Molecular genetic relationship of the 3′ untranslated region among thai dengue-3 virus, bangkok isolates, during 1973-2000

DNA and Cell Biology

Volumn 28, Issue 10, 2009, Pages 481-491

  Pankhong, Panyupa ^a,b   Weiner, David B ^b   Ramanathan, Mathura P ^b   Nisalak, Ananda ^c   Kalayanarooj, Siripen ^d   Nimmannitya, Suchitra ^d   Attatippaholkun, Watcharee ^a  

^a MAHIDOL UNIVERSITY   (Thailand)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

^c ARMED FORCES RESEARCH INSTITUTE OF MEDICAL SCIENCES   (Thailand)

^d QUEEN SIRIKIT NATIONAL INSTITUTE OF CHILD HEALTH   (Thailand)

Author keywords

[No Author keywords available]

Indexed keywords

NONSTRUCTURAL PROTEIN 5;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ANIMAL CELL; APOPTOSIS; ARTICLE; CELL LINE; CHILD; CHILD HOSPITALIZATION; CODON; CONTROLLED STUDY; DENGUE VIRUS; DENGUE VIRUS 3; DISEASE SEVERITY; DNA FLANKING REGION; GENE DELETION; GENE INSERTION; GENE SEQUENCE; GENETIC HETEROGENEITY; GENOTYPE; HUMAN; HUMAN CELL; MOLECULAR GENETICS; MOSQUITO; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PRIORITY JOURNAL; THAILAND; VIRUS ISOLATION; VIRUS REPLICATION;

3' UNTRANSLATED REGIONS; ANIMALS; BASE SEQUENCE; CELL LINE; CODON, TERMINATOR; DENGUE; DENGUE VIRUS; DNA PRIMERS; DNA, VIRAL; HUMANS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SEQUENCE HOMOLOGY, NUCLEIC ACID; SPECIES SPECIFICITY; THAILAND;

DENGUE VIRUS; DENGUE VIRUS TYPE 3;

EID: 70349448653     PISSN: 10445498     EISSN: None     Source Type: Journal    
DOI: 10.1089/dna.2008.0835     Document Type: Article

References (49)

1. Alvarez, D.E., De Lella Ezcurra, A.L., Fucito, S., and Gamarnik, A.V. (2005a). Role of RNA structures present at the 30 UTR of dengue virus on translation, RNA synthesis, and viral replication. Virology 339, 200-212.
2. Alvarez, D.E., Lodeiro, M.F., Luduena, S.J., Pietrasanta, L.I., and Gamarnik, A.V. (2005b). Long-range RNA-RNA interactions circularize the dengue virus genome. J Virol 79, 6631-6643.
3. Bhamarapravati, N. (1997). Pathology of dengue infection. In Dengue and Dengue Hemorrhagic Fever. D.J. Gubler and G. Kuno, eds. (CAB International, Wallingford, UK), pp. 115-132.
4. Boom, R., Sol, C.J.A., Solimans, M.M.M., Jansen, C.L., Wertheimvan Dillen, P.M.E., and van der Noorden, J. (1990). Rapid and simple method for purification of nucleic acids. J Clin Methods 28, 495-503.
5. Brinton, M., and Dispoto, J.H. (1988). Sequenced and secondary structure analysis of the 50-terminal region of flavivirus genome RNA. Virology 162, 290-299.
6. Brinton, M.A., Fernandez, A.V., and Amato, J. (1986). The 30- nucleotides of flavivirus genome RNA form a conserved secondary structure. Virology 153, 113-121.
7. Cahour, A., Pletnev, A., Vazielle-Falcoz, M., Rosen, L., and Lai, C.J. (1995). Growth-restricted dengue virus mutants containing deletions in the 50 noncoding region of the RNA genome. Virology 207, 68-76.
8. Cologna, R., and Rico-Hesse, R. (2003). American genotype structures decrease dengue virus output from human monocytes and dendritic cells. J Virol 77, 3929-3938.
9. Couvelard, A., Marianneau, P., Bedel, C., Drouet, M.T., Vachon, F., Henin, D., and Deuble, V. (1999). Report of a fatal cases of dengue infection with hepatitis: demonstration of dengue antigens in hepatocytes and liver apoptosis. Hum Pathol 30, 1106-1110.
10. Gubler, D.J. (1998). Dengue and dengue hemorrhagic fever. Clin Microbiol Rev 11, 480-496.
11. Hahn, C.S., Hahn, Y.S., Rice, C.M., Lee, E., Dalgarno, L., Strauss, E.G., and Strauss, J.H. (1987). Conserved elements in the 30 untranslated region of flavivirus RNAs and potential cyclization sequences. J Mol Biol 198, 33-41.
12. Holden, K.L., and Harris, E. (2004). Enhancement of dengue virus translation: role of the 30 untranslated region and the terminal 30 stem-loop domain. Virology 329, 119-133.
13. Huerre, M.R., Lan, N.T., Marianneau, P., Hue, N.B., Khun, H., Hung, N.T., Khen, N.T., Drouet, M.T., Huong, V.T., Ha, D.Q., Buisson, Y., and Deubel, V. (2001). Liver histopathology and biological correlates in five cases of fatal dengue fever in Vietnamese children. Virchows Arch 438, 107-115.
14. Jan, J.T., Chen, B.H., Ma, S.H., Liu, C.I., Tsai, H.P., Wu, H.C., Jiang, S.Y., Yang, K.D., and Shaio, M.F. (2000). Potential dengue virus-triggered apoptotic pathway in human neuroblastoma cells: arachidonic acid, superoxide anion, and NFkappaB are sequentially involved. J Virol 74, 8680-8691.
15. Khromykh, A.A., and Westaway, E.G. (1997). Subgenomic replicons of the flavivirus Kunjin: construction and applications. J Virol 71, 1497-1505.
16. Klungthong, C., Putnak, R., Mammen, M.P., Li, T., and Zhang, C. (2008). Molecular genotyping of dengue viruses by phylogenetic analysis of the sequences of individual genes. J Virol Methods 154, 175-181.
17. Lanciotti, R.S., Lewis, J.G., Gubler, D.J., and Trent, D.W. (1994). Molecular evolution and epidemiology of dengue-3 viruses. J Gen Virol 75, 65-75.
18. Leitmeyer, K.C., Vaughn, D.W., Watts, D.M., Salas, R., de C Villalobos, I., Ramos, C., and Rico-Hesse, R. (1999). Dengue virus structural differences that correlate with pathogenesis. J Virol 73, 4738-4747.
19. Lindenbach, B.D., and Rice, C.M. (2001). Flaviviridae: the viruses and their replication. In Fields Virology, fourth edition. D.M. Knipe and P.M. Howley, eds. (Lippincott Williams & Wilkins, Philadelphia, PA), pp. 991-1041.
20. Liu, X., Kim, C.N., Yang, J., Jemmerson, R., and Wang, X. (1996). Induction of apoptotic program in cell-free extracts: requirement for dATP and cytochrome c. Cell 86, 147-157.
21. Mackenzie, J.S., Gubler, D.J., and Petersen, L.R. (2004). Emerging flaviviruses: the spread and resurgence of Japanese encephalitis, West Nile and dengue viruses. Nat Med 10, S98-S109.
22. Mandl, C.W., Holzmann, H., Meixner, T., Rauscher, S., Stadler, P.F., Allison, S.L., and Heinz, F.X. (1998). Spontaneous and engineered deletions in the 30 noncoding region of tick-borne encephalitis virus: construction of highly attenuated mutants of a flavivirus. J Virol 72, 2132-2140.
23. Marianneau, P., Cardona, A., Edelman, L., Deubel, V., and Despres, P. (1997). Dengue virus replication in human hepatoma cells activates NF-kB which in turn induces apoptotic cell death. J Virol 71, 3244-3249.
24. Markoff, L. (2003). 50- and 30-noncoding regions in flavivirus RNA. Adv Virus Res 59, 177-228.
25. Mathews, D.H., Sabina, J., Zuker, M., and Turner, D.H. (1999). Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 288, 911-940.
26. Men, R., Bray, M., Clark, D., Chanock, R.M., and Lai, C.J. (1996). Dengue type 4 virus mutants containing deletions in the 30 noncoding region of the RNA genome: analysis of growth restriction in cell culture and altered viremia pattern and immunogenicity in Rhesus monkeys. J Virol 70, 3930-3937.
27. Morita, K., Tanaka, M., and Igarashi, A. (1991). Rapid identification of dengue virus serotypes by using polymerase chain reaction. J Clin Microbiol 29, 2107-2110.
28. Nicholson, W.D., Ali, A., Thornberry, N.A., Vailancourt, J.P., Ding, C.K., Gallant, M., Gareau, Y., Griffin, P.R., Labelle, M., Lazebnik, Y.A., Munday, N.A., Raju, S.M., Smulson, M.E., Yamin, T.-T., Yu, V.L., and Miller, D.K. (1995). Identification and inhibition of the ICE=CED-3 protease necessary for mammalian apoptosis. Nature 376, 37-43.
29. Nimmannitya, S. (1987). Clinical spectrum and management of dengue haemorrhagic fever. Southeast Asian J Trop Med Public Health 18, 392-397.
30. Nisalak, A., Endy, T.P., Nimmannitya, S., Kalayanarooj, S., Thisayakorn, U., Scott, R.M., Burke, D.S., Hoke, C.H., Innis, B.L., and Vaughn, D.W. (2003). Serotype-specific dengue virus circulation and dengue disease in Bangkok, Thailand from 1973 to 1999. Am J Trop Med Hyg 68, 191-202.
31. Proutski, V., Gould, E.A., and Holmes, E.C. (1997). Secondary structure of the 30 untranslated region of flaviviruses: similarities and differences. Nucleic Acids Res 25, 1194-1202.
32. Raekiansyah, M., Pramesyanti, A., Bela, B., Kosasih, H., Ma'roef, C.N., Tobing, S.Y., Rudiman, P.I., Alisjahbana, B., Endi, T.P., Green, S., Kalayanarooj, S., Rothman, A.L., and Sudiro, T.M. (2005). Genetic variations and relationship among dengue virus type 3 strains isolated from patients with mild or severe form of dengue disease in Indonesia and Thailand. Southeast Asian J Trop Med Public Health 36, 1187-1197.
33. Reed, J.C. (1997). Cytochrome c: can't live with it-can't live without it. Cell 91, 559-562.
34. Rodriguez-Roche, R., Alvarez, M., Holmes, E.C., Bernardo, L., Kouri, G., Gould, E.A., Halstead, S., and Guzman, M.G. (2005). Dengue virus type 3, Cuba, 2000-2002. Emerg Infect Dis 11, 773-774.
35. Shi, P.Y., Li, W., and Brinton, M.A. (1996). Cell proteins bind specifically to West Nile virus minus-strand 30 stem-loop RNA. J Virol 70, 6278-6287.
36. Shi, P.Y., Tilgner, M., and Lo, M.K. (2002). Construction and characterization of subgenomic replicons of New York strain of West Nile virus. Virology 296, 219-233.
37. Shurtleff, A.C., Beasley, D.W., Chen, J.J., Ni, H., Suderman, M.T., Wang, H., Xu, R., Wang, E., Weaver, S.C., Watts, D.M., Russell, K.L., and Barrett, A.D. (2001). Genetic variation in the 30 non-coding region of dengue viruses. Virology 281, 75-87.
38. Sithisarn, P., Suksanpaisan, L., Thepparit, C., and Smith, D.R. (2003). Behavior of the dengue virus in solution. J Med Virol 71, 532-539.
39. Swofford, D. (2002). PAUP , Phylogenetic Analysis Using Parsimony (and Other Methods) 4.0b10 (Sinauer, Sunderland, MA).
40. Tajima, S., Nukui, Y., Ito, M., Takasaki, T., and Kurane, I. (2006). Nineteen nucleotides in the variable region of 30 nontranslated region are dispensable for the replication of dengue type 1 virus in vitro. Virus Res 116, 38-44.
41. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., and Higgins, D.G. (1997). The clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24, 4876-4882.
42. Wallner, G., Mandi, C.W., Kunz, C., and Heinz, F.X. (1995). The flavivirus 30 non-coding region: extensive size heterogeneity independent of evolutionary relationships among strains of tick-borne encephalitis. Virology 213, 169-178.
43. Wichmann, O., Hongsiriwon, S., Bowonwatanuwong, C., Chotivanich, K., Sukthana, Y., and Pukrittayakamee, S. (2004). Risk factors and clinical features associated with severe dengue infection in adults and children during the 2001 epidemic in Chonburi, Thailand. Trop Med Int Health 9, 1022-1029.
44. Wittke, V., Robb, T.E., Thu, H.M., Nisalak, A., Nimmannitya, S., Kalayanarooj, S., Vaughn, D.W., Endy, T.P., Holmes, E.C., and Aaskov, J.G. (2002). Extinction and rapid emergence of strains of dengue 3 virus during an interepidemic period. Virology 301, 148-156.
45. Yocupicio-Monroy, R.M.E., Medina, F., del Valle, J.R., and del Angel, R.M. (2003). Cellular proteins from human monocytes bind to dengue 4 virus minus-strand 30 untranslated region RNA. J Virol 77, 3067-3076.
46. You, S., and Padmanabhan, R. (1999). A novel in vitro replication system for dengue virus. Initiation of RNA synthesis at the 30- end of exogenous viral RNA templates requires 50- and 30-terminal complementary sequence motifs of the viral RNA. J Biol Chem 274, 33714-33722.
47. Zeng, L., Falgout, B., and Markoff, L. (1998). Identification of specific nucleotide sequences within the conserved 30-SL in the dengue type 2 virus genome required for replication. JVirol 72, 7510-7522.
48. Zhang, C., Mammen, M.P., Jr., Chinnawirotpisan, P., Klungthong, C., Rodpradit, P., Monkongdee, P., Nimmannitya, S., Kalayanarooj, S., and Holmes, E.C. (2005). Clade replacements in dengue virus serotypes 1 and 3 are associated with changing serotype prevalence. J Virol 79, 15123-15130.
49. Zuker, M. (2003). Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31, 3406-3415.