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For: Cristina J, Fajardo A, Soñora M, Moratorio G, Musto H. A detailed comparative analysis of codon usage bias in Zika virus. Virus Res 2016;223:147-52. [PMID: 27449601 DOI: 10.1016/j.virusres.2016.06.022] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 06/08/2016] [Accepted: 06/14/2016] [Indexed: 12/01/2022]
Number Cited by Other Article(s)
1
Tan X, Zhou W, Jing S, Shen W, Lu B. Decoding codon usage in human papillomavirus type 59. Virus Genes 2025;61:313-323. [PMID: 40038214 PMCID: PMC12052745 DOI: 10.1007/s11262-025-02148-0] [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: 12/11/2024] [Accepted: 02/24/2025] [Indexed: 03/06/2025]
2
Rahman SU, Hu Y, Rehman HU, Alrashed MM, Attia KA, Ullah U, Liang H. Analysis of synonymous codon usage bias of Lassa virus. Virus Res 2025;353:199528. [PMID: 39832535 PMCID: PMC11815952 DOI: 10.1016/j.virusres.2025.199528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 11/17/2024] [Accepted: 01/17/2025] [Indexed: 01/22/2025]
3
Eldin P, David A, Hirtz C, Battini JL, Briant L. SARS-CoV-2 Displays a Suboptimal Codon Usage Bias for Efficient Translation in Human Cells Diverted by Hijacking the tRNA Epitranscriptome. Int J Mol Sci 2024;25:11614. [PMID: 39519170 PMCID: PMC11546939 DOI: 10.3390/ijms252111614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2024] [Revised: 10/25/2024] [Accepted: 10/26/2024] [Indexed: 11/16/2024]  Open
4
Aktürk Dizman Y. Exploring Codon Usage Patterns and Influencing Factors in Ranavirus DNA Polymerase Genes. J Basic Microbiol 2024;64:e2400289. [PMID: 39099168 DOI: 10.1002/jobm.202400289] [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: 05/17/2024] [Revised: 07/05/2024] [Accepted: 07/20/2024] [Indexed: 08/06/2024]
5
Aktürk Dizman Y. Analysis of codon usage bias of exonuclease genes in invertebrate iridescent viruses. Virology 2024;593:110030. [PMID: 38402641 DOI: 10.1016/j.virol.2024.110030] [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: 10/10/2023] [Revised: 02/04/2024] [Accepted: 02/13/2024] [Indexed: 02/27/2024]
6
Subong BJJ, Ozawa T. Bio-Chemoinformatics-Driven Analysis of nsp7 and nsp8 Mutations and Their Effects on Viral Replication Protein Complex Stability. Curr Issues Mol Biol 2024;46:2598-2619. [PMID: 38534781 PMCID: PMC10968879 DOI: 10.3390/cimb46030165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 03/28/2024]  Open
7
Wang H, Liu S, Lv Y, Wei W. Codon usage bias of Venezuelan equine encephalitis virus and its host adaption. Virus Res 2023;328:199081. [PMID: 36854361 DOI: 10.1016/j.virusres.2023.199081] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 09/14/2022] [Accepted: 02/24/2023] [Indexed: 03/02/2023]
8
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
9
Bai H, Ata G, Sun Q, Rahman SU, Tao S. Natural selection pressure exerted on "Silent" mutations during the evolution of SARS-CoV-2: Evidence from codon usage and RNA structure. Virus Res 2023;323:198966. [PMID: 36244617 PMCID: PMC9561399 DOI: 10.1016/j.virusres.2022.198966] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 01/25/2023]
10
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
11
Simón D, Cristina J, Musto H. An overview of dinucleotide and codon usage in all viruses. Arch Virol 2022;167:1443-1448. [PMID: 35467158 DOI: 10.1007/s00705-022-05454-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/05/2022] [Indexed: 11/30/2022]
12
Beelagi MS, Kumar SRS, Indrabalan UB, Patil SS, Prasad A, Suresh KP, Kollur SP, Jayappa VS, Kakkalameli SB, Srinivasa C, Venkataravana PA, Shivamallu C. Synonymous codon usage pattern among the S, M, and L segments in Crimean-congo hemorrhagic fever virus. Bioinformation 2021;17:479-491. [PMID: 34602775 PMCID: PMC8450151 DOI: 10.6026/97320630017479] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 11/23/2022]  Open
13
Nguyen TH, Wang D, Rahman SU, Bai H, Yao X, Chen D, Tao S. Analysis of codon usage patterns and influencing factors in rice tungro bacilliform virus. INFECTION GENETICS AND EVOLUTION 2021;90:104750. [PMID: 33548490 DOI: 10.1016/j.meegid.2021.104750] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/08/2021] [Accepted: 01/29/2021] [Indexed: 12/17/2022]
14
Xu Q, Chen H, Sun W, Zhu D, Zhang Y, Chen JL, Chen Y. Genome-wide analysis of the synonymous codon usage pattern of Streptococcus suis. Microb Pathog 2021;150:104732. [PMID: 33429052 DOI: 10.1016/j.micpath.2021.104732] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 12/30/2020] [Accepted: 01/03/2021] [Indexed: 01/21/2023]
15
Codon usage bias in the H gene of canine distemper virus. Microb Pathog 2020;149:104511. [PMID: 32961282 DOI: 10.1016/j.micpath.2020.104511] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/30/2020] [Accepted: 09/16/2020] [Indexed: 12/25/2022]
16
Silverj A, Rota-Stabelli O. On the correct interpretation of similarity index in codon usage studies: Comparison with four other metrics and implications for Zika and West Nile virus. Virus Res 2020;286:198097. [DOI: 10.1016/j.virusres.2020.198097] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/15/2020] [Accepted: 07/15/2020] [Indexed: 12/11/2022]
17
Shi SL, Xia RX. Codon Usage in the Iflaviridae Family Is Not Diverse Though the Family Members Are Isolated from Diverse Host Taxa. Viruses 2019;11:E1087. [PMID: 31766648 PMCID: PMC6950266 DOI: 10.3390/v11121087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 11/17/2019] [Accepted: 11/20/2019] [Indexed: 12/12/2022]  Open
18
Tao J, Yao H. Comprehensive analysis of the codon usage patterns of polyprotein of Zika virus. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019;150:43-49. [PMID: 31054849 DOI: 10.1016/j.pbiomolbio.2019.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 02/25/2019] [Accepted: 05/01/2019] [Indexed: 01/05/2023]
19
Je M, Kim H, Son HS. Analysis of the codon usage pattern of the RdRP gene of mycovirus infecting Aspergillus spp. Virol J 2019;16:10. [PMID: 30651145 PMCID: PMC6335760 DOI: 10.1186/s12985-019-1115-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 01/01/2019] [Indexed: 12/21/2022]  Open
20
Tian L, Shen X, Murphy RW, Shen Y. The adaptation of codon usage of +ssRNA viruses to their hosts. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2018;63:175-179. [PMID: 29864509 PMCID: PMC7106036 DOI: 10.1016/j.meegid.2018.05.034] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 05/16/2018] [Accepted: 05/31/2018] [Indexed: 02/05/2023]
21
Freire CCDM, Palmisano G, Braconi CT, Cugola FR, Russo FB, Beltrão-Braga PC, Iamarino A, Lima Neto DFD, Sall AA, Rosa-Fernandes L, Larsen MR, Zanotto PMDA. NS1 codon usage adaptation to humans in pandemic Zika virus. Mem Inst Oswaldo Cruz 2018;113:e170385. [PMID: 29768530 PMCID: PMC5942634 DOI: 10.1590/0074-02760170385] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 02/20/2018] [Indexed: 01/08/2023]  Open
22
Paul P, Malakar AK, Chakraborty S. Codon usage vis-a-vis start and stop codon context analysis of three dicot species. J Genet 2018. [DOI: 10.1007/s12041-018-0892-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
23
Lin D, Li L, Xie T, Yin Q, Saksena N, Wu R, Li W, Dai G, Ma J, Zhou X, Chen X. Codon usage variation of Zika virus: The potential roles of NS2B and NS4A in its global pandemic. Virus Res 2018;247:71-83. [PMID: 29428601 DOI: 10.1016/j.virusres.2018.01.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 01/26/2018] [Accepted: 01/29/2018] [Indexed: 12/18/2022]
24
Takaaki K, Tatsuo S. Analysis of factors affecting codon usage bias in human papillomavirus. ACTA ACUST UNITED AC 2018. [DOI: 10.5897/jbsa2017.0106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
25
Analysis of codon usage bias of Crimean-Congo hemorrhagic fever virus and its adaptation to hosts. INFECTION GENETICS AND EVOLUTION 2017;58:1-16. [PMID: 29198972 DOI: 10.1016/j.meegid.2017.11.027] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 11/02/2017] [Accepted: 11/28/2017] [Indexed: 01/05/2023]
26
Chen Y, Xu Q, Tan C, Li X, Chi X, Cai B, Yu Z, Ma Y, Chen JL. Genomic analysis of codon usage shows influence of mutation pressure, natural selection, and host features on Senecavirus A evolution. Microb Pathog 2017;112:313-319. [PMID: 28943149 PMCID: PMC7172466 DOI: 10.1016/j.micpath.2017.09.040] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 09/16/2017] [Accepted: 09/18/2017] [Indexed: 11/24/2022]
27
Göertz GP, Abbo SR, Fros JJ, Pijlman GP. Functional RNA during Zika virus infection. Virus Res 2017;254:41-53. [PMID: 28864425 DOI: 10.1016/j.virusres.2017.08.015] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 08/28/2017] [Accepted: 08/28/2017] [Indexed: 12/24/2022]
28
Hussain S, Rasool ST. Analysis of synonymous codon usage in Zika virus. Acta Trop 2017;173:136-146. [PMID: 28606821 DOI: 10.1016/j.actatropica.2017.06.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 06/04/2017] [Accepted: 06/07/2017] [Indexed: 01/11/2023]
29
Piontkivska H, Frederick M, Miyamoto MM, Wayne ML. RNA editing by the host ADAR system affects the molecular evolution of the Zika virus. Ecol Evol 2017. [PMID: 28649357 PMCID: PMC5478085 DOI: 10.1002/ece3.3033] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
30
Codon usage bias and evolutionary analyses of Zika virus genomes. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0549-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
31
Singh NK, Tyagi A. A detailed analysis of codon usage patterns and influencing factors in Zika virus. Arch Virol 2017;162:1963-1973. [PMID: 28324177 DOI: 10.1007/s00705-017-3324-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Accepted: 02/12/2017] [Indexed: 02/01/2023]
32
Khrustalev VV, Khrustaleva TA, Sharma N, Giri R. Mutational Pressure in Zika Virus: Local ADAR-Editing Areas Associated with Pauses in Translation and Replication. Front Cell Infect Microbiol 2017;7:44. [PMID: 28275585 PMCID: PMC5319961 DOI: 10.3389/fcimb.2017.00044] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/07/2017] [Indexed: 12/21/2022]  Open
33
Wang H, Liu S, Zhang B, Wei W. Analysis of Synonymous Codon Usage Bias of Zika Virus and Its Adaption to the Hosts. PLoS One 2016;11:e0166260. [PMID: 27893824 PMCID: PMC5125587 DOI: 10.1371/journal.pone.0166260] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 10/25/2016] [Indexed: 11/19/2022]  Open
34
Fajardo Á, Cristina J, Moreno P. Emergence and Spreading Potential of Zika Virus. Front Microbiol 2016;7:1667. [PMID: 27812357 PMCID: PMC5071320 DOI: 10.3389/fmicb.2016.01667] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 10/05/2016] [Indexed: 12/31/2022]  Open
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