An optimized circular polymerase extension reaction-based method for functional analysis of SARS-CoV-2

BACKGROUND: Reverse genetics systems have been crucial for studying specific viral genes and their relevance in the virus lifecycle, and become important tools for the rational attenuation of viruses and thereby for vaccine design. Recent rapid progress has been made in the establishment of reverse genetics systems for functional analysis of SARS-CoV-2, a coronavirus that causes the ongoing COVID-19 pandemic that has resulted in detrimental public health and economic burden. Among the different reverse genetics approaches, circular polymerase extension reaction (CPER) has become one of the leading methodologies to generate recombinant SARS-CoV-2 infectious clones. Although CPER has greatly facilitated SARS-CoV-2 analysis, it still has certain intrinsic limitations that impede the efficiency and robustness of virus rescue. RESULTS: We developed an optimized CPER methodology which, through the use of a modified linker plasmid and by performing DNA nick ligation and direct transfection of permissive cells, overcomes certain intrinsic limitations of the ‘traditional’ CPER approaches for SARS-CoV-2, allowing for efficient virus rescue. CONCLUSIONS: The herein described optimized CPER system may facilitate research studies to assess the contribution of SARS-CoV-2 genes and individual motifs or residues to virus replication, pathogenesis and immune escape, and may also be adapted to other viruses. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12985-023-02025-y.