Complete genome sequencing of dengue virus type 1 isolated in Buenos Aires, Argentina

Virus Research

Volumn 101, Issue 2, 2004, Pages 135-145

  Barrero, Paola R ^a   Mistchenko, Alicia S ^a  

^a HOSPITAL DE NIÑOS RICARDO GUTIÉRREZ   (Argentina)

Author keywords

Dengue; Molecular epidemiology; Sequencing

Indexed keywords

POLYPROTEIN; STRUCTURAL PROTEIN;

3' UNTRANSLATED REGION; ARGENTINA; ARTICLE; BRAZIL; CELL CULTURE; CELL ISOLATION; CONTROLLED STUDY; DENGUE VIRUS; EPIDEMIC; GENE MUTATION; GENE SEQUENCE; GENETIC ANALYSIS; GENOME; GENOTYPE; HUMAN; HUMAN CELL; MOLECULAR CLONING; NUCLEOTIDE SEQUENCE; PARAGUAY; PHENOTYPE; PHYLOGENY; PRESSURE; PRIORITY JOURNAL; PROTEIN PURIFICATION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEROTYPE; STRUCTURAL GENE; VIRUS DETECTION; VIRUS ISOLATION; VIRUS TRANSMISSION;

3' UNTRANSLATED REGIONS; ARGENTINA; CELL LINE; DENGUE VIRUS; GENES, VIRAL; GENOME, VIRAL; GENOMICS; HUMANS; MOLECULAR SEQUENCE DATA; MUTATION, MISSENSE; NUCLEIC ACID CONFORMATION; PHYLOGENY; PLAQUE ASSAY; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, VIRAL; SELECTION (GENETICS); SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY; VARIATION (GENETICS); VIRAL NONSTRUCTURAL PROTEINS; VIRAL STRUCTURAL PROTEINS;

ARTHROPODA; DENGUE VIRUS; DENGUE VIRUS TYPE 1;

EID: 1642282713     PISSN: 01681702     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.virusres.2003.12.033     Document Type: Article

References (59)

1. Avilés G., Rangeón G., Vorndam V., Briones A., Baroni P., Enria D., Sabattini M.S. Dengue reemergence in Argentina. Emerg. Infect. Dis. 5:1999;575-578.
2. Avilés G., Rowe J., Meissner J., Manzur Caffarena J.C., Enria D., St. Jeor S. Phylogenetic relationships of dengue-1 viruses from Argentina and Paraguay. Arch. Virol. 147:2002;2075-2087.
3. Boletín Epidemiológico República del Paraguay, 1999. Ministerio de Salud Pública y Bienestar social. Noviembre Año 5, N 17, 1-8, Asunción.
4. Boletín Epidemiológico República del Paraguay, 2000. Ministerio de Salud Pública y Bienestar social. Junio Año 6, N 19, 1-8, Asunción.
5. Boletín Epidemiológico Nacional, 2000-2001. Ministerio de Salud República Argentina.
6. Brinkworth R.I., Fairlie D.P., Leung D., Young P.R. Homology model of the dengue 2 virus NS3 protease: putative interactions with both substrate and NS2B cofactor. J. Gen. Virol. 80:1999;1167-1177.
7. Chen Y., Maguire T., Marks R.M. Demonstration of binding of dengue virus envelope protein to target cells. J. Virol. 70:1996;8765-8772.
8. Chomczynski P., Sacchi N. Single-step method of RNA isolation by guanidium thiocyanate-phenol-chloroform extraction. Anal. Biochem. 162:1987;156-159.
9. Desprès P., Frenkiel M.P., Deubel V. Differences between cell membrne fusion activities of two dengue type-1 isolates reflects modifications of viral structure. Virology. 196:1993;209-219.
10. Domingo E., Holland J.J. RNA virus mutations and fitness for survival. Ann. Rev. Microbiol. 51:1997;151-178.
11. dos Santos C.N.D., Rocha C.F.S., Cordeiro M., Fragoso S.P., Rey F., Deubel V., Desprès P. Genome analysis of dengue type-1 virus isolated between 1990 and 2001 in Brazil reveals a remarkable conservation of the structural proteins but amino acid differences in the non-structural proteins. Virus Res. 90:2002;197-205.
12. Egloff M.P., Benarroch D., Selisko B., Romette J.L., Canard B. An RNA cap (nucleoside-2′-O-)-methyltransferase in the flavivirus RNA polymerase NS5: crystal structure and functional characterization. EMBO J. 21:2002;2257-2768.
13. Falconar A.K.I. Identification of an epitope on the dengue virus membrane (M) protein defined by cross-protective monoclonal antibodies: design of an improved epitope sequence based on common determinants present in both E and M proteins. Arch. Virol. 144:1999;2313-2330.
14. Felsestein J. PHYLIP - phylogeny inference package. Cladistics. 5:1989;164-166.
15. Goncalvez A.P., Escalante A.A., Pujol F.H., Ludert J.E., Tovar D., Salas R.A., Liprandi F. Diversity and evolution of the envelope gene of dengue virus type 1. Virology. 303:2002;110-119.
16. Gubler D.J. Epidemic dengue/dengue hemorrhagic fever as a public health. Trends Microbiol. 10:2002;100-103.
17. Guzmán M.G., Kourí G. Dengue: an update. Lancet Infect. Dis. 2:2002;33-42.
18. Heinz F.X., Allison S.L. The machinery for flavivirus fusion with host cell membranes. Curr. Opin. Microbiol. 4:2001;450-455.
19. Holmes E.C., Worobey M., Rambaut A. Phylogenetic evidence for recombination in dengue virus. Mol. Biol. E. 16:1999;405-409.
20. Holmes E.C., Burch S.S. The causes and consequences of genetic variation in dengue virus. Trends Microbiol. 8:2000;74-77.
21. Jenkins G.M., Pagel M., Gould E.A., Zanotto P.M., de A., Holmes E.C. Evolution of base composition and codon usage bias in the genus Flavivirus. J. Mol. E. 52:2001;383-390.
22. Jianmin Z., Linn M.L., Bulich R., Gentry M.K., Aaskov J.G. Analysis of functional epitopes on the dengue 2 envelope (E) protein using monoclonal IgM antibodies. Arch. Virol. 140:1995;899-913.
23. Johansson M., Brooks A.J., Jans D.A., Vasudevan S.G. A small region of the dengue virus-encoded RNA-dependent RNA polymerase, NS5, confers interaction with both the nuclear transport receptor importin-beta and the viral helicase, NS3. J. Gen. Virol. 82:2001;735-745.
24. Khromykh A.A., Meka H., Guyatt K.J., Westaway E.G. Essential role of cyclization sequences in flavivirus RNA replication. J. Virol. 75:2001;6719-6728.
25. Lanciotti R.S., Callisher C.H., Gubler D.J., Chang G.J., Vorndam A.V. Rapid detection and typing of dengue viruses from clinical samples by using reverse transcriptase-polymerase chain reaction. J. Clin. Microbiol. 30:1992;545-551.
26. Leitmeyer K.C., Vaughn D.W., Watts D.M., Salas R., Villalobos I., Ramos C., Ricco-Hesse R. Dengue virus structural differences that correlate with pathogenesis. J. Virol. 73:1999;4738-4747.
27. Lole K.S., Bollinger R.C., Paranjape R.S., Gadkari D., Kulkarni S.S., Novak N.G., Ingersoll R., Sheppard H.W., Ray S.C. Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J. Virol. 73:1999;152-160.
28. Marchler-Bauer A., Anderson J.B., DeWeese-Scott C., Fedorova N.D., Geer L.Y., He S., Hurwitz D.I., Jackson J.D., Jacobs A.R., Lanczycki C.J., Liebert C.A., Liu C., Madej T., Marchler G.H., Mazumder R., Nikolskaya A.N., Panchenko A.R., Rao B.S., Shoemaker B.A., Simonyan V., Song J.S., Thiessen P.A., Vasudevan S., Wang Y., Yamashita R.A., Yin J.J., Bryant S.H. CDD: a curated entrez database of conserved domain alignments. Nucl. Acids Res. 31:2003;383-387.
29. Martin D., Rybicki E. RDP detection of recombination amongst aligned sequences. Bioinformatics. 16:2000;562-563.
30. Mathews D.H., Sabina J., Zuker M., Turner D.H. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288:1999;911-940.
31. Matzura O., Wennborg A. RNAdraw: an integrated program for RNA secondary structure calculation and analysis under 32-bit Microsoft Windows. Comput. Appl. Biosci. 12:1996;247-249.
32. Miagostovich M.P., dos Santos F.B., de Simone T.S., Costa E.V., Filippis A.M.B., Schatzmayr H.G., Nogueira R.M.R. Genetic characterization of dengue virus type 3 isolates in the State of Rio de Janeiro, 2001. Brazil J. Med. Biol. Res. 35:2002;869-872.
33. Nogueira R.M.R., Miagostovich M.P., Lampe E., Souza R.W., Zagne S.M.O., Schatzmayr H.G. Dengue epidemic in the state of Rio de Janeiro, Brazil, 1990-1991: co-circulation of dengue-1 and dengue-2. Epidemiol. Infect. 111:1993;163-170.
34. Ohta T., Tachida H. Theoretical study of near neutrality. I. Heterozygosity and rate of mutant substitution. Genetics. 126:1990;219-229.
35. Page R.D.M. Treeview: An application to display phylogenetic trees on personal computers. Comput. Appl. Biosci. 12:1996;357-358.
36. Posada D., Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics. 14:1998;817-818.
37. Proutski V., Gould E.A., Holmes E.C. Secondary structure of the 3′ unstranlated region of flaviviruses: similarities and differences. Nucl. Acids Res. 25:1997;1194-1202.
38. Proutski V., Gritsun T.S., Gould E.A., Holmes E.C. Biological consequences of deletions within the 3′ untranslated region of flaviviruses may be due to rearrangements of RNA secondary structure. Virus Res. 64:1999;107-123.
39. Puri B., Nelson W.M., Henchal E.A., Hoke C.H., Eckels K.H., Dubois D.R., Porter K.R., Hayes C.G. Molecular analysis of dengue virus attenuation after serial passage in primary dog kidney cells. J. Gen. Virol. 78:1997;2287-2291.
40. Rey F.A., Heinz F.X., Mandl C., Kunz C., Harrison S.C. The envelope glycoprotein from Tick encephalitis virus at 2. Å resolution Nature. 375:1995;291-298.
41. Rice, C.M., 1996. Flaviviridae: the viruses and their replication. In: Fields, B.N., Knipe, D.M., Chanock, R.M., Hirsch, M.S, Melnick, J.L, Monath, T.P., Roizman, B. (Eds.), Fields Virology, third ed. Lippincot-Raven, Philadelphia.
42. Rigau-Pérez J.G., Clark G.G., Gubler D.J., Reiter P., Sanders E.J., Vorndam A.V. Dengue and dengue haemorrhagic fever. Lancet. 352:1998;971-977.
43. Roehrig J.T., Risi P.A., Brubaker J.R., Hunt A.R., Beaty B.J., Trent D.W., Mathews J.H. T-helper cell epitopes on the E-glycoprotein of dengue 2 Jamaica virus. Virology. 198:1994;31-38.
44. Rozas J., Rozas R. DNASP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics. 15:1999;174-175.
45. Sala M., Wain-Hobson S. Are RNA viruses adapting or merely changing? J. Mol. E. 51:2000;12-20.
46. Shurtleff A.C., Beasley D.W.C., Chen J.J.Y., Ni H., Suderman M.T., Wang H., Xu R., Wang E., Weaver S.C., Watts D.M., Russell K.L., Barrett A.D.T. Genetic variation in the 3′ non-coding region of dengue viruses. Virology. 281:2001;75-87.
47. Smith D.B., McAllister J., Casino C., Simmonds P. Virus quasispecies: making a mountain out of a molehill. J. Gen. Virol. 78:1997;1511-1519.
48. Swofford, D.L., 1998. PAUP*. Phylogenetic Analysis Using Parsimony (* and Other Methods). version 4. Sinauer Associates, Sunderland, Massachusetts.
49. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 123:1989;585-595.
50. Tamura K., Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. E. 10:1993;512-526.
51. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl. Acids Res. 24:1997;4876-4882.
52. Tolou H.J.G., Durand J.-P., Mercier V., de Pina J.J., de Mico P., Billoir F., Charrel R.N., Lamballerie X. Evidence for recombination in natural populations of dengue virus type-1 based on the analysis of complete genome sequences. J. Gen. Virol. 82:2001;1283-1290.
53. Twiddy S.S., Woelk C.H., Holmes E.C. Phylogenetic evidence for adaptative evolution of dengue viruses in nature. J. Gen. Virol. 83:2002;1679-1689.
54. Van der Stuyft P., Gianella A., Pirard M., Holzman A., Peredo C., Boelaert M., Vorndam V. Dengue serotype 2 subtype III (Jamaica) epidemic in Santa Cruz, Bolivia. Trop. Med. Int. Health. 3:1998;857-858.
55. Wang W.K., Lin S.R., Lee C.M., King C.C., Chang S.C. Dengue-3 virus in plasma is a population of closely realted genomes: quasispecies. J. Virol. 76:2002a;4662-4665.
56. Wang W.K., Sung T.L., Lee C.N., Lin T.Y., King C.C. Sequence diversity of the capsid gene and the nonstructural gene NSB of dengue-3 virus in vivo. Virology. 303:2002;181-191.
57. Wu H.C., Huang Y.L., Chao T.T., Jan J.T., Huang J.L., Chiang H.Y., King C.C., Shaio M.F. Identification of B-cell epitope of dengue virus type 1 and its application in diagnosis of patients. J. Clin. Microbiol. 39:2001;977-982.
58. Yao Z.J., Kao M.C.C., Loh K.C., Chung M.C.M. A serotype-specific epitope of dengue virus 1 identified by phage isplayed ramdom peptide library. FEMS Microbiol. Lett. 127:1995;93-98.
59. You S., Falgout B., Markoff L., Padmanabhan R. In vitro RNA synthesis from exogenous dengue viral RNA templates requires long range interactions between 5′- and 3′-terminal regions that influence RNA structure. J. Biol. Chem. 276:2001;15581-15591.