Análisis filogenético y de presión evolutiva de secuencias nucleotídicas del gen VP4 de especies de enterovirus humanos
Palabras clave:
Enterovirus humanos, secuencias nucleotídicas, gen VP4, análisis filogenético, presión selectivaResumen
El género Enterovirus es un grupo viral que afecta a un amplio rango de hospederos, entre ellos los humanos (especies A, B, C, y D), causan enfermedades respiratorias, gastrointestinales, neurológicas, y otras, y son altamente contagiosos. Los síntomas pueden ser leves o graves. El objetivo del trabajo fue analizar la variación nucleotídica, filogenética y de presión evolutiva de secuencias nucleotídicas del gen VP4 de las cuatro especies que afectan a los humanos. Se emplearon 92 secuencias nucleotídicas disponibles en la base de datos GenBank; éstas se editaron con el software BioEdit y se alinearon con Clustal W; las relaciones filogenéticas se determinaron con MEGA6, y las presiones evolutivas con los algoritmos SNAP y SLAC. Se encontró que la identidad nucleotídica mínima intra-especie fue de 43,2% (especie B) a 72,6% (especie D). Los genotipos más variables por especie fueron EV-71 (A), Echovirus 2 (B), EV-118 (C), y EV-94 (D). El análisis de presión evolutiva mostró que el gen VP4 en las cuatro especies evoluciona bajo presión selectiva negativa. Esto indicaría que la alta tasa mutacional y eventos de recombinación no tienen un rol significativo en la evolución de este gen, debido probablemente a la localización interna de la proteína VP4.
Descargas
Referencias
Racaniello VR. Picornaviridae: the viruses and their replication. In: Knipe DM, Howley PM, Cohen JI, Griffin DE, Lamb RA, Martin MA, et al., editors. Fields Virology. 1. Philadelphia: Lippincott Williams & Wilkins; 2013. p. 453-89.
Brown BA, Oberste MS, Alexander JP, Jr., Kennett ML, Pallansch MA. Molecular epidemiology and evolution of enterovirus 71 strains isolated from 1970 to 1998. Journal of virology. 1999;73(12):9969-75.
Domingo E, Ruiz-Jarabo CM, Sierra S, Arias A, Pariente N, Baranowski E, et al. Emergence and selection of RNA virus variants: memory and extinction. Virus research. 2002;82(1-2):39-44.
Burke DS. Recombination in HIV: an important viral evolutionary strategy. Emerging infectious diseases. 1997;3(3):253-9.
Oberste MS, Maher K, Pallansch MA. Evidence for frequent recombination within species human enterovirus B based on complete genomic sequences of all thirty-seven serotypes. Journal of virology. 2004;78(2):855-67.
Eigen M, Gardiner W, Schuster P, Winkler-Oswatitsch R. The origin of genetic information. Scientific American. 1981;244(4):88-92, 6, et passim.
Nei M, Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Molecular biology and evolution. 1986;3(5):418-26.
Tanaka T, Nei M. Positive darwinian selection observed at the variable-region genes of immunoglobulins. Molecular biology and evolution. 1989;6(5):447-59.
Garcia J, Espejo V, Nelson M, Sovero M, Villaran MV, Gomez J, et al. Human rhinoviruses and enteroviruses in influenza-like illness in Latin America. Virology journal. 2013;10:305.
Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser. 1999;41:95-8.
Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994;22(22):4673-80.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Molecular biology and evolution. 2013;30(12):2725-9.
Korber B. HIV Signature and Sequence Variation Analysis. Computational Analysis of HIV Molecular Sequences. Dordrecht, Netherlands: Kluwer Academic Publishers; 2000.
Pond SL, Frost SD. Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics. 2005;21(10):2531-3.
Peng Y, Leung HC, Yiu SM, Chin FY. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics. 2012;28(11):1420-8.
Pickett BE, Sadat EL, Zhang Y, Noronha JM, Squires RB, Hunt V, et al. ViPR: an open bioinformatics database and analysis resource for virology research. Nucleic Acids Res. 2012;40(Database issue):D593-8.
Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome research. 2012;22(3):568-76.
Prachayangprecha S, Schapendonk CM, Koopmans MP, Osterhaus AD, Schurch AC, Pas SD, et al. Exploring the potential of next-generation sequencing in detection of respiratory viruses. Journal of clinical microbiology. 2014;52(10):3722-30.
Chow M, Newman JF, Filman D, Hogle JM, Rowlands DJ, Brown F. Myristylation of picornavirus capsid protein VP4 and its structural significance. Nature. 1987;327(6122):482-6.
Danthi P, Tosteson M, Li QH, Chow M. Genome delivery and ion channel properties are altered in VP4 mutants of poliovirus. Journal of virology. 2003;77(9):5266-74.
Williams RC. The Probable Mutation Effect: neutral alleles and structural reduction. Human biology. 1978;50(2):173-81.
Smura TP, Junttila N, Blomqvist S, Norder H, Kaijalainen S, Paananen A, et al. Enterovirus 94, a proposed new serotype in human enterovirus species D. The Journal of general virology. 2007;88(Pt 3):849-58.
Smura T, Ylipaasto P, Klemola P, Kaijalainen S, Kyllonen L, Sordi V, et al. Cellular tropism of human enterovirus D species serotypes EV-94, EV-70, and EV-68 in vitro: implications for pathogenesis. Journal of medical virology. 2010;82(11):1940-9.
Melnick JL. Enterovirus type 71 infections: a varied clinical pattern sometimes mimicking paralytic poliomyelitis. Reviews of infectious diseases. 1984;6 Suppl 2:S387-90.
Miyamura K, Nishimura Y, Abo M, Wakita T, Shimizu H. Adaptive mutations in the genomes of enterovirus 71 strains following infection of mouse cells expressing human P-selectin glycoprotein ligand-1. The Journal of general virology. 2011;92(Pt 2):287-91.
Chen TC, Liu SC, Huang PN, Chang HY, Chern JH, Shih SR. Antiviral activity of pyridyl imidazolidinones against enterovirus 71 variants. Journal of biomedical science. 2008;15(3):291-300.
Cabello et al Análisis filogenético y de presión evolutiva de secuencias nucleotídicas del gen VP4.
Daleno C, Greenberg D, Piralla A, Scala A, Baldanti F, Principi N, et al. A novel human enterovirus C (EV-C118) identified in two children hospitalised because of acute otitis media and community-acquired pneumonia in Israel. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology. 2013;56(2):159-62.
Piralla A, Daleno C, Scala A, Greenberg D, Usonis V, Principi N, et al. Genome characterisation of enteroviruses 117 and 118: a new group within human enterovirus species C. PloS one. 2013;8(4):e60641.
Tapparel C, Junier T, Gerlach D, Van-Belle S, Turin L, Cordey S, et al. New respiratory enterovirus and recombinant rhinoviruses among circulating picornaviruses. Emerging infectious diseases. 2009;15(5):719-26.
Kim SH, Lee HY, Jang YS. Targeted Delivery of VP1 Antigen of Foot-and-mouth Disease Virus to M Cells Enhances the Antigen-specific Systemic and Mucosal Immune Response. Immune network. 2013;13(4):157-62.
Lindberg AM, Andersson P, Savolainen C, Mulders MN, Hovi T. Evolution of the genome of Human enterovirus B: incongruence between phylogenies of the VP1 and 3CD regions indicates frequent recombination within the species. The Journal of general virology. 2003;84(Pt 5):1223-35.
Zaini Z, McMinn P. A single mutation in capsid protein VP1 (Q145E) of a genogroup C4 strain of human enterovirus 71 generates a mouse-virulent phenotype. The Journal of general virology. 2012;93(Pt 9):1935-40.
Imamura T, Oshitani H. Global reemergence of enterovirus D68 as an important pathogen for acute respiratory infections. Reviews in medical virology. 2015;25(2):102-14.
Nelson R. Outbreaks of enterovirus D68 continue across the USA. The Lancet Respiratory medicine. 2014;2(10):791.
