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Porcine reproductive and respiratory syndrome virus (PRRSV) is an important swine pathogen affecting the global swine industry. The first open reading frame 5 (ORF5)-based genetic lineage classification system describing global PRRSV-2 genetic diversity was introduced over a decade ago. Although refinements have been proposed for the predominant lineage in the USA (lineage 1), PRRSV-2 phylogenetic classification system at international levels has not been thoroughly evaluated and updated since 2010.
Methods: In this study, based on analysis of 82,237 global ORF5 sequences reported during 1989–2021, we classified PRRSV-2 into 11 genetic lineages (L1‒L11) and 21 sublineages (L1A‒L1F, L1H‒L1J, L5A‒L5B, L8A‒L8E, and L9A‒L9E).
Results: The proposed classification system is flexible for growth if additional lineages, sublineages, or more granular classifications are needed. For example, for more fine-scale epidemiological investigation, L1C was further divided into five groups (L1C.1‒L1C.5), with L1C.5 corresponding to the recently emerged L1C variant. Comparison between restriction fragment length polymorphism (RFLP) typing and phylogenetic classification revealed the inaccuracy of using RFLP to determine PRRSV-2 genetic relatedness in most scenarios. Genetic homology of six commercial PRRSV-2 vaccines to each lineage/sublineage and detection frequency of vaccine-like viruses were determined. Global geographic distribution of each lineage/sublineage was presented. Temporal dynamic changes of PRRSV-2 in the USA during 1989–2021 were investigated by analyzing 73,092 ORF5 sequences.
Conclusion: In summary, this study refined PRRSV-2 ORF5-based phylogenetic classification and investigated the geographic distribution and temporal changes of PRRSV-2 at the lineage/sublineage levels. The refined classification system and molecular epidemiology data in this study will be invaluable for future characterization of PRRSV-2.
Yim-im W, Anderson TK, Paploski IAD, VanderWaal K, Gauger P, Krueger K, Shi S, Main R, Zhang J. Refining PRRSV-2 genetic classification based on global ORF5 sequences and investigation of their geographic distributions and temporal changes. Virology. 2023. https://doi.org/10.1128/spectrum.02916-23
