Mears Harriet V, Young George R, Sanderson Theo, Harvey Ruth, Barrett-Rodger Jamie, Penn Rebecca, Cowton Vanessa, Furnon Wilhelm, De Lorenzo Giuditta, Crawford Margaret, Snell Daniel M, Fowler Ashley S, Chakrabarti Anob M, Hussain Saira, Gilbride Ciarán, Emmott Edward, Finsterbusch Katja, Luptak Jakub, Peacock Thomas P, Nicod Jérôme, Patel Arvind H, Palmarini Massimo, Wall Emma, Williams Bryan, Gandhi Sonia, Swanton Charles, Bauer David L V
RNA Virus Replication Laboratory, The Francis Crick Institute, London, United Kingdom.
Bioinformatics and Biostatistics STP, The Francis Crick Institute, London, United Kingdom.
PLoS Biol. 2025 Jan 21;23(1):e3002982. doi: 10.1371/journal.pbio.3002982. eCollection 2025 Jan.
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.
冠状病毒通过一组亚基因组RNA来表达其结构基因和辅助基因，这些亚基因组RNA的合成由5'基因组前导序列和每个主体开放阅读框上游的转录调控序列（TRS）指导。在严重急性呼吸综合征冠状病毒2（SARS-CoV-2）中，TRS的共有序列为AAACGAAC；在全球SARS-CoV-2序列中搜索该基序的出现情况时，我们发现它频繁进化，尤其是在基因组的3'端。我们展示了在刺突基因上游（在开放阅读框1b的nsp16编码区域内，该区域在人类感染期间表达）以及在典型包膜基因TRS上游得到充分支持的例子，这两个区域在多个谱系中都发生了趋同进化。最常见的新TRS位于核衣壳基因的编码区域内，几乎存在于B.1.1谱系的所有病毒中，包括值得关注的变异株阿尔法、伽马、奥密克戎及其后代。在这里，我们证明这个TRS导致一种新的亚基因组mRNA的表达，该mRNA编码核衣壳截断的C末端部分，它是I型干扰素产生的拮抗剂，并在感染期间有助于病毒的适应性。当核衣壳编码序列发生突变时，与单独敲除TRS时相比，我们观察到了不同的表型。我们的研究结果表明，除了氨基酸水平外，SARS-CoV-2在功能性RNA水平上也在经历进化变化。
