Effects of <i>SADS‐CoV</i> accessory proteins NS3a, NS7a, and NS7b on viral pathogenicity: A multi‐omics investigation

<i>Swine acute diarrhea syndrome coronavirus</i> (<i>SADS-CoV</i>) 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 <i>SADS-CoV</i>. The role and specific functional mechanisms of the viral accessory proteins NS3a and NS7a/b in the pathogenicity of <i>SADS-CoV</i> remain unclear. This study utilized a reverse genetics platform with <i>SADS-CoV</i> to generate the two deletion mutant viruses <i>rSADS-ΔNS3a</i> and <i>rSADS-ΔNS7</i>, lacking the <i>NS3a</i> and <i>NS7a/b</i> 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 <i>NS3a</i> and <i>NS7a/b</i> significantly impacted the expression of genes involved in amino acid metabolism (<i>ARG1</i>, <i>NAGS</i>); carbohydrate metabolism (<i>PCK1</i>); and ECM receptor interaction (<i>LAMB3</i>), with more profound effects observed with the <i>NS7a/b</i> 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 <i>SADS-CoV</i>. Our findings provide insights into the pathogenic mechanisms of <i>SADS-CoV</i> and suggest potential targets for intervention.