RefiningPRRSV-2 genetic classificationbased on global ORF5 sequences and investigation of their geographic distributions and temporal changes

Porcine reproductive and respiratory syndrome virus (PRRSV) is an important swine pathogen affectingthe global swine industry. The firstopen reading frame 5 (ORF5)-based genetic lineage classificationsystem describing global PRRSV-2 genetic diversity was introduced over a decade ago. Although refinementshave been proposed for the predominant lineage in the USA (lineage 1), PRRSV-2 phylogenetic classificationsystem at international levels has not been thoroughly evaluated and updated since 2010. In this study, based on analysis of 82,237 global ORF5 sequences reported during 1989-2021, we classifiedPRRSV-2 into 11 genetic lineages (L1-L11) and 21 sublineages (L1A-L1F, L1H-L1J, L5A-L5B, L8A-L8E, and L9A-L9E). The proposed classificationsystem is flexiblefor growth if additional lineages, sublineages, or more granular classificationsare needed. For example, for more fine-scaleepidemiological investigation, L1C was further divided into fivegroups (L1C.1-L1C.5), with L1C.5 corresponding to the recently emerged L1C variant. Comparison between restriction fragment length polymorphism (RFLP) typing and phylogenetic classificationrevealed 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. In summary, this study refinedPRRSV-2 ORF5-based phylogenetic classificationand investigated the geographic distribution and temporal changes of PRRSV-2 at the lineage/sublineage levels. The refinedclassificationsystem and molecular epidemiology data in this study will be invaluable for future characterization of PRRSV-2.