Identification of host lncRNAs that impact Venezuelan equine encephalitis virus TC-83 replication

Venezuelan equine encephalitis virus (VEEV) causes encephalitis in humans and equids, and there are no vaccines or therapeutics for humans. In recent years, non-coding RNAs have emerged as critical regulatory factors affecting different cellular pathways. Specifically, long non-coding RNAs (lncRNAs) have been identified as regulators of antiviral pathways; however, their role in VEEV infection has not been assessed. Here, we show differential expression of several lncRNAs in primary mouse target cells infected with a vaccine strain of VEEV (TC-83) but not a pathogenic strain (TrD). Among the differentially expressed genes (DEGs), suppressing lncRNA small nucleolar RNA host gene 15 (Snhg15) resulted in a 7-fold increase in TC-83 replication in primary mouse astrocytes. Knockdown of Snhg15 during TC-83 infection resulted in the suppression of ten genes, all of which were also increased during TC-83 infection along with Snhg15. Most of these genes are involved in antiviral responses. KEGG pathway analysis confirmed the suppression of both pattern recognition receptor and inflammatory pathways after Snhg15 knockdown. However, Snhg15 suppression did not significantly alter NF-kB signaling in TC-83-infected cells. These data are the first to identify lncRNA responses in encephalitic alphavirus infection and demonstrate important roles for these overlooked RNAs in VEEV infection.IMPORTANCEAlthough many studies have reported differential expression of lncRNAs during viral infections, the lncRNA response to VEEV infection and its functional roles have not been previously characterized. In this study, we provide the first comprehensive analysis of host lncRNA expression in primary cells that are targeted during VEEV infection. We demonstrate that the expression of specific host lncRNAs is altered during VEEV infection and that modulation of these lncRNAs changes the expression of host antiviral and inflammatory pathways and impacts viral replication. These findings advance our understanding of VEEV-host interaction and shed light on previously unappreciated regulatory layers of infection. Given the absence of approved vaccines or antiviral therapies for VEEV, our work identifies novel host factors that may serve as potential targets for the development of anti-VEEV therapeutics upon further investigation.