Phylogeography and molecular epidemiology of an epidemic strain of dengue virus type 1 in Sri Lanka

American Journal of Tropical Medicine and Hygiene

Volumn 91, Issue 2, 2014, Pages 225-234

  Ocwieja, Karen E ^a   Fernando, Anira N ^a,b   Sherrill Mix, Scott ^a   Sundararaman, Sesh A ^a   Tennekoon, Rashika N ^a,b   Tippalagama, Rashmi ^a,b   Krishnananthasivam, Shivankari ^a,b   Premawansa, Gayani ^a,c   Premawansa, Sunil ^a,d   De Silva, Aruna Dharshan ^a,b  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b Department of Microbiology Perelman School of Medicine University of Pennsylvania ^*  (Sri Lanka)

^c Department of Anaesthesiology College of Anaesthesiologists and Intensivists of Sri Lanka   (Sri Lanka)

^d UNIVERSITY OF COLOMBO   (Sri Lanka)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHINA; DENGUE; DENGUE VIRUS 1; DISEASE SEVERITY; GENOME ANALYSIS; HUMAN; MAJOR CLINICAL STUDY; MOLECULAR EPIDEMIOLOGY; NONHUMAN; NUCLEOTIDE SEQUENCE; PAKISTAN; PHYLOGENY; PHYLOGEOGRAPHY; SEQUENCE ANALYSIS; SEROTYPE; SINGAPORE; SRI LANKA; THAILAND; UNINDEXED SEQUENCE; VIRUS STRAIN;

ADULT; AEDES; ANIMALS; BAYES THEOREM; DENGUE VIRUS; DISEASE OUTBREAKS; GENOTYPE; HUMANS; INSECT VECTORS; MIDDLE AGED; MOLECULAR EPIDEMIOLOGY; PHYLOGENY; PHYLOGEOGRAPHY; RNA, VIRAL; SEROTYPING; SEVERE DENGUE; SRI LANKA;

EID: 84907262097     PISSN: 00029637     EISSN: None     Source Type: Journal    
DOI: 10.4269/ajtmh.13-0523     Document Type: Article

References (55)

1. Nathan MB, D-D R, Guzman M, 2009. Dengue: Guidelines for Diagnosis, Treatment, Prevention, and Control: New Edition. Geneva: World Health Organization.
2. Bhatt S, Gething PW, Brady OJ, Messina JP, Farlow AW, Moyes CL, Drake JM, Brownstein JS, Hoen AG, Sankoh O, Myers MF, George DB, Jaenisch T, Wint GR, Simmons CP, Scott TW, Farrar JJ, Hay SI, 2013. The global distribution and burden of dengue. Nature 496: 504-507.
3. Guzman MG, Kouri G, 2002. Dengue: an update. Lancet Infect Dis 2: 33-42.
4. Halstead SB, et al., 1970. Observations related to pathogenesis of dengue hemorrhagic fever. I. Experience with classification of dengue viruses. Yale J Biol Med 42: 261-275.
5. Rothman AL, 2011. Immunity to dengue virus: a tale of original antigenic sin and tropical cytokine storms. Nat Rev Immunol 11: 532-543.
6. Whitehorn J, Simmons CP, 2011. The pathogenesis of dengue. Vaccine 29: 7221-7228.
7. Gubler DJ, 2002. The global emergence/resurgence of arboviral diseases as public health problems. Arch Med Res 33: 330-342.
8. Wilder-Smith A, Gubler DJ, 2008. Geographic expansion of dengue: the impact of international travel. Med Clin North Am 92: 1377-1390.
9. Kanakaratne N, et al., 2009. Severe dengue epidemics in Sri Lanka, 2003-2006. Emerg Infect Dis 15: 192-199.
10. 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.
11. Tissera HA, et al., 2011. New dengue virus type 1 genotype in Colombo, Sri Lanka. Emerg Infect Dis 17: 2053-2055.
12. Dissanayake VH, Gunawardena ND, Gunasekara NC, Siriwardhana DR, Senarath N, 2011. Shift in the transmission pattern of dengue serotypes and concurrent infection with more than one dengue virus serotype. Ceylon Med J 56: 176-178.
13. Sri Lankan Ministry of Health, EU, 2013. Disease Surveillance, Trends. Available at: http://www.epid.gov.lk/web/index.php?option=com- casesanddeaths&Itemid=448&lang=en. Accessed June 10, 2013.
14. Sirisena PD, Noordeen F, 2014. Evolution of dengue in Sri Lanka-changes in the virus, vector, and climate. International journal of infectious diseases: IJID: Official Publication of the International Society for Infectious Diseases 19: 6-12.
15. Sudiro TM, et al., 1997. Rapid diagnosis of dengue viremia by reverse transcriptase-polymerase chain reaction using 3'-noncoding region universal primers. Am J Trop Med Hyg 56: 424-429.
16. Lanciotti RS, Calisher CH, Gubler DJ, Chang GJ, Vorndam AV, 1992. Rapid detection and typing of dengue viruses from clinical samples by using reverse transcriptase-polymerase chain reaction. J Clin Microbiol 30: 545-551.
17. Morgulis A, et al., 2008. Database indexing for production MegaBLAST searches. Bioinformatics 24: 1757-1764.
18. Zhang Z, Schwartz S, Wagner L, Miller W, 2000. A greedy algorithm for aligning DNA sequences. J Comput Biol 7: 203-214.
19. Needleman SB, Wunsch CD, 1970. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48: 443-453.
20. Drummond AJ, Suchard MA, Xie D, Rambaut A, 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 29: 1969-1973.
21. Drummond AJ, Nicholls GK, Rodrigo AG, Solomon W, 2002. Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 161: 1307-1320.
22. Dunham EJ, Holmes EC, 2007. Inferring the timescale of dengue virus evolution under realistic models of DNA substitution. J Mol Evol 64: 656-661.
23. Rabaa MA, Ty Hang VT, Wills B, Farrar J, Simmons CP, Holmes EC, 2010. Phylogeography of recently emerged DENV-2 in southern Viet Nam. PLoS Negl Trop Dis 4: e766.
24. Rambaut A, Drummond AJ, 2007. Tracer v1.5. Available at: http://tree.bio.ed.ac.uk/software/tracer/.
25. Morariu VI, Srinivasan BV, Raykar VC, Duraiswami R, Davis LS, 2008. Automatic online tuning for fast Gaussian summation. Adv Neural Inf Process, 21 edn. 1113-1120.
26. Pond SL, Frost SD, Muse SV, 2005. HyPhy: hypothesis testing using phylogenies. Bioinformatics 21: 676-679.
27. Delport W, Poon AF, Frost SD, Kosakovsky Pond SL, 2010. Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics 26: 2455-2457.
28. Kosakovsky Pond SL, Frost SD, 2005. Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol 22: 1208-1222.
29. Pond SL, et al., 2006. Adaptation to different human populations by HIV-1 revealed by codon-based analyses. PLOS Comput Biol 2: e62.
30. Murrell B, et al., 2012. Detecting individual sites subject to episodic diversifying selection. PLoS Genet 8: e1002764.
31. Core Team R, 2013. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing.
32. Anoop M, et al., 2012. Complete genome sequencing and evolutionary analysis of dengue virus serotype 1 isolates from an outbreak in Kerala, South India. Virus Genes 45: 1-13.
33. Chen S, 2011. The origin of dengue viruses caused the DF outbreak in Guangdong province, China, in 2006. Infect Genet Evol 11: 1183-1187.
34. Zhang C, et al., 2005. Clade replacements in dengue virus serotypes 1 and 3 are associated with changing serotype prevalence. J Virol 79: 15123-15130.
35. Khan MA, et al., 2013. Emergence and diversification of dengue 2 cosmopolitan genotype in Pakistan, 2011. PLoS ONE 8: e56391.
36. Anez G, Morales-Betoulle ME, Rios M, 2011. Circulation of different lineages of dengue virus type 2 in Central America, their evolutionary time-scale and selection pressure analysis. PLoS ONE 6: e27459.
37. Holmes EC, 2003. Patterns of intra- and interhost nonsynonymous variation reveal strong purifying selection in dengue virus. J Virol 77: 11296-11298.
38. Anez G, et al., 2013. Evolutionary dynamics of West Nile virus in the United States, 1999-2011: phylogeny, selection pressure and evolutionary time-scale analysis. PLoS Negl Trop Dis 7: e2245.
39. Schreiber MJ, et al., 2009. Genomic epidemiology of a dengue virus epidemic in urban Singapore. J Virol 83: 4163-4173.
40. Twiddy SS, Holmes EC, Rambaut A, 2003. Inferring the rate and time-scale of dengue virus evolution. Mol Biol Evol 20: 122-129.
41. Valle RP, Falgout B, 1998. Mutagenesis of the NS3 protease of dengue virus type 2. J Virol 72: 624-632.
42. Murthy HM, Clum S, Padmanabhan R, 1999. Dengue virus NS3 serine protease. Crystal structure and insights into interaction of the active site with substrates by molecular modeling and structural analysis of mutational effects. J Biol Chem 274: 5573-5580.
43. Muller DA, Corrie SR, Coffey J, Young PR, Kendall MA, 2012. Surface modified microprojection arrays for the selective extraction of the dengue virus NS1 protein as a marker for disease. Anal Chem 84: 3262-3268.
44. Miller S, Sparacio S, Bartenschlager R, 2006. Subcellular localization and membrane topology of the Dengue virus type 2 Non-structural protein 4B. J Biol Chem 281: 8854-8863.
45. Modis Y, Ogata S, Clements D, Harrison SC, 2004. Structure of the dengue virus envelope protein after membrane fusion. Nature 427: 313-319.
46. Guzman MG, et al., 1995. Partial nucleotide and amino acid sequences of the envelope and the envelope/nonstructural protein-1 gene junction of four dengue-2 virus strains isolated during the 1981 Cuban epidemic. Am J Trop Med Hyg 52: 241-246.
47. Rico-Hesse R, et al., 1997. Origins of dengue type 2 viruses associated with increased pathogenicity in the Americas. Virology 230: 244-251.
48. Leitmeyer KC, et al., 1999. Dengue virus structural differences that correlate with pathogenesis. J Virol 73: 4738-4747.
49. Cologna R, Rico-Hesse R, 2003. American genotype structures decrease dengue virus output from human monocytes and dendritic cells. J Virol 77: 3929-3938.
50. Imrie A, et al., 2010. Homology of complete genome sequences for dengue virus type-1, from dengue-fever- and denguehaemorrhagicfever-Associated epidemics in Hawaii and French Polynesia. Ann Trop Med Parasitol 104: 225-235.
51. Samath F. Chinese, Sri Lankan workers mingle at sprawling Hambantota port site. Financial Times. Oct. 5, 2008 [online]. Available at: http://www.sundaytimes.lk/081005/FinancialTimes/ft343.html. Accessed April 16, 2014.
52. Mudalige D. Lanka takes over Norochcholai plant. Features, Online edition of Daily News, Lakehouse Newspapers. Aug. 10, 2011 [online]. Available at: http://archives.dailynews.lk/2011/08/10/fea10.asp. Accessed April 16, 2014.
53. Zheng K, et al., 2009. Molecular characterization of the E gene of dengue virus type 1 isolated in Guangdong province, China, in 2006. Epidemiol Infect 137: 73-78.
54. Nicolaisen LE, Desai MM, 2012. Distortions in genealogies due to purifying selection. Mol Biol Evol 29: 3589-3600.
55. Jenkins GM, Rambaut A, Pybus OG, Holmes EC, 2002. Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis. J Mol Evol 54: 156-165.