PRRSV-2 variant classification:a dynamic nomenclature for enhanced monitoring and surveillance

Existing genetic classificationsystems for porcine reproductive and respiratory syndrome virus type 2 (PRRSV-2), such as restriction fragment length polymorphisms and sub-lineages, are unreliable indicators of close genetic relatedness or lack sufficientresolution for epidemiological monitoring routinely conducted by veterinarians. Here, we outline a fine-scaleclassificationsystem for PRRSV-2 genetic variants in the United States. Based on >25,000 U.S. open reading frame 5 (ORF5) sequences, sub-lineages were divided into genetic variants using a clustering algorithm. Through classifying new sequences every 3 months and systematically identifying new variants across 8 years, we demonstrated that prospective implementation of the variant classificationsystem produced robust, reproducible results across time and can dynamically accommodate new genetic diversity arising from virus evolution. From 2015 to 2023, 118 variants were identified,with ∼48 active variants per year, of which 26 were common (detected >50 times). Mean within-variant genetic distance was 2.4% (max: 4.8%). The mean distance to the closest related variant was 4.9%. A routinely updated webtool (https://stemma.shinyapps.io/PRRSLoom-variants/) was developed and is publicly available for end users to assign newly generated sequences to a variant ID. This classificationsystem relies on U.S. sequences from 2015 onward; further effortsare required to extend this system to older or international sequences. Finally, we demonstrate how variant classificationcan better discriminate between previous and new strains on a farm, determine possible sources of new introductions into a farm/system, and track emerging variants regionally. Adoption of this classificationsystem will enhance PRRSV-2 epidemiological monitoring, research, and communication, and improve industry responses to emerging genetic variants.