Endemic dengue associated with the co-circulation of multiple viral lineages and localized density-dependent transmission

PLoS Pathogens

Volumn 7, Issue 6, 2011, Pages

  Raghwani, Jayna ^a   Rambaut, Andrew ^a,b   Holmes, Edward C ^b,c   Hang, Vu Ty ^d   Hien, Tran Tinh ^e   Farrar, Jeremy ^d,f   Wills, Bridget ^d,f   Lennon, Niall J ^g   Birren, Bruce W ^g   Henn, Matthew R ^g   Simmons, Cameron P ^d,e  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

^c PENNSYLVANIA STATE UNIVERSITY   (United States)

^d OXFORD UNIVERSITY CLINICAL RESEARCH UNIT   (Viet Nam)

^e UNIVERSITY COLLEGE LONDON HOSPITALS   (United Kingdom)

^f UNIVERSITY OF OXFORD   (United Kingdom)

^g BROAD INSTITUTE OF MIT AND HARVARD   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADOLESCENT; ARTICLE; CAMBODIA; CHILD; CHINA; DENGUE; DENGUE VIRUS 1; DISEASE TRANSMISSION; FEMALE; GENE SEQUENCE; HOST; HUMAN; MALE; MOSQUITO; PHYLOGEOGRAPHY; PRESCHOOL CHILD; RURAL POPULATION; SCHOOL CHILD; URBAN POPULATION; VIRUS TRANSMISSION; AEDES; ANIMAL; BAYES THEOREM; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; DENGUE VIRUS; DISEASE CARRIER; DNA SEQUENCE; ENDEMIC DISEASE; GENETIC VARIABILITY; GENETICS; INCIDENCE; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; POPULATION DENSITY; SOUTHEAST ASIA; TIME; VIET NAM; VIROLOGY; VIRUS GENOME;

COMPLEMENTARY DNA; VIRUS RNA;

ADOLESCENT; AEDES; ANIMALS; ASIA, SOUTHEASTERN; BASE SEQUENCE; BAYES THEOREM; CHILD; CLUSTER ANALYSIS; DENGUE; DENGUE VIRUS; DNA, COMPLEMENTARY; ENDEMIC DISEASES; FEMALE; GENETIC VARIATION; GENOME, VIRAL; HUMANS; INCIDENCE; INSECT VECTORS; MALE; MOLECULAR SEQUENCE DATA; PHYLOGEOGRAPHY; POPULATION DENSITY; RNA, VIRAL; RURAL POPULATION; SEQUENCE ANALYSIS, DNA; TIME FACTORS; URBAN POPULATION; VIETNAM;

EID: 79959834106     PISSN: 15537366     EISSN: 15537374     Source Type: Journal    
DOI: 10.1371/journal.ppat.1002064     Document Type: Article

References (45)

1. Pediatric Dengue Vaccine Initiative. Global burden of dengue. http://www.pdvi.org/about_dengue/GBD.asp. Accessed 30 November 2009.
2. Gandon S, Mackinnon MJ, Nee S, Read AF, (2001) Imperfect vaccines and the evolution of pathogen virulence. Nature 414: 751-756.
3. Webster DP, Farrar J, Rowland-Jones S, (2009) Progress towards a dengue vaccine. Lancet Infect Dis 9: 678-687.
4. Wahala WM, Donaldson EF, de Alwis R, Accavitti-Loper MA, Baric RS, et al. (2010) Natural strain variation and antibody neutralization of dengue serotype 3 viruses. PLoS Pathog 6: e1000821.
5. Shrestha B, Brien JD, Sukupolvi-Petty S, Austin SK, Edeling MA, et al. (2010) The development of therapeutic antibodies that neutralize homologous and heterologous genotypes of dengue virus type 1. PLoS Pathog 6: e1000823.
6. Sukupolvi-Petty S, Austin SK, Engle M, Brien JD, Dowd KA, et al. (2010) Structure and Function Analysis of Therapeutic Monoclonal Antibodies against Dengue Virus Type 2. J Virol 84: 9227-9239.
7. Holmes EC, Twiddy SS, (2003) The origin, emergence and evolutionary genetics of dengue virus. Infect Genet Evol 3: 19-28.
8. Messer WB, Gubler DJ, Harris E, Sivananthan K, de Silva AM, (2003) Emergence and global spread of a dengue serotype 3, subtype III virus. Emerg Infect Dis 9: 800-809.
9. Myat Thu H, Lowry K, Jiang L, Hlaing T, Holmes EC, et al. (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.
10. Rico-Hesse R, Harrison LM, Salas RA, Tovar D, Nisalak A, et al. (1997) Origins of dengue type 2 viruses associated with increased pathogenicity in the Americas. Virology 230: 244-251.
11. Bennett SN, Holmes EC, Chirivella M, Rodriguez DM, Beltran M, et al. (2006) Molecular evolution of dengue 2 virus in Puerto Rico: positive selection in the viral envelope accompanies clade reintroduction. J Gen Virol 87: 885-893.
12. McElroy K, Santiago G, Lennon N, Birren B, Henn M, et al. (2011) Endurance, refuge, and reemergence of dengue virus type II, Puerto Rico, 1986-2007. Emerg Infect Dis 17: 64-71.
13. Hang VTT, Holmes EC, Duong V, Nguyen TQ, Tran TH, et al. (2010) Emergence of the Asian 1 genotype of dengue virus serotype 2 in viet nam: in vivo fitness advantage and lineage replacement in South-East Asia. PLoS Negl Trop Dis 4: e757.
14. Rabaa MA, Ty Hang VT, Wills B, Farrar J, Simmons CP, et al. (2010) Phylogeography of recently emerged DENV-2 in southern Viet Nam. PLoS Negl Trop Dis 4: e766.
15. Schreiber MJ, Holmes EC, Ong SH, Soh HSH, Liu W, et al. (2009) Genomic Epidemiology of a Dengue Virus Epidemic in Urban Singapore. J Virol 83: 4163-4173.
16. Endy TP, Nisalak A, Chunsuttitwat S, Vaughn DW, Green S, et al. (2004) Relationship of preexisting dengue virus (DV) neutralizing antibody levels to viremia and severity of disease in a prospective cohort study of DV infection in Thailand. J Infect Dis 189: 990-1000.
17. Nagao Y, Koelle K, (2008) Decreases in dengue transmission may act to increase the incidence of dengue hemorrhagic fever. Proc Natl Acad Sci U S A 105: 2238-2243.
18. Anders KL, Nguyet NM, Van Vinh Chau N, Hung NT, Thuy TT, et al. (2011) Epidemiological Factors Associated with Dengue Shock Syndrome and Mortality in Hospitalized Dengue Patients in Ho Chi Minh City, Vietnam. Am J Trop Med Hyg 84: 127-134.
19. Cologna R, Armstrong PM, Rico-Hesse R, (2005) Selection for virulent dengue viruses occurs in humans and mosquitoes. J Virol 79: 853-859.
20. Libraty DH, Endy TP, Houng HS, Green S, Kalayanarooj S, et al. (2002) Differing influences of virus burden and immune activation on disease severity in secondary dengue-3 virus infections. J Infect Dis 185: 1213-1221.
21. Scott TW, Amerasinghe PH, Morrison AC, Lorenz LH, Clark GG, et al. (2000) Longitudinal studies of Aedes aegypti (Diptera: Culicidae) in Thailand and Puerto Rico: blood feeding frequency. J Med Entomol 37: 89-101.
22. Scott TW MA, (2003) Aedes aegypti density and the risk of dengue virus transmission. In: Takken W ST, editors. Ecological aspects for application of genetically modified mosquitoes Dordrecht, The Netherlands FRONTIS pp. 187-206.
23. Zhang C, Mammen MP Jr, Chinnawirotpisan P, Klungthong C, Rodpradit P, et al. (2005) Clade replacements in dengue virus serotypes 1 and 3 are associated with changing serotype prevalence. J Virol 79: 15123-15130.
24. Twiddy SS, Holmes EC, Rambaut A, (2003) Inferring the rate and time-scale of dengue virus evolution. Mol Biol Evol 20: 122-129.
25. Lanciotti RS, Gubler DJ, Trent DW, (1997) Molecular evolution and phylogeny of dengue-4 viruses. J Gen Virol 78: 2279-2286.
26. Lemey P, Rambaut A, Drummond AJ, Suchard MA, (2009) Bayesian Phylogeography Finds Its Roots. Plos Comput Biol 5: e1000520.
27. Lemey P, Rambaut A, Welch JJ, Suchard MA, (2010) Phylogeography Takes a Relaxed Random Walk in Continuous Space and Time. Mol Biol Evol 27: 1877-1885.
28. Russell CA, Jones TC, Barr IG, Cox NJ, Garten RJ, et al. (2008) The global circulation of seasonal influenza A (H3N2) viruses. Science 320: 340-346.
29. Ha DQ, Ninh TU, (2000) Virological Surveillance of Dengue Haemorrhagic Fever in Viet Nam, 1987-1999. Dengue Bulletin 24: 18-23.
30. Sittisombut N, Sistayanarain A, Cardosa MJ, Salminen M, Damrongdachakul S, et al. (1997) 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: 100-108.
31. Wittke V, Robb TE, Thu HM, Nisalak A, Nimmannitya S, et al. (2002) Extinction and rapid emergence of strains of dengue 3 virus during an interepidemic period. Virology 301: 148-156.
32. Russell RC, Webb CE, Williams CR, Ritchie SA, (2005) Mark-release-recapture study to measure dispersal of the mosquito Aedes aegypti in Cairns, Queensland, Australia. Med Vet Entomol 19: 451-457.
33. Reiter P, Amador MA, Anderson RA, Clark GG, (1995) Short report: dispersal of Aedes aegypti in an urban area after blood feeding as demonstrated by rubidium-marked eggs. Am J Trop Med Hyg 52: 177-179.
34. Harrington LC, Scott TW, Lerdthusnee K, Coleman RC, Costero A, et al. (2005) Dispersal of the dengue vector Aedes aegypti within and between rural communities. Am J Trop Med Hyg 72: 209-220.
35. Balmaseda A, Standish K, Mercado JC, Matute JC, Tellez Y, et al. (2010) Trends in Patterns of Dengue Transmission over 4 Years in a Pediatric Cohort Study in Nicaragua. J Infect Dis 201: 5-14.
36. Morrison AC, Minnick SL, Rocha C, Forshey BM, Stoddard ST, et al. (2010) Epidemiology of Dengue Virus in Iquitos, Peru 1999 to 2005: Interepidemic and Epidemic Patterns of Transmission. PLoS Negl Trop Dis 4: e670.
37. Hang VT, Nguyet NM, Trung DT, Tricou V, Yoksan S, et al. (2009) Diagnostic Accuracy of NS1 ELISA and Lateral Flow Rapid Tests for Dengue Sensitivity, Specificity and Relationship to Viraemia and Antibody Responses. PLoS Negl Trop Dis 3: e360.
38. Simmons CP, Dolocek C, Chau TNB, Griffiths M, Dung NTP, et al. (2007) Patterns of host genome-wide gene transcript abundance in the peripheral blood of patients with acute dengue haemorrhagic fever. J Infect Dis 195: 1097-107.
39. Swofford D, (2003) PAUP*.Phylogenetic Analysis Using Parsimony (*and other methods). Version 4. ed. Sinauer Associates. Sunderland, Mass.
40. Drummond AJ, Rambaut A, (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7: 214.
41. Shapiro B, Rambaut A, Drummond AJ, (2006) Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Mol Biol Evol 23: 7-9.
42. Drummond AJ, Ho SYW, Phillips MJ, Rambaut A, (2006) Relaxed phylogenetics and dating with confidence. PLoS Biol 4: 699-710.
43. Minin VN, Bloomquist EW, Suchard MA, (2008) Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics. Mol Biol Evol 25: 1459-1471.
44. Minin VN, Suchard MA, (2008) Counting labeled transitions in continuous-time Markov models of evolution. J Math Biol 56: 391-412.
45. O'Brien JD, Minin VN, Suchard MA, (2009) Learning to count: robust estimates for labeled distances between molecular sequences. Mol Biol Evol 26: 801-814.