Genotyping of porcine reproductive and respiratory syndrome virus in Ontario

Davor Ojkic

Animal Health Laboratory, University of Guelph, Guelph, ON. 

AHL Newsletter 2025;29(1):18.

Genetic characterization of porcine reproductive and respiratory syndrome virus type 2 (PRRSV) is typically done through open reading frame 5 (ORF5) analysis. ORF5 encodes glycoprotein 5, a highly variable component of the PRRSV envelope that is critical in the infection process and in swine immune responses. Historically, strain classification was carried out by ORF5 restriction fragment length polymorphism (RFLP) analysis; later on, ORF5 phylogenetic analysis was introduced. Although RFLP analysis corresponds with phylogenetic analysis to some extent, phylogenetic analysis provides a more stringent discrimination of PRRSV strains.

Recently, a refinement of the PRRSV lineage-based classification was proposed, which subdivided PRRSV into 11 lineages (L1‒L11) and 21 sub-lineages (L1A‒L1F, L1H‒L1J, L5A‒L5B, L8A‒L8E, and L9A‒L9E), based on ORF5 sequences. Using these criteria, an analysis of 1,777 PRRSV ORF5 sequences obtained from Ontario samples between 2015 and 2024 recognized the presence of six lineages (L1, L2, L4, L5, L7, L8). The most frequently detected lineages were L1 and L5, with 1,423 (80.08%) and 325 (17.73%) samples identified, respectively. Detection of lineages L2, L4, L7, and L8 in Ontario was infrequent (Table 1). Lineages L3, L6, L9, L10, and L11 were not detected.

Sub-lineage classification assigned 1,250 sequences into 9 sub-lineages: L1B, L1C, L1D, L1E, L1F, L1H, L5A, L8A, and L8C (Table 2). However, 525 sequences in the L1 lineage could not be definitively classified using the current criteria. Ontario PRRSV ORF5 sequences with ambiguous or undetermined L1 sub-lineage designations were labeled with an “X” (e.g., L1X, L1X.1).

Some RFLP patterns were sub-lineage-specific; for example, all 2-5-2 sequences were in the L5A sub-lineage, and all 1-8-4 sequences were in the L1H sub-lineage. On the other hand, the RFLP pattern 1-1-1 was detected in four sub-lineages, and 1-1-2 was detected in five sub-lineages (Table 3).

Table 1. Lineage classification of PRRSV ORF5 sequences from Ontario, 2015-2024.

Table 2. Sub-lineage classification of PRRSV ORF5 sequences from Ontario, 2015-2024.

Table 3.  Top 10 most frequent RFLP patterns of PRRSV ORF5 sequences from Ontario, 2015-2024.

Reference

1.Yim-Im W, et al. Refining PRRSV-2 genetic classification based on global ORF5 sequences. Microbiol Spectr 2023;11(6):e02916-23.