Synonymous and Biased Codon Usage by MERS CoV Papain-Like and 3CL-Proteases

Kandeel, Mahmoud; Altaher, Abdallah

doi:10.1248/bpb.b17-00168

Cited by 10 publications

(9 citation statements)

References 32 publications

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“…In addition, A or T nucleotides were the most predominant nucleotides at the 3rd position of codons. This is in agreement with the previous studies of CoVs 25,31 …”

Section: Discussionsupporting

confidence: 94%

From SARS and MERS CoVs to SARS‐CoV‐2: Moving toward more biased codon usage in viral structural and nonstructural genes

Kandeel

Ibrahim

Fayez

et al. 2020

Journal of Medical Virology

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176

139

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Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging disease with fatal outcomes. In this study, a fundamental knowledge gap question is to be resolved by evaluating the differences in biological and pathogenic aspects of SARS-CoV-2 and the changes in SARS-CoV-2 in comparison with the two prior major COV epidemics, SARS and Middle East respiratory syndrome (MERS) coronaviruses. Methods: The genome composition, nucleotide analysis, codon usage indices, relative synonymous codons usage, and effective number of codons (ENc) were analyzed in the four structural genes; Spike (S), Envelope (E), membrane (M), and Nucleocapsid (N) genes, and two of the most important nonstructural genes comprising RNA-dependent RNA polymerase and main protease (Mpro) of SARS-CoV-2, Beta-CoV from pangolins, bat SARS, MERS, and SARS CoVs. Results: SARS-CoV-2 prefers pyrimidine rich codons to purines. Most highfrequency codons were ending with A or T, while the low frequency and rare codons were ending with G or C. SARS-CoV-2 structural proteins showed 5 to 20 lower ENc values, compared with SARS, bat SARS, and MERS CoVs. This implies higher codon bias and higher gene expression efficiency of SARS-CoV-2 structural proteins. SARS-CoV-2 encoded the highest number of over-biased and negatively biased codons. Pangolin Beta-CoV showed little differences with SARS-CoV-2 ENc values, compared with SARS, bat SARS, and MERS CoV. Conclusion: Extreme bias and lower ENc values of SARS-CoV-2, especially in Spike, Envelope, and Mpro genes, are suggestive for higher gene expression efficiency, compared with SARS, bat SARS, and MERS CoVs.

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“…In addition, A or T nucleotides were the most predominant nucleotides at the 3rd position of codons. This is in agreement with the previous studies of CoVs 25,31 …”

Section: Discussionsupporting

confidence: 94%

From SARS and MERS CoVs to SARS‐CoV‐2: Moving toward more biased codon usage in viral structural and nonstructural genes

Kandeel

Ibrahim

Fayez

et al. 2020

Journal of Medical Virology

Self Cite

176

139

View full text Add to dashboard Cite

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“…This suggests that the RNA viruses with high ENc values adapt to the host with various preferred codons (Jenkins and Holmes, 2003). The positively biased or represented codons of the present study are similar to the two other studies on MERS CoV proteases and pandemic influenza virus (H1N1 and in H3N2) (Kumar et al, 2016;Kandeel and Altaher, 2017). In zika virus and tembusu virus codon usage was driven by the mutation bias (Cristina et al, 2015;Zhou et al, 2015) while in Parvoviridae and pedCoV it was dominated by selection pressure (Shi et al, 2013;Chen et al, 2014b).…”

Section: Discussionsupporting

confidence: 86%

Analysis of preferred codon usage in the coronavirus N genes and their implications for genome evolution and vaccine design

Sheikh

Al‐Taher

Al‐Nazawi

et al. 2020

Journal of Virological Methods

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The nucleocapsid (N) protein of a coronavirus plays a crucial role in virus assembly and in its RNA transcription. It is important to characterize a virus at the nucleotide level to discover the virus's genomic sequence variations and similarities relative to other viruses that could have an impact on the functions of its genes and proteins. This entails a comprehensive and comparative analysis of the viral genomes of interest for preferred nucleotides, codon bias, nucleotide changes at the 3 rd position (NT3s), synonymous codon usage and relative synonymous codon usage. In this study, the variations in the N proteins among 13 different coronaviruses (CoVs) were analysed at the nucleotide and amino acid levels in an attempt to reveal how these viruses adapt to their hosts relative to their preferred codon usage in the N genes. The results revealed that, overall, eighteen amino acids had different preferred codons and eight of these were over-biased. The N genes had a higher AT% over GC% and the values of their effective number of codons ranged from 40.43 to 53.85, indicating a slight codon bias. Neutrality plots and correlation analyses showed a very high level of GC3s/GC correlation in porcine epidemic diarrhea CoV (pedCoV), followed by Middle East respiratory syndrome-CoV (MERS CoV), porcine delta CoV (dCoV), bat CoV (bCoV) and feline CoV (fCoV) with r values 0.81, 0.68, -0.47, 0.98 and 0.58, respectively. These data implied a high rate of evolution of the CoV genomes and a strong influence of mutation on evolutionary selection in the CoV N genes. This type of genetic analysis would be useful for evaluating a virus's host adaptation, evolution and is thus of value to vaccine design strategies.

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“…In all of its structural genes, SARS-CoV-2 prefers pyrimidine rich codons to purines, and most high-frequency codons ended with A or T. The low-frequency codons ended with G or C [61]. This is in agreement with previous studies of CoVs [62]. SARS-CoV-2 structural proteins showed 5-20 lower ENc values compared to SARS, bat SARS and MERS CoVs.…”

Section: Sars-cov-2 Genomics and Variationsupporting

confidence: 90%

Update of the current knowledge on genetics, evolution, immunopathogenesis, and transmission for coronavirus disease 19 (COVID-19)

Tizaoui¹,

Zidi²,

Lee³

et al. 2020

Int. J. Biol. Sci.

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In December 2019, an acute respiratory disease caused by novel species of coronavirus (SARS-CoV-2), emerged in China and has spread throughout the world. On 11 th March 2020, the World Health Organization (WHO) officially declared coronavirus disease 19 (COVID-19) a pandemic, severe coronavirus-mediated human disease. Based on genomic and phylogenetic studies, SARS-CoV-2 might originate from bat coronaviruses and infects humans directly or through intermediate zoonotic hosts. However, the exact origin or the host intermediate remains unknown. Genetically, SARS-CoV-2 is similar to several existing coronaviruses, particularly SARS-CoV, but differs by silent and non-silent mutations. The virus uses different transmission routes and targets cells and tissues with angiotensin-converting enzyme 2 (ACE2) protein, which makes it contagious. COVID-19 shares both the main clinical features and excessive/dysregulated cell responses with the two previous Middle East respiratory syndrome coronavirus (MERS) and severe acute respiratory syndrome coronavirus (SARS) epidemics. In this review, we provide an update of the current knowledge on the COVID-19 pandemic. Gaining a deeper understanding of SARS-CoV-2 structure, transmission routes, and molecular responses, will assist in the prevention and control of COVID-19 outbreaks in the future.

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Synonymous and Biased Codon Usage by MERS CoV Papain-Like and 3CL-Proteases

Cited by 10 publications

References 32 publications

From SARS and MERS CoVs to SARS‐CoV‐2: Moving toward more biased codon usage in viral structural and nonstructural genes

From SARS and MERS CoVs to SARS‐CoV‐2: Moving toward more biased codon usage in viral structural and nonstructural genes

Analysis of preferred codon usage in the coronavirus N genes and their implications for genome evolution and vaccine design

Update of the current knowledge on genetics, evolution, immunopathogenesis, and transmission for coronavirus disease 19 (COVID-19)

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