Journal Article

Emergence of SARS-CoV-2 subgenomic RNAs that enhance viral fitness and immune evasion

Emmott, Edward, Crawford, Margaret, Furnon, Wilhelm, Gilbride, Ciarán, Wall, Emma, Sanderson, Theo, Mears, Harriet V., Chakrabarti, Anob M., Harvey, Ruth, Finsterbusch, Katja, Hussain, Saira, Williams, Bryan, Snell, Daniel M., Palmarini, Massimo, Patel, Arvind H., Bauer, David L. V., Swanton, Charles, Young, George R., Penn, Rebecca, Luptak, Jakub, Nicod, Jérôme, Gandhi, Sonia, De Lorenzo, Giuditta, Barrett-Rodger, Jamie, Cowton, Vanessa, Peacock, Thomas P., Fowler, Ashley S.

2025

Overview

Coronaviruses express their structural and accessory genes via a set of subgenomic RNAs, whose synthesis is directed by transcription regulatory sequences (TRSs) in the 5′ genomic leader and upstream of each body open reading frame. In SARS-CoV-2, the TRS has the consensus AAACGAAC; upon searching for emergence of this motif in the global SARS-CoV-2 sequences, we find that it evolves frequently, especially in the 3′ end of the genome. We show well-supported examples upstream of the Spike gene—within the nsp16 coding region of ORF1b—which is expressed during human infection, and upstream of the canonical Envelope gene TRS, both of which have evolved convergently in multiple lineages. The most frequent neo-TRS is within the coding region of the Nucleocapsid gene, and is present in virtually all viruses from the B.1.1 lineage, including the variants of concern Alpha, Gamma, Omicron and descendants thereof. Here, we demonstrate that this TRS leads to the expression of a novel subgenomic mRNA encoding a truncated C-terminal portion of Nucleocapsid, which is an antagonist of type I interferon production and contributes to viral fitness during infection. We observe distinct phenotypes when the Nucleocapsid coding sequence is mutated compared to when the TRS alone is ablated. Our findings demonstrate that SARS-CoV-2 is undergoing evolutionary changes at the functional RNA level in addition to the amino acid level.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Ablation / Amino acids / Biology and life sciences / Cell culture / Coronaviruses / COVID-19 / COVID-19 - immunology / COVID-19 - virology / Data analysis / Disease transmission / Env gene / Evolution, Molecular / Gene expression / Genetic Fitness / Genome, Viral / Genomes / Health aspects / Humans / Immune Evasion - genetics / Infections / Medical research / Medicine and health sciences / Mutation / Nucleocapsids / Open Reading Frames / Phenotypes / Regulatory sequences / Regulatory Sequences, Nucleic Acid / Research and Analysis Methods / RNA / RNA polymerase / RNA, Viral - genetics / SARS-CoV-2 - genetics / SARS-CoV-2 - immunology / SARS-CoV-2 - physiology / Severe acute respiratory syndrome coronavirus 2 / Spike Glycoprotein, Coronavirus - genetics / Viral diseases