Identification of mechanisms underlying the attenuation of viruses by codon pair deoptimization

• Applicant: Privatdozent Dr. Michael Veit, since 7/2020
• Subject Area: Virology ; Veterinary Medical Science
• Term: from 2019 to 2023
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 424925074

• Final Report Year: 2024

Final Report Abstract

Codon pair deoptimization (CPD) is a promising technique for rapidly developing safe and effective live attenuated virus vaccines. This method involves making precise changes to viral genomes without altering the amino acid sequences of encoded proteins, resulting in attenuated viruses that elicit similar immune responses to the original pathogens. CPD works by replacing original genomic segments with recoded ones designed to contain an increased number of statistically underrepresented codon pairs in the virus host's genome. These underrepresented pairs are thought to slow down viral protein production, impacting virus fitness. However, CPD also unintentionally increases CpG dinucleotides in recoded sequences, and it was unclear whether attenuation resulted from increased underrepresented codon pairs, CpG dinucleotides, or other factors. Using Influenza A virus as a model, we generated virus mutants with differently recoded genetic segments encoding neuraminidase, a crucial enzyme for viral spread. Our research revealed that suboptimal codon pairs were primarily responsible for decreased virus replication fitness, while CpG dinucleotides played no significant role in attenuation. We discovered that suboptimal codon pairs reduce viral RNA stability and mRNA translation efficiency, resulting in decreased protein production and impaired viral replication. These findings confirm that CPD can be reliably used to design safer and more effective vaccines. Furthermore, understanding how codon pairs influence mRNA stability and protein production opens up new possibilities in biotechnology. Manipulating codon pair bias could be used to either decrease mRNA stability and protein production for virus attenuation or enhance these processes for applications such as mRNA vaccine production.

Publications

• Mechanism of Virus Attenuation by Codon Pair Deoptimization. Cell Reports, 31(4), 107586.
  Groenke, Nicole; Trimpert, Jakob; Merz, Sophie; Conradie, Andelé M.; Wyler, Emanuel; Zhang, Hongwei; Hazapis, Orsalia-Georgia; Rausch, Sebastian; Landthaler, Markus; Osterrieder, Nikolaus & Kunec, Dusan
  
• Development of safe and highly protective live-attenuated SARS-CoV-2 vaccine candidates by genome recoding. Cell Reports, 36(5), 109493.
  Trimpert, Jakob; Dietert, Kristina; Firsching, Theresa C.; Ebert, Nadine; Thi, Nhu Thao Tran; Vladimirova, Daria; Kaufer, Susanne; Labroussaa, Fabien; Abdelgawad, Azza; Conradie, Andelé; Höfler, Thomas; Adler, Julia M.; Bertzbach, Luca D.; Jores, Joerg; Gruber, Achim D.; Thiel, Volker; Osterrieder, Nikolaus & Kunec, Dusan
  
• Live attenuated virus vaccine protects against SARS-CoV-2 variants of concern B.1.1.7 (Alpha) and B.1.351 (Beta). Science Advances, 7(49).
  Trimpert, Jakob; Adler, Julia M.; Eschke, Kathrin; Abdelgawad, Azza; Firsching, Theresa C.; Ebert, Nadine; Thao, Tran Thi Nhu; Gruber, Achim D.; Thiel, Volker; Osterrieder, Nikolaus & Kunec, Dusan
  
• Synthetically recoded virus sCPD9 – A tool to accelerate SARS-CoV-2 research under biosafety level 2 conditions. Computational and Structural Biotechnology Journal, 20, 4376-4380.
  Kunec, Dusan; Osterrieder, Nikolaus & Trimpert, Jakob
  
• A non-transmissible live attenuated SARS-CoV-2 vaccine. Molecular Therapy, 31(8), 2391-2407.
  Adler, Julia M.; Martin, Vidal Ricardo; Voß, Anne; Kunder, Sandra; Nascimento, Mariana; Abdelgawad, Azza; Langner, Christine; Vladimirova, Daria; Osterrieder, Nikolaus; Gruber, Achim D.; Kunec, Dusan & Trimpert, Jakob
  
• Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters. Nature Microbiology, 8(5), 860-874.
  Nouailles, Geraldine; Adler, Julia M.; Pennitz, Peter; Peidli, Stefan; Teixeira, Alves Luiz Gustavo; Baumgardt, Morris; Bushe, Judith; Voss, Anne; Langenhagen, Alina; Langner, Christine; Martin, Vidal Ricardo; Pott, Fabian; Kazmierski, Julia; Ebenig, Aileen; Lange, Mona V.; Mühlebach, Michael D.; Goekeri, Cengiz; Simmons, Szandor; Xing, Na ... & Trimpert, Jakob
  
• An intranasal live-attenuated SARS-CoV-2 vaccine limits virus transmission. Nature Communications, 15(1).
  Adler, Julia M.; Martin, Vidal Ricardo; Langner, Christine; Vladimirova, Daria; Abdelgawad, Azza; Kunecova, Daniela; Lin, Xiaoyuan; Nouailles, Geraldine; Voss, Anne; Kunder, Sandra; Gruber, Achim D.; Wu, Haibo; Osterrieder, Nikolaus; Kunec, Dusan & Trimpert, Jakob