Mutation in position of 32 (G>U) of S2M differentiate human SARS-CoV2 from Bat Coronavirus

Abstract

The new Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a zoonotic pathogen that has rapidly mutated and become transmissible to humans. There is little existing data on the mutations in SARS-CoV-2 and the impact of these polymorphisms on its transmission and viral load. In this study, the SARS-CoV-2 genomic sequence was analyzed to identify variants within the 3’UTR region of its cis-regulatory RNA elements. A 43-nucleotide genetic element with a highly conserved stem-loop II-like motif (S2M), was discovered. The research revealed 32 G>U and 16 G>U/A mutations located within the S2M sequence in human SARS-CoV-2 models. These polymorphisms appear to make the S2M secondary and tertiary structures in human SARS-CoV-2 models less stable when compared to the S2M structures of bat/pangolin models. This grants the RNA structures more flexibility, which could be one of its escape mechanisms from host defenses or facilitate its entry into host proteins and enzymes. While this S2M sequence may not be omnipresent across all human SARS-CoV-2 models, when present, its sequence is always highly conserved. It may be used as a potential target for the development of vaccines and therapeutic agents.

The highly conserved stem-loop II motif is important for the lifecycle of astroviruses but dispensable for SARS-CoV-2

“…In contrast, seasonal human coronaviruses (HKU1, 229E, OC43, and NL63) and Middle Eastern respiratory syndrome coronavirus (MERS-CoV) do not contain an s2m 3 . Interestingly, the reference SARS-CoV-2 genome and all subsequent variants of concern encode a unique genetic variant with a uracil at position 32 in the s2m that is distinct from other s2m sequences and is predicted to perturb the secondary structure [19][20][21][22][23] . Additional genetic variants or deletions of the s2m have been periodically detected from clinical isolates [23][24][25][26] .…”

The stem loop 2 motif is a site of vulnerability for SARS-CoV-2

“…When considering s2m as a target for virus inhibition, it is also worth noting that while it is a remarkably stable genomic element, conserved across multiple groups of single-stranded (+) sense RNA viruses, some mutations can arise over time. In the SARS-CoV-2 sequences from Covid-19 patient samples, some s2m polymorphisms have been detected at positions 15 and 31, predicted to destabilise the stem loop structure (Vahed et al, 2020; Yeh and Contreras, 2020). Using a combination of several gapmers together offers a potential strategy to guard against emerging resistance.…”

“…1A), in contrast to the overall 20 % genome-wide sequence difference (Kim et al, 2020). The s2m sequence is also highly conserved in the clinical isolates from patients that have tested positive for SARS-CoV-2 during the current pandemic, although with a few isolated exceptions (GSAID database https://www.gisaid.org; UCSC genome browser; Vahed et al,2020; Yeh and Contreras, 2020). The high degree of s2m sequence conservation is likely to be a direct consequence of a requirement to sustain an elaborate and conserved three-dimensional structure.…”

Impacts of 203/204: RG>KR mutation in the N protein of SARS-CoV-2

“…Sequences from residues 1-419 for N-protein native Sequence ID: YP_009724397.2 and mutant sequence ID: QIQ08827.1 were used in this study. All of the structures were visualized using PYMOL Chimera software Version 1.7.4 (30). The calculation procedure was almost the same as that in our previous works (31-34).…”