SARS-CoV-2: gone with the evolution

Starting at the end, evolution is erasing the imprinted CGG-CGG genetic footrprint on theSARS-CoV-2 acquired with the furin cleavage site. CGG-CGG is the original code ofthe arginine pair inthe polybasic furin cleavage site of the viralS protein. CGG-CGGis the heart of the 12nucleotide length sequence that properly inserted into the S gene encoded the PRRA motif in the early viruses. In Omicron it isHRRA. In terms of functionality, this arginine dimer in the SARS-CoV-2 S proteinis untouchable , but its code is very unfavourable for the virus. So it is plausiblethat asolution for the virus should go through an argininebias codon usage in the furin site. The aimof this study was to going onwith the longitudinal study on the evolution of this furin site arginine dimer, so essential for the virus. However, the surprise has been to discover that at least in the CQ.2 lineage, based on theavailable GISAID genomes, the original CGG-CGG arginine code has been lost and optimized in the 99.65 % of cases. It is worth noting thatthe new codon usage matches the arginine pair of the SARS-CoV-2 furin clevage site and arginine pairsof other viral proteins ( e.g. , nsp13, nucleocapsid) of both SARS-CoV-2and bat coronaviruses.