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Rapid Reconstruction Method for Large RNA Virus Genomes During an Outbreak

Colorized scanning electron micrograph of a VERO E6 cell (blue-green) exhibiting elongated cell projections and signs of apoptosis, after infection with SARS-COV-2 virus particles (yellow), which were isolated from a patient sample. Credit: NIAID

In a new study published in Nature, research led by scientists at the Institute of Virology and Immunology (IVI) and the University of Bern 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.

Although homologous recombination in yeast has already been used for the generation of a number of molecular virus clones and vaccine development in the past, large RNA virus genomes, such as from Coronaviruses, are cumbersome to clone and manipulate in E. coli due to size and occasional instability. Therefore, an alternative rapid and robust reverse genetics platform for RNA viruses would benefit the research community.

Here, researchers generated viral subgenomic fragments 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 the researchers have been able to engineer and resurrect chemically-synthesized clones of the recent epidemic SARS-CoV-2 in only a week after receipt of the synthetic DNA fragments.

The technical advance described here allows a rapid response to emerging viruses as it enables the generation and functional characterization of evolving RNA virus variants—in real-time—during an outbreak.

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

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