Scarless SARS-CoV-2 Genome Engineering and Variant Analysis

Abstract

In addition to causing cold and flu-like symptoms, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) can also cause chronic longer-term diseases. Antiviral drugs, especially used combinatorially, have the potential to reduce the severity of individual infections and prevent the development of chronic disease. One of the safest and most versatile reverse genetics systems for SARS-CoV-2 studies is a bacterial artificial chromosome (BAC)-based system harboring the WA1 strain full-length genome and attenuating deletions in the accessory open reading frame 3a and 7b proteins (ORF3a and ORF7b, respectively). Here, a scarless genome engineering technique called En Passant mutagenesis was used to change one amino acid in the viral main protease (Mpro P132) into the residue present in contemporary Omicron strains (H132), in order to more accurately study protease inhibitors and resistance mechanisms. This recombinant, attenuated viral system yields antiviral EC50 values for the active component of approved drugs including nirmatrelvir (Paxlovid) and ensitrelvir (Xocova) and, importantly, also enables a parallel assessment of drug efflux. For instance, the antiviral potency of nirmatrelvir improves 50-fold by inhibiting the P-Glycoprotein (P-Gp) transporter with ritonavir or tariquidar, whereas the potency of ensitrelvir is unaffected. This system also enables the safe isolation and characterization of viral variants with reduced sensitivity to drugs, as evidenced by Mpro M49L compromising the efficacy of ensitrelvir. Together, these systems combine to provide safe, reliable, and quantitative approaches for Mpro variant analysis and drug testing without the biosafety concerns of conducting these experiments using wildtype isolates. IMPORTANCE Safe genetic systems for studying coronavirus biology and developing next generation antivirals are important. One of the most versatile systems leverages a bacterial artificial chromosome to efficiently propagate and engineer a full-length SARS-CoV-2 genome. This system is also safe because it has crippling deletion mutations that limit virus replication to a small number of cell lines. Here, we use a genome engineering technology to change a single amino acid in the viruses’ main protease enzyme to match that of circulating Omicron isolates. The resulting attenuated virus was also used to demonstrate antiviral efficacy of approved drugs and uncover mutants with reduced drug sensitivity. The emergent mutants match those in a subset of circulating strains further demonstrating broad relevance.