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Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform

Author

Listed:
  • Tran Thao

    (Institute of Virology and Immunology (IVI)
    University of Bern
    University of Bern)

  • Fabien Labroussaa

    (University of Bern
    University of Bern)

  • Nadine Ebert

    (Institute of Virology and Immunology (IVI)
    University of Bern)

  • Philip V’kovski

    (Institute of Virology and Immunology (IVI)
    University of Bern)

  • Hanspeter Stalder

    (Institute of Virology and Immunology (IVI)
    University of Bern)

  • Jasmine Portmann

    (Institute of Virology and Immunology (IVI)
    University of Bern)

  • Jenna Kelly

    (Institute of Virology and Immunology (IVI)
    University of Bern)

  • Silvio Steiner

    (Institute of Virology and Immunology (IVI)
    University of Bern
    University of Bern)

  • Melle Holwerda

    (Institute of Virology and Immunology (IVI)
    University of Bern
    University of Bern
    University of Bern)

  • Annika Kratzel

    (Institute of Virology and Immunology (IVI)
    University of Bern
    University of Bern)

  • Mitra Gultom

    (Institute of Virology and Immunology (IVI)
    University of Bern
    University of Bern
    University of Bern)

  • Kimberly Schmied

    (Institute of Virology and Immunology (IVI)
    University of Bern)

  • Laura Laloli

    (Institute of Virology and Immunology (IVI)
    University of Bern
    University of Bern
    University of Bern)

  • Linda Hüsser

    (Institute of Virology and Immunology (IVI)
    University of Bern)

  • Manon Wider

    (University of Bern)

  • Stephanie Pfaender

    (Institute of Virology and Immunology (IVI)
    University of Bern
    Ruhr-Universität Bochum)

  • Dagny Hirt

    (Institute of Virology and Immunology (IVI)
    University of Bern)

  • Valentina Cippà

    (University of Bern
    University of Bern)

  • Silvia Crespo-Pomar

    (University of Bern
    University of Bern)

  • Simon Schröder

    (corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health)

  • Doreen Muth

    (corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health
    associated partner Charité)

  • Daniela Niemeyer

    (corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health
    associated partner Charité)

  • Victor M. Corman

    (corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health
    associated partner Charité)

  • Marcel A. Müller

    (corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health
    associated partner Charité
    Sechenov University)

  • Christian Drosten

    (corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health
    associated partner Charité)

  • Ronald Dijkman

    (Institute of Virology and Immunology (IVI)
    University of Bern
    University of Bern)

  • Joerg Jores

    (University of Bern
    University of Bern)

  • Volker Thiel

    (Institute of Virology and Immunology (IVI)
    University of Bern)

Abstract

Reverse genetics has been an indispensable tool to gain insights into viral pathogenesis and vaccine development. The genomes of large RNA viruses, such as those from coronaviruses, are cumbersome to clone and manipulate in Escherichia coli owing to the size and occasional instability of the genome1–3. Therefore, an alternative rapid and robust reverse-genetics platform for RNA viruses would benefit the research community. Here we show the full functionality of a yeast-based synthetic genomics platform to genetically reconstruct diverse RNA viruses, including members of the Coronaviridae, Flaviviridae and Pneumoviridae families. Viral subgenomic fragments were generated using viral isolates, cloned viral DNA, clinical samples or synthetic DNA, and these fragments were then reassembled in one step in Saccharomyces cerevisiae using transformation-associated recombination cloning to maintain the genome as a yeast artificial chromosome. T7 RNA polymerase was then used to generate infectious RNA to rescue viable virus. Using this platform, we were able to engineer and generate chemically synthesized clones of the virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)4, which has caused the recent pandemic of coronavirus disease (COVID-19), in only a week after receipt of the synthetic DNA fragments. The technical advance that we describe here facilitates rapid responses to emerging viruses as it enables the real-time generation and functional characterization of evolving RNA virus variants during an outbreak.

Suggested Citation

  • Tran Thao & Fabien Labroussaa & Nadine Ebert & Philip V’kovski & Hanspeter Stalder & Jasmine Portmann & Jenna Kelly & Silvio Steiner & Melle Holwerda & Annika Kratzel & Mitra Gultom & Kimberly Schmied, 2020. "Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform," Nature, Nature, vol. 582(7813), pages 561-565, June.
  • Handle: RePEc:nat:nature:v:582:y:2020:i:7813:d:10.1038_s41586-020-2294-9
    DOI: 10.1038/s41586-020-2294-9
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    Citations

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    Cited by:

    1. Xi Zhang & Te Zhang & Xin Wei & Zhanpeng Xiao & Weiwen Zhang, 2024. "Reducing potential dual-use risks in synthetic biology laboratory research: a dynamic model of analysis," Palgrave Communications, Palgrave Macmillan, vol. 11(1), pages 1-14, December.
    2. Guilherme Dias de Melo & Victoire Perraud & Flavio Alvarez & Alba Vieites-Prado & Seonhee Kim & Lauriane Kergoat & Anthony Coleon & Bettina Salome Trüeb & Magali Tichit & Aurèle Piazza & Agnès Thierry, 2023. "Neuroinvasion and anosmia are independent phenomena upon infection with SARS-CoV-2 and its variants," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    3. Ruipeng Lei & Enya Qing & Abby Odle & Meng Yuan & Chaminda D. Gunawardene & Timothy J. C. Tan & Natalie So & Wenhao O. Ouyang & Ian A. Wilson & Tom Gallagher & Stanley Perlman & Nicholas C. Wu & Lok-Y, 2024. "Functional and antigenic characterization of SARS-CoV-2 spike fusion peptide by deep mutational scanning," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    4. Akshay J. Maheshwari & Jonathan Calles & Sean K. Waterton & Drew Endy, 2023. "Engineering tRNA abundances for synthetic cellular systems," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    5. Bo Qin & Ziheng Li & Kaiming Tang & Tongyun Wang & Yubin Xie & Sylvain Aumonier & Meitian Wang & Shuofeng Yuan & Sheng Cui, 2023. "Identification of the SARS-unique domain of SARS-CoV-2 as an antiviral target," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    6. Urszula Radzikowska & Andrzej Eljaszewicz & Ge Tan & Nino Stocker & Anja Heider & Patrick Westermann & Silvio Steiner & Anita Dreher & Paulina Wawrzyniak & Beate Rückert & Juan Rodriguez-Coira & Damir, 2023. "Rhinovirus-induced epithelial RIG-I inflammasome suppresses antiviral immunity and promotes inflammation in asthma and COVID-19," Nature Communications, Nature, vol. 14(1), pages 1-22, December.
    7. Yang Liu & Xianwen Zhang & Jianying Liu & Hongjie Xia & Jing Zou & Antonio E. Muruato & Sivakumar Periasamy & Chaitanya Kurhade & Jessica A. Plante & Nathen E. Bopp & Birte Kalveram & Alexander Bukrey, 2022. "A live-attenuated SARS-CoV-2 vaccine candidate with accessory protein deletions," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    8. Oskar Staufer & Gösta Gantner & Ilia Platzman & Klaus Tanner & Imre Berger & Joachim P. Spatz, 2022. "Bottom-up assembly of viral replication cycles," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    9. G. Tuba Barut & Nico Joel Halwe & Adriano Taddeo & Jenna N. Kelly & Jacob Schön & Nadine Ebert & Lorenz Ulrich & Christelle Devisme & Silvio Steiner & Bettina Salome Trüeb & Bernd Hoffmann & Inês Bere, 2022. "The spike gene is a major determinant for the SARS-CoV-2 Omicron-BA.1 phenotype," Nature Communications, Nature, vol. 13(1), pages 1-14, December.

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