The origin, emergence and evolutionary genetics of dengue virus

Infection, Genetics and Evolution

Volumn 3, Issue 1, 2003, Pages 19-28

  Holmes, Edward C ^a   Twiddy, S Susanna ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Demographic history; Dengue virus; Emerging disease; Molecular clock; Positive selection; Virulence

Indexed keywords

DENGUE VIRUS; DISEASE SEVERITY; ENDEMIC DISEASE; EPIDEMIOLOGY; GENETIC SELECTION; GENETIC VARIABILITY; IMMUNOLOGY; MOLECULAR EVOLUTION; NONHUMAN; PHENOTYPIC VARIATION; PRIORITY JOURNAL; PROSPECTIVE STUDY; REVIEW; SEQUENCE ANALYSIS; SEROTYPE; STATISTICS; STRAIN DIFFERENCE; VIRAL GENETICS; VIRUS TRANSMISSION; VIRUS VIRULENCE;

ANIMALS; DENGUE VIRUS; EVOLUTION, MOLECULAR; GENOTYPE; HUMANS; PHYLOGENY; SELECTION (GENETICS); VARIATION (GENETICS); VIRULENCE;

DENGUE VIRUS; PRIMATES;

EID: 0037404062     PISSN: 15671348     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1567-1348(03)00004-2     Document Type: Review

References (88)

1. AbuBakar S.Wong P.-F.Chan Y.-F.Emergence of dengue virus type 4 genotype IIA in Malaysia J. Gen. Virol. 83 2002 2437-2442.
2. Armstrong P.M.Rico-Hesse R.Differential susceptibility of Aedes aegypti to infection by the American and Southeast Asian genotypes of dengue type 2 virus Vector Borne Zoo. Dis. 1 2001 159-168.
3. Barnes W.J.S.Rosen L.Fatal hemorrhagic disease and shock associated with primary dengue infection on a Pacific island Am. J. Trop. Med. Hyg. 23 1974 495-506.
4. Becher P.Orlich M.Thiel H.J.RNA recombination between persisting pestivirus and a vaccine strain: generation of cytopathogenic virus and induction of lethal disease J. Virol. 75 2001 6256-6264.
5. Bielefeldt-Ohmann H.Pathogenesis of dengue virus diseases: missing pieces in the jigsaw Trends Microbiol. 5 1997 409-413.
6. Billoir F.de Chesse R.Tolou H.de Micco P.Gould E.A.de Lamballerie X.Phylogeny of the genus Flavivirus using complete coding sequences of arthropod-borne viruses with no known vector J. Gen. Virol. 81 2000 781-790.
7. Burke D.S.Nisalak A.Johnson D.E.Scott R.M.A prospective study of dengue infections in Bangkok Am. J. Trop. Med. Hyg. 38 1988 172-180.
8. Chiewsilp P.Scott R.M.Bharamapravati N.Histocompatibility antigens and dengue hemorrhagic fever Am. J. Trop. Med. Hyg. 30 1981 1100-1105.
9. Chungue E.Deubel V.Cassar O.Laille M.Martin P.M.Molecular epidemiology of dengue 3 viruses and genetic relatedness among dengue 3 strains isolated from patients with mild or severe form of dengue fever in French Polynesia J. Gen. Virol. 74 1993 2765-2770.
10. Chungue E.Cassar O.Drouet M.T.Guzmán M.G.Laille M.Rosen L.Deubel V.Molecular epidemiology of dengue-1 and dengue-4 viruses J. Gen. Virol. 76 1995 1877-1884.
11. Diamond M.S.Edgil D.Roberts T.G.Lu B.Harris E.Infection of human cells by dengue virus is modulated by different cell types and viral strains J. Virol. 74 2000 7814-7823.
12. Drake J.W.Holland J.J.Mutation rates among RNA viruses Proc. Natl. Acad. Sci. U.S.A. 96 1999 13910-13913.
13. Ferguson N.Anderson R.Gupta S.The effect of antibody-dependent enhancement on the transmission dynamics and persistence of multiple-strain pathogens Proc. Natl. Acad. Sci. U.S.A. 96 1999 790-794.
14. Gaunt M.W.Sall A.A.de Lamballerie X.Falconar A.K.I.Dzhivanian T.I.Gould E.A.Phylogenetic relationships of flaviviruses correlate with their epidemiology, disease association and biogeography J. Gen. Virol. 82 2001 1867-1876.
15. Gubler D.J.Dengue and dengue haemorrhagic fever Clin. Micro. Rev. 11 1998 480-496.
16. Gubler D.J.Reed D.Rosen L.Hitchcock J.C.Jr.Epidemiologic, clinical, and virologic observations on dengue in the Kingdom of Tonga Am. J. Trop. Med. Hyg. 27 1978 581-589.
17. Gubler D.J.Suharyono W.Lubis I.Eram S.Gunarso S.Epidemic dengue 3 in Central Java, associated with low viremia in man Am. J. Trop. Med. Hyg. 30 1981 1094-1099.
18. Guzmán M.G.Kouŕ G.P.Bravo J.Calunga M.Soler M.Vazquez S.Venereo C.Dengue hemorrhagic fever in Cuba I. Serological confirmation of clinical diagnosis Trans. Roy. Soc. Trop. Med. Hyg. 78 1984a 235-238.
19. Guzmán M.G.Kouŕ G.P.Bravo J.Soler M.Vazquez S.Santos M.Villaescusa R.Basanta P.Indan G.Ballester J.M.Dengue hemorrhagic fever in Cuba II. Clinical investigations Trans. Roy. Soc. Trop. Med. Hyg. 78 1984b 236-241.
20. Halstead S.B.Dengue haemorrhagic fever-a public health problem and a field for research Bull. World Health 58 1980 1-21.
21. Halstead S.B.Pathogenesis of dengue: challenges to molecular biology Science 239 1988 476-481.
22. Halstead S.B.Sreit T.G.Lafontant J.G.Putvatana R.Russell K.Sun W.Kanesa-Thasan N.Hayes C.G.Watts D.M.Haiti: absence of dengue hemorrhagic fever despite hyperendemic dengue virus transmission Am. J. Trop. Med. Hyg. 65 2001 180-183.
23. Hayes E.B.Gubler D.J.Dengue and dengue hemorrhagic fever Ped. Infect. Dis. J. 11 1992 311-317.
24. Holmes E.C.Burch S.S.The causes and consequences of genetic variation in dengue virus Trends Microbiol. 8 2000 74-77.
25. Holmes E.C.Worobey M.Rambaut A.Phylogenetic evidence for recombination in dengue virus Mol. Biol. E 16 1999 405-409.
26. Jenkins G.M.Pagel M.Gould E.A.Zanottode P.M.A.Holmes E.C.Evolution of base composition and codon usage bias in the genus Flavivirus J. Mol. E 52 2001 383-390.
27. Jenkins G.M.Rambaut A.Pybus O.G.Holmes E.C.Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis J. Mol. E 54 2002 152-161.
28. Kalinina O.Norder H.Mukomolov S.Magnius L.O.A natural intergenotypic recombinant of hepatitis C virus identified in St. Petersburg J. Virol. 76 2002 4034-4043.
29. Kho L.K.Wulur H.Jahja E.C.Gubler D.J.DHF accompanied by encephalopathy in Jakarta Southeast Asian J. Trop. Med. Pub. Health 12 1981 83-86.
30. Kliks S.Antibody-enhanced infection of monocytes as the pathogenetic mechanism for severe dengue illness AIDS Res. Hum. Retro. 6 1990 993-998.
31. Kliks S.C.Nimmannitya S.Nisalak A.Burke D.S.Evidence that maternal dengue antibodies are important in the development of dengue hemorrhagic fever in infants Am. J. Trop. Med. Hyg. 38 1988 411-419.
32. Kochel T.J.Watts D.M.Halstead S.B.Hayes C.G.Espinoza A.Felices V.Caceda R.Bautista C.T.Montoya Y.Douglas S.Russell K.L.Effect of dengue-1 antibodies on American dengue-2 viral infection and dengue haemorrhagic fever Lancet 360 2002 310-312.
33. Korber B.Muldoon M.Theiler J.Gao F.Gupta R.Lapedes A.Hahn B.H.Wolinksy S.Bhattacharya T.Timing the ancestor of the HIV-1 pandemic strains Science 288 2000 1789-1796.
34. Kouŕ G.Más P.Guzmán M.G.Soler M.Goyenechea A.Morier L.Dengue haemorrhagic fever in Cuba, 1981. Rapid diagnosis of the etiological agent Bull. Panamerican Health Org. 17 1983 126-132.
35. Kouŕ G.Guzmán M.G.Valdés L.Carbonel I.del Rosaria D.Vazquez S.Laferté J.Delgada J.Cabrera M.V.Reemergence of dengue in Cuba: a 1997 epidemic in Santiago de Cuba Emerg. Infect. Dis. 4 1998 89-92.
36. Kuno G.Chang G.-J.J.Tsuchiya K.R.Karabatsos N.Cropp C.B.Phylogeny of the genus Flavivirus J. Virol. 72 1998 73-83.
37. Kurane I.Ennis F.A.Cytokines in dengue virus infections: role of cytokines in the pathogenesis of dengue hemorrhagic fever Sem. Virol. 5 1994 443-448.
38. Kurane I.Takasaki T.Dengue fever and dengue haemorrhagic fever: challenges of controlling an enemy still at large Rev. Med. Virol. 11 2001 301-311.
39. Lai M.M.C.RNA recombination in animal and plant viruses Microbiol. Rev. 56 1992 61-79.
40. Lanciotti R.S.Lewis J.G.Gubler D.J.Trent D.W.Molecular evolution and epidemiology of dengue-3 viruses J. Gen. Virol. 75 1994 65-75.
41. Lanciotti R.S.Gubler D.J.Trent D.W.Molecular evolution and phylogeny of dengue-4 viruses J. Gen. Virol. 78 1997 2279-2286.
42. Leitmeyer K.C.Vaughn D.W.Watts D.M.Salas R.Villalobos de Chacon I.Ramos C.Rico-Hesse R.Dengue virus structural differences that correlate with pathogenesis J. Virol. 73 1999 4738-4747.
43. Lewis J.A.Chang G.-J.Lanciotti R.S.Kinney R.M.Mayer L.W.Trent D.W.Phylogenetic relationships of dengue-2 viruses Virology 197 1993 216-224.
44. Loke H.Bethell D.B.Phuong C.X.T.Dung M.Schneider J.White N.J.Day N.P.J.Farrar J.Hill A.V.S.Strong HLA class I-restricted T cell responses in dengue hemorrhagic fever: a double-edged sword? J. Infect. Dis. 184 2001 1369-1373.
45. Lorono-Pino M.A.Cropp C.B.Farfan J.A.Vorndam A.V.Rodŕguez-Angulo E.M.Rosado-Paredes D.P.Flores-Flores L.F.Beaty B.J.Gubler D.J.Common occurrence of concurrent infections by multiple dengue virus serotypes Am. J. Trop. Med. Hyg. 61 1999 725-730.
46. Monath T.P.Wands J.R.Hill L.J.Brown N.V.Marciniak R.A.Wong M.A.Gentry M.K.Burke D.S.Grant J.A.Trent D.W.Geographic classification of dengue-2 virus strains by antigen signature analysis Virology 154 1986 313-324.
47. Monath T.P.Dengue: the risk to developed and developing countries Proc. Natl. Acad. Sci. U.S.A. 91 1994 2395-2400.
48. Pandey B.D.Igarashi A.Severity-related molecular differences among 19 strains of dengue type 2 virus Microbiol. Immunol. 44 2000 179-188.
49. Peiris J.S.M.Dittus W.P.J.Ratnayake C.B.Seroepidemiology of dengue and other arboviruses in a natural population of toque macaques (Macaca sinica) at Polonnaruwa, Sri Lanka J. Med. Primatol. 22 1993 240-245.
50. Proutski V.Gaunt M.W.Gould E.A.Holmes E.C.Secondary structure of the 3′-untranslated region of yellow fever virus: implications for virulence, attenuation and vaccine development J. Gen. Virol. 78 1997 1543-1549.
51. Proutski V. Gritsun T.S. Gould E.A. Holmes E.C. Biological consequences of deletions within the 3′-UTR of flaviviruses may be due to rearrangements of RNA secondary structure Virus Res. 64 1999 107-123.
52. Pryor M.J. Carr J.I. Hocking H. Davidson A.D. Li P. Wright P.J. Replication of dengue virus type 2 in human monocyte-derived macrophages: comparisons of isolates and recombinant viruses with substitutions at amino acid 390 in the envelope glycoprotein Am. J. Trop. Med. Hyg. 65 2001 427-434.
53. Rambaut A.Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies Bioinformatics 16 2000 395-399.
54. Reed D. Maguire T. Mataika J. Type 1 dengue with hemorrhagic disease in Fiji: epidemiologic findings Am. J. Trop. Med. Hyg. 26 1977 784-791.
55. Rico-Hesse R.Molecular evolution and distribution of dengue viruses type 1 and 2 in nature Virology 174 1990 479-493.
56. Rico-Hesse R.Harrison L.M.Salas R.A.Tovar D.Nisalak A.Ramos C.Boshell J.de Mesa M.T.R.Nogueira R.M.R.da Rosa A.T.Origins of dengue type 2 viruses associated with increased pathogenicity in the Americas Virology 230 1997 244-251.
57. Rico-Hesse R.Harrison L.M.Nisalak A.Vaughn D.W.Kalayanarooj S.Green S.Rothman A.L.Ennis F.A.Molecular evolution of dengue type 2 virus in Thailand Am. J. Trop. Med. Hyg. 58 1998 96-101.
58. Rodhain F.The role of monkeys in the biology of dengue and yellow fever Comp. Immunol. Micro. Infect. Dis. 14 1991 9-19.
59. Rosen L.The Emperor's New Clothes revisited, or reflections on the pathogenesis of dengue hemorrhagic fever Am. J. Trop. Med. Hyg. 26 1977 337-343.
60. Rudnick A.Ecology of dengue virus Asian J. Infect. Dis. 2 1978 156-160.
61. Rudnick, A., 1984. The ecology of the dengue virus complex in peninsular Malaysia. In: Pang, T., Pathmanathan, R. (Eds.), Proceedings of the International Conference on Dengue/DHF. University of Malaya Press, Kuala Lumpur, p. 7.
62. Sanchez I.J.Ruiz B.H.A single nucleotide change in the E protein gene of dengue virus 2 Mexican strain affects neurovirulence in mice J. Gen. Virol. 77 1996 2541-2545.
63. Sangkawibha N. Rohanasuphot S. Ahandrik S. Viriyapongse S. Jatanasen S. Salitul V. Phanthumachinda B. Halstead S.B. Risk factors in dengue shock syndrome: a prospective epidemiologic study in Rayong, Thailand. I. The 1980 outbreak Am. J. Epidemiol. 120 1984 653-669.
64. Scott R.M. Nimmannitya S. Bancroft W.H.Mansuwan P.Shock syndrome in primary dengue infections Am. J. Trop. Med. Hyg. 25 1976 866-874.
65. 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′ noncoding region of dengue viruses Virology 281 2001 75-87.
66. Sittisombut N.Sistayanarain A.Cardosa M.J.Salminen M.Damrongdachakul S.Kalayanarooj S.Rojanasuphot S.Supawadee J.Maneekarn N.Possible occurrence of a genetic bottleneck in dengue serotype 2 viruses between the 1980 and 1987 epidemic seasons in Bangkok, Thailand Am. J. Trop. Med. Hyg. 57 1997 100-108.
67. Solomon T. Dung N.M. Vaughn D.W. Kneen R. Thao L.T.T. Raengsakulrach B. Loan H.T. Day N.P.J. Farrar J. Myint K.S.A. Warrell M.J. James W.S. Nisalak A. White N.J. Neurological manifestations of dengue infection Lancet 355 2000 1053-1059.
68. Swofford, D.L., 2002. PAUP. Phylogenetic Analysis Using Parsimony (and Other Methods). Version 4. Sinauer Associates, Sunderland, MA.
69. Thein S. Aung M.M. Shwe T.N. Aye M. Zaw A. Aye K. Aye K.M. Aaskov J.G. Risk factors in dengue shock syndrome Am. J. Trop. Med. Hyg. 56 1997 566-572.
70. Toulou H.J.G. Coussinier-Paris P. Durand J.-P. Mercier V. de Pina J.-J. de Micco P. Billoir F. Charrel R.N. de 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.
71. Trent D.W. Grant J.A. Rosen L. Monath T.P. Genetic variation among dengue 2 viruses of different geographic origin Virology 128 1983 271-284.
72. Twiddy, S.S., Holmes, E.C., 2003. The extent of homologous recombination in the genus Flavivirus. J. Gen. Virol. 84, 429-440.
73. Twiddy S.S. Farrar J.J. Chau N.V. Wills B. Gould E.A. Gritsun T. Lloyd G. Holmes E.C. Phylogenetic relationships and differential selection pressures among genotypes of dengue-2 virus Virology 298 2002a 63-72.
74. Twiddy S.S. Woelk C.H. Holmes E.C. Phylogenetic evidence for adaptive evolution of dengue viruses in nature J. Gen. Virol. 83 2002b 1679-1689.
75. Twiddy, S.S., Pybus, O.G., Holmes, E.C., 2003a. Comparative population dynamics of mosquito-borne flaviviruses. Infect. Genet. Evol., in press.
76. Twiddy, S.S., Rambaut, A., Holmes, E.C., 2003b. Inferring the rate and time-scale of dengue virus evolution. Mol. Biol. Evol. 20, 122-129.
77. Uzcategui N.Y. Camacho D. Comach G. Cuello de Uzcategui R. Holmes E.C. Gould E.A. Molecular epidemiology of dengue type 2 virus in Venezuela: evidence for in situ virus evolution and recombination J. Gen. Virol. 82 2001 2945-2953.
78. Vaughn D.W. Green S. Kalayanarooj S. Innis B.L. Nimmannitya S. Suntayakorn S. Endy T.P. Raengsakulrach B. Rothman A.L. Ennis F.A. Nisalak A. Dengue viremia titer, antibody response pattern, and virus serotype correlate with disease severity J. Infect. Dis. 181 2000 2-9
79. Wang E. Ni H. Xu R. Barrett A.D.T. Watowich S.J. Gubler D.J. Weaver S.C. Evolutionary relationships of endemic/epidemic and sylvatic dengue viruses J. Virol. 74 2000 3227-3234
80. Wang W.-K. Lin S.-R. Lee C.-M. King C.-C. Chang S.-C. Dengue type 3 virus in plasma is a population of closely related genomes: quasispecies J. Virol. 76 2002 4662-4665.
81. Watts D.M. Porter K.R. Putvatana P. Vasquez B. Calampa C. Hayes C.G. Halstead S.B. Failure of secondary infection with American genotype dengue 2 to cause dengue haemorrhagic fever Lancet 354 1999 1431-1434.
82. World Health Organisation (WHO), 2002. Fact sheet: dengue and dengue haemorrhagic fever. World Health Organization, Geneva.
83. Wittke V. Robb T.E. Thu H.M. Nimmannitya S. Kalayanrooj S. Vaughn D.W. Endy T.P. Holmes E.C. Aaskov J.G. Extinction and rapid emergence of strains of dengue 3 virus during an interepidemic period Virology 301 2002 148-156.
84. Wolfe N.D. Kilbourn A.M. Karesh W.B. Rahman H.A. Bosi E.J. Cropp B.E. Andau M. Spielman A. Gubler D.J. Sylvatic transmission of arboviruses among Bornean orangutans Am. J. Trop. Hyg. Med. 64 2001 310-316.
85. Worobey M. Holmes E.C. Homologous recombination and the molecular evolution of GB virus C/hepatitis G virus Mol. Biol. E 18 2001 254-261.
86. Worobey M. Rambaut A. Holmes E.C. Widespread intra-serotype recombination in natural populations of dengue virus Proc. Natl. Acad. Sci. U.S.A. 96 1999 7352-7357.
87. Zanotto P.M. de A. Gould E.A. Gao G.F. Harvey P.H. Holmes E.C. Population dynamics of flaviviruses revealed by molecular phylogenies Proc. Natl. Acad. Sci. U.S.A. 93 1996 548-553
88. Zeng L. Kurane I. Okamoto Y. Ennis F.A. Brinton M.A. Identification of amino acids involved in recognition by dengue virus NS3-specific, HLA-DR15-restricted cytotoxic CD4+ T-cell clones J. Virol. 70 1996 3108-3117.