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For: Butt AM, Nasrullah I, Qamar R, Tong Y. Evolution of codon usage in Zika virus genomes is host and vector specific. Emerg Microbes Infect 2016;5:e107. [PMID: 27729643 DOI: 10.1038/emi.2016.106] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 08/21/2016] [Accepted: 08/25/2016] [Indexed: 12/12/2022]
Number Cited by Other Article(s)
1
Han S, Li S, Li L, Li S. Genetic characterization of four bacteriophages of Salmonella enterica derived from different geographic regions in China via genomic comparison. Res Vet Sci 2025;189:105608. [PMID: 40199046 DOI: 10.1016/j.rvsc.2025.105608] [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: 07/06/2024] [Revised: 09/27/2024] [Accepted: 03/07/2025] [Indexed: 04/10/2025]
2
Oyeniran KA, Tenibiaje MO. Detectable episodic positive selection in the virion strand a-strain Maize streak virus genes may have a role in its host adaptation. Virus Genes 2025:10.1007/s11262-025-02157-z. [PMID: 40237943 DOI: 10.1007/s11262-025-02157-z] [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: 11/06/2024] [Accepted: 04/06/2025] [Indexed: 04/18/2025]
3
Feng X, Liu Z, Mo Y, Zhang S, Ma XX. Role of nucleotide pair frequency and synonymous codon usage in the evolution of bovine viral diarrhea virus. Arch Virol 2025;170:64. [PMID: 40011265 DOI: 10.1007/s00705-025-06250-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2024] [Accepted: 11/26/2024] [Indexed: 02/28/2025]
4
Mohan G, Choudhury A, Bhat J, Phartyal R, Lal R, Verma M. Human Riboviruses: A Comprehensive Study. J Mol Evol 2025;93:11-37. [PMID: 39739017 DOI: 10.1007/s00239-024-10221-9] [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: 06/03/2024] [Accepted: 11/20/2024] [Indexed: 01/02/2025]
5
Thomas PD, Ferrer MF, Lozano MJ, Gómez RM. A study on the codon usage bias of arenavirus common genes. Front Microbiol 2025;15:1490076. [PMID: 39917269 PMCID: PMC11799557 DOI: 10.3389/fmicb.2024.1490076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2024] [Accepted: 12/30/2024] [Indexed: 02/09/2025]  Open
6
Guo F, Tan H, Yang J, Jia R, Wang R, Wu L, Pan F, Kang K, Xie W, Li Y, Fan K. Insight into the codon usage patterns and adaptation of Tembusu Virus. Poult Sci 2025;104:104651. [PMID: 39667183 PMCID: PMC11699206 DOI: 10.1016/j.psj.2024.104651] [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: 07/29/2024] [Revised: 12/05/2024] [Accepted: 12/06/2024] [Indexed: 12/14/2024]  Open
7
Sun M, Wang J, Smagghe G, Dai R, Wang X, Yang Y, Li M, You S. Description of mitochondrial genomes and phylogenetic analysis of Megophthalminae (Hemiptera: Cicadellidae). JOURNAL OF INSECT SCIENCE (ONLINE) 2024;24:9. [PMID: 39657582 PMCID: PMC11631095 DOI: 10.1093/jisesa/ieae109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2024] [Revised: 09/20/2024] [Accepted: 10/30/2024] [Indexed: 12/12/2024]
8
Zhao Y, Su X, He D. Codon Usage Analysis Reveals Distinct Evolutionary Patterns and Host Adaptation Strategies in Duck Hepatitis Virus 1 (DHV-1) Phylogroups. Viruses 2024;16:1380. [PMID: 39339856 PMCID: PMC11437458 DOI: 10.3390/v16091380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Revised: 08/18/2024] [Accepted: 08/28/2024] [Indexed: 09/30/2024]  Open
9
Shan KJ, Wu C, Tang X, Lu R, Hu Y, Tan W, Lu J. Molecular Evolution of Protein Sequences and Codon Usage in Monkeypox Viruses. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024;22:qzad003. [PMID: 38862422 PMCID: PMC11425058 DOI: 10.1093/gpbjnl/qzad003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/06/2023] [Accepted: 10/11/2023] [Indexed: 06/13/2024]
10
Kaushik R, Kumar N, Yadav P, Sircar S, Shete-Aich A, Singh A, Tomar S, Launey T, Malik YS. Comprehensive Genomics Investigation of Neboviruses Reveals Distinct Codon Usage Patterns and Host Specificity. Microorganisms 2024;12:696. [PMID: 38674640 PMCID: PMC11052288 DOI: 10.3390/microorganisms12040696] [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: 03/06/2024] [Revised: 03/24/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024]  Open
11
Yang Q, Xin C, Xiao QS, Lin YT, Li L, Zhao JL. Codon usage bias in chloroplast genes implicate adaptive evolution of four ginger species. FRONTIERS IN PLANT SCIENCE 2023;14:1304264. [PMID: 38169692 PMCID: PMC10758403 DOI: 10.3389/fpls.2023.1304264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024]
12
Guo F, Yang J, Abd El-Aty AM, Wang R, Ju X. Base composition, adaptation, and evolution of goose astroviruses: codon-based investigation. Poult Sci 2023;102:103029. [PMID: 37713803 PMCID: PMC10511809 DOI: 10.1016/j.psj.2023.103029] [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: 03/24/2023] [Revised: 07/24/2023] [Accepted: 08/11/2023] [Indexed: 09/01/2023]  Open
13
Li G, Chen X, Li X, Liang Y, Li X, Liang W, Yan Z, Wang Y, Wang Y, Luo J, Guo XF, Zhu XT. Analyzing the Evolution and Host Adaptation of the Rabies Virus from the Perspective of Codon Usage Bias. Transbound Emerg Dis 2023;2023:4667253. [PMID: 40303686 PMCID: PMC12016951 DOI: 10.1155/2023/4667253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/02/2023] [Accepted: 09/12/2023] [Indexed: 05/02/2025]
14
Aktürk Dizman Y. Codon usage bias analysis of the gene encoding NAD+-dependent DNA ligase protein of Invertebrate iridescent virus 6. Arch Microbiol 2023;205:352. [PMID: 37812231 DOI: 10.1007/s00203-023-03688-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 09/18/2023] [Indexed: 10/10/2023]
15
Rani S, Mamathashree MN, Bharthi I U, Patil SS, Krishnamoorthy P, Shueb M, Pandey RK, Suresh KP. Comprehensive examination on codon usage bias pattern of the Bovine Ephemeral fever virus. J Biomol Struct Dyn 2023;42:10593-10603. [PMID: 37705249 DOI: 10.1080/07391102.2023.2258220] [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: 05/30/2023] [Accepted: 09/02/2023] [Indexed: 09/15/2023]
16
Wang L, Zhao H, Wang Z, Ding S, Qin L, Jiang R, Deng X, He Z, Li L. An Evolutionary Perspective of Codon Usage Pattern, Dinucleotide Composition and Codon Pair Bias in Prunus Necrotic Ringspot Virus. Genes (Basel) 2023;14:1712. [PMID: 37761852 PMCID: PMC10530913 DOI: 10.3390/genes14091712] [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: 07/31/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023]  Open
17
Wu X, Shan K, Zan F, Tang X, Qian Z, Lu J. Optimization and Deoptimization of Codons in SARS-CoV-2 and Related Implications for Vaccine Development. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023;10:e2205445. [PMID: 37267926 PMCID: PMC10427376 DOI: 10.1002/advs.202205445] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 04/08/2023] [Indexed: 06/04/2023]
18
Zhou J, Wang X, Zhou Z, Wang S. Insights into the Evolution and Host Adaptation of the Monkeypox Virus from a Codon Usage Perspective: Focus on the Ongoing 2022 Outbreak. Int J Mol Sci 2023;24:11524. [PMID: 37511283 PMCID: PMC10380431 DOI: 10.3390/ijms241411524] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023]  Open
19
Noor F, Ashfaq UA, Bakar A, Qasim M, Masoud MS, Alshammari A, Alharbi M, Riaz MS. Identification and characterization of codon usage pattern and influencing factors in HFRS-causing hantaviruses. Front Immunol 2023;14:1131647. [PMID: 37492567 PMCID: PMC10364125 DOI: 10.3389/fimmu.2023.1131647] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 06/22/2023] [Indexed: 07/27/2023]  Open
20
Xin W, Guo Z, Wang L, Li Y, Shangguan H, Xue K, Chen H, Yang H, Zhao L, Ge J. Multiple genotypes infection and molecular characterization of Torque teno neovison virus: A novel Anelloviridae of mink in China. Res Vet Sci 2023;161:145-155. [PMID: 37384973 DOI: 10.1016/j.rvsc.2023.06.021] [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: 04/11/2023] [Revised: 06/23/2023] [Accepted: 06/23/2023] [Indexed: 07/01/2023]
21
Chen L, Jiang W, Wu W, Zhang S, Cai J, Lv T, Xiang B, Lin Q, Liao M, Ding C, Ren T. Insights into the Epidemiology, Phylodynamics, and Evolutionary Changes of Lineage GI-7 Infectious Bronchitis Virus. Transbound Emerg Dis 2023;2023:9520616. [PMID: 40303710 PMCID: PMC12016960 DOI: 10.1155/2023/9520616] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/10/2023] [Accepted: 05/11/2023] [Indexed: 05/02/2025]
22
Khandia R, Khan AA, Karuvantevida N, Gurjar P, Rzhepakovsky IV, Legaz I. Insights into Synonymous Codon Usage Bias in Hepatitis C Virus and Its Adaptation to Hosts. Pathogens 2023;12:pathogens12020325. [PMID: 36839597 PMCID: PMC9961758 DOI: 10.3390/pathogens12020325] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/25/2023] [Accepted: 02/02/2023] [Indexed: 02/17/2023]  Open
23
Pu F, Wang R, Yang X, Hu X, Wang J, Zhang L, Zhao Y, Zhang D, Liu Z, Liu J. Nucleotide and codon usage biases involved in the evolution of African swine fever virus: A comparative genomics analysis. J Basic Microbiol 2023;63:499-518. [PMID: 36782108 DOI: 10.1002/jobm.202200624] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/05/2023] [Accepted: 01/21/2023] [Indexed: 02/15/2023]
24
Zhou J, Xing Y, Zhou Z, Wang S. A comprehensive analysis of Usutu virus (USUV) genomes revealed lineage-specific codon usage patterns and host adaptations. Front Microbiol 2023;13:967999. [PMID: 36713228 PMCID: PMC9878346 DOI: 10.3389/fmicb.2022.967999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 12/19/2022] [Indexed: 01/15/2023]  Open
25
Rahman SU, Rehman HU, Rahman IU, Khan MA, Rahim F, Ali H, Chen D, Ma W. Evolution of codon usage in Taenia saginata genomes and its impact on the host. Front Vet Sci 2023;9:1021440. [PMID: 36713873 PMCID: PMC9875090 DOI: 10.3389/fvets.2022.1021440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 10/03/2022] [Indexed: 01/13/2023]  Open
26
Rahman SU, Rehman HU, Rahman IU, Rauf A, Alshammari A, Alharbi M, Haq NU, Suleria HAR, Raza SHA. Analysis of codon usage bias of lumpy skin disease virus causing livestock infection. Front Vet Sci 2022;9:1071097. [PMID: 36544551 PMCID: PMC9762553 DOI: 10.3389/fvets.2022.1071097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 11/10/2022] [Indexed: 12/07/2022]  Open
27
Gao Y, Lu Y, Song Y, Jing L. Analysis of codon usage bias of WRKY transcription factors in Helianthus annuus. BMC Genom Data 2022;23:46. [PMID: 35725374 PMCID: PMC9210703 DOI: 10.1186/s12863-022-01064-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 06/13/2022] [Indexed: 11/10/2022]  Open
28
Bansal S, Mallikarjuna MG, Balamurugan A, Nayaka SC, Prakash G. Composition and Codon Usage Pattern Results in Divergence of the Zinc Binuclear Cluster (Zn(II)2Cys6) Sequences among Ascomycetes Plant Pathogenic Fungi. J Fungi (Basel) 2022;8:1134. [PMID: 36354901 PMCID: PMC9694491 DOI: 10.3390/jof8111134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/22/2022] [Accepted: 10/23/2022] [Indexed: 07/29/2023]  Open
29
Qin L, Ding S, Wang Z, Jiang R, He Z. Host Plants Shape the Codon Usage Pattern of Turnip Mosaic Virus. Viruses 2022;14:v14102267. [PMID: 36298822 PMCID: PMC9607058 DOI: 10.3390/v14102267] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 01/25/2023]  Open
30
Sophiarani Y, Chakraborty S. Comparison of compositional constraints: Nuclear genome vs plasmid genome of Pseudomonas syringae pv. tomato DC3000. J Biosci 2022. [DOI: 10.1007/s12038-022-00296-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
31
Fan Y, Guo D, Zhao S, Wei Q, Li Y, Lin T. Human genes with relative synonymous codon usage analogous to that of polyomaviruses are involved in the mechanism of polyomavirus nephropathy. Front Cell Infect Microbiol 2022;12:992201. [PMID: 36159639 PMCID: PMC9492876 DOI: 10.3389/fcimb.2022.992201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/12/2022] [Indexed: 11/28/2022]  Open
32
Wang X, Sun J, Lu L, Pu FY, Zhang DR, Xie FQ. Evolutionary dynamics of codon usages for peste des petits ruminants virus. Front Vet Sci 2022;9:968034. [PMID: 36032280 PMCID: PMC9412750 DOI: 10.3389/fvets.2022.968034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022]  Open
33
Feng JL, Wu LW, Wang Q, Pan YJ, Li BL, Lin YL, Yao H. Comparison Analysis Based on Complete Chloroplast Genomes and Insights into Plastid Phylogenomic of Four Iris Species. BIOMED RESEARCH INTERNATIONAL 2022;2022:2194021. [PMID: 35937412 PMCID: PMC9348943 DOI: 10.1155/2022/2194021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 06/06/2022] [Accepted: 07/05/2022] [Indexed: 11/17/2022]
34
Wang Q, Lyu X, Cheng J, Fu Y, Lin Y, Abdoulaye AH, Jiang D, Xie J. Codon Usage Provides Insights into the Adaptive Evolution of Mycoviruses in Their Associated Fungi Host. Int J Mol Sci 2022;23:7441. [PMID: 35806445 PMCID: PMC9267111 DOI: 10.3390/ijms23137441] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 11/16/2022]  Open
35
Wang X, Sun J, Zheng Y, Xie F. Dispersion of synonymous codon usage patterns in hepatitis E virus genomes derived from various hosts. J Basic Microbiol 2022;62:975-983. [PMID: 35778820 DOI: 10.1002/jobm.202200072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 05/01/2022] [Accepted: 06/11/2022] [Indexed: 11/09/2022]
36
Sarkar I, Dey P, Rathore SS, Singh GD, Singh RP. Global genomic and proteomic analysis indicates co-evolution of Neisseria species and with their human host. World J Microbiol Biotechnol 2022;38:149. [PMID: 35773545 DOI: 10.1007/s11274-022-03338-w] [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: 11/24/2021] [Accepted: 06/11/2022] [Indexed: 11/30/2022]
37
Tyagi N, Sardar R, Gupta D. Natural selection plays a significant role in governing the codon usage bias in the novel SARS-CoV-2 variants of concern (VOC). PeerJ 2022;10:e13562. [PMID: 35765592 PMCID: PMC9233899 DOI: 10.7717/peerj.13562] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 05/19/2022] [Indexed: 01/17/2023]  Open
38
Li B, Wu H, Miao Z, Hu L, Zhou L, Lu Y. Codon Usage of Hepatitis E Viruses: A Comprehensive Analysis. Front Microbiol 2022;13:938651. [PMID: 35801104 PMCID: PMC9253588 DOI: 10.3389/fmicb.2022.938651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 05/30/2022] [Indexed: 11/25/2022]  Open
39
He Z, Qin L, Xu X, Ding S. Evolution and host adaptability of plant RNA viruses: Research insights on compositional biases. Comput Struct Biotechnol J 2022;20:2600-2610. [PMID: 35685354 PMCID: PMC9160401 DOI: 10.1016/j.csbj.2022.05.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 01/23/2023]  Open
40
Nambou K, Anakpa M, Tong YS. Human genes with codon usage bias similar to that of the nonstructural protein 1 gene of influenza A viruses are conjointly involved in the infectious pathogenesis of influenza A viruses. Genetica 2022;150:97-115. [PMID: 35396627 PMCID: PMC8992787 DOI: 10.1007/s10709-022-00155-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 03/24/2022] [Indexed: 11/27/2022]
41
Zu Z, Lin H, Hu Y, Zheng X, Chen C, Zhao Y, He N. The genetic evolution and codon usage pattern of severe fever with thrombocytopenia syndrome virus. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022;99:105238. [PMID: 35144005 DOI: 10.1016/j.meegid.2022.105238] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 01/04/2022] [Accepted: 02/03/2022] [Indexed: 06/14/2023]
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Joshi A, Krishnan S, Kaushik V. Codon usage studies and epitope-based peptide vaccine prediction against Tropheryma whipplei. J Genet Eng Biotechnol 2022;20:41. [PMID: 35254546 PMCID: PMC8899776 DOI: 10.1186/s43141-022-00324-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/22/2022] [Indexed: 12/18/2022]
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Evolution of Viral Pathogens Follows a Linear Order. Microbiol Spectr 2022;10:e0165521. [PMID: 35107326 PMCID: PMC8809352 DOI: 10.1128/spectrum.01655-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]  Open
44
Comprehensive Analysis of Codon Usage Patterns in Chinese Porcine Circoviruses Based on Their Major Protein-Coding Sequences. Viruses 2022;14:v14010081. [PMID: 35062285 PMCID: PMC8778832 DOI: 10.3390/v14010081] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/31/2021] [Accepted: 12/31/2021] [Indexed: 01/01/2023]  Open
45
Nair RR, Mohan M, Rudramurthy GR, Vivekanandam R, Satheshkumar PS. Strategies and Patterns of Codon Bias in Molluscum Contagiosum Virus. Pathogens 2021;10:1649. [PMID: 34959603 PMCID: PMC8703355 DOI: 10.3390/pathogens10121649] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 11/22/2022]  Open
46
Zhang Z, Guo F, Roy A, Yang J, Luo W, Shen X, Irwin DM, Chen RA, Shen Y. Evolutionary perspectives and adaptation dynamics of human seasonal influenza viruses from 2009 to 2019: An insight from codon usage. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021;96:105067. [PMID: 34487866 DOI: 10.1016/j.meegid.2021.105067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/28/2021] [Accepted: 09/01/2021] [Indexed: 06/13/2023]
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Li Y, Wang R, Wang H, Pu F, Feng X, Jin L, Ma Z, Ma XX. Codon Usage Bias in Autophagy-Related Gene 13 in Eukaryotes: Uncovering the Genetic Divergence by the Interplay Between Nucleotides and Codon Usages. Front Cell Infect Microbiol 2021;11:771010. [PMID: 34804999 PMCID: PMC8602353 DOI: 10.3389/fcimb.2021.771010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 10/12/2021] [Indexed: 12/15/2022]  Open
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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: 3.8] [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
49
Ramos-González PL, Pons T, Chabi-Jesus C, Arena GD, Freitas-Astua J. Poorly Conserved P15 Proteins of Cileviruses Retain Elements of Common Ancestry and Putative Functionality: A Theoretical Assessment on the Evolution of Cilevirus Genomes. FRONTIERS IN PLANT SCIENCE 2021;12:771983. [PMID: 34804105 PMCID: PMC8602818 DOI: 10.3389/fpls.2021.771983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
50
Yi K, Kim SY, Bleazard T, Kim T, Youk J, Ju YS. Mutational spectrum of SARS-CoV-2 during the global pandemic. Exp Mol Med 2021;53:1229-1237. [PMID: 34453107 PMCID: PMC8393781 DOI: 10.1038/s12276-021-00658-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/29/2021] [Accepted: 05/11/2021] [Indexed: 02/07/2023]  Open
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