HP-PRRSV is attenuated by de-optimization of codon pair bias in its RNA-dependent RNA polymerase nsp9 gene

There is an urgent need to develop new vaccines against highly pathogenic PRRS virus (HP-PRRSV) variant in China. The actual use of each codon pairs is more or less frequent than that of the statistical prediction and codon pair bias (CPB) usage affects gene translation. We “shuffled” the existing codons in HP-PRRSV genes GP5, M, nsp2 and nsp9, so that the CPB of these genes could be more negative. De-optimization of nsp9, the RNA-dependent RNA polymerase, significantly decreased PRRSV replication in porcine alveolar macrophages (PAMs). In vitro study showed that HV-nsp9min and HV-nsp29min were remarkably attenuated in PAMs, and inoculation of pigs with 2 ml⁎105.0 TCID50/ml of HV-nsp9min or HV-nsp29min did not cause PRRS. Importantly, pigs immunized with HV-nsp29min were fully protected against different HP-PRRSV strains׳ lethal challenges. Our results imply that the CPB de-optimized HV-nsp29min has the potential to be used as a live vaccine candidate against HP-PRRSV.