Analysis of Rapidly Emerging Variants in Structured Regions of the SARS-CoV-2 Genome

Abstract

<jats:title>Abstract</jats:title><jats:p>The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has motivated a widespread effort to understand its epidemiology and pathogenic mechanisms. Modern high-throughput sequencing technology has led to the deposition of vast numbers of SARS-CoV-2 genome sequences in curated repositories, which have been useful in mapping the spread of the virus around the globe. They also provide a unique opportunity to observe virus evolution in real time. Here, we evaluate two cohorts of SARS-CoV-2 genomic sequences to identify rapidly emerging variants within structured cis-regulatory elements of the SARS-CoV-2 genome. Overall, twenty variants are present at a minor allele frequency of at least 0.5%. Several enhance the stability of Stem Loop 1 in the 5’UTR, including a set of co-occurring variants that extend its length. One appears to modulate the stability of the frameshifting pseudoknot between ORF1a and ORF1b, and another perturbs a bi-stable molecular switch in the 3’UTR. Finally, five variants destabilize structured elements within the 3’UTR hypervariable region, including the S2M stem loop, raising questions as to the functional relevance of these structures in viral replication. Two of the most abundant variants appear to be caused by RNA editing, suggesting host-viral defense contributes to SARS-CoV-2 genome heterogeneity. This analysis has implications for the development of therapeutics that target viral cis-regulatory RNA structures or sequences, as rapidly emerging variations in these regions could lead to drug resistance.</jats:p>

Programmed −1 Ribosomal Frameshifting in coronaviruses: A therapeutic target

“…Historically, a series of molecular genetics and biochemical analyses of the Avian Infectious Bronchitis Virus −1 PRF signal established the foundation for much of our understanding of this phenomenon ( Brierley et al, 2007 ; Brierley and Pennell, 2001 ). Analyses of SARS-CoV-2 sequence variations reveal the highly conserved nature of the −1 PRF signal; the vast majority of variants are very infrequently represented in the population, supporting the importance of this element for viral fitness ( Ryder et al, 2020 ). Functional studies of single-nucleotide polymorphisms seen in different regions of the pseudoknot found that most of them had little effect on −1 PRF efficiency ( Neupane et al, 2020 ), with only a few leading to significant decreases, including a ~2-fold decrease from C13476U and C13501U in stem 1 ( Sun et al, 2020 ) and a roughly 3-fold decrease from U13494C in stem 2 ( Neupane et al, 2020 ); notably, each of these mutations involved converting G:C pairs to G:U (or vice versa), and hence would be expected to leave the secondary structure unchanged.…”

The short- and long-range RNA-RNA Interactome of SARS-CoV-2

“…For example, interactions between promoters and enhancers dictate the rate of transcription along the eukaryotic genome (Rowley and Corces, 2018) . Great effort is being made to reveal the structural landscapes of the SARS-CoV-2 genome (Andrews et al, 2020;Huston et al, 2020;Kelly et al, 2020;Lan et al, 2020;Manfredonia et al, 2020;Ryder, 2020;Sanders et al, 2020;Sun et al, 2020) .…”

Analysis of SARS‐CoV‐2 mutations in Mexico, Belize, and isolated regions of Guatemala and its implication in the diagnosis

“…We found a mutation in the noncoding regions 5ʹ‐UTR (C241T), this type of mutation in UTRs of SARS‐Cov‐2 has been studied recently, suggesting that C241T in 5ʹ‐UTR appeared early during the outbreak, and could be key in virus replication and RNA folding, 46 affecting the steam‐loop 5b (SL5b) 47,48 and the host defense 49 . The intergenic mutation A29700G located between ORF3a and E genes might emerge through adenosine deaminase acting on RNA (ADAR) and could be important in the antiviral response 28,35,50 reducing the stability in the RNA fold 29 …”