Codon usage bias in the H gene of canine distemper virus

Wang, Xin; Xu, Weihua; Fan, Kewei; Chiu, Hung-chuan; Huang, Cuiqin

doi:10.1016/j.micpath.2020.104511

Cited by 12 publications

(13 citation statements)

References 49 publications

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“…The CA & TG and CG & TA dinucleotides were seen to be over and underrepresented, respectively in S, M segments whereas in the L segment CT dinucleotide was an addition to overrepresented codons. Similar results were observed in the previous study [9,15]. Further, a total of 7 (ACG, CCG, TCG, TGC, AGC, GGC, and TGC), 11(ACG, CCG, CGC, GCG, TCG, AGC, CGC, GCA, GCG, and TGC), and 10 (AGC, CGC, GCA, GCG, GGC, TGC, CCG, CGC, GCG, and TCG) RSCU codons were containing underrepresented CG dinucleotide in S, M, and L segment respectively, signifying all these codons are not favourably preferred.…”

Section: Discussionsupporting

confidence: 93%

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Synonymous codon usage pattern among the S, M, and L segments in crimean-congo hemorrhagic fever causing virus

et al. 2021

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Crimean-congo hemorrhagic fever (CCHF) virus is one among the major zoonosis viral diseases that use the Hyalomma ticks as their transmission vector to cause viral infection to the human and mammalian community. The fatality of infectious is high across the world especially in Africa, Asia, Middle East, and Europe. This study regarding codon usage bias of S, M, and L segments of the CCHF virus pertaining to the host Homo sapiens, reveals in-depth information about the evolutionary characteristics of CCHFV. Relative Synonymous Codon Usage (RSCU), Effective number of codons (ENC) were calculated, to determine the codon usage pattern in each segment. Correlation analysis between Codon adaptation index (CAI), GRAVY (Hydrophobicity), AROMO (Aromaticity), and nucleotide composition revealed bias in the codon usage pattern. There was no strong codon bias found among any segments of the CCHF virus, indicating both the factors i.e., natural selection and mutational pressure shapes the codon usage bias.

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Section: Discussionsupporting

confidence: 93%

“…The same technique was carried out for each S, M, L segments of the CCHF virus by plotting the GC12 values against GC3 values. The regression line on the neutrality plot is indicative of the mutational pressure [15] [14].…”

Section: Neutrality Plot Analysismentioning

confidence: 99%

Synonymous codon usage pattern among the S, M, and L segments in crimean-congo hemorrhagic fever causing virus

et al. 2021

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“…Where the frequency of nucleotides X and Y is denoted as f x and f y respectively. The expected frequency of the dinucleotide XY is denoted as f y f x and the observed frequency of dinucleotide XY is denoted as f xy [ 9 ].…”

Section: Methodsmentioning

confidence: 99%

“…Natural selection, nucleotide base content, genetic mutation, and drift are some of the factors that are closely related to the codon bias in the molecular evolution of the agent/organisms. The codon usage experienced during the process of molecular evolution, is efficient in changing the production of proteins and mutations in the genes [ 5 - 9 ]. Therefore, codon usage analysis provides details on how it affects the evolution pattern, environmental adaptation, response to the immune system, and virus survival among the hosts and virus [ 7 , 10 ].…”

Section: Introductionmentioning

confidence: 99%

Analysis of codon usage bias of classical swine fever virus

et al. 2021

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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.

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“…Studies have found that low codon usage bias reduces the competition for the synthesis mechanism between viruses and hosts, which is conducive to the expression of viral genes in host cells. We consider that the same three narcissus virus CP gene low codon bias is conducive to better adapting to its host [ 52 , 53 ].…”

Section: Discussionmentioning

confidence: 99%

Synonymous Codon Usage Analysis of Three Narcissus Potyviruses

Ding

Guo³

et al. 2022

Viruses

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Narcissus degeneration virus (NDV), narcissus late season yellows virus (NLSYV) and narcissus yellow stripe virus (NYSV), which belong to the genus Potyvirus of the family Potyviridae, cause significant losses in the ornamental value and quality of narcissus. Several previous studies have explored the genetic diversity and evolution rate of narcissus viruses, but the analysis of the synonymous codons of the narcissus viruses is still unclear. Herein, the coat protein (CP) of three viruses is used to analyze the viruses’ phylogeny and codon usage pattern. Phylogenetic analysis showed that NYSV, NDV and NLSYV isolates were divided into five, three and five clusters, respectively, and these clusters seemed to reflect the geographic distribution. The effective number of codon (ENC) values indicated a weak codon usage bias in the CP coding region of the three narcissus viruses. ENC-plot and neutrality analysis showed that the codon usage bias of the three narcissus viruses is all mainly influenced by natural selection compared with the mutation pressure. The three narcissus viruses shared the same best optimal codon (CCA) and the synonymous codon prefers to use codons ending with A/U, compared to C/G. Our study shows the codon analysis of different viruses on the same host for the first time, which indicates the importance of the evolutionary-based design to control these viruses.

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Codon usage bias in the H gene of canine distemper virus

Cited by 12 publications

References 49 publications

Synonymous codon usage pattern among the S, M, and L segments in crimean-congo hemorrhagic fever causing virus

Synonymous codon usage pattern among the S, M, and L segments in crimean-congo hemorrhagic fever causing virus

Analysis of codon usage bias of classical swine fever virus

Synonymous Codon Usage Analysis of Three Narcissus Potyviruses

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