scholarly journals Multivariate analyses of codon usage of SARS-CoV-2 and other betacoronaviruses

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Haogao Gu ◽  
Daniel K W Chu ◽  
Malik Peiris ◽  
Leo L M Poon
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Codon Usage ◽  
Influenza A ◽  
Multivariate Analyses ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Health Concern ◽  
Codon Usage Pattern ◽  
Usage Pattern ◽  
Influenza A Viruses

Abstract Coronavirus disease 2019 (COVID-19) is a global health concern as it continues to spread within China and beyond. The causative agent of this disease, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), belongs to the genus Betacoronavirus, which also includes severe acute respiratory syndrome-related coronavirus (SARSr-CoV) and Middle East respiratory syndrome-related coronavirus (MERSr-CoV). Codon usage of viral genes are believed to be subjected to different selection pressures in different host environments. Previous studies on codon usage of influenza A viruses helped identify viral host origins and evolution trends, however, similar studies on coronaviruses are lacking. In this study, we compared the codon usage bias using global correspondence analysis (CA), within-group CA and between-group CA. We found that the bat RaTG13 virus best matched the overall codon usage pattern of SARS-CoV-2 in orf1ab, spike and nucleocapsid genes, while the pangolin P1E virus had a more similar codon usage in membrane gene. The amino acid usage pattern of SARS-CoV-2 was generally found similar to bat and human SARSr-CoVs. However, we found greater synonymous codon usage differences between SARS-CoV-2 and its phylogenetic relatives on spike and membrane genes, suggesting these two genes of SARS-CoV-2 are subjected to different evolutionary pressures.

scholarly journals Multivariate Analyses of Codon Usage of SARS-CoV-2 and other betacoronaviruses

2020 ◽  
Author(s):  
Haogao Gu ◽  
Daniel Chu ◽  
Malik Peiris ◽  
Leo L.M. Poon
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Codon Usage ◽  
Correspondence Analysis ◽  
Influenza A ◽  
Multivariate Analyses ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Health Concern ◽  
Influenza A Viruses ◽  
Viral Sequences

AbstractCoronavirus disease 2019 (COVID-19) is a global health concern as it continues to spread within China and beyond. The causative agent of this disease, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), belongs to the genus Betacoronavirus which also includes severe acute respiratory syndrome related coronavirus (SARSr-CoV) and Middle East respiratory syndrome related coronavirus (MERSr-CoV). Codon usage of viral genes are believed to be subjected to different selection pressures in different host environments. Previous studies on codon usage of influenza A viruses can help identify viral host origins and evolution trends, however, similar studies on coronaviruses are lacking. In this study, global correspondence analysis (CA), within-group correspondence analysis (WCA) and between-group correspondence analysis (BCA) were performed among different genes in coronavirus viral sequences. The amino acid usage pattern of SARS-CoV-2 was generally found similar to bat and human SARSr-CoVs. However, we found greater synonymous codon usage differences between SARS-CoV-2 and its phylogenetic relatives on spike and membrane genes, suggesting these two genes of SARS-CoV-2 are subjected to different evolutionary pressures.

Synonymous codon usage pattern analysis of Hepatitis D virus

2013 ◽  
Vol 173 (2) ◽  
pp. 350-353 ◽  
Author(s):  
Arghya Kamal Bishal ◽  
Rashmi Mukherjee ◽  
Chandan Chakraborty
Keyword(s):  
Codon Usage ◽  
Pattern Analysis ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Codon Usage Pattern ◽  
Usage Pattern ◽  
Hepatitis D ◽  
Hepatitis D Virus

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.

Analysis of synonymous codon usage in H5N1 virus and other influenza A viruses

Biosystems ◽  
2005 ◽  
Vol 81 (1) ◽  
pp. 77-86 ◽  
Author(s):  
Tong Zhou ◽  
Wanjun Gu ◽  
Jianmin Ma ◽  
Xiao Sun ◽  
Zuhong Lu
Keyword(s):  
Codon Usage ◽  
Influenza A ◽  
H5n1 Virus ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Influenza A Viruses

scholarly journals Phylogenetic and Codon Usage Analysis for Capsid and Replicase Genes of Porcine Circovirus 3

2021 ◽  
Author(s):  
Xianglong Yu ◽  
Kuipeng Gao ◽  
Molin Pi ◽  
Huizi Li ◽  
Wenxia Zhong ◽  
...  
Keyword(s):  
Codon Usage ◽  
Synonymous Codon ◽  
Economic Loss ◽  
Porcine Circovirus Type ◽  
Synonymous Codon Usage ◽  
Porcine Circovirus ◽  
Codon Usage Pattern ◽  
Usage Pattern ◽  
Swine Industry ◽  
Usage Analysis

Abstract Porcine circovirus type 3 (PCV3) is a highly contagious virus belonging to the family Circoviridae that causes the severe dermatitis and nephropathy syndrome. To date, PCV3 has a worldwide distribution and bring huge economic loss in swine industry. Replicase protein (Rep) and capsid protein (Cap) are two major proteins of PCV3. Considering that the large number of new PCV3 isolates were reported in the past few years and the research for the codon usage pattern of Rep and Cap genes was still a gap, phylogenetic and codon usage analysis of these two genes was performed. Phylogenetic analysis with all strains showed no clear clusters were displayed, but almost all strains of one genotype were separated into same clade. Relative synonymous codon usage (RSCU) analysis revealed that the codon usage bias existed and effective number of codon (ENC) analysis showed that the bias was slight low. ENC-GC3s plot indicated that mutational pressure and other factors both play a role in PCV3 codon usage and neutrality plot analysis showed that natural selection was the main force influencing the codon usage pattern. In summary, the results provided the important basic data on codon usage pattern of Rep and Cap genes, and a better understanding of the evolution and potential origin of PCV3.

In silico Analysis of Synonymous Codon Usage Pattern of Rhizobium etli CFN 42

2014 ◽  
Vol 86 (2) ◽  
pp. 385-393
Author(s):  
Mohammad Samir Farooqi ◽  
R. K. Sanjukta ◽  
Dwijesh Chandra Mishra ◽  
Dhananjaya Pratap Singh ◽  
Anil Rai ◽  
...  
Keyword(s):  
Codon Usage ◽  
In Silico ◽  
Synonymous Codon ◽  
In Silico Analysis ◽  
Synonymous Codon Usage ◽  
Codon Usage Pattern ◽  
Usage Pattern ◽  
Rhizobium Etli ◽  
Silico Analysis
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