Reassessment of PRRSV-2 ORF5 sequence diversity in Japan identifies a previously unrecognized candidate lineage-level clade.

Authors

Osamu Taira, Ryosuke Takai, Yoriko Yonezawa, Nobuyuki Tsutsumi, Katsuaki Sugiura

Published in

Archives of virology. Volume 171. Issue 8. Jul 23, 2026. Epub Jul 23, 2026.

Abstract

Porcine reproductive and respiratory syndrome virus type 2 (PRRSV-2) exhibits extensive genetic diversity, and ORF5-based classification provides a standardized framework for global molecular surveillance. In a previous nationwide study in Japan, lineage 4 (L4) was identified as a dominant lineage exhibiting unexpectedly high genetic diversity. This observation motivated a focused reassessment of L4-assigned viruses to determine whether this heterogeneity reflected within-lineage diversification or deeper phylogenetic separation. In this study, we re-evaluated PRRSV-2 ORF5 sequences previously assigned to L4 in Japan using maximum-likelihood phylogenetic reconstruction and pairwise nucleotide distance analyses consistent with the global ORF5 classification framework. Following sequence de-duplication, 321 L4-assigned ORF5 sequences were analyzed together with global reference datasets. Phylogenetic analysis revealed two divergent clades within the L4-assigned population. One clade contained the global L4 reference sequences, whereas the other formed a distinct monophyletic group composed predominantly of Japanese sequences and supported by bootstrap values ≥ 85% at its defining node. Pairwise uncorrected nucleotide p-distance analysis showed that divergence between the two clades exceeded the 11% ORF5 lineage demarcation threshold (median between-clade p-distance = 0.133). Based on combined phylogenetic and genetic distance evidence, we report this distinct clade, provisionally designated JPL-A, as a candidate lineage-level clade separate from the major L4 clade. These findings indicate that contemporary PRRSV-2 diversity in Japan includes a lineage-level group not fully represented in historical global references and highlight the value of regional surveillance data in refining standardized ORF5-based classification resources.

PMID:
42489934
Bibliographic data and abstract were imported from PubMed on 23 Jul 2026.

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