Genomic characterization of a NADC30-like PRRSV strain harboring a unique "111+2+1+19" amino acid deletion in NSP2 in northern Xinjiang, China, 2026.

Abstract

To clarify the genetic evolutionary characteristics of porcine reproductive and respiratory syndrome virus (PRRSV) circulating in northern Xinjiang, China, in 2026, this study employed third-generation sequencing technology to determine the complete genome sequences of locally prevalent PRRSV strains and conducted systematic analyses of their molecular features. Porcine serum samples were collected from pig farms in northern Xinjiang, China, in 2026, and four PRRSV-2-positive samples were identified via fluorescent RT-PCR. Whole-genome sequencing was performed using the CycloneSEQ nanopore single-molecule sequencing platform. After obtaining the complete viral genome sequences, bioinformatics software including MEGA 12, DNASTAR, RDP4, and SimPlot 3.5.1 were used for phylogenetic analysis, homology comparison, key amino acid variation analysis, and recombination event identification. One high-quality complete PRRSV-2 genome sequence, designated XJ/PRRSV-2/2026-1 (15,009 bp in full length), was successfully obtained, along with three additional low-quality sequences used as references. Phylogenetic analysis revealed that all sequences belonged to Sublineage 1.8 (NADC30-like) of PRRSV-2. Homology analysis revealed that this strain shared the highest nucleotide identity (87.5%) with the NADC30 reference strain, with the ORF1a gene exhibiting the most significant variation, particularly within the NSP2 region. Amino acid sequence alignment revealed that the NSP2 region exhibits a discontinuous deletion pattern of "111 + 2+1 + 19", characterized by an additional two-amino-acid deletion at positions 467-468 compared to the typical "111 + 1+19" deletion of NADC30-like strains. Amino acid variations in the GP5 protein were concentrated in the signal peptide region (aa 1-31) and the C-epitope region (aa 53-62), containing three potential N-glycosylation sites (34 NSSS, 44 NLTI, 51 NGTD) and two transmembrane regions. Recombination analysis confirmed that this strain is a recombinant strain derived from NADC30, JXA1, and ATCC VR-2332, with three recombination breakpoints identified. This study presents a whole-genome characterization of an NADC30-like recombinant PRRSV strain detected from northern Xinjiang, China. A novel NSP2 deletion pattern and critical amino acid substitutions in the GP5 protein were identified. These observations are consistent with previous regional molecular epidemiological surveillance and may serve as a basis for broader investigations into the genetic evolution of PRRSV.