#07-125

Complete

Date Full Report Received

01/07/2009

Date Abstract Report Received

01/07/2009

Investigation

Institution: , ,
Primary Investigator:

The PRRSV strain database (http://prrsvdb.org) has been supported by the National Pork Board for four years. The database (PRRSVdb; 9,531 sequences) is available for queries in order to obtain detailed information about PRRSV sequences (percent similarity to vaccines or other database isolates, ORF5 RFLP analysis, year and state of isolation, phylogenetic relationships, GenBank submission numbers, relevant clinical information if provided by the respective veterinary diagnostic laboratory (VDL)). The project directly addresses the NPB directive to implement a National PRRSV Sequence Database and has relevance to a number of PRRS Initiative efforts such as surveying potentially new field strains for vaccines, examining sequence conservation among various isolates for improvement of diagnostics, epitope evaluation and assessment of virus spread locally, nationally and internationally. The database is comprised presently of four veterinary diagnostic laboratories sequenced isolates and those independently deposited in GenBank. In addition, the software interface of the database has been updated to provide additional flexibility to the PRRSVdb. This flex-based web interface provides improved phylogeny viewing and user-uploaded sequence analysis, either dependent or independent of the database. This research is currently the result of several sources: the National Pork Board, the National Animal Disease Center-USDA-ARS (Kay Faaberg), the Minnesota Veterinary Diagnostic Laboratory (MVDL; James Collins and the Molecular Diagnostic Section), South Dakota Animal Disease Research & Diagnostic Laboratory (Jane Christopher-Hennings, Travis Clement), Hong Kong University (Frederick Leung, Hon Chung Chau) and the Manitoba Veterinary Services Branch (Andre Hamel) with software engineers (Trevor Wennblom, John Crow) formerly located at the Center for Biomedical Research Informatics (CBRI) of the University of Minnesota. Since the CBRI was eliminated, Trevor Wennblom moved to the Minnesota Supercomputing Institute and has worked off hours on the PRRSV Database and John Crow (Co-PI) relocated to the National Center for Genome Resources (NCGR) in Santa Fe, New Mexico. At present, the PRRSV Database has not received additional funding and thus has been forced to stop development. John Crow is currently paying monthly fees for database maintenance and online publication to Slicehost (http://www.slicehost.com), a database warehouse management firm, out of his personal funds at a rate of $38/month.