VirOligo: a database of virus-specific oligonucleotides

Area of Science:

• Virology
• Bioinformatics
• Molecular Biology

Background:

• Accurate detection of viral nucleic acids is crucial for diagnosing and managing viral infections.
• A centralized resource for virus-specific oligonucleotides, including primers and probes, is needed to support diagnostic and research efforts.
• Bovine respiratory disease (BRD) is a significant economic concern in cattle production, necessitating efficient diagnostic tools.

Purpose of the Study:

• To establish and present the VirOligo database, a curated collection of virus-specific oligonucleotides.
• To provide a comprehensive resource for PCR primers and hybridization probes used in the detection of viral nucleic acids.
• To focus initially on viruses associated with bovine respiratory disease.

Main Methods:

• Compilation of oligonucleotide data from peer-reviewed English-language publications.
• Inclusion of experimental conditions for oligonucleotide detection.
• Integration of links to external databases such as PubMed, GenBank, NCBI Taxonomy, and BLAST for comprehensive information retrieval.

Main Results:

• The VirOligo database contains a complete listing of oligonucleotides specific to viruses associated with bovine respiratory disease as of July 2001.
• Included viruses encompass bovine herpesvirus types 1, 3, 4, and 5, bovine viral diarrhea virus, bovine parainfluenza 3 virus, bovine respiratory syncytial virus, bovine adenovirus, bovine rhinovirus, bovine coronavirus, bovine reovirus, bovine enterovirus, and alcelaphine herpesvirus-1.
• Each entry links to relevant external databases for further information.

Conclusions:

• VirOligo serves as a valuable resource for researchers and diagnosticians working with viral nucleic acid detection.
• The database facilitates the identification and selection of appropriate oligonucleotides for specific viral targets.
• The VirOligo database is expandable to include other viruses, enhancing its utility for a broader range of research applications.