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bioRxiv · 10.1101/2024.08.28.610093

Identification of a new ORF3a-E fusion subgenomic RNA of SARS-CoV-2 and its biological features in the infection process

Zhang, Y.·Zheng, H.·Li, J.·Zhang, X.·Li, H.·Zhao, X.·Zhang, Z.·Li, Y.·Chen, k.·Peng, S.·Shi, H.·Liu, L.
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Abstract

Subgenomic RNAs (sgRNAs) are discontinuous transcription products of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that are involved in viral gene expression and replication, but their exact functions are still being studied. Here, we report the identification of a new type of sgRNA, the fusion ORF3a-E-sgRNA, involved in the infection process of SARS-CoV-2. This sgRNA codes both ORF3a and E and can be detected throughout the viral life cycle in SARS-CoV-2-infected cells with high copy numbers. ORF3a-E-sgRNA guides more ORF3a translation and promotes the expression of cellular ribosomal protein S3 (RPS3) and the binding of eukaryotic translation initiation factor 4E (eIF4E). Single-cell sequencing of a SARS-CoV-2-infected human bronchial epithelial cell line (16HBE) revealed that maintenance of this stable translational environment by ORF3a-E-sgRNA is important for the SARS-CoV-2 assembly and release capabilities and is also beneficial for viral evasion of host innate immunity. More importantly, the transcription level of ORF3a-E-sgRNA contributes to differences in infection processes between the Wuhan strain and XBB strain of SARS-CoV-2.

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Zhang, Y., Zheng, H., Li, J., Zhang, X., Li, H., Zhao, X., Zhang, Z., Li, Y., Chen, k., Peng, S., Shi, H., Liu, L.. 2024-08-28. Identification of a new ORF3a-E fusion subgenomic RNA of SARS-CoV-2 and its biological features in the infection process. https://doi.org/10.1101/2024.08.28.610093

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