piRNAs Are a New COVID-19-Fighting Tool

Abstract A prolonged pandemic with numerous human casualties requires a rapid search for means to control the various strains of SARS-CoV-2. Since only part of the human population is affected by coronaviruses, there are probably endogenous compounds preventing the spread of these viral pathogens. We investigated the effect of piRNA (PIWI-interacting RNAs) molecules on SARS-CoV-2 (NC_045512.2) coronavirus expression, which can inhibit protein synthesis on the genomic RNA (gRNA) of the virus and simultaneously prevent viral gRNA replication. A 28-nt cluster of 70 piRNA binding sites (BSs) in the SARS-CoV-2 gRNA region encoding the LETIQITIS oligopeptide of the ORF1ab protein was identified. The second cluster of BS 39 piRNAs with a length of 31 nt in the gRNA region encodes the RATLQAIASEF oligopeptide of the ORF1ab protein. The third cluster of 24 piRNA BSs 31 nt long in the gRNA region encodes the oligopeptide PKLQSSQAWQP of the ORF1ab protein. Twelve piRNAs were identified that strongly interact with the gRNA sites of the virus from 4670 nt to 29024 nt. Based on the identified functionally important endogenous piRNAs, synthetic piRNAs (spiRNAs) are proposed that will suppress the multiplication of the coronavirus even more strongly. These spiRNAs and selected endogenous piRNAs have little effect on human 17494 protein-coding genes, indicating a low probability of side effects. spiRNA and piRNA kits are proposed to control the SARS-CoV-2 strain. The piRNA and spiRNA selection methodology created for the control of SARS-CoV-2 coronavirus NC_045512.2 can be used to control all strains of coronavirus.