Phylogenetic reconstruction of dengue virus type 2 in Colombia

Virology Journal

Volumn 9, Issue , 2012, Pages

  Méndez, Jairo A ^a,c   Usme Ciro, José A ^b   Domingo, Cristina ^d,e   Rey, Gloria J ^a   Sánchez, Juan A ^c   Tenorio, Antonio ^d   Gallego Gomez, Juan C ^b  

^a INSTITUTO NACIONAL DE SALUD   (Colombia)

^b UNIVERSIDAD DE ANTIOQUIA   (Colombia)

^c UNIVERSIDAD DE LOS ANDES   (Colombia)

^d INSTITUTO DE SALUD CARLOS III   (Spain)

^e ROBERT KOCH INSTITUTE   (Germany)

Author keywords

Colombia; Dengue virus; Evolution; Genotype; Phylogenetic; Serotype

Indexed keywords

ENVELOPE PROTEIN; E GLYCOPROTEIN, DENGUE VIRUS TYPE 2; E-GLYCOPROTEIN, DENGUE VIRUS TYPE 2; VIRUS ENVELOPE PROTEIN; VIRUS RNA;

ARTICLE; CARBOXY TERMINAL SEQUENCE; COLOMBIA; DENGUE; DENGUE VIRUS 2; GENE SEQUENCE; GENOTYPE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; VIRUS GENE; CLASSIFICATION; DENGUE VIRUS; GENETICS; HUMAN; ISOLATION AND PURIFICATION; MOLECULAR EPIDEMIOLOGY; VIROLOGY;

DENGUE VIRUS; DENGUE VIRUS TYPE 2;

COLOMBIA; DENGUE; DENGUE VIRUS; GENOTYPE; HUMANS; MOLECULAR EPIDEMIOLOGY; PHYLOGENY; RNA, VIRAL; VIRAL ENVELOPE PROTEINS;

EID: 84860838808     PISSN: None     EISSN: 1743422X     Source Type: Journal    
DOI: 10.1186/1743-422X-9-64     Document Type: Article

References (65)

1. Dengue and dengue hemorrhagic fever: its history and resurgence as a global public health problem. Gubler D, Dengue and dengue hemorrhagic feve Oxford: CAB International, Gubler DJ, Kuno G, 1997
2. Origins of dengue type 2 viruses associated with increased pathogenicity in the Americas. Rico-Hesse R, Harrison LM, Salas RA, Tovar D, Nisalak A, Ramos C, Boshell J, de Mesa MT, Nogueira RMR, da Rosa AT, Virology 1997 230 244 251 10.1006/viro.1997.8504 9143280 (Pubitemid 27211855)
3. Dengue viral infections: pathogenesis and epidemiology. McBride WJ, Bielefeldt-Ohmann H, Microbes Infect 2000 2 1041 1050 10.1016/S1286-4579(00) 01258-2 10967284 (Pubitemid 30664218)
4. Dengue guidelines for diagnosis, treatment, prevention and control. World Health Organization, Special Program for Research and Training in Tropical Diseases France, World Health Organization 2009
5. A timeline for dengue in the Americas to December 31, 2000 and noted first occurrences. Schneider JMPH, Droll D, Division of Disease Prevention and Control Pan American Health Organization 2001
6. Dengue en Colombia. Boshell J, Biomedica 1986 6 101 106
7. Pathogenesis of Dengue: Challenges to Molecular Biology. Halstead SB, Sci 1988 239 476 481 10.1126/science.3277268 (Pubitemid 18084309)
8. Dengue hemorrhagic fever in Cuba. II. Clinical Investigations. Guzman MG, Kouri DJ, Bravo J, Soler M, Vasquez S, Santos M, Villaescusa R, Basanta P, Indan G, Ballester JM, Trans Royal Soc Trop Med Hyg 1984 78 239 241 10.1016/0035-9203(84)90286-4
9. Dengue virus 3 genotype 1 assosiated with dengue fever and dengue hemorrhagic fever, Brazil. Barcelos L, Batista A, Portela G, Paiva B, Germano J, Bonjardim CA, Peregrino PC, Geessien E, Emerg Infect Dis 2008 14 314 316 10.3201/eid1402.070278 18258129 (Pubitemid 351213686)
10. Dengue virus structural differences that correlate with pathogenesis. Leitmeyer KC, J Virol 1999 73 4738 4747 10233934 (Pubitemid 29246733)
11. Genetic variation and microevolution of dengue 2 virus in Southeast Asia. Trent DW, Grant JA, Monath TP, Manske CL, Corina M, Fox GE, Virol 1989 172 523 535 10.1016/0042-6822(89)90195-5 (Pubitemid 19255974)
12. Molecular evolution and distribution of dengue viruses type 1 and 2 in nature. Rico-Hesse R, Virol 1990 174 479 493 10.1016/0042-6822(90)90102-W (Pubitemid 20060152)
13. Phylogenetic relationships of dengue-2 viruses. Lewis JA, Chang GJ, Lanciotti RS, Kinney RM, Mayer LW, Trent DW, Virol 1993 197 216 224 10.1006/viro.1993.1582
14. Molecular epidemiology of dengue-1 and dengue-4 viruses. Chunge E, Cassar O, Drouet MT, Guzman MG, Laille M, Rosen L, Deubel V, J Gen Virol 1995 76 1877 1884 10.1099/0022-1317-76-7-1877 9049396
15. Molecular evolution and phylogeny of dengue-4 viruses. Lanciotti RS, Gubler DJ, Trent DW, J Gen Virol 1997 78 2279 84 9292015
16. Molecular evolution of dengue type 2 virus in Thailand. Rico-Hesse R, Harrison LM, Nisalak A, Vaughn DW, Kalayanarooj S, Green S, Rothman AL, Ennis FA, AmJTrop Med Hyg 1998 58 96 101 (Pubitemid 28071417)
17. Molecular epidemiology of dengue viruses in Brazil. Nogueira RM, Miagostovich MP, Goncalvez H, Cad Saude Publica 2000 16 205 211 10.1590/S0102-311X2000000100021 10738165
18. Phylogenetic relationships and differential selection pressures among genotypes of dengue-2 virus. Twiddy SS, Farrar JJ, Chau NV, Wills B, Gould EA, Gritsun T, Lloyd G, Holmes EC, Virol 2002 298 63 72 10.1006/viro.2002.1447 (Pubitemid 34734880)
19. Molecular evolution and phylogeny of dengue type 4 virus in the Caribbean. Foster JE, Bennett SN, Vaughan H, Vorndam V, McMillan WO, Carrington CVF, Virol 2003 306 126 34 10.1016/S0042-6822(02)00033-8 (Pubitemid 36293403)
20. The origin, emergence and evolutionary genetics of dengue virus. Holmes EC, Twiddy SS, Infect Genet Evol 2003 3 19 28 10.1016/S1567-1348(03)00004-2 12797969 (Pubitemid 36437583)
21. Molecular epidemiological study of dengue virus type 1 in Taiwan. Hwang KP, Chu PY, Tung YC, Wang HL, Yueh YY, Wu YC, Chin C, Lin KH, J Med Virol 2003 70 404 409 10.1002/jmv.10410 12767004 (Pubitemid 36638054)
22. Molecular epidemiology of dengue virus type 3 in Venezuela. Uzcategui NY, Comach G, Camacho D, Salcedo M, de Quintana MC, Jimenez M, Siera G, Cuello R, James WS, Turner S, Holmes EC, Gould EA, J Gen Virol 2003 84 1569 1575 10.1099/vir.0.18807-0 12771427 (Pubitemid 36675528)
23. Phylogeography and molecular evolution of dengue 2 in the Caribbean basin, 1981-2000. Foster JE, Bennett SN, Carrington CVF, Vaughan H, McMillan WO, Virol 2004 324 48 59 10.1016/j.virol.2004.03.020 (Pubitemid 38737398)
24. Introduction of the American/Asian genotype of dengue 2 virus into the Yucatan State of Mexico. Lorõo-Pino MA, Farfan-Ale JA, Zapata-Peraza AL, Rosado-Paredes EP, Flores-Flores LF, García-Reján JE, AmJTrop Med Hyg 2004 71 485 492 (Pubitemid 39458343)
25. Genotipificacián y análisis filogenético de cepas colombianas del virus dengue tipo 2. Méndez JA, Bernal MP, Calvache D, Boshell J, NOVA 2003 1 37 43
26. Use of a Short Fragment of the C-Terminal E Gene for Detection and Characterization of Two New Lineages of Dengue Virus 1 in India. Domingo C, Palacios G, Jabado O, Reyes N, Niedrig M, Gascán J, Cabrerizo M, Lipkin WI, Tenorio A, J Clin Microbiol 2006 44 1519 1529 10.1128/JCM.44.4.1519-1529. 2006 16597885
27. Simultaneous circulation of genotypes I and III of dengue virus 3 in Colombia. Usme-Ciro JA, Mendez JA, Tenorio A, Rey Gloria J, Domingo C, Gallego-Gomez JC, Virol J 2008 5 101 110 10.1186/1743-422X-5-101 18764951
28. Phylogenetic studies reveal existence of multiple lineages of a single genotype of DENV-1 (genotype III) in India during 1956-2007. Kukreti H, Dash PK, Parida M, Chaudhary A, Saxena P, Rautela RS, Mittal V, Chhabra M, Bhattacharya D, Lal S, Rao PVL, Rai A, Virol J 2009 6 1 10.1186/1743-422X-6-1 19126194
29. Phylogenetic history demonstrates two different lineages of dengue type 1 virus in Colombia. Mendez JA, Usme-Ciro JA, Domingo C, Rey GJ, Sanchez JA, Tenorio A, Gallego-Gomez JC, Virol J 2010 7 226 10.1186/1743-422X-7-226 20836894
30. The reinvasion of Colombia by Aedes aegypti: aspects to remember. Groot H, AmJTrop Med Hyg 1980 29 330 338 (Pubitemid 10114307)
31. Dengue en Colombia: epidemiologia, estrategias de intervencián y perspectivas del problema. Padilla JC, Rojas D, Sáenz R, Rojas D, Bello B, Méndez JA, Ministerio de la Proteccián Social-Instituto Nacional de Salud Colombia 2010
32. Boletín de vigilancia de Dengue en Colombia. Instituto Nacional de Salud, 2011 No. 01 de
33. A New Tool for the Diagnosis and Molecular Surveillance of Dengue Infections in Clinical Samples. Domingo C, Palacios G, Niedrig M, Cabrerizo M, Jabado O, Reyes N, Lipkin WI, Tenorio A, Dengue Bulletin 2004 28 87 95 (Pubitemid 40716029)
34. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions specific gap penalties and weight matrix choice. Thompson JD, Higgins DG, Gibson TJ, Nucleic Acids Res 1994 22 4673 4680 10.1093/nar/22.22.4673 7984417 (Pubitemid 24354800)
35. MEGA4: Molecuar Evolutionary Genetics Analysis (MEGA) software version 4.0. Tamura K, Dudley J, Nei M, Kumar S, Mol Biol Evol 2007 24 1596 1599 10.1093/molbev/msm092 17488738 (Pubitemid 47236692)
36. Population dynamics of flaviviruses revealed by molecular phylogenies. Zanotto PM, Gould EA, Gao GF, Harvey PH, Holemes EC, Proc Natl Acad Sci USA 1996 93 548 53 10.1073/pnas.93.2.548 8570593 (Pubitemid 26041125)
37. Inferring the rate and time-scale of dengue virus evolution. Twiddy SS, Holmes EC, Rambaut A, Mol Biol Evol 2003 20 122 129 10.1093/molbev/msg010 12519914 (Pubitemid 36077906)
38. Molecular evolution of dengue viruses: Contributions of phylogenetics to understanding the history and epidemiology of the preeminent arboviral disease. Weaver SC, Vasilakis N, Inf Gen & Evol 2009 9 523 540 10.1016/j.meegid.2009. 02.003 21255527
39. Detection and genetic relationship of dengue virus sequences in seventeen-year-old paraffin-embedded samples from Cuba. Sariol CA, Pelegrino JL, Martinez A, Arteaga E, Kouri G, Guzman MG, AmJTrop Med Hyg 1999 61 994 1000 (Pubitemid 30084127)
40. Partial nucleotide and amino acid sequences of the envelope and the envelope/nonstructural protein-1 gene junction of four dengue-2 virus strains isolated during the 1981 Cuban epidemic. Guzman MG, Deubel V, Pelegrino JL, Rosario D, Marrero M, Sariol C, Kouri G, AmJTrop Med Hyg 1995 52 241 246
41. Failure of secondary infection eith American genotype dengue 2 to cause dengue hemorrhagic fever. Watts DM, Porter KR, Putvatana P, Vasquez B, Calampa C, Hayes CG, Halstead SB, Lancet 1999 354 1431 1434 10.1016/S0140-6736(99)04015- 5 10543670 (Pubitemid 29494755)
42. The phylogeography of human viruses. Holmes EC, Mol Ecol 2004 13 745 756 10.1046/j.1365-294X.2003.02051.x 15012753 (Pubitemid 38394011)
43. Lineage extinction and replacement in dengue type 1 virus populations are due to stochastic events rather than to natural selection. Myat TH, Lowry K, Jiang L, Hlaing T, Holmes EC, Aascov J, Virol 2005 336 163 172 10.1016/j.virol.2005.03.018 (Pubitemid 40693951)
44. Invasion and maintenance of dengue virus type 2 and type 4 in the Americas. Carrington CVF, Foster JE, Pybus OG, Bennett SN, Holmes EC, J Virol 2005 79 14680 14687 10.1128/JVI.79.23.14680-14687.2005 16282468 (Pubitemid 41636266)
45. Molecular epidemiology of dengue 2 viruses inthe Philippines: genotype shift and local evolution. Salda LTD, Parquet MDC, Matias RR, Natividad FF, Kobayashi N, Morita K, AmJTrop Med Hyg 2005 73 796 802 (Pubitemid 41446732)
46. Molecular evolution of dengue 2 virus in Puerto Rico: Positive selection in the viral envelope accompanies clade reintroduction. Bennett SN, Holmes EC, Chirivella M, Rodríguez DM, Beltrán M, Vorndam V, Gubler DJ, McMillan WO, J Gen Virol 2006 87 885 893 131 10.1099/vir.0.81309-0 16528038
47. RNA virus mutations and fitness for survival. Domingo E, Holland JJ, Annu Rev Microbiol 1997 51 151 178 10.1146/annurev.micro.51.1.151 9343347 (Pubitemid 27433046)
48. The causes and consequences of genetic variation in dengue virus. Holmes EC, Burch SS, Trends Microbiol 2000 8 74 7 10.1016/S0966-842X(99)01669-8 10664600 (Pubitemid 30100330)
49. Phylogenetic evidence for adaptive evolution of dengue viruses in nature. Twiddy SS, Woelk CH, Holmes EC, J Gen Virol 2002 83 1679 1689 12075087 (Pubitemid 34716274)
50. Selection-driven evolution of emergent dengue virus. Bennett SN, Holmes EC, Chirivella M, Rodríguez DM, Beltrán M, Vorndam V, Gubler DJ, McMillan WO, Mol Biol Evol 2003 20 1650 1658 10.1093/molbev/msg182 12832629 (Pubitemid 41070827)
51. Patterns of intra- and interhost nonsynonymous variation reveal strong purifying selection in dengue virus. Holmes EC, J Virol 2003 77 11296 11298 10.1128/JVI.77.20.11296-11298.2003 14512579 (Pubitemid 37204321)
52. Arbovirus evolution in viv is constrained by host alternation. Coffey LL, Vasilakis N, Brault AC, Powers AM, Tripet F, Weaver SC, PNAS 2008 105 6970 6975 10.1073/pnas.0712130105 18458341 (Pubitemid 351754514)
53. Mosquitoes put the brake on arbovirus evolution: Experimental evolution reveals slower mutation accumulation in Mosquito than vertebrate cells. Vasilakis N, Deardorff ER, Kenney JL, Rossi S, Hanley K, Weaver S, PLoS Pathogens 2009 5 1 18
54. Evolutionary relationships of endemic/epidemic and sylvatic dengue viruses. Wang E, Ni H, Xu R, Barrett ADT, Watowich SJ, Gubler DJ, Weaver SC, J Virol 2000 74 3227 3234 10.1128/JVI.74.7.3227-3234.2000 10708439 (Pubitemid 30143747)
55. Basic concepts in RNA virus evolution. Domingo E, Escarmis C, Sevilla N, Moya A, Elena SF, Quer J, Novella IS, Holland JJ, FASEB J 1996 10 859 864 8666162 (Pubitemid 26184164)
56. Mutation rates among RNA viruses. Drake JW, Holland JJ, Proc Natl Acad Sci USA 1999 96 13910 13913 10.1073/pnas.96.24.13910 10570172
57. Evolution of the sequence composition of flaviviruses. Shubert AM, Putoni C, Inf Gen & Evol 2010 10 129 136 10.1016/j.meegid.2009.11.004 21255527
58. Modeltest: testing the model of DNA substitution. Posada D, Crandall KA, Bioinformatics 1998 14 817 818 10.1093/bioinformatics/14.9.817 9918953 (Pubitemid 28552116)
59. Convert sequence formats using ReadSeq. Gilbert DG, http://iubio.bio. indiana.edu/soft/molbio/readseq/java/
60. PALM: A paralleled and integrated framework for Phylogenetic inference with Automatic Likelihood Model selectors. Chen SH, Su SY, Lo CZ, Chen KH, Huang TJ, Kuo BH, Lin CY, PLoS One 2009 4 12 8116 10.1371/journal.pone.0008116 19997614
61. BEAST: Bayesian evolutionary analysis by sampling trees. Drummond A, Rambaut A, BMC Evol Biol 2007 7 214 221 10.1186/1471-2148-7-214 17996036 (Pubitemid 351253125)
62. Bayesian inference of phylogeny: a non-technical primer. Archibald JK, Mort ME, Crawford DJ, Taxon 2003 52 187 191 10.2307/3647388 (Pubitemid 36844604)
63. Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies. Rambaut A, Bioinformatics 2000 16 395 399 10.1093/bioinformatics/16.4.395 10869038 (Pubitemid 30417084)
64. Relaxed phylogenetics and dating with confidence. Drummond A, Ho SYW, Phillips MJ, Rambaut A, PLoS Biology 2006 4 1 11 10.1371/journal.pbio.0040001 (Pubitemid 43128324)
65. Bayesian phylogeography finds its roots. Lemey P, Rambaut A, Drummond A, Suchard MA, PLoS Computational Biology 2009 5 1000520 10.1371/journal.pcbi. 1000520 19779555