1 Introduction

The (+)RNA genome of the pandemic SARS-CoV-2 virus is about 30,000 nucleotides long [1]. Since December 2019, when the original strain (WuhanHu-1) has emerged, the SARS-CoV-2 acquired more than 10,000 recorded nucleotide mutations [2], with an estimated mutation rate between 0.0004 and 0.002 mutations per nucleotide per year [3]. The current release of the GISAID database contains more than 14 million SARS-CoV-2 sequences [4] and allows the tracking of the evolution of the virus with unprecedented precision. As widely discussed, SARS-CoV-2 is being shaped by the pressure exerted by neutralizing antibodies and applied upon the receptor-binding domain of the Spike (S) protein [5]. It should be, however, noted that antibodies are far from being the only adversarial factor encountered by the virus upon infection. In particular, the binding of host miRNA to other (+)RNA viruses provides a substantial evolutionary pressure [6] as these molecules suppress both the translation and the replication of virus along with altering some aspects of their pathogenesis [7–9].
Several works have predicted interactions of the SARS-CoV-2 single-stranded
(+)RNA virus with multiple human miRNAs [10–13]. A majority of studies have not, however, taken into account the ability of the SARS-CoV-2 virus to evolve, and, accordingly, to selectively alter its miRNA binding regions, especially these enriched in binding seeds. Only a few published works utilized the sequences from various Variants of Concern (VOCs) [14]. Human genomes encode many miRNAs, a majority of which display differential expression in human tissues. It is obvious that only miRNA species expressed in replication-permissive host cells will be relevant to SARS-CoV-2 evolution. In humans, the SARS-CoV-2 virus predominantly replicates in the type 2 alveocytes of the lung. In addition, significant clinical data indicate the presence of the virus in the intestinal epithelium, which expresses both ACE2 and TMPRSS2 [15]. Moreover, intestinal viral persistence is commonly detected. It is now recognized that long-term residence of SARS-CoV-2 in the human gut supports low-intensity inflammation, which contributes to the complications of COVID-19, collectively known as post-COVID or long COVID [16]. For three years of the pandemic, the SARS-CoV-2 virus has significantly mutated. Due to the degeneracy of the genetic code, many mutations have not led to a change in the sequence of viral proteins and, therefore, are classified as silent [17]. Nevertheless, silent nucleotide changes have managed to get fixed in the virus genome. In evolution, the fixation of the mutation may take place either by chance, or under the influence of the selective forces acting upon RNA itself rather than on the encoded proteins. The binding of the cellular miRNAs to the viral genome may be capable of exerting such pressure. The hypothesis that the evolutionary pressure exerted by binding of miRNA species expressed in human lung and intestinal tissue has shaped up the genome of the current variants of SARS-CoV-2 virus dominating the globe was tested.