Beyond Variant Evolution: Structurally and Functionally Conserved Regions in the 5′UTR of SARS-CoV-2 as Resilient Antiviral Targets

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a positive-sense RNA virus, and its genome includes a highly conserved 5′ untranslated region (5′UTR). This region contains the so-called ‘leader sequence’, a crucial genomic region responsible for the viral replication and the synthesis of all subgenomic RNAs (sgRNAs). It has been demonstrated that targeting highly conserved genomic regions is essential for developing broad-spectrum antiviral therapies that resist viral mutation and evasion. Hypothesis: Given the high level of nucleotide homology between SARS-CoV and SARS-CoV-2, particularly in essential regions like the 5′UTR, the identification of a perfect sequence alignment across SARS-CoV-2 variants within this conserved region would provide a robust, mutation-resistant target for novel RNA-based drugs, such as small interfering RNAs (siRNAs) or microRNAs (miRNAs). Materials and Methods: Sequence alignment was performed across the different SARS-CoV-2 strains (i.e., the different variants that have appeared so far) to identify conserved genomic areas, leading to the selection of potential target sites for antiviral molecules. Specifically, computational analyses were utilized to map available binding sites for human miRNAs within the SARS-CoV-2 5′UTR. Results: Comparative alignments revealed that the leader sequence/5′UTR region is highly stable and conserved in all the considered SARS-CoV-2 sequences, representing a common therapeutic target across different variants and strains. Discussion: The perfect alignment observed in the 5′UTR confirms that this region is a highly critical target, less prone to mutations in all the considered variants. This property makes the region ideal for therapeutic intervention using non-coding RNAs. If endogenous miRNAs were found to bind this region (e.g., miR-638, miR-3150b-3p, etc.) and promote viral replication similarly to mechanisms observed in viruses like hepatitis C virus (HCV), their activity could be inhibited using chemically modified antisense analogs, such as locked nucleic acid (LNA) oligonucleotides.