Molecular characterization of porcine reproductive and respiratory syndrome virus in Henan and Shanxi, China, during 2023–2024

Porcine reproductive and respiratory syndrome virus (PRRSV) is responsible for one of the most prevalent and economically damaging diseases in the pig industry. Surveillance of its epidemic profile and genetic Characteristics is critical for developing effective control strategies. In this study, 213 clinical samples were collected from pigs displaying typical symptoms of porcine reproductive and respiratory syndrome from swine farms of varying sizes in 13 cities of Henan and Shanxi provinces, China, between 2023 and 2024. All samples were screened via RT-PCR, and the ORF5 and Nsp2 genes of the viruses found in positive samples were sequenced and analyzed. The results revealed a PRRSV positivity rate of 19.72% (42/213). Phylogenetic analysis based on ORF5 showed that all 35 sequenced strains belong to the genotype PRRSV-2, with 27 strains clustering within sublineage 1.8 (NADC30-like), five in sublineage 5.1 (VR2332-like), and the remaining strains distributed among sublineages 8.7 (HP-PRRSV-like), 1.5 (NADC34-like), and 3.5 (QYYZ-like), indicating the dominance of NADC30-like strains in Henan and Shanxi provinces. Additionally, Nsp2 gene analysis of 10 selected strains (sublineages 5.1 and 1.8) revealed a unique 131-amino-acid (aa) deletion in the hypervariable region. Notably, two novel discontinuous deletions were identified: a 7-aa deletion (PVSLGGD) at positions 216-222 and a 3-aa deletion (GVL) at positions 453-455. Additionally, strains HNLY-6, HNLY-11, and HNLY-14 exhibited evidence of possible recombination events between NADC30-like and VR2332-like strains. These findings provide critical insights into the epidemiology of PRRSV in Henan and Shanxi provinces from 2023 to 2024, supporting the development of targeted prevention and control strategies.