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

## TL;DR

This paper identifies a conserved region in SARS-CoV-2's genome that could serve as a stable target for antiviral drugs, resistant to mutations.

## Contribution

The study proposes using the conserved 5′UTR region of SARS-CoV-2 as a mutation-resistant target for RNA-based antiviral therapies.

## Key findings

- The 5′UTR region of SARS-CoV-2 is highly conserved across all variants, making it a stable target for antiviral drugs.
- Computational analysis identified potential miRNA binding sites in the 5′UTR region that could be inhibited to block viral replication.
- Endogenous miRNAs like miR-638 and miR-3150b-3p may bind the 5′UTR and promote replication, suggesting chemically modified antisense analogs could be effective.

## Abstract

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.