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Gaunt ER, Digard P. Compositional biases in RNA viruses: Causes, consequences and applications. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1679. [PMID: 34155814 PMCID: PMC8420353 DOI: 10.1002/wrna.1679] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/29/2021] [Accepted: 05/31/2021] [Indexed: 01/05/2023]
Abstract
If each of the four nucleotides were represented equally in the genomes of viruses and the hosts they infect, each base would occur at a frequency of 25%. However, this is not observed in nature. Similarly, the order of nucleotides is not random (e.g., in the human genome, guanine follows cytosine at a frequency of ~0.0125, or a quarter the number of times predicted by random representation). Codon usage and codon order are also nonrandom. Furthermore, nucleotide and codon biases vary between species. Such biases have various drivers, including cellular proteins that recognize specific patterns in nucleic acids, that once triggered, induce mutations or invoke intrinsic or innate immune responses. In this review we examine the types of compositional biases identified in viral genomes and current understanding of the evolutionary mechanisms underpinning these trends. Finally, we consider the potential for large scale synonymous recoding strategies to engineer RNA virus vaccines, including those with pandemic potential, such as influenza A virus and Severe Acute Respiratory Syndrome Coronavirus Virus 2. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Evolution and Genomics > Computational Analyses of RNA RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition.
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Affiliation(s)
- Eleanor R. Gaunt
- Department of Infection and ImmunityThe Roslin Institute, The University of EdinburghEdinburghUK
| | - Paul Digard
- Department of Infection and ImmunityThe Roslin Institute, The University of EdinburghEdinburghUK
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2
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Wang G, Zheng C. Zinc finger proteins in the host-virus interplay: multifaceted functions based on their nucleic acid-binding property. FEMS Microbiol Rev 2021; 45:fuaa059. [PMID: 33175962 DOI: 10.1093/femsre/fuaa059] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/07/2020] [Indexed: 12/14/2022] Open
Abstract
Zinc finger proteins (ZFPs) are a huge family comprised of massive, structurally diverse proteins characterized by zinc ion coordinating. They engage in the host-virus interplay in-depth and occupy a significant portion of the host antiviral arsenal. Nucleic acid-binding is the basic property of certain ZFPs, which draws increasing attention due to their immense influence on viral infections. ZFPs exert multiple roles on the viral replications and host cell transcription profiles by recognizing viral genomes and host mRNAs. Their roles could be either antiviral or proviral and were separately discussed. Our review covers the recent research progress and provides a comprehensive understanding of ZFPs in antiviral immunity based on their DNA/RNA binding property.
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Affiliation(s)
- Guanming Wang
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, No.1 Xue Yuan Road, University Town, FuZhou Fujian, 350108, China
| | - Chunfu Zheng
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, No.1 Xue Yuan Road, University Town, FuZhou Fujian, 350108, China
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Dr NW, Calgary, Alberta, Canada, AB T2N 4N1
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Pintó RM, Pérez-Rodríguez FJ, Costafreda MI, Chavarria-Miró G, Guix S, Ribes E, Bosch A. Pathogenicity and virulence of hepatitis A virus. Virulence 2021; 12:1174-1185. [PMID: 33843464 PMCID: PMC8043188 DOI: 10.1080/21505594.2021.1910442] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Hepatitis A is an acute infection of the liver, which is mostly asymptomatic in children and increases the severity with age. Although in most patients the infection resolves completely, in a few of them it may follow a prolonged or relapsed course or even a fulminant form. The reason for these different outcomes is unknown, but it is generally accepted that host factors such as the immunological status, age and the occurrence of underlaying hepatic diseases are the main determinants of the severity. However, it cannot be ruled out that some virus traits may also contribute to the severe clinical outcomes. In this review, we will analyze which genetic determinants of the virus may determine virulence, in the context of a paradigmatic virus in terms of its genomic, molecular, replicative, and evolutionary features.
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Affiliation(s)
- Rosa M Pintó
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, and Institute of Nutrition and Safety, University of Barcelona, Barcelona, Spain
| | - Francisco-Javier Pérez-Rodríguez
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, and Institute of Nutrition and Safety, University of Barcelona, Barcelona, Spain.,Present Address: Division of Infectious Diseases, Laboratory of Virology, University of Geneva Hospitals, Geneva, Switzerland
| | - Maria-Isabel Costafreda
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, and Institute of Nutrition and Safety, University of Barcelona, Barcelona, Spain
| | - Gemma Chavarria-Miró
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, and Institute of Nutrition and Safety, University of Barcelona, Barcelona, Spain
| | - Susana Guix
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, and Institute of Nutrition and Safety, University of Barcelona, Barcelona, Spain
| | - Enric Ribes
- Enteric Virus Laboratory, Department of Cell Biology, Physiology and Immunology, University of Barcelona, Barcelona, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, and Institute of Nutrition and Safety, University of Barcelona, Barcelona, Spain
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Deb B, Uddin A, Chakraborty S. Composition, codon usage pattern, protein properties, and influencing factors in the genomes of members of the family Anelloviridae. Arch Virol 2021; 166:461-474. [PMID: 33392821 PMCID: PMC7779081 DOI: 10.1007/s00705-020-04890-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 10/02/2020] [Indexed: 01/31/2023]
Abstract
The present study was carried out on 62 genome sequences of members of the family Anelloviridae, as there have been no reports of genome analysis of these DNA viruses using a bioinformatics approach. The genes were found to be rich in AC content with low codon usage bias (CUB). Relative synonymous codon usage (RSCU) values identified the preferred codons for each amino acid in the family. The codon AGA was overrepresented, while the codons TCG, TTG, CGG, CGT, ACG, GCG and GAT were underrepresented in all of the genomes. A significant correlation was found between the effective number of codons (ENC) and base constraints, indicating that compositional properties might have influenced the CUB. A highly significant correlation was observed between the overall base content and the base content at the third codon position, indicating that mutations might have affected the CUB. A highly significant positive correlation was observed between GC12 and GC3 (r = 0.904, p < 0.01), which indicated that directional mutation pressure influenced all three codon positions. A neutrality plot revealed that the contribution of mutation and natural selection in determining the CUB was 58.6% and 41.4%, respectively.
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Affiliation(s)
- Bornali Deb
- Department of Biotechnology, Assam University, Silchar, Assam 788150 India
| | - Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi, Assam 788150 India
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Sheikh A, Al-Taher A, Al-Nazawi M, Al-Mubarak AI, Kandeel M. Analysis of preferred codon usage in the coronavirus N genes and their implications for genome evolution and vaccine design. J Virol Methods 2020; 277:113806. [PMID: 31911390 PMCID: PMC7119019 DOI: 10.1016/j.jviromet.2019.113806] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 11/24/2019] [Accepted: 12/20/2019] [Indexed: 02/08/2023]
Abstract
The nucleotide variations among the N genes of 13 different coronaviruses (CoVs) were interpreted. Overall, 18 amino acids observed with varying preferred codons. The effective number of codon values ranged from 40.43 to 53.85, revealing a slight codon bias. A highly significant correlation between GC3s and ENc values was observed in porcine epidemic diarrhea CoV, followed by Middle East respiratory syndrome CoV.
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 3rd 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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Affiliation(s)
- Abdullah Sheikh
- The Camel Research Center, King Faisal University, Alhofuf, Alahsa 31982, Saudi Arabia
| | - Abdulla Al-Taher
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Alhofuf, Alahsa 31982, Saudi Arabia
| | - Mohammed Al-Nazawi
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Alhofuf, Alahsa 31982, Saudi Arabia
| | - Abdullah I Al-Mubarak
- Department of Microbiology, College of Veterinary Medicine, King Faisal University, Alhofuf, Alahsa 31982, Saudi Arabia
| | - Mahmoud Kandeel
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Alhofuf, Alahsa 31982, Saudi Arabia; Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
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Xu X, Li P, Zhang Y, Wang X, Xu J, Wu X, Shen Y, Guo D, Li Y, Yao L, Li L, Song B, Ma J, Liu X, Xu S, Zhang H, Wu Z, Cao H. Comprehensive analysis of synonymous codon usage patterns in orf3 gene of porcine epidemic diarrhea virus in China. Res Vet Sci 2019; 127:42-46. [PMID: 31677415 PMCID: PMC7172109 DOI: 10.1016/j.rvsc.2019.09.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 09/24/2019] [Accepted: 09/26/2019] [Indexed: 11/15/2022]
Abstract
The ORF3 protein of porcine epidemic diarrhea virus (PEDV) is found to function as an ion channel which influences virus virulence and production. Taking consideration of the importance of PEDV orf3 gene, we have performed comprehensive analysis to investigate its synonymous codon usage patterns. In this study, the results of base composition analysis showed A/T rich and G/C poor in PEDV orf3 genes, and the most abundant base was nucleotide T. The relative synonymous codon usage value in each codon revealed that codon usage bias existed. The mean ENC value of each gene was 48.75, indicating a low codon usage bias, as well as a relatively instable change in PEDV orf3 genes. The general correlation analysis between base composition and codon usage bias indicated that mutational bias has an impact on the PEDV codon usage bias. Neutral analysis suggested that natural selection pressure takes a more important influence than mutational bias in shaping codon usage bias. Moreover, other factors including hydrophobicity and aromaticity have been also found to influence the codon usage variation among the PEDV orf3 genes. This study not only represents the most systematic analysis of codon usage patterns in PEDV orf3 genes, but also provides a basic shaping mechanism of the codon usage bias. ORF3 genes are A/T rich and C/G poor, and codon usage bias existed. Natural selection pressure plays a more important role than mutational bias in codon usage bias. Hydrophobicity and aromaticity also influence the codon usage variation.
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Affiliation(s)
- Xin Xu
- College of Life Science and Technology, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Biotechnology Center, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Branch of Animal Husbandry and Veterinary of HeiLongJiang Academy of Agricultural Sciences, Qiqihar 161005, China
| | - Pengfei Li
- Department of Nephrology, The Fifth Affiliated Hospital of Harbin Medical University, Daqing 163319, China
| | - Yating Zhang
- College of Life Science and Technology, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Biotechnology Center, HeiLongJiang BaYi Agricultural University, Daqing 163319, China
| | - Xianhe Wang
- College of Life Science and Technology, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Biotechnology Center, HeiLongJiang BaYi Agricultural University, Daqing 163319, China
| | - Jiaxin Xu
- College of Life Science and Technology, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Biotechnology Center, HeiLongJiang BaYi Agricultural University, Daqing 163319, China
| | - Xuening Wu
- College of Life Science and Technology, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Biotechnology Center, HeiLongJiang BaYi Agricultural University, Daqing 163319, China
| | - Yujiang Shen
- College of Life Science and Technology, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Biotechnology Center, HeiLongJiang BaYi Agricultural University, Daqing 163319, China
| | - Dexuan Guo
- College of Life Science and Technology, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Biotechnology Center, HeiLongJiang BaYi Agricultural University, Daqing 163319, China
| | - Yuchang Li
- College of Life Science and Technology, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Biotechnology Center, HeiLongJiang BaYi Agricultural University, Daqing 163319, China
| | - Lili Yao
- College of Life Science and Technology, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Biotechnology Center, HeiLongJiang BaYi Agricultural University, Daqing 163319, China
| | - Liyang Li
- College of Life Science and Technology, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Biotechnology Center, HeiLongJiang BaYi Agricultural University, Daqing 163319, China
| | - Baifen Song
- College of Life Science and Technology, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Biotechnology Center, HeiLongJiang BaYi Agricultural University, Daqing 163319, China
| | - Jinzhu Ma
- College of Life Science and Technology, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Biotechnology Center, HeiLongJiang BaYi Agricultural University, Daqing 163319, China
| | - Xinyang Liu
- College of Life Science and Technology, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Biotechnology Center, HeiLongJiang BaYi Agricultural University, Daqing 163319, China
| | - Shuyan Xu
- College of Science, HeiLongJiang BaYi Agricultural University, Daqing 163319, China
| | - Hua Zhang
- College of Life Science and Technology, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150069, China; Biotechnology Center, HeiLongJiang BaYi Agricultural University, Daqing 163319, China.
| | - Zhijun Wu
- College of Life Science and Technology, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Biotechnology Center, HeiLongJiang BaYi Agricultural University, Daqing 163319, China.
| | - Hongwei Cao
- College of Life Science and Technology, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Biotechnology Center, HeiLongJiang BaYi Agricultural University, Daqing 163319, China.
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Deka H, Nath D, Uddin A, Chakraborty S. DNA compositional dynamics and codon usage patterns of M1 and M2 matrix protein genes in influenza A virus. INFECTION GENETICS AND EVOLUTION 2018; 67:7-16. [PMID: 30367980 DOI: 10.1016/j.meegid.2018.10.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/11/2018] [Accepted: 10/23/2018] [Indexed: 11/30/2022]
Abstract
Influenza A virus subtype H3N2 has been a serious health issue across the globe with approximately 36 thousand annual casualties in the United States of America only. Co-circulation in avian, swine and human hosts has led to frequent mutations in the virus genome, due to which development of successful antivirals against the virus has become a formidable challenge. Recently, focussed research is being carried out targeting the matrix proteins of this strain as vaccine candidates. This study is carried out to unravel the key features of the genes encoding the matrix proteins that manoeuvre the codon usage profile in the H3N2 strains. The findings reveal differential codon choice for both matrix protein 1 and matrix protein 2. The overall codon usage bias is less pronounced in both the datasets which is evident from higher value of effective number of codons (>55). Comparison of the codon usage for both the genes under study with that of humans revealed that the viral codon usage is not fully optimized for the human host conditions. Both the genes enrolled in the study showed variation which was reflected in almost all the indices used for codon usage studies. Neutrality analysis revealed a weak role of mutation pressure while selection was the major contributor towards codon usage.
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Affiliation(s)
- Himangshu Deka
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India
| | - Durbba Nath
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India
| | - Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Hailakandi 788150, Assam, India.
| | - Supriyo Chakraborty
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India.
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Pintó RM, Pérez-Rodríguez FJ, D'Andrea L, de Castellarnau M, Guix S, Bosch A. Hepatitis A Virus Codon Usage: Implications for Translation Kinetics and Capsid Folding. Cold Spring Harb Perspect Med 2018. [PMID: 29530949 DOI: 10.1101/cshperspect.a031781] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Codon usage bias is universal to all genomes. Hepatitis A virus (HAV) codon usage is highly biased and deoptimized with respect to its host. Accordingly, HAV is unable to induce cellular translational shutoff and its internal ribosome entry site (IRES) is inefficient. Codon usage deoptimization may be seen as a hawk (host cell) versus dove (HAV) game strategy for accessing transfer RNA (tRNA). HAV avoids use of abundant host cell codons and thereby eludes competition for the corresponding tRNAs. Instead, codons that are abundant or rare in cellular messenger RNAs (mRNAs) are used relatively rarely in its genome, although intermediately abundant host cell codons are abundant in the viral genome. Rare codons in the capsid coding region slow down the translation elongation rate, and in doing so intrinsically modulate capsid folding, which is critical to the stability of a virus transmitted through the fecal-oral route. HAV is a paradigmatic example of what has been proposed as a codon usage "code" for protein structure.
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Affiliation(s)
- Rosa M Pintó
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028 Barcelona, Spain.,Enteric Virus Laboratory, Institute of Nutrition and Food Safety, Campus Torribera, University of Barcelona, 08921 Santa Coloma de Gramanet, Spain
| | - Francisco-Javier Pérez-Rodríguez
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028 Barcelona, Spain.,Enteric Virus Laboratory, Institute of Nutrition and Food Safety, Campus Torribera, University of Barcelona, 08921 Santa Coloma de Gramanet, Spain
| | - Lucia D'Andrea
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028 Barcelona, Spain.,Enteric Virus Laboratory, Institute of Nutrition and Food Safety, Campus Torribera, University of Barcelona, 08921 Santa Coloma de Gramanet, Spain
| | - Montserrat de Castellarnau
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028 Barcelona, Spain.,Enteric Virus Laboratory, Institute of Nutrition and Food Safety, Campus Torribera, University of Barcelona, 08921 Santa Coloma de Gramanet, Spain
| | - Susana Guix
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028 Barcelona, Spain.,Enteric Virus Laboratory, Institute of Nutrition and Food Safety, Campus Torribera, University of Barcelona, 08921 Santa Coloma de Gramanet, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028 Barcelona, Spain.,Enteric Virus Laboratory, Institute of Nutrition and Food Safety, Campus Torribera, University of Barcelona, 08921 Santa Coloma de Gramanet, Spain
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Karumathil S, Raveendran NT, Ganesh D, Kumar Ns S, Nair RR, Dirisala VR. Evolution of Synonymous Codon Usage Bias in West African and Central African Strains of Monkeypox Virus. Evol Bioinform Online 2018; 14:1176934318761368. [PMID: 29551886 PMCID: PMC5846927 DOI: 10.1177/1176934318761368] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 02/01/2018] [Indexed: 12/17/2022] Open
Abstract
The evolution of bias in synonymous codon usage in chosen monkeypox viral genomes and the factors influencing its diversification have not been reported so far. In this study, various trends associated with synonymous codon usage in chosen monkeypox viral genomes were investigated, and the results are reported. Identification of factors that influence codon usage in chosen monkeypox viral genomes was done using various codon usage indices, such as the relative synonymous codon usage, the effective number of codons, and the codon adaptation index. The Spearman rank correlation analysis and a correspondence analysis were used for correlating various factors with codon usage. The results revealed that mutational pressure due to compositional constraints, gene expression level, and selection at the codon level for utilization of putative optimal codons are major factors influencing synonymous codon usage bias in monkeypox viral genomes. A cluster analysis of relative synonymous codon usage values revealed a grouping of more virulent strains as one major cluster (Central African strains) and a grouping of less virulent strains (West African strains) as another major cluster, indicating a relationship between virulence and synonymous codon usage bias. This study concluded that a balance between the mutational pressure acting at the base composition level and the selection pressure acting at the amino acid level frames synonymous codon usage bias in the chosen monkeypox viruses. The natural selection from the host does not seem to have influenced the synonymous codon usage bias in the analyzed monkeypox viral genomes.
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Affiliation(s)
- Sudeesh Karumathil
- Centre for Evolutionary Ecology, Aushmath Biosciences, Coimbatore, India
| | - Nimal T Raveendran
- Amrita Centre for Nanosciences, Amrita Vishwa Vidyapeetham, Kochi, India
| | - Doss Ganesh
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | | | - Rahul R Nair
- Centre for Evolutionary Ecology, Aushmath Biosciences, Coimbatore, India
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Analysis of the codon usage pattern in Middle East Respiratory Syndrome Coronavirus. Oncotarget 2017; 8:110337-110349. [PMID: 29299151 PMCID: PMC5746386 DOI: 10.18632/oncotarget.22738] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 10/27/2017] [Indexed: 11/25/2022] Open
Abstract
Middle East Respiratory Syndrome Coronavirus (MERS-CoV), which first broken out in Jeddah in 2012, causes a severe acute respiratory illness with a high mortality rate. To better understand the molecular characteristics of isolated MERS-CoV genomes, we first analysed the codon usage pattern of the zoonotic MERS-CoV strains comprehensively to gain an insight into the mechanism of cross-species transmission. We found that MERS human/camel isolates showed a low codon usage bias. Both mutation and nature selection pressure have contributed to this low codon usage bias, with the former being the main determining factor. We also observed that gene function, evolution time and the different host species of the virus all contributed to the bias of MERS-CoV, to some extent. Additionally, the codon usage pattern of MERS-CoV isolates is different from other related Nidovirales viruses isolated from bats and hedgehogs. In the future, more epidemiological surveys are required to examine the factors that resulted in the emergence and outbreak of this virus.
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Shi SL, Jiang YR, Yang RS, Wang Y, Qin L. Codon usage in Alphabaculovirus and Betabaculovirus hosted by the same insect species is weak, selection dominated and exhibits no more similar patterns than expected. INFECTION GENETICS AND EVOLUTION 2016; 44:412-417. [PMID: 27484795 PMCID: PMC7106102 DOI: 10.1016/j.meegid.2016.07.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 07/16/2016] [Accepted: 07/29/2016] [Indexed: 11/26/2022]
Abstract
Mutations shape synonymous codon usage bias in certain organism genomes, while selection shapes it in others. Lepidopteran-specific Alphabaculovirus and Betabaculovirus are two large genera in the family of Baculoviridae. In this study, we analyzed the codon usage patterns in 17 baculoviruses, including 10 alphabaculoviruses and 7 betabaculoviruses, which were isolated from seven insect species, and we characterized the codon usage patterns between Alphabaculovirus and Betabaculovirus. Our results show that all the baculoviruses possessed a general weak trend of codon bias. The differences of ENc (effective number of codons) values, nucleotide contents and the impacts of nucleotide content on ENc value within alpha-/betabaculovirus pairs were independent of whether the host species are the same or different. Furthermore, the majority of amino acid sequences adopted codons unequally in all viruses, but the numbers of common preferred codons between alpha- and betabaculoviruses hosted by the same insect species were not significantly different from the differences observed between alpha- and betabaculoviruses hosted by different insect species. In addition, the amino acids that adopt the same synonymous codon composition between alpha- and betabaculoviruses hosted by the same insect species were statistically as few as those between alpha- and betabaculoviruses hosted by different insect species. Correspondence analysis revealed that no major factors resulted in the codon bias in these baculoviruses, implying multiple minor influential factors exist. Neutrality plot analysis indicated that selection pressure dominated mutations in shaping the codon usage. However, the levels of selection pressure were not significantly different among viruses hosted by the same insect species. We expect that evolution would cause the alpha- and betabaculoviruses hosted by the same insect species to share more patterns, but this effect was not observed.
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Affiliation(s)
- Sheng-Lin Shi
- Insect Resource Engineering Research Center of Liaoning Province, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China.
| | - Yi-Ren Jiang
- Insect Resource Engineering Research Center of Liaoning Province, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China.
| | - Rui-Sheng Yang
- Insect Resource Engineering Research Center of Liaoning Province, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China.
| | - Yong Wang
- Insect Resource Engineering Research Center of Liaoning Province, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China.
| | - Li Qin
- Insect Resource Engineering Research Center of Liaoning Province, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China.
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Karniychuk UU. Analysis of the synonymous codon usage bias in recently emerged enterovirus D68 strains. Virus Res 2016; 223:73-9. [PMID: 27364082 DOI: 10.1016/j.virusres.2016.06.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 05/09/2016] [Accepted: 06/24/2016] [Indexed: 11/30/2022]
Abstract
Understanding the codon usage pattern of a pathogen and relationship between pathogen and host's codon usage patterns has fundamental and applied interests. Enterovirus D68 (EV-D68) is an emerging pathogen with a potentially high public health significance. In the present study, the synonymous codon usage bias of 27 recently emerged, and historical EV-D68 strains was analyzed. In contrast to previously studied enteroviruses (enterovirus 71 and poliovirus), EV-D68 and human host have a high discrepancy between favored codons. Analysis of viral synonymous codon usage bias metrics, viral nucleotide/dinucleotide compositional parameters, and viral protein properties showed that mutational pressure is more involved in shaping the synonymous codon usage bias of EV-D68 than translation selection. Computation of codon adaptation indices allowed to estimate expression potential of the EV-D68 genome in several commonly used laboratory animals. This approach requires experimental validation and may provide an auxiliary tool for the rational selection of laboratory animals to model emerging viral diseases. Enterovirus D68 genome compositional and codon usage data can be useful for further pathogenesis, animal model, and vaccine design studies.
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Affiliation(s)
- Uladzimir U Karniychuk
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada.
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Chen Y, Shi Y, Deng H, Gu T, Xu J, Ou J, Jiang Z, Jiao Y, Zou T, Wang C. Characterization of the porcine epidemic diarrhea virus codon usage bias. INFECTION GENETICS AND EVOLUTION 2014; 28:95-100. [PMID: 25239728 PMCID: PMC7185563 DOI: 10.1016/j.meegid.2014.09.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Revised: 08/26/2014] [Accepted: 09/01/2014] [Indexed: 11/15/2022]
Abstract
Codon usage bias of porcine epidemic diarrhea virus is low. Mutational bias and natural selection pressure influence codon usage bias of porcine epidemic diarrhea virus. Natural selection plays an increasingly significant role during evolution of porcine epidemic diarrhea virus.
Porcine epidemic diarrhea virus (PEDV) has been responsible for several recent outbreaks of porcine epidemic diarrhea (PED) and has caused great economic loss in the swine-raising industry. Considering the significance of PEDV, a systemic analysis was performed to study its codon usage patterns. The relative synonymous codon usage value of each codon revealed that codon usage bias exists and that PEDV tends to use codons that end in T. The mean ENC value of 47.91 indicates that the codon usage bias is low. However, we still wanted to identify the cause of this codon usage bias. A correlation analysis between the codon compositions (A3s, T3s, G3s, C3s, and GC3s), the ENC values, and the nucleotide contents (A%, T%, G%, C%, and GC%) indicated that mutational bias plays role in shaping the PEDV codon usage bias. This was further confirmed by a principal component analysis between the codon compositions and the axis values. Using the Gravy, Aroma, and CAI values, a role of natural selection in the PEDV codon usage pattern was also identified. Neutral analysis indicated that natural selection pressure plays a more important role than mutational bias in codon usage bias. Natural selection also plays an increasingly significant role during PEDV evolution. Additionally, gene function and geographic distribution also influence the codon usage bias to a degree.
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Affiliation(s)
- Ye Chen
- Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Yuzhen Shi
- Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Hongjuan Deng
- Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Ting Gu
- Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Jian Xu
- Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Jinxin Ou
- Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Zhiguo Jiang
- Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Yiren Jiao
- Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Tan Zou
- Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Chong Wang
- Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China.
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15
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Abstract
Hepatitis A virus (HAV) is a faeco-orally transmitted picornavirus and is one of the main causes of acute hepatitis worldwide. An overview of the molecular biology of HAV is presented with an emphasis on recent findings. Immune evasion strategies and a possible correlation between HAV and atopy are discussed as well. Despite the availability of efficient vaccines, antiviral drugs targeting HAV are required to treat severe cases of fulminant hepatitis, contain outbreaks, and halt the potential spread of vaccine-escape variants. Additionally, such drugs could be used to shorten the period of illness and decrease associated economical costs. Several known inhibitors of HAV with various mechanisms of action will be discussed. Since none of these molecules is readily useable in the clinic and since the availability of an anti-HAV drug would be of clinical importance, increased efforts should be targeted toward discovery and development of such antivirals.
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Affiliation(s)
- Yannick Debing
- Rega Institute for Medical ResearchUniversity of LeuvenLeuvenBelgium
| | - Johan Neyts
- Rega Institute for Medical ResearchUniversity of LeuvenLeuvenBelgium
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16
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Hepatitis A virus adaptation to cellular shutoff is driven by dynamic adjustments of codon usage and results in the selection of populations with altered capsids. J Virol 2014; 88:5029-41. [PMID: 24554668 DOI: 10.1128/jvi.00087-14] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Hepatitis A virus (HAV) has a highly biased and deoptimized codon usage compared to the host cell and fails to inhibit host protein synthesis. It has been proposed that an optimal combination of abundant and rare codons controls the translation speed required for the correct capsid folding. The artificial shutoff host protein synthesis results in the selection of variants containing mutations in the HAV capsid coding region critical for folding, stability, and function. Here, we show that these capsid mutations resulted in changes in their antigenicity; in a reduced stability to high temperature, low pH, and biliary salts; and in an increased efficacy of cell entry. In conclusion, the adaptation to cellular shutoff resulted in the selection of large-plaque-producing virus populations. IMPORTANCE HAV has a naturally deoptimized codon usage with respect to that of its cell host and is unable to shut down the cellular translation. This fact contributes to the low replication rate of the virus, in addition to other factors such as the highly inefficient internal ribosome entry site (IRES), and explains the outstanding physical stability of this pathogen in the environment mediated by a folding-dependent highly cohesive capsid. Adaptation to artificially induced cellular transcription shutoff resulted in a redeoptimization of its capsid codon usage, instead of an optimization. These genomic changes are related to an overall change of capsid folding, which in turn induces changes in the cell entry process. Remarkably, the adaptation to cellular shutoff allowed the virus to significantly increase its RNA uncoating efficiency, resulting in the selection of large-plaque-producing populations. However, these populations produced much-debilitated virions.
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17
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Atkinson NJ, Witteveldt J, Evans DJ, Simmonds P. The influence of CpG and UpA dinucleotide frequencies on RNA virus replication and characterization of the innate cellular pathways underlying virus attenuation and enhanced replication. Nucleic Acids Res 2014; 42:4527-45. [PMID: 24470146 PMCID: PMC3985648 DOI: 10.1093/nar/gku075] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Most RNA viruses infecting mammals and other vertebrates show profound suppression of CpG and UpA dinucleotide frequencies. To investigate this functionally, mutants of the picornavirus, echovirus 7 (E7), were constructed with altered CpG and UpA compositions in two 1.1–1.3 Kbase regions. Those with increased frequencies of CpG and UpA showed impaired replication kinetics and higher RNA/infectivity ratios compared with wild-type virus. Remarkably, mutants with CpGs and UpAs removed showed enhanced replication, larger plaques and rapidly outcompeted wild-type virus on co-infections. Luciferase-expressing E7 sub-genomic replicons with CpGs and UpAs removed from the reporter gene showed 100-fold greater luminescence. E7 and mutants were equivalently sensitive to exogenously added interferon-β, showed no evidence for differential recognition by ADAR1 or pattern recognition receptors RIG-I, MDA5 or PKR. However, kinase inhibitors roscovitine and C16 partially or entirely reversed the attenuated phenotype of high CpG and UpA mutants, potentially through inhibition of currently uncharacterized pattern recognition receptors that respond to RNA composition. Generating viruses with enhanced replication kinetics has applications in vaccine production and reporter gene construction. More fundamentally, the findings introduce a new evolutionary paradigm where dinucleotide composition of viral genomes is subjected to selection pressures independently of coding capacity and profoundly influences host–pathogen interactions.
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Affiliation(s)
- Nicky J Atkinson
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK and School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
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18
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Hepatitis A virus: host interactions, molecular epidemiology and evolution. INFECTION GENETICS AND EVOLUTION 2013; 21:227-43. [PMID: 24200587 DOI: 10.1016/j.meegid.2013.10.023] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2013] [Revised: 10/25/2013] [Accepted: 10/26/2013] [Indexed: 12/16/2022]
Abstract
Infection with hepatitis A virus (HAV) is the commonest viral cause of liver disease and presents an important public health problem worldwide. Several unique HAV properties and molecular mechanisms of its interaction with host were recently discovered and should aid in clarifying the pathogenesis of hepatitis A. Genetic characterization of HAV strains have resulted in the identification of different genotypes and subtypes, which exhibit a characteristic worldwide distribution. Shifts in HAV endemicity occurring in different parts of the world, introduction of genetically diverse strains from geographically distant regions, genotype displacement observed in some countries and population expansion detected in the last decades of the 20th century using phylogenetic analysis are important factors contributing to the complex dynamics of HAV infections worldwide. Strong selection pressures, some of which, like usage of deoptimized codons, are unique to HAV, limit genetic variability of the virus. Analysis of subgenomic regions has been proven useful for outbreak investigations. However, sharing short sequences among epidemiologically unrelated strains indicates that specific identification of HAV strains for molecular surveillance can be achieved only using whole-genome sequences. Here, we present up-to-date information on the HAV molecular epidemiology and evolution, and highlight the most relevant features of the HAV-host interactions.
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19
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Martrus G, Nevot M, Andres C, Clotet B, Martinez MA. Changes in codon-pair bias of human immunodeficiency virus type 1 have profound effects on virus replication in cell culture. Retrovirology 2013; 10:78. [PMID: 23885919 PMCID: PMC3726367 DOI: 10.1186/1742-4690-10-78] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 07/18/2013] [Indexed: 11/29/2022] Open
Abstract
Background Human immunodeficiency virus type 1 (HIV-1) has a biased nucleotide composition different from human genes. This raises the question of how evolution has chosen the nucleotide sequence of HIV-1 that is observed today, or to what extent the actual encoding contributes to virus replication capacity, evolvability and pathogenesis. Here, we applied the previously described synthetic attenuated virus engineering (SAVE) approach to HIV-1. Results Using synonymous codon pairs, we rationally recoded and codon pair–optimized and deoptimized different moieties of the HIV-1 gag and pol genes. Deoptimized viruses had significantly lower viral replication capacity in MT-4 and peripheral blood mononuclear cells (PBMCs). Varying degrees of ex vivo attenuation were obtained, depending upon both the specific deoptimized region and the number of deoptimized codons. A protease optimized virus carrying 38 synonymous mutations was not attenuated and displayed a replication capacity similar to that of the wild-type virus in MT-4 cells and PBMCs. Although attenuation is based on several tens of nucleotide changes, deoptimized HIV-1 reverted to wild-type virulence after serial passages in MT-4 cells. Remarkably, no reversion was observed in the optimized virus. Conclusion These data demonstrate that SAVE is a useful strategy to phenotypically affect the replicative properties of HIV-1.
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Affiliation(s)
- Gloria Martrus
- Fundació irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), Badalona 08916, Spain
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20
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A detailed comparative analysis on the overall codon usage patterns in West Nile virus. INFECTION GENETICS AND EVOLUTION 2013; 14:396-400. [PMID: 23333335 DOI: 10.1016/j.meegid.2013.01.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 01/02/2013] [Accepted: 01/03/2013] [Indexed: 11/22/2022]
Abstract
West Nile virus (WNV) is a member of the family Flaviviridae and its genome consists of an 11-kb single-stranded, positive-sense RNA. WNV is maintained in an enzootic cycle between mosquitoes and birds, but can also infect and cause disease in horses and humans, which serve as incidental dead-end hosts. Understanding the extent and causes of biases in codon usage is essential to the comprehension of viral evolution. In this study, we performed a comprehensive analysis of 449 WNV strains, for which complete genome sequences are available. Effective number of codons (ENC) indicates that the overall codon usage among WNV strains is only slightly biased. Codon adaptation index (CAI) values found for WNV genes are different from the CAI values found for human genes. The relative synonymous codon usage among WNV strains isolated from birds, equines, humans and mosquitoes are roughly similar and are influenced by the relative dinucleotide frequencies. Taking together, the results of this work suggest that WNV genomic biases are the result of the evolution of genome composition, the need to escape the antiviral cell responses and a dynamic process of mutation and selection to re-adapt its codon usage to different environments.
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21
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Goñi N, Iriarte A, Comas V, Soñora M, Moreno P, Moratorio G, Musto H, Cristina J. Pandemic influenza A virus codon usage revisited: biases, adaptation and implications for vaccine strain development. Virol J 2012; 9:263. [PMID: 23134595 PMCID: PMC3543350 DOI: 10.1186/1743-422x-9-263] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 11/02/2012] [Indexed: 11/20/2022] Open
Abstract
Background Influenza A virus (IAV) is a member of the family Orthomyxoviridae and contains eight segments of a single-stranded RNA genome with negative polarity. The first influenza pandemic of this century was declared in April of 2009, with the emergence of a novel H1N1 IAV strain (H1N1pdm) in Mexico and USA. Understanding the extent and causes of biases in codon usage is essential to the understanding of viral evolution. A comprehensive study to investigate the effect of selection pressure imposed by the human host on the codon usage of an emerging, pandemic IAV strain and the trends in viral codon usage involved over the pandemic time period is much needed. Results We performed a comprehensive codon usage analysis of 310 IAV strains from the pandemic of 2009. Highly biased codon usage for Ala, Arg, Pro, Thr and Ser were found. Codon usage is strongly influenced by underlying biases in base composition. When correspondence analysis (COA) on relative synonymous codon usage (RSCU) is applied, the distribution of IAV ORFs in the plane defined by the first two major dimensional factors showed that different strains are located at different places, suggesting that IAV codon usage also reflects an evolutionary process. Conclusions A general association between codon usage bias, base composition and poor adaptation of the virus to the respective host tRNA pool, suggests that mutational pressure is the main force shaping H1N1 pdm IAV codon usage. A dynamic process is observed in the variation of codon usage of the strains enrolled in these studies. These results suggest a balance of mutational bias and natural selection, which allow the virus to explore and re-adapt its codon usage to different environments. Recoding of IAV taking into account codon bias, base composition and adaptation to host tRNA may provide important clues to develop new and appropriate vaccines.
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Affiliation(s)
- Natalia Goñi
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo, 11400, Uruguay
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22
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Shi SL, Jiang YR, Liu YQ, Xia RX, Qin L. Selective pressure dominates the synonymous codon usage in parvoviridae. Virus Genes 2012; 46:10-9. [PMID: 22996735 DOI: 10.1007/s11262-012-0818-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2012] [Accepted: 09/05/2012] [Indexed: 12/16/2022]
Abstract
Parvoviridae is a family of small non-enveloped viruses and divided into two subfamilies. The family members infect a wide range of organisms from insects to humans and some of the members (e.g., nonpathogenic adeno-associated viruses) are effective gene therapy delivery vectors. We detailed the synonymous codon usage pattern of Parvoviridae family from the available 58 sequenced genomes through multivariate statistical methods. Our results revealed that nine viruses showed some degree of strong codon bias, and the others possessed a general weak trend of codon bias. ENc-plot and neutrality plot results showed that selective pressure dominated over mutation in shapes coding sequence's composition. The overall GC content and GC content at the third synonymous codon position were the principal determinants behind the variations within the codon usage patterns, as they both significantly correlated with the first axis of correspondence analysis. In addition, gene length had no direct influence on the codon usage pattern. Densovirinae subfamily and Parvovirinae subfamily possessed nine identical preferred codons, though most of the two subfamilies codon usage frequencies were significantly different. The result of cluster analysis based on synonymous codon usage was discordant with that of taxonomic classification. Adeno-associated viruses formed a separated clade far from other Parvoviridae members in the dendrogram. Thus, we concluded that natural selection rather than mutation pressure accounts for the main factor that affects the codon bias in Parvoviridae family.
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Affiliation(s)
- Sheng-Lin Shi
- Postdoctoral Station of Plant Protection, Shenyang Agricultural University, No.120 Dongling Road, Shenyang, P.R.China.
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23
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Genetic characterization and codon usage bias of full-length Hepatitis E virus sequences shed new lights on genotypic distribution, host restriction and genome evolution. INFECTION GENETICS AND EVOLUTION 2012; 12:1842-53. [PMID: 22951575 DOI: 10.1016/j.meegid.2012.07.021] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2012] [Revised: 07/27/2012] [Accepted: 07/29/2012] [Indexed: 02/08/2023]
Abstract
Hepatitis E virus (HEV) is present in different species and ecological niches. It has been divided into 4 major mammalian genotypes. In this study, 3 new full-length genomes of swine HEV were sequenced and the results did not reveal any particular host determinant in comparison with human isolates belonging to the same genotype. Nucleotide composition and codon usage bias were determined to characterize HEV host restriction and genome evolution. Peculiar nucleotide bias was observed for A and C nucleotides in all HEV genotypes. Apart from the ORF1 hypervariable region and the ORF2/3 overlapping region, no nucleotide bias was observed between the 3 codon positions. CpG dinucleotides were also shown to be under-represented in HEV as in most RNA viruses. The effective number of codon used in HEV genome was high, indicating a lack of codon bias. Correspondence analysis of the relative synonymous codon usage was performed and demonstrated that evolution of HEV is not driven by geographical or host factors, but is representative of HEV phylogeny. These results confirm that HEV genome evolution is mainly based on mutational pressure. Natural selection, for instance involving fine-tuning translation kinetics and escape from the host immune system, may also play a role in shaping the HEV genome, particularly in the ORF1 hypervariable region and the ORF2/3 overlapping region. These regions might be involved in host restriction. Finally this study revealed the need to re-evaluate the possible subtyping classification.
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24
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High codon adaptation in citrus tristeza virus to its citrus host. Virol J 2012; 9:113. [PMID: 22698086 PMCID: PMC3416656 DOI: 10.1186/1743-422x-9-113] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Accepted: 06/14/2012] [Indexed: 01/29/2023] Open
Abstract
Background Citrus tristeza virus (CTV), a member of the genus Closterovirus within the family Closteroviridae, is the causal agent of citrus tristeza disease. Previous studies revealed that the negative selection, RNA recombination and gene flow were the most important forces that drove CTV evolution. However, the CTV codon usage was not studied and thus its role in CTV evolution remains unknown. Results A detailed comparative analysis of CTV codon usage pattern was done in this study. Results of the study show that although in general CTV does not have a high degree of codon usage bias, the codon usage of CTV has a high level of resemblance to its host codon usage. In addition, our data indicate that the codon usage resemblance is only observed for the woody plant-infecting closteroviruses but not the closteroviruses infecting the herbaceous host plants, suggesting the existence of different virus-host interactions between the herbaceous plant-infecting and woody plant-infecting closteroviruses. Conclusion Based on the results, we suggest that in addition to RNA recombination, negative selection and gene flow, host plant codon usage selection can also affect CTV evolution.
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25
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Pintó RM, D'Andrea L, Pérez-Rodriguez FJ, Costafreda MI, Ribes E, Guix S, Bosch A. Hepatitis A virus evolution and the potential emergence of new variants escaping the presently available vaccines. Future Microbiol 2012; 7:331-46. [PMID: 22393888 DOI: 10.2217/fmb.12.5] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Hepatitis A is the most common infection of the liver worldwide and is fecal-orally transmitted. Its incidence tends to decrease with improvements in hygiene conditions but at the same time its severity increases. Hepatitis A virus is the causative agent of acute hepatitis in humans and belongs to the Hepatovirus genus in the Picornaviridae family, and it has very unique characteristics. This article reviews some molecular and biological properties that allow the virus to live in a very quiescent way and to build an extremely stable capsid that is able to persist in and out of the body. Additionally, the relationship between the genomic composition and the structural and antigenic properties of the capsid is discussed, and the potential emergence of antigenic variants is evaluated from an evolutionary perspective.
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Affiliation(s)
- Rosa M Pintó
- Enteric Virus Laboratory, School of Biology, University of Barcelona, Barcelona, Spain.
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26
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Lukashev AN, Drexler JF, Belalov IS, Eschbach-Bludau M, Baumgarte S, Drosten C. Genetic variation and recombination in Aichi virus. J Gen Virol 2012; 93:1226-1235. [DOI: 10.1099/vir.0.040311-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Aichi virus (AiV), a member of the genus Kobuvirus in the family Picornaviridae, causes gastroenteritis in humans. It was noted that AiV differs from other picornaviruses in its unusually high C content and a very high degree of genome-ordered RNA secondary structures. However, the genetic variability and mutational restrictions on a full-genome scale have not been studied. In addition to the available five complete AiV genomes, we determined here another five complete coding sequences of AiV sampled in Germany, 2004. Distinctive AiV genetic features included a low incidence of recombination along the genome without obvious hotspots or spared regions and very low rates of synonymous and non-synonymous variation, supporting an absence of AiV serotypes. In addition, the absence of recombination between AiV genotypes A and B suggested the existence of reproductive isolation between taxonomic units below the species level. In contrast to most other picornaviruses, AiV genomes strongly avoided the UpA dinucleotide, while there was no obvious selection against the CpG dinucleotide. AiV genomes also appeared to contain a codon usage bias (CUB) apparent as an effective number of codons of 39.5, which was amongst the most extreme among RNA viruses. A set of sequence scrambling algorithms was developed to determine the origin of CUB in AiV. While in most picornaviruses the genomic dinucleotide content contributed significantly to CUB, in AiV its extreme nucleotide content, i.e. 57 % third codon position C, was the main driving force behind the apparent CUB.
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Affiliation(s)
- Alexander N. Lukashev
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Jan Felix Drexler
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Ilya S. Belalov
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia
| | | | | | - Christian Drosten
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
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27
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Hu JS, Wang QQ, Zhang J, Chen HT, Xu ZW, Zhu L, Ding YZ, Ma LN, Xu K, Gu YX, Liu YS. The characteristic of codon usage pattern and its evolution of hepatitis C virus. INFECTION GENETICS AND EVOLUTION 2011; 11:2098-102. [DOI: 10.1016/j.meegid.2011.08.025] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 08/22/2011] [Accepted: 08/24/2011] [Indexed: 01/29/2023]
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