PRRSV-2 variant classification: a dynamic nomenclature for enhanced monitoring and surveillance
Authors: VanderWaal Kimberly , Pamornchainavakul Nakarin , Kikuti Mariana , Zhang Jianqiang , Zeller Michael , Trevisan Giovani , Rossow Stephanie , Schwartz Mark , Linhares Daniel C.L. , Holtkamp Derald J. , da Silva João Paulo Herrera , Corzo Cesar A. , Baker Julia P. , Anderson Tavis K. , Makau Dennis N. , Paploski Igor A.D. 
Published: August 2024

AbstractExisting genetic classification systems for porcine reproductive and respiratory syndrome virus 2 (PRRSV-2), such as restriction fragment length polymorphisms (RFLPs) and sub-lineages, are unreliable indicators of genetic relatedness or lack sufficient resolution for epidemiological monitoring routinely conducted by veterinarians. Here, we outline a fine-scale classification system for PRRSV-2 genetic variants in the U.S. 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 three months and systematically identifying new variants across eight years, we demonstrated that prospective implementation of the variant classification system produced robust, reproducible results across time and can dynamically accommodate new genetic diversity arising from virus evolution. From 2015 and 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 classification system relies on U.S. sequences from 2015 onwards; further efforts are required to extend this system to older or international sequences. Finally, we demonstrate how variant classification can 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 classification system will enhance PRRSV-2 epidemiological monitoring, research, and communication, and improve industry responses to emerging genetic variants.ImportanceThe development and implementation of a fine-scale classification system for PRRSV-2 genetic variants represents a significant advancement for monitoring PRRSV-2 occurrence in the swine industry. Based on systematically-applied criteria for variant identification using national-scale sequence data, this system addresses the shortcomings of existing classification methods by offering higher resolution and adaptability to capture emerging variants. This system provides a stable and reproducible method for classifying PRRSV-2 variants, facilitated by a freely available and regularly updated webtool for use by veterinarians and diagnostic labs. Although currently based on U.S. PRRSV-2 ORF5 sequences, this system can be expanded to include sequences from other countries, paving the way for a standardized global classification system. By enabling accurate and improved discrimination of PRRSV-2 genetic variants, this classification system significantly enhances the ability to monitor, research, and respond to PRRSV-2 outbreaks, ultimately supporting better management and control strategies in the swine industry.