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Rapid PRRSV-2 ORF5-based lineage classification using Nextclade.

Michael A Zeller1, Jennifer Chang2, Giovani Trevisan1

  • 1Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA, United States.

Frontiers in Veterinary Science
|September 30, 2024
PubMed
Summary
This summary is machine-generated.

A new genetic nomenclature for Porcine Reproductive and Respiratory Syndrome Virus type 2 (PRRSV-2) enables standardized lineage classification. This system, integrated with Nextclade, aids in identifying mutations and comparing strains to vaccines for improved swine health management.

Keywords:
ORF5PRRSVclassificationlineagesublineage

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Area of Science:

  • Veterinary Virology
  • Molecular Epidemiology
  • Bioinformatics

Background:

  • Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) poses a significant global threat to swine health and the agricultural economy.
  • Existing genetic characterization of PRRSV-2 is fragmented, hindering effective global surveillance and control strategies.
  • A standardized genetic nomenclature is crucial for consistent PRRSV-2 lineage identification and tracking.

Purpose of the Study:

  • To establish and implement a standard genetic nomenclature for PRRSV-2 ORF5-based genetic lineages.
  • To develop a user-friendly bioinformatics tool for rapid PRRSV-2 lineage classification and analysis.
  • To facilitate the comparison of contemporary PRRSV-2 strains with historical data and vaccine sequences.

Main Methods:

  • Development of a PRRSV-2 ORF5-based genetic nomenclature, extending previous classifications.
  • Creation of a scaffold sequence dataset including historical/contemporary strains and vaccines for Nextclade v3.0.
  • Utilized the Augur pipeline with DQ478308.1 as a reference for phylogenetic analysis and classifier generation.

Main Results:

  • A functional Nextclade classifier for PRRSV-2 ORF5 lineage assignment is now available via Nextstrain and PRRSView.
  • The classifier provides phylogenetic classification, sequence metrics (quality, mutations), and confidential user analysis.
  • Submitted sequences are phylogenetically placed, allowing comparison with reference viruses, vaccine strains, and metadata.

Conclusions:

  • The implemented Nextclade workflow offers a standardized and efficient method for PRRSV-2 lineage classification.
  • This tool aids in identifying key mutations and comparing current PRRSV-2 strains to relevant vaccines.
  • Enhanced PRRSV-2 surveillance and control strategies can be supported through this standardized classification system.