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Citation: Kai Wu, Dehe Wang, Junhao Wang, Yu Zhou. Translation landscape of SARS-CoV-2 noncanonical subgenomic RNAs [J].VIROLOGICA SINICA, 2022, 37(6) : 813-822.  http://dx.doi.org/10.1016/j.virs.2022.09.003

Translation landscape of SARS-CoV-2 noncanonical subgenomic RNAs

  • Corresponding author: Yu Zhou, yu.zhou@whu.edu.cn
  • Received Date: 05 July 2022
    Accepted Date: 01 September 2022
    Available online: 06 September 2022
  • The ongoing COVID-19 pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with a positive-stranded RNA genome. Current proteomic studies of SARS-CoV-2 mainly focus on the proteins encoded by its genomic RNA (gRNA) or canonical subgenomic RNAs (sgRNAs). Here, we systematically investigated the translation landscape of SARS-CoV-2, especially its noncanonical sgRNAs. We first constructed a strict pipeline, named vipep, for identifying reliable peptides derived from RNA viruses using RNA-seq and mass spectrometry data. We applied vipep to analyze 24 sets of mass spectrometry data related to SARS-CoV-2 infection. In addition to known canonical proteins, we identified many noncanonical sgRNA-derived peptides, which stably increase after viral infection. Furthermore, we explored the potential functions of those proteins encoded by noncanonical sgRNAs and found that they can bind to viral RNAs and may have immunogenic activity. The generalized vipep pipeline is applicable to any RNA viruses and these results have expanded the SARSCoV-2 translation map, providing new insights for understanding the functions of SARS-CoV-2 sgRNAs.

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    Translation landscape of SARS-CoV-2 noncanonical subgenomic RNAs

      Corresponding author: Yu Zhou, yu.zhou@whu.edu.cn
    • a State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China;
    • b TaiKang Center for Life and Medical Sciences, RNA Institute, Wuhan University, Wuhan, 430072, China;
    • c Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China;
    • d Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, China

    Abstract: The ongoing COVID-19 pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with a positive-stranded RNA genome. Current proteomic studies of SARS-CoV-2 mainly focus on the proteins encoded by its genomic RNA (gRNA) or canonical subgenomic RNAs (sgRNAs). Here, we systematically investigated the translation landscape of SARS-CoV-2, especially its noncanonical sgRNAs. We first constructed a strict pipeline, named vipep, for identifying reliable peptides derived from RNA viruses using RNA-seq and mass spectrometry data. We applied vipep to analyze 24 sets of mass spectrometry data related to SARS-CoV-2 infection. In addition to known canonical proteins, we identified many noncanonical sgRNA-derived peptides, which stably increase after viral infection. Furthermore, we explored the potential functions of those proteins encoded by noncanonical sgRNAs and found that they can bind to viral RNAs and may have immunogenic activity. The generalized vipep pipeline is applicable to any RNA viruses and these results have expanded the SARSCoV-2 translation map, providing new insights for understanding the functions of SARS-CoV-2 sgRNAs.

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