Effects of SADS-CoV accessory proteins NS3a, NS7a, and NS7b on viral pathogenicity: A multi-omics investigation

Swine acute diarrhea syndrome coronavirus (SADS-CoV) is an emerging, novel porcine coronavirus that causes acute diarrhea and vomiting in piglets, leading to significant neonatal morbidity and a mortality rate exceeding 90%. To date, no comprehensive studies have systematically elucidated the multi-omics regulatory networks of the accessory proteins of SADS-CoV. The role and specific functional mechanisms of the viral accessory proteins NS3a and NS7a/b in the pathogenicity of SADS-CoV remain unclear. This study utilized a reverse genetics platform with SADS-CoV to generate the two deletion mutant viruses rSADS-ΔNS3a and rSADS-ΔNS7, lacking the NS3a and NS7a/b genes, respectively. Transcriptomic and metabolomic analyses were the first-ever performed on porcine ileal epithelial cell line IPI-2I infected with the mutants, revealing differentially expressed genes and metabolites in comparison with the wild-type virus. The deletion of NS3a and NS7a/b significantly impacted the expression of genes involved in amino acid metabolism (ARG1, NAGS); carbohydrate metabolism (PCK1); and ECM receptor interaction (LAMB3), with more profound effects observed with the NS7a/b deletion. Metabolomic analysis further confirmed that NS3a and NS7a/b primarily affect lipid, amino acid, and carbohydrate metabolism. Animal experiments in piglets demonstrated that the loss of these proteins attenuated the virulence of SADS-CoV. Our findings provide insights into the pathogenic mechanisms of SADS-CoV and suggest potential targets for intervention.