Genetic evolutionary and pathogenicity analyses of a novel porcine reproductive and respiratory syndrome virus 1 strain SC202404 that emerged in Southwestern China

The porcine reproductive and respiratory syndrome virus 1 (PRRSV-1) was first reported in China in 1997, and its prevalence has increased rapidly in recent years. However, information on the genetic evolution and pathogenicity of the newly emerged PRRSV-1 isolates in China remains limited. To further our knowledge about the novel isolate, SC202404 was selected to analyze its potential evolutionary history, regional circulation, and pathogenicity for piglets. The PRRSV SC202404 strain was isolated from diseased pigs in Sichuan Province, Southwestern China in 2024. Complete genomic sequence analyses were conducted using the DNASTAR 7.0 software. The phylogenetic relationship of the PRRSV-1 strains was constructed using the maximum likelihood method in MEGA X. The Bayesian molecular divergence time estimation was analyzed using BEAST v10.5.0 software. Recombination events were detected using RDP V4.26 and SIMPLOT software v3.5.1. Five piglets in the challenge group were inoculated intranasally (2 mL) and intramuscularly (1 mL) with SC202404 (1 × 105.5 TCID50/mL). Rectal temperatures and clinical symptoms were monitored and scored daily after challenge. The serum was collected for viremia detection by RT‒qPCR and PRRSV-specific antibody levels by ELISA kit. The histopathological examination of tissues were performed using H&E staining. A genome comparative analysis revealed that SC202404 shares the highest nucleotide similarity (94.5%) with the PRRSV-1 BJEU06-1-like strain TZJ226, which was identified in a pig farm in Henan Province in 2020. A genomic sequence alignment showed that SC202404 has the same unique 25 aa premature termination in GP3, and a consecutive deletion of 6 aa in GP4 as the TZJ226 strain. Evolutionary analyses conducted on ORF5 sequences using Bayesian phylodynamic models estimated the time of emergence of the SC202404 strain as 2014–2015, which is earlier than the emergence of the TZJ226 strain. Moreover, recombination analyses revealed that SC202404 is a minor parent strain of the recombinant virus TZJ226. Therefore, we hypothesize that the SC202404 and TZJ226 strains might share a common evolutionary origin, potentially suggesting a transmission link or regional circulation between Sichuan and Henan provinces. Furthermore, an animal challenge study in piglets showed that SC202404 infection caused a transient fever, and moderate hemorrhagic and interstitial pneumonia, which indicated that the new virus exhibits moderate pathogenicity to piglets. A novel PRRSV-1 strain, SC202404, with unique molecular markers in GP3 and GP4, was isolated from Sichuan Province in 2024. Animal challenge study in piglets showed that SC202404 is a moderate virulent strain. Our study aids in understanding the genetic evolution of the novel PRRSV-1 strain SC202404 and highlights the importance of preventing and controlling PRRSV-1 strains in China.