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

Abstract

Reverse genetics has been an indispensable tool revolutionising insights into viral pathogenesis and vaccine development. Large RNA virus genomes, such as from Coronaviruses, are cumbersome to clone and manipulate in E. coli due to size and occasional instability1–3. 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 Paramyxoviridae families. Viral subgenomic fragments were generated using viral isolates, cloned viral DNA, clinical samples, or synthetic DNA, and reassembled in one step in Saccharomyces cerevisiae using transformation associated recombination (TAR) cloning to maintain the genome as a yeast artificial chromosome (YAC). T7-RNA polymerase has been used to generate infectious RNA to rescue viable virus. Based on this platform we have been able to engineer and resurrect chemically-synthetized clones of the recent epidemic SARS-CoV-24 in only a week after receipt of the synthetic DNA fragments. The technical advance we describe here allows a rapidly response to emerging viruses as it enables the generation and functional characterization of evolving RNA virus variants—in real-time—during an outbreak.

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Correspondence to Joerg Jores or Volker Thiel.

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Supplementary Information

This file contains a full guide to the Supplementary Information, which includes full legends for Supplementary Figures 1-2, Supplementary Data 1 and Supplementary Table 1.

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Supplementary Figure 1

Reconstruction of the different viral genomes in yeast using TAR cloning – see Supplementary Information document for full legend.

Supplementary Figure 2

Raw data of all the uncropped agarose gels used in this study. Red rectangles indicate gel parts that were cropped for display in Supplementary Fig. 1.

Supplementary Data 1

Nucleotide sequences of synthetic DNA fragments used to reconstruct recombinant SARS-CoV-2 and SARS-CoV-2-GFP.

Supplementary Table 1

A list of primers used in the study.

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Thao, T.T.N., Labroussaa, F., Ebert, N. et al. Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform. Nature (2020). https://doi.org/10.1038/s41586-020-2294-9

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