Co-Infection of PRRSV-1 and PRRSV-2 in a Single Sow: Complete Genome Characterization Reveals a Novel CH-1a-Backbone Recombinant with an NADC30-Derived Nsp2 in China

Porcine reproductive and respiratory syndrome virus (PRRSV) has the characteristics of a fast evolution rate and high genetic heterogeneity. PRRSV-1 and PRRSV-2 are co-circulating, and the threat they pose to the health of pigs worldwide continues to rise. In this study, two PRRSV strains with significantly different genetic backgrounds, namely SHEU-2022 (PRRSV-1, full length 15,050 nt) and SHCH-2023 (PRRSV-2, full length 15,019 nt), were simultaneously isolated from a single serum sample of a co-infected sow in Shanghai, China, and their whole-genome characteristics were analyzed. SHEU-2022 clustered with indigenous PRRSV-1 isolates in China, harbored a unique 15-nt deletion in the ORF3-ORF4 overlapping region, carried an additional N-glycosylation site on GP5, and replicated only in porcine alveolar macrophages (PAMs) under the conditions used. SHCH-2023 is a novel recombinant strain with a CH-1a-like (lineage 8) genome backbone and two NADC30-derived fragments—one in Nsp2 (sublineage 1.8) carrying the characteristic 131-amino acid deletion and one in the GP2/E region; it replicated in both PAMs and Marc-145 cells, though this may partly reflect the enrichment procedure. No PRRSV-1/PRRSV-2 recombination was detected between the two co-infected strains.