scholarly journals Characterization of codon usage pattern in novel coronavirus 2019-nCoV

2020 ◽  
Author(s):  
Wei Hou
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
International Health ◽  
Bioinformatic Analysis ◽  
Viral Pneumonia ◽  
Codon Usage Pattern ◽  
Usage Pattern ◽  
Potential Value ◽  
Novel Coronavirus

Abstract The outbreak of viral pneumonia in China due to a novel coronavirus 2019-nCoV poses significant threats to international health. In this study we perform bioinformatic analysis to take a snapshot of the codon usage pattern of 2019-nCoV and uncover that this novel coronavirus has a relatively low codon usage bias. The information from this research may not only be helpful to get new insights into the evolution of 2019-nCoV, but also have potential value for developing coronavirus vaccines.

scholarly journals Characterization of Codon Usage Pattern in Novel Coronavirus SARS-CoV-2

2020 ◽  
Author(s):  
Wei Hou
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
International Health ◽  
Bioinformatic Analysis ◽  
Codon Usage Pattern ◽  
Usage Pattern ◽  
Potential Value ◽  
Novel Coronavirus

Abstract The outbreak of COVID-19 due to a novel coronavirus SARS-CoV-2 has posed significant threats to international health. In this study we perform bioinformatic analysis to take a snapshot of the codon usage pattern of SARS-CoV-2 and uncover that this novel coronavirus has a relatively low codon usage bias. The information from this research may not only be helpful to get new insights into the evolution of SARS-CoV-2, but also have potential value for developing coronavirus vaccines.

scholarly journals Characterization of codon usage pattern in SARS-CoV-2

2020 ◽  
Vol 17 (1) ◽  
Author(s):  
Wei Hou
Keyword(s):  
Codon Usage ◽  
International Health ◽  
Bioinformatic Analysis ◽  
Codon Usage Pattern ◽  
Slight Variation ◽  
Usage Pattern ◽  
Mutation Pressure ◽  
Genetic Traits ◽  
Human Coronaviruses ◽  
Novel Coronavirus

Abstract The outbreak of coronavirus disease 2019 (COVID-19) due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed significant threats to international health. The genetic traits as well as evolutionary processes in this novel coronavirus are not fully characterized, and their roles in viral pathogenesis are yet largely unknown. To get a better picture of the codon architecture of this newly emerging coronavirus, in this study we perform bioinformatic analysis, based on publicly available nucleotide sequences of SARS-CoV-2 along with those of other members of human coronaviruses as well as non-human coronaviruses in different hosts, to take a snapshot of the genome-wide codon usage pattern of SARS-CoV-2 and uncover that all over-represented codons end with A/U and this newly emerging coronavirus has a relatively low codon usage bias, which is shaped by both mutation pressure and natural selection. Additionally, there is slight variation in the codon usage pattern among the SARS-CoV-2 isolates from different geo-locations. Furthermore, the overall codon usage pattern of SARS-CoV-2 is generally similar to that of its phylogenetic relatives among non-human betacoronaviruses such as RaTG13. Taken together, we comprehensively analyze the characteristics of codon usage pattern in SARS-CoV-2 via bioinformatic approaches. The information from this research may not only be helpful to get new insights into the evolution of SARS-CoV-2, but also have potential value for developing coronavirus vaccines.

scholarly journals Characterization of Codon Usage Pattern in SARS-CoV-2

2020 ◽  
Author(s):  
Wei Hou
Keyword(s):  
Codon Usage ◽  
International Health ◽  
Bioinformatic Analysis ◽  
Codon Usage Pattern ◽  
Slight Variation ◽  
Usage Pattern ◽  
Mutation Pressure ◽  
Genetic Traits ◽  
Human Coronaviruses ◽  
Novel Coronavirus

Abstract The outbreak of coronavirus disease 2019 (COVID-19) due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed significant threats to international health. The genetic traits as well as evolutionary processes in this novel coronavirus are not fully characterized, and their roles in viral pathogenesis are yet largely unknown. To get a better picture of the codon architecture of this newly emerging coronavirus, in this study we perform bioinformatic analysis, based on publicly available nucleotide sequences of SARS-CoV-2 along with those of other members of human coronaviruses as well as non-human coronaviruses in different hosts, to take a snapshot of the genome-wide codon usage pattern of SARS-CoV-2 and uncover that all over-represented codons end with A/U and this newly emerging coronavirus has a relatively low codon usage bias, which is shaped by both mutation pressure and natural selection. Additionally, there is slight variation in the codon usage pattern among the SARS-CoV-2 isolates from different geo-locations. Furthermore, the overall codon usage pattern of SARS-CoV-2 is generally similar to that of its phylogenetic relatives among non-human betacoronaviruses such as RaTG13. Taken together, we comprehensively analyze the characteristics of codon usage pattern in SARS-CoV-2 via bioinformatic approaches. The information from this research may not only be helpful to get new insights into the evolution of SARS-CoV-2, but also have potential value for developing coronavirus vaccines.

scholarly journals Analysis of codon usage bias of classical swine fever virus

2021 ◽  
pp. 1450-1458
Author(s):  
Sharanagouda S. Patil ◽  
Uma Bharathi Indrabalan ◽  
Kuralayanapalya Puttahonnappa Suresh ◽  
Bibek Ranjan Shome
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Synonymous Codon ◽  
Principal Component ◽  
Infectious Agent ◽  
Classical Swine Fever ◽  
Economic Loss ◽  
Codon Usage Pattern ◽  
Usage Pattern ◽  
Coding Regions

Background and Aim: Classical swine fever (CSF), caused by CSF virus (CSFV), is a highly contagious disease in pigs causing 100% mortality in susceptible adult pigs and piglets. High mortality rate in pigs causes huge economic loss to pig farmers. CSFV has a positive-sense RNA genome of 12.3 kb in length flanked by untranslated regions at 5' and 3' end. The genome codes for a large polyprotein of 3900 amino acids coding for 11 viral proteins. The 1300 codons in the polyprotein are coded by different combinations of three nucleotides which help the infectious agent to evolve itself and adapt to the host environment. This study performed and employed various methods/techniques to estimate the changes occurring in the process of CSFV evolution by analyzing the codon usage pattern. Materials and Methods: The evolution of viruses is widely studied by analyzing their nucleotides and coding regions/ codons using various methods. A total of 115 complete coding regions of CSFVs including one complete genome from our laboratory (MH734359) were included in this study and analysis was carried out using various methods in estimating codon usage bias and evolution. This study elaborates on the factors that influence the codon usage pattern. Results: The effective number of codons (ENC) and relative synonymous codon usage showed the presence of codon usage bias. The mononucleotide (A) has a higher frequency compared to the other mononucleotides (G, C, and T). The dinucleotides CG and CC are underrepresented and overrepresented. The codons CGT was underrepresented and AGG was overrepresented. The codon adaptation index value of 0.71 was obtained indicating that there is a similarity in the codon usage bias. The principal component analysis, ENC-plot, Neutrality plot, and Parity Rule 2 plot produced in this article indicate that the CSFV is influenced by the codon usage bias. The mutational pressure and natural selection are the important factors that influence the codon usage bias. Conclusion: The study provides useful information on the codon usage analysis of CSFV and may be utilized to understand the host adaptation to virus environment and its evolution. Further, such findings help in new gene discovery, design of primers/probes, design of transgenes, determination of the origin of species, prediction of gene expression level, and gene function of CSFV. To the best of our knowledge, this is the first study on codon usage bias involving such a large number of complete CSFVs including one sequence of CSFV from India.

scholarly journals Genome-wide codon usage pattern analysis reveals the correlation between codon usage bias and gene expression in Cuscuta australis

Genomics ◽  
2020 ◽  
Vol 112 (4) ◽  
pp. 2695-2702 ◽  
Author(s):  
Xu-Yuan Liu ◽  
Yu Li ◽  
Kai-Kai Ji ◽  
Jie Zhu ◽  
Peng Ling ◽  
...  
Keyword(s):  
Gene Expression ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Pattern Analysis ◽  
Codon Usage Pattern ◽  
Usage Pattern ◽  
Genome Wide

Characterization of codon usage pattern and influencing factors in Japanese encephalitis virus

2016 ◽  
Vol 221 ◽  
pp. 58-65 ◽  
Author(s):  
Niraj K. Singh ◽  
Anuj Tyagi ◽  
Rajinder Kaur ◽  
Ramneek Verma ◽  
Praveen K. Gupta
Keyword(s):  
Codon Usage ◽  
Japanese Encephalitis Virus ◽  
Influencing Factors ◽  
Japanese Encephalitis ◽  
Encephalitis Virus ◽  
Codon Usage Pattern ◽  
Usage Pattern

scholarly journals The codon usage pattern of the novel coronavirus is drastically different from those of other pathogenic viruses

2020 ◽  
Author(s):  
Xiaolong Wang
Keyword(s):  
Codon Usage ◽  
World Health ◽  
Codon Usage Pattern ◽  
The Novel ◽  
Usage Pattern ◽  
Intermediate Hosts ◽  
Usage Patterns ◽  
Pathogenic Viruses ◽  
Novel Coronavirus ◽  
Health Organization

Abstract The current outbreak of a novel coronavirus (COVID-19) has caused thousands of deaths and has been declared to be a worldwide pandemic by the World Health Organization. There have been various disputes but the origin of COVID-19 is not clear. Here we analyzed the similarities of codon usage patterns between humans and pathogenic viruses, such as human immunodeficiency virus (HIV), highly pathogenic avian influenza (HPAI), SARS, MERS, and COVID-19. In HIVs, HPAIs, SARS, and MERS, codon usages are highly similar to that of humans; in contrast, the codon usage pattern of COVID-19 is drastically different from those of humans and other pathogenic viruses. Besides, coronaviruses have been evolving in two opposite directions: human-preferred codons are adopted to substitute less-preferred ones in SARS and MERS but are substituted by less-preferred ones in COVID-19. The unique codon usage pattern suggesting that COVID-19 was evolved in an intermediate host, in which its codon usage pattern becomes drastically different from that of bats or humans, and its pathogenicity is weakened compared with SARS ad MERS COVs. Finally, we appeal to international cooperation to eliminate the epidemic by cutting off the transmission routes among humans and to search for the origin and intermediate hosts of the novel coronavirus to prevent future animal-to-human transmission.

scholarly journals Comparative studies of codon usage profile of Anisakis simplex (Nematoda) and Carassius gibelio (Prussian carp)

2022 ◽  
Vol 43 (1) ◽  
pp. 123-132
Author(s):  
W. Ahmed ◽  
◽  
S. Gupta ◽  
I. Mukherjee ◽  
V.K. Babu ◽  
...  
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Similar Pattern ◽  
Synonymous Codon ◽  
Anisakis Simplex ◽  
Codon Usage Pattern ◽  
Usage Pattern ◽  
Prussian Carp ◽  
Evolutionary Forces ◽  
Carassius Gibelio

Aim: The aim of the present study was to understand the molecular relationship between nematode (parasite) and fish (host) through codon usage bias (CUB) analysis. Methodology: The Codon usage bias analysis has been performed in fish Carassius gibelio (Prussian carp) and nematode fish parasite Anisakis simplex. The complete coding sequences (CDS) of C. gibelio (Prussian carp) and A. simplex (Nematode) were retrieved from National Center for Biotechnology Information and followed to that we have performed bioinformatics analysis to understand the codon usage pattern between host and parasite. Results: Different CUB indices like Relative synonymous codon usage (RSCU), Effective number of codons (ENC), Codon adaptation index (CAI) and Codon bias index (CBI) revealed a similar pattern in the codon usage in C. gibelio and A. simplex. In addition, inclusive analysis using different plots (ENC, parity, neutrality) had shown the influence of both the evolutionary forces i.e mutational and translational selection on codon usage pattern. This describes the role of evolutionary forces in determining the conserved genome to establish species-specific function-level differences for efficient survival. Interpretation: The present study elucidated the association between Carassiusgibelio (host) and Anisakis simplex (parasite) based on the similar pattern of codon usage bias between both the species.

Characterization of Codon Usage Bias in the UL55 Gene of Duck Enteritis Virus

2011 ◽  
Vol 204-210 ◽  
pp. 649-662 ◽  
Author(s):  
Ying Wu ◽  
An Chun Cheng ◽  
Ming Shu Wang ◽  
De Kang Zhu ◽  
Xiao Yue Chen
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Duck Enteritis Virus ◽  
Codon Usage Pattern ◽  
Usage Pattern ◽  
E Coli ◽  
Usage Patterns ◽  
Enteritis Virus

The analysis of codon usage may improve our understanding of the evolution and pathogenesis of DEV（Duck enteritis virus） and allow reengineering of target gene to improve their expression for gene therapy.In this study,we calculated the codon usage bias in DEV UL55 gene and performed a comparative analysis of synonymous codon usage patterns in other 26 related viruses by EMBOSS CUSP program and Codon W on line.Moreover,statistical methods were used to investigate the correlations of these related parameters. By comparing synonymous codon usage patterns in different viruses,we observed that synonymous codon usage pattern in these virus is virus specific and phylogenetically conserved, with a strong bias towards the codons with A and T at the third codon position. Phylogenetic analysis based on codon usage pattern suggested that DEV UL55 gene was clustered with the avian Alphaherpesvirus but diverged to form a single branch. The Neutrality-plot suggested GC12 and GC3s adopt the same mutation pattern,meanwhile,the ENC-plot revealed that the genetic heterogeneity in UL55 genes is constrained by the G+C content, while translational selection and gene length have no or micro effect on the variations of synonymous codon usage in these virus genes.Furthermore, we compared the codon preferences of DEV with those of E. coli, yeast and Homo sapiens.Data suggested the eukaryotes system such as human system may be more suitable for the expression of DEV UL55 gene in vitro. If the yeast and E. coli expression system are wanted for the expression of DEV UL55 gene ,codon optimization of the DEV UL55 gene may be required.

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