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Wang Y, Chi C, Zhang J, Zhang K, Deng D, Zheng W, Chen N, Meurens F, Zhu J. Systematic analysis of the codon usage patterns of African swine fever virus genome coding sequences reveals its host adaptation phenotype. Microb Genom 2024; 10:001186. [PMID: 38270515 PMCID: PMC10868601 DOI: 10.1099/mgen.0.001186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 01/09/2024] [Indexed: 01/26/2024] Open
Abstract
African swine fever (ASF) is a severe haemorrhagic disease caused by the African swine fever virus (ASFV), transmitted by ticks, resulting in high mortality among domestic pigs and wild boars. The global spread of ASFV poses significant economic threats to the swine industry. This study employs diverse analytical methods to explore ASFV's evolution and host adaptation, focusing on codon usage patterns and associated factors. Utilizing phylogenetic analysis methods including neighbour-joining and maximum-likelihood, 64 ASFV strains were categorized into four clades. Codon usage bias (CUB) is modest in ASFV coding sequences. This research identifies multiple factors - such as nucleotide composition, mutational pressures, natural selection and geographical diversity - contributing to the formation of CUB in ASFV. Analysis of relative synonymous codon usage reveals CUB variations within clades and among ASFVs and their hosts. Both Codon Adaptation Index and Similarity Index analyses confirm that ASFV strains are highly adapted to soft ticks (Ornithodoros moubata) but less so to domestic pigs, which could be a result of the long-term co-evolution of ASFV with ticks. This study sheds light on the factors influencing ASFV's codon usage and fitness dynamics, enriching our understanding of its evolution, adaptation and host interactions.
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Affiliation(s)
- Yuening Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, 225009, PR China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China
| | - Chenglin Chi
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, 225009, PR China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China
| | - Jiajia Zhang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, 225009, PR China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China
| | - Kaili Zhang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, 225009, PR China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China
| | - Dafu Deng
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, 225009, PR China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China
| | - Wanglong Zheng
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, 225009, PR China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China
| | - Nanhua Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, 225009, PR China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China
| | - François Meurens
- Swine and Poultry Infectious Diseases Research Center, Faculty of Veterinary Medicine, University of Montreal, St. Hyacinthe, QC, J2S 2M2, Canada
- Department of Veterinary Microbiology and Immunology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E2, Canada
| | - Jianzhong Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, 225009, PR China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China
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Wu H, Li B, Miao Z, Hu L, Zhou L, Lu Y. Codon usage of host-specific P genotypes (VP4) in group A rotavirus. BMC Genomics 2022; 23:518. [PMID: 35842571 PMCID: PMC9288207 DOI: 10.1186/s12864-022-08730-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 06/30/2022] [Indexed: 11/26/2022] Open
Abstract
Background Group A rotavirus (RVA) is a common causative agent of acute gastroenteritis in infants and young children worldwide. RVA P genotypes, determined by VP4 sequences, have been confirmed to infect humans and animals. However, their codon usage patterns that are essential to obtain insights into the viral evolution, host adaptability, and genetic characterization remained unclear, especially across animal hosts. Results We performed a comprehensive codon usage analysis of eight host-specific RVA P genotypes, including human RVA (P[4] and P[8]), porcine RVA (P[13] and P[23]), and zoonotic RVA (P[1], P[6], P[7] and P[19]), based on 233 VP4 complete coding sequences. Nucleotide composition, relative synonymous codon usage (RSCU), and effective number of codons (ENC) were calculated. Principal component analysis (PCA) based on RSCU values was used to explore the codon usage patterns of different RVA P genotypes. In addition, mutation pressure and natural selection were identified by using ENC-plot, parity rule 2 plot, and neutrality plot analyses. All VP4 sequences preferred using A/U nucleotides (A: 0.354-0.377, U: 0.267-0.314) than G/C nucleotides across genotypes. Similarly, majority of commonly used synonymous codons were likely to end with A/U nucleotides (A: 9/18-12/18, U: 6/18-9/18). In PCA, human, porcine, and zoonotic genotypes clustered separately in terms of RSCU values, indicating the host-specific codon usage patterns; however, porcine and zoonotic genotypes were partly overlapped. Human genotypes, P[4] and P[8], had stronger codon usage bias, as indicated by more over-represented codons and lower ENC, compared to porcine and zoonotic genotypes. Moreover, natural selection was determined to be a predominant driver in shaping the codon usage bias across the eight P genotypes. In addition, mutation pressure contributed to the codon usage bias of human genotypes. Conclusions Our study identified a strong codon usage bias of human RVA P genotypes attributable to both natural selection and mutation pressure, whereas similar codon usage bias between porcine and zoonotic genotypes predominantly attributable to natural selection. It further suggests possible cross-species transmission. Therefore, it warrants further surveillance of RVA P genotypes for early identification of zoonotic infection. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08730-2.
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Affiliation(s)
- Han Wu
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety (Fudan University), School of Public Health, Fudan University, Shanghai, 200032, China
| | - Bingzhe Li
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety (Fudan University), School of Public Health, Fudan University, Shanghai, 200032, China
| | - Ziping Miao
- Institute of Communicable Diseases Prevention and Control, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310052, Zhejiang, China
| | - Linjie Hu
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety (Fudan University), School of Public Health, Fudan University, Shanghai, 200032, China
| | - Lu Zhou
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety (Fudan University), School of Public Health, Fudan University, Shanghai, 200032, China
| | - Yihan Lu
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety (Fudan University), School of Public Health, Fudan University, Shanghai, 200032, China.
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Si F, Jiang L, Yu R, Wei W, Li Z. Study on the Characteristic Codon Usage Pattern in Porcine Epidemic Diarrhea Virus Genomes and Its Host Adaptation Phenotype. Front Microbiol 2021; 12:738082. [PMID: 34733253 PMCID: PMC8558211 DOI: 10.3389/fmicb.2021.738082] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 09/20/2021] [Indexed: 11/29/2022] Open
Abstract
Porcine epidemic diarrhea virus (PEDV), which classified in the genus Alphacoronavirus, family Coronaviridae, is one of the most important pathogens that cause heavy economic losses in pig industry. Although intensive mutation and recombination analysis of PEDV strains were provided, systematic genome analysis were needed to elucidate the evolution mechanism and codon usage adaptation profiles of the pathogen. Here, a comprehensive investigation was carried out to reveal the systematic evolutionary processes of synonymous codon usage and host-adapted evolution phenotype of PEDV genome. We found a low codon usage bias (CUB) in PEDV genome and that nucleotide compositions, natural selection, mutation pressure and geographical diversity shapes the codon usage patterns of PEDV, with natural selection dominated the overall codon usage bias in PEDV than the others. By using the relative codon deoptimization index (RCDI) and similarity index (SiD) analysis, we observed that genotype II PEDV strains showed the highest level of adaptation phenotype to Sus scrofa than another divergent clade. To the best of our knowledge, this is the first comprehensive report elaborating the codon usage and host adaptation of PEDV. The findings offer an insight into our understanding of factors involved in PEDV evolution, adaptation and fitness toward their hosts.
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Affiliation(s)
- Fusheng Si
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Engineering Research Center of Breeding Pig, Institute of Animal Science and Veterinary Medicine, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Li Jiang
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Ruisong Yu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Engineering Research Center of Breeding Pig, Institute of Animal Science and Veterinary Medicine, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Wenqiang Wei
- Department of Microbiology, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Zhen Li
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Engineering Research Center of Breeding Pig, Institute of Animal Science and Veterinary Medicine, Shanghai Academy of Agricultural Sciences, Shanghai, China
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Hoxie I, Dennehy JJ. Rotavirus A Genome Segments Show Distinct Segregation and Codon Usage Patterns. Viruses 2021; 13:v13081460. [PMID: 34452326 PMCID: PMC8402926 DOI: 10.3390/v13081460] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 12/29/2022] Open
Abstract
Reassortment of the Rotavirus A (RVA) 11-segment dsRNA genome may generate new genome constellations that allow RVA to expand its host range or evade immune responses. Reassortment may also produce phylogenetic incongruities and weakly linked evolutionary histories across the 11 segments, obscuring reassortment-specific epistasis and changes in substitution rates. To determine the co-segregation patterns of RVA segments, we generated time-scaled phylogenetic trees for each of the 11 segments of 789 complete RVA genomes isolated from mammalian hosts and compared the segments’ geodesic distances. We found that segments 4 (VP4) and 9 (VP7) occupied significantly different tree spaces from each other and from the rest of the genome. By contrast, segments 10 and 11 (NSP4 and NSP5/6) occupied nearly indistinguishable tree spaces, suggesting strong co-segregation. Host-species barriers appeared to vary by segment, with segment 9 (VP7) presenting the weakest association with host species. Bayesian Skyride plots were generated for each segment to compare relative genetic diversity among segments over time. All segments showed a dramatic decrease in diversity around 2007 coinciding with the introduction of RVA vaccines. To assess selection pressures, codon adaptation indices and relative codon deoptimization indices were calculated with respect to different host genomes. Codon usage varied by segment with segment 11 (NSP5) exhibiting significantly higher adaptation to host genomes. Furthermore, RVA codon usage patterns appeared optimized for expression in humans and birds relative to the other hosts examined, suggesting that translational efficiency is not a barrier in RVA zoonosis.
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Affiliation(s)
- Irene Hoxie
- Biology Department, The Graduate Center, The City University of New York, New York, NY 10016, USA;
- Biology Department, Queens College, The City University of New York, Flushing, New York, NY 11367, USA
- Correspondence:
| | - John J. Dennehy
- Biology Department, The Graduate Center, The City University of New York, New York, NY 10016, USA;
- Biology Department, Queens College, The City University of New York, Flushing, New York, NY 11367, USA
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Kumar N, Bera BC, Greenbaum BD, Bhatia S, Sood R, Selvaraj P, Anand T, Tripathi BN, Virmani N. Revelation of Influencing Factors in Overall Codon Usage Bias of Equine Influenza Viruses. PLoS One 2016; 11:e0154376. [PMID: 27119730 PMCID: PMC4847779 DOI: 10.1371/journal.pone.0154376] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 04/12/2016] [Indexed: 11/18/2022] Open
Abstract
Equine influenza viruses (EIVs) of H3N8 subtype are culprits of severe acute respiratory infections in horses, and are still responsible for significant outbreaks worldwide. Adaptability of influenza viruses to a particular host is significantly influenced by their codon usage preference, due to an absolute dependence on the host cellular machinery for their replication. In the present study, we analyzed genome-wide codon usage patterns in 92 EIV strains, including both H3N8 and H7N7 subtypes by computing several codon usage indices and applying multivariate statistical methods. Relative synonymous codon usage (RSCU) analysis disclosed bias of preferred synonymous codons towards A/U-ended codons. The overall codon usage bias in EIVs was slightly lower, and mainly affected by the nucleotide compositional constraints as inferred from the RSCU and effective number of codon (ENc) analysis. Our data suggested that codon usage pattern in EIVs is governed by the interplay of mutation pressure, natural selection from its hosts and undefined factors. The H7N7 subtype was found less fit to its host (horse) in comparison to H3N8, by possessing higher codon bias, lower mutation pressure and much less adaptation to tRNA pool of equine cells. To the best of our knowledge, this is the first report describing the codon usage analysis of the complete genomes of EIVs. The outcome of our study is likely to enhance our understanding of factors involved in viral adaptation, evolution, and fitness towards their hosts.
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MESH Headings
- Adaptation, Physiological/genetics
- Animals
- Biological Evolution
- Codon
- Gene Expression Regulation, Viral
- Genetic Code
- Genome, Viral
- Horse Diseases/virology
- Horses
- Host-Pathogen Interactions
- Influenza A Virus, H3N8 Subtype/genetics
- Influenza A Virus, H3N8 Subtype/metabolism
- Influenza A Virus, H7N7 Subtype/genetics
- Influenza A Virus, H7N7 Subtype/metabolism
- Models, Statistical
- Mutation Rate
- Orthomyxoviridae Infections/veterinary
- Orthomyxoviridae Infections/virology
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Species Specificity
- Virus Replication
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Affiliation(s)
- Naveen Kumar
- Immunology Lab, National Institute of High Security Animal Diseases (NIHSAD), Bhopal, Madhya Pradesh, India
| | - Bidhan Chandra Bera
- Biotechnology Lab, Veterinary Type Culture Collection, National Research Center on Equines (NRCE), Hisar, Haryana, India
| | - Benjamin D. Greenbaum
- Tisch Cancer Institute, Departments of Medicine, Hematology and Medical Pathology, and Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Sandeep Bhatia
- Immunology Lab, National Institute of High Security Animal Diseases (NIHSAD), Bhopal, Madhya Pradesh, India
| | - Richa Sood
- Immunology Lab, National Institute of High Security Animal Diseases (NIHSAD), Bhopal, Madhya Pradesh, India
| | - Pavulraj Selvaraj
- Equine Pathology Lab, National Research Center on Equines (NRCE), Hisar, Haryana, India
| | - Taruna Anand
- Biotechnology Lab, Veterinary Type Culture Collection, National Research Center on Equines (NRCE), Hisar, Haryana, India
| | | | - Nitin Virmani
- Equine Pathology Lab, National Research Center on Equines (NRCE), Hisar, Haryana, India
- * E-mail:
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Analysis of codon usage pattern evolution in avian rotaviruses and their preferred host. INFECTION GENETICS AND EVOLUTION 2015; 34:17-25. [PMID: 26086995 DOI: 10.1016/j.meegid.2015.06.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 05/26/2015] [Accepted: 06/14/2015] [Indexed: 10/23/2022]
Abstract
Rotavirus infection is a worldwide problem, with occurrence of highly divergent viruses classified in 8 species (A-H). We report here the evolution assessment of codon usage patterns in virus-host system in avian rotavirus (AvRV) of species RVA, RVD, RVF and RVG (preferentially affecting birds). The nucleotide contents, codon usage bias (CUB), relative synonymous codon usage (RSCU), and effective number of codons (ENCs) values were investigated targeting overexpressing major inner capsid viral protein (VP6) of these AvRV species. The results confirm that the evolutionary characteristics influences the rotavirus (RV) genetic diversity and impact of host's natural selection on the AvRVs codons. Synonymous codon usage patterns were evaluated following multivariate statistical procedures on all available AvRV coding gene sequences. RSCU trees accommodated all AvRV species and preferred host sequences in one topology confirming greater imminence of AvRVs with the host chicken cell genes. Similarly, the codon adaptation index (CAI) results also displayed a higher adaptation of AvRVs to its chicken host. The codon preference analysis of RVs revealed that VP6 gene express more proficiently in the yeast system, whereas, codon optimization might be required for the effectual expression in Escherichia coli and Homo sapiens. The findings provide basic evidence on the dynamics of AvRV evolution and its host adaptation, which could be exploited for additional research on avian species in future.
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Tatsumi M, Nagaoka Y, Tsugawa T, Yoto Y, Hori T, Tsutsumi H. Longitudinal analysis of VP7 gene of group A human rotavirus G2P[4] strains circulating in the pre-vaccine era in Sapporo, Japan from 1991 to 2011. Microbiol Immunol 2014; 58:540-4. [PMID: 25040726 DOI: 10.1111/1348-0421.12182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 07/03/2014] [Accepted: 07/14/2014] [Indexed: 11/27/2022]
Abstract
Sequence analysis of the VP7 gene in 23 group A human rotavirus G2P[4] strains obtained during 1991-2011, that is, the pre-vaccine era, in Sapporo, Japan showed considerable genetic diversity, mainly in variable regions. Recent G2P[4] epidemic strains were located in sublineage IVa with a distinctive substitution of D96N. This study provides background data on the genetic variability of G2P[4] rotavirus-VP7 gene prior to the widespread use of rotavirus vaccines in Japan.
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Affiliation(s)
- Masatoshi Tatsumi
- Department of Pediatrics, Sapporo Medical University School of Medicine, South-1, West-16, Sapporo, 060-8543, Japan; Otaru Kyokai Hospital, Otaru City, Japan
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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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Luo XL, Xu JG, Ye CY. Analysis of synonymous codon usage inShigella flexneri2a strain 301 and otherShigellaandEscherichia colistrains. Can J Microbiol 2011; 57:1016-23. [DOI: 10.1139/w11-095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this study, we analysed synonymous codon usage in Shigella flexneri 2a strain 301 (Sf301) and performed a comparative analysis of synonymous codon usage patterns in Sf301 and other strains of Shigella and Escherichia coli . Although there was a significant variety in codon usage bias among different Sf301 genes, there was a slight but observable codon usage bias that could primarily be attributable to mutational pressure and translational selection. In addition, the relative abundance of dinucleotides in Sf301 was observed to be independent of the overall base composition but was still caused by differential mutational pressure; this also shaped codon usage. By comparing the relative synonymous codon usage values across different Shigella and E. coli strains, we suggested that the synonymous codon usage pattern in the Shigella genomes was strain specific. This study represents a comprehensive analysis of Shigella codon usage patterns and provides a basic understanding of the mechanisms underlying codon usage bias.
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Affiliation(s)
- Xue Lian Luo
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, People’s Republic of China
| | - Jian Guo Xu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, People’s Republic of China
| | - Chang Yun Ye
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, People’s Republic of China
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Doan YH, Nakagomi T, Cunliffe NA, Pandey BD, Sherchand JB, Nakagomi O. The occurrence of amino acid substitutions D96N and S242N in VP7 of emergent G2P[4] rotaviruses in Nepal in 2004-2005: a global and evolutionary perspective. Arch Virol 2011; 156:1969-78. [DOI: 10.1007/s00705-011-1083-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 07/22/2011] [Indexed: 02/01/2023]
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