biostudies-arrayexpressProfessor Stephen GriffinHomo sapiensHISAT2https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16855Interplay between type I interferon (IFN) driven innate responses and viral antagonism strongly influences SARS-CoV-2 transmission and the COVID-19 disease course. Hence, variant adaptation includes diminished induction of IFN stimulated genes (ISG) and/or evasion of their effector functions. Exogenous IFN treatment “rewires” innate responses to drive virus elimination, yet therapeutic trials to date have been unremarkable. Resolving this paradox could translate to variant-agnostic innate immunotherapy. By contrast, oncolytic viruses (OV) exhibit profoundly attenuated innate antagonism, resulting in potent IFN responses despite the inherently immunosuppressive nature of tumour microenvironments. Moreover, OV only undergo lytic replication within innate-deficient malignant cells, and not in cells where sufficient innate responses exist. This, combined with previous studies showing that OV suppressed replication of underlying oncogenic viruses in tumours, we explored whether clinical grade oncolytic Orthoreovirus (Reo) superinfection could eliminate SARS-CoV-2 from immune-competent lung epithelial cell lines in the absence of toxicity. Reo exerted profound activation of innate responses, including when SARS-CoV-2 infection was already established, rewiring cells towards an antiviral state emulating that of Reo infection alone. Both intracellular and paracrine mechanisms induced ISG repertoires including multiple known anti-SARS-CoV-2 effectors, as well as others that remain unvalidated. Amongst these, we demonstrate the first direct evidence that MX2 and XAF1 restrict SARS-CoV-2 replication. Thus, with an excellent safety record, self-amplification, and respiratory tract tropism, we propose that Reo superinfection may provide a tractable alternative to recombinant cytokines for innate antiviral immunotherapy.biostudies-arrayexpressSequencing - Libraries were pooled and sequenced via Illumina NovaSeq 6000 producing paired-end 150 bp reads. Image data transformed into Raw data (fq) using CASAVA base recognition (calling). Reads with adapter contamination, uncertain nucleotides >10%, and low quality nucleotides >50% were removed.Nucleic Acid Extraction - RNA was purified using TRIzol according to manufacturers instructions.Growth Protocol - cells were cultured at 37 °C in a humidified atmosphere at 5 % CO2 in Dulbecco's modified Eagle medium (DMEM) containing high glucose and supplemented with 10 % (v/v) heat-inactivated foetal bovine serum (FBS) and 1 % (v/v) non-essential amino acids.Sample Treatment - A549 AT cells were infected with SARS-CoV-2 (Eng/2) at 0.5 PFU/cell. Reo were administered either 12 h before SARS-CoV-2 infection (pretreatment), at 0 hpi (same time), or 6 hpi (5 PFU/cell). Cells were incubated for 24 h following SARS-CoV-2 infection.Sample Collection - Cells were washed three times in PBS and lysed with TRIzol according to manufacturers instructions.Library Construction - Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - HISAT2 software was used to map the clean reads to the Homo sapiens (GRCh38/hg38) genome.Data Transformation - Gene expression was determined by generating FPKM; distribution of gene expression and FKPM was checked; sample correlation was determined via the Pearson Correlation coefficient between samples; PCA analysis on FPKM was determined.UnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000Interplay between type I interferon (IFN) driven innate responses and viral antagonism strongly influences SARS-CoV-2 transmission and the COVID-19 disease course. Hence, variant adaptation includes diminished induction of IFN stimulated genes (ISG) and/or evasion of their effector functions. Exogenous IFN treatment “rewires” innate responses to drive virus elimination, yet therapeutic trials to date have been unremarkable. Resolving this paradox could translate to variant-agnostic innate immunotherapy. By contrast, oncolytic viruses (OV) exhibit profoundly attenuated innate antagonism, resulting in potent IFN responses despite the inherently immunosuppressive nature of tumour microenvironments. Moreover, OV only undergo lytic replication within innate-deficient malignant cells, and not in cells where sufficient innate responses exist. This, combined with previous studies showing that OV suppressed replication of underlying oncogenic viruses in tumours, we explored whether clinical grade oncolytic Orthoreovirus (Reo) superinfection could eliminate SARS-CoV-2 from immune-competent lung epithelial cell lines in the absence of toxicity. Reo exerted profound activation of innate responses, including when SARS-CoV-2 infection was already established, rewiring cells towards an antiviral state emulating that of Reo infection alone. Both intracellular and paracrine mechanisms induced ISG repertoires including multiple known anti-SARS-CoV-2 effectors, as well as others that remain unvalidated. Amongst these, we demonstrate the first direct evidence that MX2 and XAF1 restrict SARS-CoV-2 replication. Thus, with an excellent safety record, self-amplification, and respiratory tract tropism, we propose that Reo superinfection may provide a tractable alternative to recombinant cytokines for innate antiviral immunotherapy.RNA-seq of coding RNAHomo sapiensOncolytic Reovirus mediates innate-driven SARS-CoV-2 elimination in the absence of cell toxicityProfessor Stephen GriffinSamantha Garcia-Cardenas, Gemma Swinscoe, Amy Moran, Liam Barningham, Graham Cook, Adel Samson, Sam Wilson, Michael Malim, Russell Hughes, Stephen GriffinfalseOncolytic Reovirus mediates innate-driven SARS-CoV-2 elimination in the absence of cell toxicityInterplay between type I interferon (IFN) driven innate responses and viral antagonism strongly influences SARS-CoV-2 transmission and the COVID-19 disease course. Hence, variant adaptation includes diminished induction of IFN stimulated genes (ISG) and/or evasion of their effector functions. Exogenous IFN treatment “rewires” innate responses to drive virus elimination, yet therapeutic trials to date have been unremarkable. Resolving this paradox could translate to variant-agnostic innate immunotherapy. By contrast, oncolytic viruses (OV) exhibit profoundly attenuated innate antagonism, resulting in potent IFN responses despite the inherently immunosuppressive nature of tumour microenvironments. Moreover, OV only undergo lytic replication within innate-deficient malignant cells, and not in cells where sufficient innate responses exist. This, combined with previous studies showing that OV suppressed replication of underlying oncogenic viruses in tumours, we explored whether clinical grade oncolytic Orthoreovirus (Reo) superinfection could eliminate SARS-CoV-2 from immune-competent lung epithelial cell lines in the absence of toxicity. Reo exerted profound activation of innate responses, including when SARS-CoV-2 infection was already established, rewiring cells towards an antiviral state emulating that of Reo infection alone. Both intracellular and paracrine mechanisms induced ISG repertoires including multiple known anti-SARS-CoV-2 effectors, as well as others that remain unvalidated. Amongst these, we demonstrate the first direct evidence that MX2 and XAF1 restrict SARS-CoV-2 replication. Thus, with an excellent safety record, self-amplification, and respiratory tract tropism, we propose that Reo superinfection may provide a tractable alternative to recombinant cytokines for innate antiviral immunotherapy.2026-04-15T00:00:00Z2026-04-17T01:01:32.491Z2026-03-30T17:40:38.305ZE-MTAB-16855ERP191570EFO_0002944EFO_0004170EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184EFO_000396910.64898/2025.12.17.694833