Comparative analysis of full-length genomic sequences of 10 dengue serotype 1 viruses associated with different genotypes, epidemics, and disease severity isolated in Thailand over 22 years

American Journal of Tropical Medicine and Hygiene

Volumn 83, Issue 5, 2010, Pages 1156-1165

  Tang, Yuxin ^a   Rodpradit, Prinyada ^b   Chinnawirotpisan, Piyawan ^b   Mammen Jr , Mammen P ^b   Li, Tao ^a   Lynch, Julia A ^a   Putnak, Robert ^a   Zhang, Chunlin ^a,b  

^a WALTER REED ARMY INSTITUTE OF RESEARCH   (United States)

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

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; AMINO ACID SUBSTITUTION; ARTICLE; CASE REPORT; DENGUE VIRUS 1; DISEASE SEVERITY; DISEASE TRANSMISSION; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC VARIABILITY; HUMAN; NONHUMAN; SEQUENCE ANALYSIS; THAILAND; VIRUS GENE; VIRUS ISOLATION; CHEMISTRY; CHILD; CLASSIFICATION; COMPARATIVE STUDY; DENGUE; DENGUE VIRUS; EPIDEMIC; FEMALE; GENETICS; GENOTYPE; HOSPITALIZATION; INFANT; MALE; NUCLEOTIDE SEQUENCE; PATHOGENICITY; PRESCHOOL CHILD; TIME; VIROLOGY; VIRUS GENOME;

DENGUE VIRUS;

VIRUS RNA;

AMINO ACID SUBSTITUTION; BASE SEQUENCE; CHILD; CHILD, PRESCHOOL; DENGUE; DENGUE VIRUS; DISEASE OUTBREAKS; FEMALE; GENOME, VIRAL; GENOTYPE; HUMANS; INFANT; MALE; RNA, VIRAL; SEVERITY OF ILLNESS INDEX; THAILAND; TIME FACTORS;

EID: 79952045479     PISSN: 00029637     EISSN: None     Source Type: Journal    
DOI: 10.4269/ajtmh.2010.10-0052     Document Type: Article

References (60)

1. Jennifer LK, Harris E, 2008. Global spread and persistence of dengue. Annu Rev Microbiol 62: 71-92.
2. Gubler DJ, 1998. Dengue and dengue hemorrhagic fever. Clin Microbiol Rev 11: 480-496. (Pubitemid 28379096)
3. World Health Organization, 2007. TDR Report of Dengue Scientific Working Group. TDR/SWG/08, Geneva. Available at: http://www.who.int/tdr/publications/ publications/swg-dengue-2.htm. Accessed July 2008.
4. Gubler DJ, 2006. Dengue/dengue haemorrhagic fever: history and current status. Novartis Found Symp 277: 3-16; discussion 16-22, 71-73, 251-253.
5. Myat Thu H, Lowry K, Jiang L, Hlaing T, Holmes EC, Aaskov J, 2005. Lineage extinction and replacement in dengue type 1 virus populations are due to stochastic events rather than to natural selection. Virology 336: 163-172. (Pubitemid 40693951)
6. Zhang C, Mammen MP Jr, Chinnawirotpisan P, Klungthong C, Rodpradit P, Monkongdee P, Nimmannitya S, Kalayanarooj S, Holmes EC, 2005. Clade replacements in dengue virus serotypes 1 and 3 are associated with changing serotype prevalence. J Virol 79: 15123-15130. (Pubitemid 43032295)
7. Domingo E, Holland JJ, 1994. Mutation rates and rapid evolution of RNA viruses. Morse SS, ed. The Evolutionary Biology of Viruses. New York: Raven Press, 161-184.
8. Drakes JW, Holland JJ, 1999. Mutation rates among RNA viruses. Proc Natl Acad Sci USA 96: 13910-13913.
9. Adams B, Holmes EC, Zhang C, Mammen MP Jr, Nimmannitya S, Kalayanarooj S, Boots M, 2006. Cross-protective immunity can account for the alternating epidemic pattern of dengue virus serotypes circulating in Bangkok. Proc Natl Acad Sci USA 103: 14234-14239. (Pubitemid 44453009)
10. Nisalak A, Endy TP, Nimmannitya S, Kalayanarooj S, Thisayakorn U, Scott RM, Burke DS, Hoke CH, Innis BL, Vaughn DW, 2003. Serotype-specific dengue virus circulation and dengue disease in Bangkok, Thailand from 1973 to 1999. Am J Trop Med Hyg 68: 191-202. (Pubitemid 38240545)
11. Halstead SB, Scanlon JE, Umpaivit P, Udomsakdi S, 1969. Dengue and chikungunya virus infection in man in Thailand, 1962-1964. IV. Epidemiologic studies in the Bangkok metropolitan area. Am J Trop Med Hyg 18: 997-1021.
12. Nimmannitya SHS, Cohen S, Margiontta MR, 1969. Dengue and chikungunya virus infection in man in Thailand, 1962-1964. I. Observation on hospitalized patients with hemorrhagic fever. Am J Trop Med Hyg 18: 954-971.
13. Halstead SB, Udomsakdi S, Scanlon JE, Rohitayodhin S, 1969. Dengue and chikungunya virus infection in man in Thailand, 1962-1964. V. Epidemiologic observations outside Bangkok. Am J Trop Med Hyg 18: 1022-1033.
14. Klungthong C, Zhang C, Mammen MP Jr, Ubol S, Holmes EC, 2004. The molecular epidemiology of dengue virus serotype 4 in Bangkok, Thailand. Virology 329: 168-179. (Pubitemid 39346038)
15. Zhang C, Mammen MP Jr, Chinnawirotpisan P, Klungthong C, Rodpradit P, Nisalak A, Vaughn DW, Nimmannitya S, Kalayanarooj S, Holmes EC, 2006. Structure and age of genetic diversity of dengue virus type 2 in Thailand. J Gen Virol 87: 873-883.
16. Zhao R, Chinnawirotpisan P, Klungthong C, Zhang C, Putnak R, 2010. Evidence for inter- and intra-genotypic variations in dengue type 4 viruses representing predominant and non-predominant genitypes co-circulating in Thailand from 1997 to 2001. Virus Genes 41: 5-13.
17. Holmes EC, 2003. Patterns of intra- and interhost nonsynonymous variation reveal strong purifying selection in dengue virus. J Virol 77: 11296-11298. (Pubitemid 37204321)
18. Markoff L, 2003. 5′- and 3′-noncoding regions in flavivirus RNA. Adv Virus Res 59: 177-228.
19. Zhou Y, Mammen MP Jr, Klungthong C, Chinnawirotpisan P, Vaughn DW, Nimmannitya S, Kalayanarooj S, Holmes EC, Zhang C, 2006. Comparative analysis reveals no consistent association between the secondary structure of the 3′-untranslated region of dengue viruses and disease syndrome. J Gen Virol 87: 2595-2603.
20. Zuo Z, Liew OW, Chen G, Chong PC, Lee SH, Chen K, Jiang H, Puah CM, Zhu W, 2009. Mechanism of NS2B-mediated activation of NS3pro in dengue virus: molecular dynamics simulations and bioassays. J Virol 83: 1060-1070.
21. Hasegawa H, Yoshida M, Shiosaka T, Fujita S, Kobayashi Y, 1992. Mutations in the envelope protein of Japanese encephalitis virus affect entry into cultured cells and virulence in mice. Virology 191: 158-165.
22. Jiang WR, Lowe A, Reid S, Could EA, 1993. Single amino acid codon changes in louping ill virus antibody-resistant mutants with reduced neurovirulence. J Gen Virol 74: 931-935. (Pubitemid 23154299)
23. Mandl CW, Guirakhoo F, Holzmann H, Heinz FX, Kunz C, 1989. Antigenic structure of the flavivirus envelop protein E at the molecular level, using tick-bone encephalitis virus as a model. J Virol 63: 564-571. (Pubitemid 19057220)
24. Leitmeyer KC, Vaughn DW, Watts DM, Salas R, Villalobos I, Chacon de, Ramos C, Rico-Hesse R, 1999. Dengue virus structural differences that correlate with pathogenesis. J Virol 73: 4738-4747. (Pubitemid 29246733)
25. Bulich R, Aaskov JG, 1992. Nuclear localization of dengue 2 virus core protein detected with monoclonal antibodies. J Gen Virol 73: 2999-3003.
26. Makino Y, Tadano M, Anzai T, Ma SP, Yasuda S, Fukunaga T, 1989. Detection of dengue 4 virus core protein in the nucleus. II. Antibody against dengue 4 core protein produced by a recombinant baculovirus reacts with the antigen in the nucleus. J Gen Virol 70: 1417-1425. (Pubitemid 19165603)
27. Tadano M, Makino Y, Fukunaga T, Okuno Y, Fukai K, 1989. Detection of dengue 4 virus core protein in the nucleus. I. A monoclonal antibody to dengue 4 virus reacts with the antigen in the nucleus and cytoplasm. J Gen Virol 70: 1409-1415. (Pubitemid 19165602)
28. Sangiambut S, Keelapang P, Aaskov J, Puttikhunt C, Kasinrerk W, Malasit P, Sittisombut N, 2008. Multiple regions in dengue virus capsid protein contribute to nuclear localization during virus infection. J Gen Virol 89: 1254-1264.
29. Hsieh TY, Matsumoto M, Chou H. C, Schneider R, Hwang S. B, Lee AS, Lai MM, 1998. Hepatitis C virus core protein interacts with heterogeneous nuclear ribonucleoprotein K. J Biol Chem 273: 17651-17659. (Pubitemid 28355103)
30. Chang CJ, Luh HW, Wang SH, Lin HJ, Lee SC, Hu ST, 2001. The heterogeneous nuclear ribonucleoprotein K (hnRNP K) interacts with dengue virus core protein. DNA Cell Biol 20: 569-577.
31. Michelotti EF, Michelotti GA, Aronsohn AI, Levens D, 1996. Heterogeneous nuclear ribonucleoprotein K is a transcription factor. Mol Cell Biol 16: 2350-2360. (Pubitemid 26123756)
32. Prendergast GC, 1999. Mechanism of apoptosis by c-Myc. Oncogene 18: 2967-2987.
33. Lee E, Weir RC, Dalgarno L, 1997. Changes in the dengue virus major envelope protein on passaging and their localization on the three-dimensional structure of the protein. Virology 232: 281-290. (Pubitemid 27293571)
34. Nayak V, Dessau M, Kucera K, Anthony K, Ledizet M, Modis Y, 2009. Crystal structure of dengue virus type 1 envelope protein in the postfusion conformation and its implications for membrane fusion. J Virol 83: 4338-4344.
35. Twiddy SS, Woelk CH, Holmes EC, 2002. Phylogenetic evidence for adaptive evolution of dengue viruses in nature. J Gen Virol 83: 1679-1689. (Pubitemid 34716274)
36. Wengler G, Czaya G, Farber PM, Hegemann JH, 1991. In vitro synthesis of West Nile virus proteins indicates that the aminoterminal segment of the NS3 protein contains the active centre of the protease which cleaves the viral polyprotein after multiple basic amino acids. J Gen Virol 72: 851-858.
37. Chambers TJ, Nestorowicz A, Amberg SM, Rice CM, 1993. Mutagenesis of the yellow fever virus NS2B protein: effects on proteolytic processing, NS2B-NS3 complex formation, and viral replication. J Virol 67: 6797-6807. (Pubitemid 23309150)
38. Li H, Clum S, You S, Ebner KE, Padmanabhan R, 1999. The serine protease and RNA-stimulated nucleoside triphosphatase and RNA helicase functional domains of dengue virus type 2 NS3 converge within a region of 20 amino acids. J Virol 73: 3108-3116. (Pubitemid 29135701)
39. Yusof R, Clum S, Wetzel M, Murthy HM, Padmanabhan R, 2000. Purified NS2B/NS3 serine protease of dengue virus type 2 exhibits cofactor NS2B dependence for cleavage of substrates with dibasic amino acids in vitro. J Biol Chem 275: 9963-9969. (Pubitemid 30202042)
40. Bartelma G, Padmanabhan R, 2002. Expression, purification, and characterization of the RNA 5′-triphosphatase activity of dengue virus type 2 nonstructural protein 3. Virology 299: 122-132. (Pubitemid 35007517)
41. Benarroch D, Selisko B, Locatelli GA, Maga G, Romette JL, Canard B, 2004. The RNA helicase, nucleotide 5′-triphosphatase, and RNA 5′-triphosphatase activities of Dengue virus protein NS3 are Mg2+-dependent and require a functional Walker B motif in the helicase catalytic core. Virology 328: 208-218. (Pubitemid 39349470)
42. Walker JE, Saraste M, Runswick MJ, Gay NJ, 1982. Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J 1: 945-951.
43. Singleton MR, Wigley DB, 2002. Modularity and specialization in superfamily 1 and 2 helicases. J Bacteriol 184: 1819-1826. (Pubitemid 34275522)
44. Sampath A, Xu T, Chao A, Luo D, Lescar J, Vasudevan SG, 2006. Structure-based mutational analysis of the NS3 helicase from dengue virus. J Virol 80: 6686-6690. (Pubitemid 43927471)
45. Roosendaal J, Westaway EG, Khromykh A, Mackenzie JM, 2006. Regulated cleavages at the West Nile virus NS4A-2K-NS4B junctions play a major role in rearranging cytoplasmic membranes and golgi trafficking of the NS4A protein. J Virol 80: 4623-4632.
46. Brooks AJ, Johansson M, John AV, Xu Y, Jans DA, Vasudevan SG, 2002. The interdomain region of dengue NS5 protein that binds to the viral helicase NS3 contains independently functional importin beta 1 and importin alpha/beta-recognized nuclear localization signals. J Biol Chem 277: 36399-36407.
47. Kapoor M, Zhang L, Ramachandra M, Kusukawa J, Ebner KE, Padmanabhan R, 1995. Association between NS3 and NS5 proteins of dengue virus type 2 in the putative RNA replicase is linked to differential phosphorylation of NS5. J Biol Chem 270: 19100-19106.
48. Yap TL, Xu T, Chen YL, Malet H, Egloff MP, Canard B, Vasudevan SG, Lescar J, 2007. Crystal structure of the dengue virus RNA-dependent RNA polymerase catalytic domain at 1.85-angstrom resolution. J Virol 81: 4753-4765. (Pubitemid 46668672)
49. Medin CL, Fitzgerald KA, Rothman AL, 2005. Dengue virus nonstructural protein NS5 induces interleukin-8 transcription and secretion. J Virol 79: 11053-11061. (Pubitemid 41170646)
50. Khabar KSA-ZF, Al-Ahdal MN, Murayama T, Dhalla M, Mukaida N, Taha M, Al-Sedairy ST, Siddiqui Y, Kessie G, Matsushima K, 1997. The alpha chemokine, interleukin 8, inhibits the antiviral action of interferon alpha. J Exp Med 186: 1077-1085. (Pubitemid 27441151)
51. Pryor MJ, Rawlinson SM, Butcher RE, Barton CL, Waterhouse TA, Vasudevan SG, Bardin PG, Wright PJ, Jans DA, Davidson AD, 2007. Nuclear localization of dengue virus nonstructural protein 5 through its importin alpha/beta-recognized nuclear localization sequences is integral to viral infection. Traffic 8: 795-807. (Pubitemid 46971628)
52. Chambers TJ, McCourt DW, Rice CM, 1989. Yellow fever virus proteins NS2A, NS2B, and NS4B: identification and partial N-terminal amino acid sequence analysis. Virology 169: 100-109.
53. Kümmerer B, Rice CM, 2002. Mutations in yellow fever virus nonstructural protein NS2A selectively block production of infectious particles. J Virol 76: 4773-4784. (Pubitemid 34441683)
54. Leung JY, Pijlman GP, Kondratieva N, Hyde J, Mackenzie JM, Khromykh AA, 2008. Role of nonstructural protein NS2A in flavivirus assembly. J Virol 82: 4731-4741. (Pubitemid 351657035)
55. Munoz-Jordan JL, Laurent-Rolle M, Ashour J, Martinez-Sobrido L, Ashok M, Lipkin WI, Garcia-Sastre A, 2005. Inhibition of alpha/beta interferon signaling by the NS4B protein of flaviviruses. J Virol 79: 8004-8013. (Pubitemid 40853504)
56. Munoz-Jordan JL, Sanchez-Burgos GG, Laurent-Rolle M, Garcia-Sastre A, 2003. Inhibition of interferon signaling by dengue virus. Proc Natl Acad Sci USA 100: 14333-14338. (Pubitemid 37499237)
57. Umareddy I, Chao A, Sampath A, Gu F, Vasudevan SG, 2006. Dengue virus NS4B interacts with NS3 and dissociates it from single-stranded RNA. J Gen Virol 87: 2605-2614.
58. Jones M, Davidson A, Hibbert L, Gruenwald P, Schlaak J, Ball S, Foster GR, Jacobs M, 2005. Dengue virus inhibits alpha interferon signaling by reducing STAT2 expression. J Virol 79: 5414-5420. (Pubitemid 40548209)
59. Miller S, Kastner S, Krijnse-Locker J, Buhler S, Bartenschlager R, 2007. The non-structural protein 4A of dengue virus is an integral membrane protein inducing membrane alterations in a 2K-regulated manner. J Biol Chem 282: 8873-8882. (Pubitemid 47093477)
60. Lindenbach BD, Rice CM, 1999. Genetic interaction of flavivirus nonstructural proteins NS1 and NS4A as a determinant of replicase function. J Virol 73: 4611-4621. (Pubitemid 29246719)