Genotyping atypical porcine pestivirus using NS5a

Area of Science:

• Veterinary Virology
• Molecular Epidemiology
• Genomics

Background:

• Atypical porcine pestivirus (APPV) emerged in 2014, causing congenital tremors in pigs.
• Molecular epidemiology is crucial for APPV monitoring and control, relying on genome sequencing and phylogenetic analysis.
• Existing studies use varied genes for APPV phylogeny, lacking a standardized classification system for global strains.

Purpose of the Study:

• To propose a standardized taxonomy for APPV strains at genotype, subgenotype, and isolate levels.
• To evaluate the suitability of different viral genes for APPV phylogenetic analysis.
• To establish reliable classification thresholds for APPV genetic diversity.

Main Methods:

• Analysis of 76 whole APPV genomes and 16 partial polyprotein coding sequences.
• Assessment of genetic variability and suitability of individual genes for phylogenetic studies.
• Determination of pairwise identity thresholds and genetic distances for classification.

Main Results:

• The NS5a coding sequence is identified as the most suitable gene for APPV strain tracing, mirroring whole genome phylogenetic information.
• A proposed genotyping scheme includes three genotypes and seven subgenotypes within genotype 1.
• Established pairwise identity thresholds: 84%-91% for subgenotype and 80% for genotype separation using whole genomes; 82%-91% for subgenotype and 76% for genotype using NS5a.

Conclusions:

• The NS5a gene offers a robust alternative to whole genome sequencing for APPV molecular epidemiology.
• The proposed classification strategy provides clear segregation of APPV genotypes, subgenotypes, and isolates.
• This improved phylogenetic basis aids in understanding APPV genetic diversity and controlling disease outbreaks.