VI - 2021 DP - 2021 Dec 15 TI - The United States Swine Pathogen Database: integrating veterinary diagnostic laboratory sequence data to monitor emerging pathogens of swine. LID - 10.1093/database/baab078 [doi] LID - baab078 AB - Veterinary diagnostic laboratories 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 but are not publicly available as data may be associated with sensitive information. However, these data can be used for field-relevant vaccines; determining where and when pathogens are spreading; have relevance to research in molecular and comparative virology; and are a component in pandemic preparedness efforts. We have developed a centralized sequence database that integrates private clinical data using PRRSV data as an exemplar, alongside publicly available genomic information. We implemented the Tripal toolkit, a collection of Drupal modules that are used to manage, visualize and disseminate biological data stored within the Chado database schema. New sequences sourced from diagnostic laboratories contain: genomic information; date of collection; collection location; and a unique identifier. Users can download annotated genomic sequences 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, custom annotation pipelines have determined species, the location of open reading frames and nonstructural proteins and the occurrence of putative frame shifts. Eighteen swine pathogens have been curated. The database provides researchers 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 and how these novel strains are disseminated in the USA and abroad. Database URLhttps://swinepathogendb.org. CI - Published by Oxford University Press 2021. This work is written by (a) US Government employee(s) and is in the public domain in the US. FAU - Anderson, Tavis K AU - Anderson TK AUID- ORCID: 0000-0002-3138-5535 AD - Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, 1920 Dayton Avenue, Ames, IA 50010, USA. FAU - Inderski, Blake AU - Inderski B AD - Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, 1920 Dayton Avenue, Ames, IA 50010, USA. FAU - Diel, Diego G AU - Diel DG AD - Department of Veterinary & Biomedical Sciences, South Dakota State University, 1155 North Campus Drive, Brookings, SD 57007, USA. AD - South Dakota Animal Disease Research & Diagnostic Laboratory, South Dakota State University, 1155 North Campus Drive, Brookings, SD 57007, USA. AD - Diego G. Diel, Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA. FAU - Hause, Benjamin M AU - Hause BM AD - Department of Veterinary & Biomedical Sciences, South Dakota State University, 1155 North Campus Drive, Brookings, SD 57007, USA. AD - South Dakota Animal Disease Research & Diagnostic Laboratory, South Dakota State University, 1155 North Campus Drive, Brookings, SD 57007, USA. FAU - Porter, Elizabeth G AU - Porter EG AD - Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA. AD - Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA. FAU - Clement, Travis AU - Clement T AD - Department of Veterinary & Biomedical Sciences, South Dakota State University, 1155 North Campus Drive, Brookings, SD 57007, USA. AD - South Dakota Animal Disease Research & Diagnostic Laboratory, South Dakota State University, 1155 North Campus Drive, Brookings, SD 57007, USA. FAU - Nelson, Eric A AU - Nelson EA AD - Department of Veterinary & Biomedical Sciences, South Dakota State University, 1155 North Campus Drive, Brookings, SD 57007, USA. AD - South Dakota Animal Disease Research & Diagnostic Laboratory, South Dakota State University, 1155 North Campus Drive, Brookings, SD 57007, USA. FAU - Bai, Jianfa AU - Bai J AD - Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA. AD - Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA. FAU - Christopher-Hennings, Jane AU - Christopher-Hennings J AD - Department of Veterinary & Biomedical Sciences, South Dakota State University, 1155 North Campus Drive, Brookings, SD 57007, USA. AD - South Dakota Animal Disease Research & Diagnostic Laboratory, South Dakota State University, 1155 North Campus Drive, Brookings, SD 57007, USA. FAU - Gauger, Phillip C AU - Gauger PC AD - Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA. AD - Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA. FAU - Zhang, Jianqiang AU - Zhang J AD - Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA. AD - Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA. FAU - Harmon, Karen M AU - Harmon KM AD - Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA. AD - Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA. FAU - Main, Rodger AU - Main R AD - Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA. AD - Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA. FAU - Lager, Kelly M AU - Lager KM AD - Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, 1920 Dayton Avenue, Ames, IA 50010, USA. FAU - Faaberg, Kay S AU - Faaberg KS AD - Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, 1920 Dayton Avenue, Ames, IA 50010, USA. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - England TA - Database (Oxford) JT - Database : the journal of biological databases and curation JID - 101517697 SB - IM MH - Animals MH - Genomics MH - Humans MH - Laboratories MH - Open Reading Frames MH - Phylogeny MH - *Porcine Reproductive and Respiratory Syndrome MH - *Porcine respiratory and reproductive syndrome virus MH - Swine MH - United States PMC - PMC8903347 EDAT- 2022/02/16 06:00 MHDA- 2022/04/30 06:00 PMCR- 2021/12/15 CRDT- 2022/02/15 05:37 PHST- 2021/04/20 00:00 [received] PHST- 2021/11/04 00:00 [revised] PHST- 2021/11/29 00:00 [accepted] PHST- 2022/02/15 05:37 [entrez] PHST- 2022/02/16 06:00 [pubmed] PHST- 2022/04/30 06:00 [medline] PHST- 2021/12/15 00:00 [pmc-release] AID - 6462938 [pii] AID - baab078 [pii] AID - 10.1093/database/baab078 [doi] PST - ppublish SO - Database (Oxford). 2021 Dec 15;2021:baab078. doi: 10.1093/database/baab078.