In Silico Study of piRNA Interactions with the SARS-CoV-2 Genome

Int J Mol Sci. 2022 Aug 31;23(17):9919. doi: 10.3390/ijms23179919.


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. It has been shown that piRNA (PIWI-interacting RNAs) interact with the mRNA of human genes and can block protein synthesis at the stage of translation. Estimated the effects of piRNA on SARS-CoV-2 genomic RNA (gRNA) in silico. A cluster of 13 piRNA binding sites (BS) in the SARS-CoV-2 gRNA region encoding the oligopeptide was identified. The second cluster of BSs 39 piRNAs also encodes the oligopeptide. The third cluster of 24 piRNA BS encodes the oligopeptide. Twelve piRNAs were identified that strongly interact with the gRNA. 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. The piRNA and spiRNA selection methodology created for the control of SARS-CoV-2 (NC_045512.2) can be used to control all strains of SARS-CoV-2.

Keywords: COVID-19; SARS-CoV-2; coronavirus genome; drug target; miRNA; piRNA.

MeSH terms

  • COVID-19* / genetics
  • Genome
  • Humans
  • RNA, Guide, Kinetoplastida
  • RNA, Small Interfering / genetics
  • RNA, Small Interfering / metabolism
  • SARS-CoV-2* / genetics


  • RNA, Guide
  • RNA, Small Interfering