ISU PRRSView

ISU PRRSView provides analytical information from Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) sequence data, utilizing Nextclade for rapid lineage classification and phylogenetic analysis to inform PRRSV research and veterinary decision-making.

Key Features:

• Nextclade-based lineage classification: Rapid PRRSV-2 ORF5-based lineage classification using a scaffold sequence dataset designed for Nextclade v3.0.
• Phylogenetic placement: Submitted sequences are grafted to the reference tree using phylogenetic placement, enabling comparison to nearby sequences of reference viruses and vaccine strains.
• Sequence quality metrics: Provides classification quality and notable mutations relative to the DQ478308.1 reference strain.
• Metadata comparisons: Additional comparisons between sequences can be made with metadata including year, country, and RFLP typing incorporated in the dataset.
• Local analysis: Sequences are not uploaded to a server, ensuring analysis remains strictly confidential to the user.

Scientific Applications:

• PRRSV-2 lineage assignment: Rapidly assign standardized genetic lineage classifications to PRRSV-2 ORF5 sequences on demand.
• Mutation identification: Identify mutations of interest relative to the reference strain and nearby sequences.
• Vaccine strain comparison: Compare contemporary strains to relevant historical and contemporary vaccine strains included in the scaffold dataset.
• Global PRRSV characterization: Facilitate use of the Yim-Im et al. 2023 standard genetic nomenclature for global PRRSV-2 characterization.

Methodology:

Scaffold sequences including historical and contemporary vaccines were synthesized into a dataset for Nextclade v3.0, with metadata for year, country, and RFLP typing incorporated. These scaffold sequences were processed through the Augur pipeline using DQ478308.1 as a reference strain for rooting and comparison.