Evidence Supporting That C-to-U RNA Editing Is the Major Force That Drives SARS-CoV-2 Evolution

Wang, Jinxiang; Wu, Liqun; Pu, Xiaoxin; Cao, Meiling

doi:10.1007/s00239-023-10097-1

Cited by 5 publications

(5 citation statements)

References 48 publications

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“…A total of 94.0% of all As in the SARS-CoV-2 genome have mutated at some time to a G (Table 4), and 70% of total A>G mutations were first observed by the end of September 2020 (Figure 5). The prevalence of C>U and A>G mutations is consistent with the predominant role of host deaminases in causing a significant portion of SARS-CoV-2 mutations [14,17,18,64].…”

Section: Snv Signature Analysissupporting

confidence: 68%

“…By mid-April 2020, 70% of all C>U mutations had already been observed (Figure 5). In addition, C>U mutations are the most frequent mutations on average [17], and they have been observed in the largest number of variants, pangolin lineages, and countries (Figure S10). All of this evidence supports the role of C>U mutations as a driving mechanism in the evolution of SARS-CoV-2 [63].…”

Section: Snv Signature Analysismentioning

confidence: 99%

“…Mutations in SARS-CoV-2 can be caused by RNA-dependent RNA polymerase (RdRp) replication errors or by host deaminases that deaminate unpaired nitrogenous bases [1]. At the start of the pandemic, the prevalence of C>U mutations and other evidence suggested that RNA editing is the major source of SARS-CoV-2 mutation [12][13][14][15][16][17]. Since then, the role of RNA editing in SARS-CoV-2 evolution has been experimentally demonstrated [18][19][20].…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

The Mutational Landscape of SARS-CoV-2

Saldivar-Espinoza,

Garcia-Segura,

Novau-Ferré

et al. 2023

IJMS

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Mutation research is crucial for detecting and treating SARS-CoV-2 and developing vaccines. Using over 5,300,000 sequences from SARS-CoV-2 genomes and custom Python programs, we analyzed the mutational landscape of SARS-CoV-2. Although almost every nucleotide in the SARS-CoV-2 genome has mutated at some time, the substantial differences in the frequency and regularity of mutations warrant further examination. C>U mutations are the most common. They are found in the largest number of variants, pangolin lineages, and countries, which indicates that they are a driving force behind the evolution of SARS-CoV-2. Not all SARS-CoV-2 genes have mutated in the same way. Fewer non-synonymous single nucleotide variations are found in genes that encode proteins with a critical role in virus replication than in genes with ancillary roles. Some genes, such as spike (S) and nucleocapsid (N), show more non-synonymous mutations than others. Although the prevalence of mutations in the target regions of COVID-19 diagnostic RT-qPCR tests is generally low, in some cases, such as for some primers that bind to the N gene, it is significant. Therefore, ongoing monitoring of SARS-CoV-2 mutations is crucial. The SARS-CoV-2 Mutation Portal provides access to a database of SARS-CoV-2 mutations.

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Section: Snv Signature Analysissupporting

confidence: 68%

Section: Snv Signature Analysismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

The Mutational Landscape of SARS-CoV-2

Saldivar-Espinoza,

Garcia-Segura,

Novau-Ferré

et al. 2023

IJMS

View full text Add to dashboard Cite

show abstract

“…The leading and characteristic mutations of RdRp reported for Omicron are A1892T, I189V, P314L, K38R, T492I, and V57V (Bansal and Kumar, 2022). Subsequent changes in RNA editing and RNA replication errors are the main reasons for the emergence of further mutations (Wang et al, 2023), such as P323L caused by the 14408C>T mutation on RdRp, which results in high mutation rates throughout the rest of the viral genome, despite being predicted to increase the protein stability. In addition, mutations A97V and A185V can alter the secondary structure of a protein (Rahimi et al, 2021).…”

Section: Rdrpmentioning

confidence: 99%

Molecular evolutionary analysis of the SARS-CoV-2 through the mutation analysis of Spike, Envelope and RdRp proteins

Omerkić Dautović,

Džuho,

Ašić

2024

GenApp

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COVID-19 pandemic, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), was declared in 2020 by the World Health Organization. New mutations have been identified, leading to various variants of this virus, including Alpha, Beta, Gamma, Delta, and Omicron, which are classified as variants of concern (VOCs) and have raised considerable concerns for global public health. Such constant spread and changes in the genome of the virus require continuous monitoring. This research focuses on the evolution of SARS-CoV-2 through a detailed presentation of the viral genome, protein structure and interpretation, with the presentation of phylogenetic characteristics and patterns. We obtained the sequence data from the European region focusing on the S, E, and RdRp proteins from the publicly available NCBI database. We next used the MEGA11 package to generate the multiple sequence alignments and create phylogenetic trees. The SWISS-MODEL server was connected to the Protein Data Bank to obtained tertiary structure images of all the proteins presented in the paper. Stability studies of obtained mutations were performed via MUpro online tool. The results indicate a substantial impact of the Omicron variant relative to others, particularly concerning the alterations and mutations observed in the spike (S) protein, which is crucial in the infection process.

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“…The relative mutational impact between RdRp (RNA-dependent RNA polymerase), which introduces errors during replication, and RNA editing enzymes, remains unclear [17][18][19]. Recent studies revealed an enrichment of C-to-U substitutions and, to a lesser extent, A-to-G substitutions in the SARS-CoV-2 genome, offering evidence for RNA editing by APOBEC and potentially by ADAR enzymes [20][21][22][23][24][25]. However, the full extent of this editing can only be conclusively established through experiments using ADAR and APOBEC knock-out cell lines [26,27].…”

Section: Introductionmentioning

confidence: 99%

RNAsselem: a Python Package for Descriptive Analysis of RNA Secondary Structure Elements in Viral Genomes

Kazanov,

Matveev,

Ponomarev

et al. 2023

Preprint

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Recent advancements in experimental and computational methods for RNA secondary structure detection have revealed the crucial role of RNA structural elements in diverse molecular processes within living cells. It has been demonstrated that the secondary structure of the entire viral genome is often responsible for performing crucial functions in the viral life cycle and also influences virus evolution. To investigate the role of viral RNA secondary structure, alongside experimental techniques, the use of bioinformatics tools is important for analyzing various secondary structure patterns, including hairpin loops, internal loops, multifurcations, external loops, bulges, stems, and pseudoknots. Here, we have introduced a Python package for analyzing RNA secondary structure elements in viral genomes, which includes the recognition of common secondary structure patterns, the generation of descriptive statistics for these structural elements, and the provision of their basic properties. We applied the developed package to analyze the secondary structures of complete viral genomes collected from the literature, aiming to gain insights into viral function and evolution. Both the package and the collection of secondary structures of viral genomes are available at http://github.com/KazanovLab/RNAsselem.

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Evidence Supporting That C-to-U RNA Editing Is the Major Force That Drives SARS-CoV-2 Evolution

Cited by 5 publications

References 48 publications

The Mutational Landscape of SARS-CoV-2

The Mutational Landscape of SARS-CoV-2

Molecular evolutionary analysis of the SARS-CoV-2 through the mutation analysis of Spike, Envelope and RdRp proteins

RNAsselem: a Python Package for Descriptive Analysis of RNA Secondary Structure Elements in Viral Genomes

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