H5N8流感病毒密码子偏爱性及聚类分析
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摘要
目的探索H5N8流感病毒相关蛋白的密码子偏爱性及其变化趋势。方法运用CUSP、CodonW等生物信息软件对2000年以来的H5N8流行株相关蛋白的编码序列进行密码子偏爱性分析,并以重要的人类流感病毒作为参照进行聚类分析。结果 H5N8流感病毒相关蛋白的有效密码子数目(ENC)值均较高,密码子偏性总体较低;相关蛋白的偏爱密码子有差异性。ENC-Plot及中性分析显示,H5N8在进化过程中主要受自然选择因素的影响。聚类分析显示,除NA蛋白的密码子偏爱性相对稳定外,其他蛋白在2010、2014、2016年流行株发生了明显改变。结论近年来H5N8在环境压力下发生快速突变,其跨物种感染人的风险进一步加强,而NA密码子偏爱性变化可能是监测的重点。
Objective To examine the codon usage bias of H5N8 influenza virus and its changes. Methods Bioinformatic software such as CUSP and CodonW were used to analyze the codon bias of the coding sequences of proteins related to strains of H5N8 prevalent since 2000,and clustering analysis was performed with reference to other key strains of the human influenza virus. Results The number of effective codons(ENC)of H5N8 influenza virus-related proteins ranged from 43-56,which is close to 61.Codon optimality differed significantly among related proteins.ENC-plot analysis and neutral analysis indicated that H5N8 was mainly influenced by natural selection over the course of its evolution.The results of cluster analysis indicated that proteins besides the NA protein had a series of significant mutations in 2010,2014,and 2016. Conclusion Over the past few years,H5N8 has undergone rapid mutations while under environmental pressure.It has a greater risk of crossing species to infect humans,and changes in NA codon usage bias may be a key way to monitor H5N8 outbreaks.
Objective To examine the codon usage bias of H5N8 influenza virus and its changes. Methods Bioinformatic software such as CUSP and CodonW were used to analyze the codon bias of the coding sequences of proteins related to strains of H5N8 prevalent since 2000,and clustering analysis was performed with reference to other key strains of the human influenza virus. Results The number of effective codons(ENC)of H5N8 influenza virus-related proteins ranged from 43-56,which is close to 61.Codon optimality differed significantly among related proteins.ENC-plot analysis and neutral analysis indicated that H5N8 was mainly influenced by natural selection over the course of its evolution.The results of cluster analysis indicated that proteins besides the NA protein had a series of significant mutations in 2010,2014,and 2016. Conclusion Over the past few years,H5N8 has undergone rapid mutations while under environmental pressure.It has a greater risk of crossing species to infect humans,and changes in NA codon usage bias may be a key way to monitor H5N8 outbreaks.
引文
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[4]Pasick J,Berhane Y,Joseph T,et al.Reassortant highly pathogenic influenza A H5N2virus containing gene segments related to Eurasian H5N8in British Columbia,Canada,2014[J].Sci Rep,2015(5):9484.
[5]El-Shesheny R,Barman S,Feeroz MM,et al.Genesis of influenza A(H5N8)viruses[J].Emerg Infect Dis,2017,23(8):1368.
[6]Xu W,Dai Y,Hua C,et al.Genomic signature analysis of the recently emerged highly pathogenic A(H5N8)avian influenza virus:implying an evolutionary trend for bird-to-human transmission[J].Microbes Infect,2017,19(2):597-604.
[7]Nasrullah I,Butt AM,Tahir S,et al.Genomic analysis of codon usage shows influence of mutation pressure,natural selection,and host features on Marburg virus evolution[J].BMC Evol Biol,2015(15):174.
[8]Wei L,He J,Jia X,et al.Analysis of codon usage bias of mitochondrial genome in Bombyx mori and its relation to evolution[J].BMC Evol Biol,2014(14):262.
[9]Bera BC,Virmani N,Kumar N,et al.Genetic and codon usage bias analyses of polymerase genes of equine influenza virus and its relation to evolution[J].BMC Genomics,2017,18(1):652.
[10]Marra MA,Jones SJ,Astell CR,et al.The Genome sequence of the SARS-associated coronavirus[J].Science,2003,300(5624):1399-404.
[11]Castells M,Victoria M,Colina R,et al.Genome-wide analysis of codon usage bias in Bovine Coronavirus[J].Virology J,2017,14(1):115.
[12]Wright F.The'effective number of codons'used in a gene[J].Gene,1990,87(1):23-9.
[13]Bae YA.Codon usage patterns of tyrosinase genes in Clonorchis sinensis[J].Kor J Parasitol,2017,55(2):175.
[14]Chen Y,Li X,Chi X,et al.Comprehensive analysis of the codon usage patterns in the envelope glycoprotein E2gene of the classical swine fever virus[J].PLoS One,2017,12(9):e183646.
[15]Huang X,Xu J,Chen L,et al.Analysis of transcriptome data reveals multifactor constraint on codon usage in Taenia multiceps[J].BMC Genomics,2017,18(1):308.
[16]Zhao Y,Zheng H,Xu A,et al.Analysis of codon usage bias of envelope glycoprotein genes in nuclear polyhedrosis virus(NPV)and its relation to evolution[J].BMC Genomics,2016,17(1):677.
[17]Yang H,Carney PJ,Mishin VP,et al.Molecular characterizations of surface proteins hemagglutinin and neuraminidase from recent H5Nx avian influenza viruses[J].J Virol,2016,90(12):5770-84.
[18]Mazumder TH,Chakraborty S.Gaining insights into the codon usage patterns of TP53Gene across eight mammalian species[J].PloS One,2015,10(3):e121709.
[19]Zhou J,Ding Y,He Y,et al.The effect of multiple evolutionary selections on synonymous codon usage of genes in the Mycoplasma bovis genome[J].PloS One,2014,9(10):e108949.
[20]Goni N,Iriarte A,Comas V,et al.Pandemic influenza A virus codon usage revisited:biases,adaptation and implications for vaccine strain development[J].Virol J,2012(9):263.
[21]Wong EH,Smith DK,Rabadan R,et al.Codon usage bias and the evolution of influenza A viruses[J].BMC Evol Biol,2010(10):253.
[22]Who.Assessment of risk associated with influenza A(H5N8)virus[Z].2016.