Single amino acid substitution in RdRp reduces viral recombination frequency of NADC30-like porcine reproductive and respiratory syndrome virus type 2.

Porcine reproductive and respiratory syndrome (PRRS) is one of the most significant diseases, causing tremendous economic losses to the global swine industry. Accumulating evidence indicates that recombination between PRRSV-2 strains, particularly those involving NADC30-like PRRSV-2 variants, has been responsible for outbreaks across several countries. However, the key proteins or amino acids associated with PRRSV-2 recombination remain unclear. In this study, two representative PRRSV-2 strains (the NADC30-like HeB108 strain from lineage 1 and the HP-PRRSV HuN4 strain from lineage 8) were serially passaged in the presence of ribavirin. Amino acid substitutions associated with ribavirin resistance were identified in the RNA-dependent RNA polymerase (RdRp) and helicase of the passaged viruses. Using the infectious clones PRRSV-2 HeB108 and HuN4, ribavirin-resistant mutants with single or multiple amino acid substitutions were generated. Notably, the mutants HeB108-VGSS and HuN4-TNII, with multiple amino acid substitutions, showed higher fidelity and lower pathogenicity in infected piglets than their parental viruses. Furthermore, the potential decreased recombination risk correlated with increased polymerase fidelity. In an inter-lineage co-infection assay on primary alveolar macrophages, the I360V substitution in RdRp reduced the recombination frequency of NADC30-like PRRSV-2 HeB108 as determined by both Sanger sequencing and nanopore long-read RNA sequencing. The results identified a key amino acid associated with viral recombination in NADC30-like PRRSV-2 and provide an editing target for developing safer vaccines that are less prone to recombination.