Evolution and heterogeneity of multiple serotypes of Dengue virus in Pakistan, 2006-2011

Virology Journal

Volumn 10, Issue , 2013, Pages

  Koo, Carmen ^a   Nasir, Amna ^b   Hapuarachchi, Hapuarachchige Chanditha ^a   Lee, Kim Sung ^a   Hasan, Zahra ^b   Ng, Lee Ching ^a   Khan, Erum ^b  

^a NATIONAL ENVIRONMENT AGENCY   (Singapore)

^b AGA KHAN UNIVERSITY   (Pakistan)

Author keywords

Dengue; Diversity; Evolution; Genome; Molecular epidemiology; Pakistan; Phylogenetics

Indexed keywords

AMINO ACID SUBSTITUTION; ARTICLE; CLADISTICS; DENGUE; DENGUE VIRUS; DENGUE VIRUS 1; DENGUE VIRUS 2; DENGUE VIRUS 3; DENGUE VIRUS 4; DIVERSIFYING SELECTION; ENVELOPE GENE; GENE CLUSTER; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC HETEROGENEITY; GENETIC SIMILARITY; GENETIC VARIABILITY; GENOME ANALYSIS; GEOGRAPHIC DISTRIBUTION; HUMAN; HUMAN TISSUE; MOLECULAR EPIDEMIOLOGY; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; PAKISTAN; PHYLOGENY; POLYMERASE CHAIN REACTION; SEROTYPE; VIRUS GENOME; VIRUS ISOLATION; VIRUS LOAD; VIRUS PURIFICATION; VIRUS TRANSMISSION;

DENGUE VIRUS;

CLUSTER ANALYSIS; COHORT STUDIES; DENGUE; DENGUE VIRUS; GENETIC VARIATION; HUMANS; MOLECULAR EPIDEMIOLOGY; MOLECULAR SEQUENCE DATA; PAKISTAN; PHYLOGEOGRAPHY; RNA, VIRAL; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY;

EID: 84883274852     PISSN: None     EISSN: 1743422X     Source Type: Journal    
DOI: 10.1186/1743-422X-10-275     Document Type: Article

References (47)

1. Flavivirus genome organization, expression, and replication. Chambers TJ, Hahn CS, Galler R, Rice CM, Annu Rev Microbiol 1990 44 649 688 10.1146/annurev.mi.44.100190.003245 2174669
2. Fight against dengue in India: progresses and challenges. Gupta B, Reddy BP, Parasitol Res 2013 112 1367 1378 10.1007/s00436-013-3342-2 23455936
3. Shift in the transmission pattern of dengue serotypes and concurrent infection with more than one dengue virus serotype. Dissanayake VH, Gunawardena ND, Gunasekara NC, Siriwardhana DR, Senarath N, Ceylon Med J 2011 56 176 178 22298216
4. Dengue virus and Japanese Encephalitis virus epidemiological shifts in Nepal: a case of opposing trends. Dumre SP, Shakya G, Na-Bangchang K, Eursitthichai V, Grams HR, Upreti SR, Ghimire P, Kc K, Nisaluk A, Gibbons RV, Fernandez S, Am J Trop Med Hyg 2013 88 677 680 10.4269/ajtmh.12-0436 23419366
5. Dengue fever in the Indian Subcontinent: an overview. Raheel U, Faheem M, Riaz MN, Kanwal N, Javed F, Zaidi N, Qadri I, J Infect Dev Ctries 2011 5 239 247 21537064
6. A review of dengue as an emerging disease in Pakistan. Rasheed SB, Butlin RK, Boots M, Public Health 2013 127 11 17 10.1016/j.puhe.2012.09.006 23219263
7. Dengue Fever (DF) in Pakistan. Jahan F, Asia Pac Fam Med 2011 10 1 10.1186/1447-056X-10-1 21349169
8. Demographic and clinical features of dengue fever in Pakistan from 2003-2007: a retrospective cross-sectional study. Khan E, Kisat M, Khan N, Nasir A, Ayub S, Hasan R, PLoS One 2010 5 12505 10.1371/journal.pone.0012505
9. A brief review on dengue molecular virology, diagnosis, treatment and prevalence in Pakistan. Idrees S, Ashfaq UA, Genet Vaccines Ther 2012 10 6 10.1186/1479-0556-10-6 22929369
10. West Nile virus in Pakistan. 1. Sero-epidemiological studies in Punjab Province. Hayes CG, Baqar S, Ahmed T, Chowdhry MA, Reisen WK, Trans R Soc Trop Med Hyg 1982 76 431 436 10.1016/0035-9203(82)90130-4 6926759
11. Dengue haemorrhagic fever outbreak in Karachi, Pakistan, 1994. Chan YC, Salahuddin NI, Khan J, Tan HC, Seah CL, Li J, Chow VT, Trans R Soc Trop Med Hyg 1995 89 619 620 10.1016/0035-9203(95)90412-3 8594672
12. Dengue virus infection among children with undifferentiated fever in Karachi. Akram DS, Igarashi A, Takasu T, Indian J Pediatr 1998 65 735 740 10.1007/BF02731055 10773930
13. Expansion of epidemic dengue viral infections to Pakistan. Paul RE, Patel AY, Mirza S, Fisher-Hoch SP, Luby SP, Int J Infect Dis 1998 2 197 201 10.1016/S1201-9712(98)90052-2 9763501
14. Dengue virus serotype 3, Karachi, Pakistan. Jamil B, Hasan R, Zafar A, Bewley K, Chamberlain J, Mioulet V, Rowlands M, Hewson R, Emerg Infect Dis 2007 13 182 183 10.3201/eid1301.060376 17370547
15. Co-circulations of two genotypes of dengue virus in 2006 out-break of dengue hemorrhagic fever in Karachi, Pakistan. Khan E, Hasan R, Mehraj V, Nasir A, Siddiqui J, Hewson R, J Clin Virol 2008 43 176 179 10.1016/j.jcv.2008.06.003 18639489
16. Serotype and genotype analysis of dengue virus by sequencing followed by phylogenetic analysis using samples from three mini outbreaks-2007-2009 in Pakistan. Fatima Z, Idrees M, Bajwa MA, Tahir Z, Ullah O, Zia MQ, Hussain A, Akram M, Khubaib B, Afzal S, et al. BMC Microbiol 2011 11 200 10.1186/1471-2180-11-200 21906394
17. Emergence and diversification of dengue 2 cosmopolitan genotype in pakistan, 2011. Khan MA, Ellis EM, Tissera HA, Alvi MY, Rahman FF, Masud F, Chow A, Howe S, Dhanasekaran V, Ellis BR, Gubler DJ, PLoS One 2013 8 56391 10.1371/journal.pone.0056391 23520453
18. Rapid evolution of RNA viruses. Steinhauer DA, Holland JJ, Annu Rev Microbiol 1987 41 409 433 10.1146/annurev.mi.41.100187.002205 3318675
19. Unifying the epidemiological and evolutionary dynamics of pathogens. Grenfell BT, Pybus OG, Gog JR, Wood JL, Daly JM, Mumford JA, Holmes EC, Science 2004 303 327 332 10.1126/science.1090727 14726583
20. Inferring the rate and time-scale of dengue virus evolution. Twiddy SS, Holmes EC, Rambaut A, Mol Biol Evol 2003 20 122 129 10.1093/molbev/msg010 12519914
21. Sequence analyses of NS3 genes of recent Pakistan and Singapore strains of dengue virus types 1 and 2. Chow VT, Yong R, Chan YC, Res Virol 1997 148 17 20 10.1016/S0923-2516(97)81907-3 9017828
22. Prevalence and molecular characterization of dengue viruses serotypes in 2010 epidemic. Mahmood N, Rana MY, Qureshi Z, Mujtaba G, Shaukat U, Am J Med Sci 2012 343 61 64 10.1097/MAJ.0b013e3182217001 21760476
23. Crystal structure of the dengue virus RNA-dependent RNA polymerase catalytic domain at 1.85-angstrom resolution. Yap TL, Xu T, Chen YL, Malet H, Egloff MP, Canard B, Vasudevan SG, Lescar J, J Virol 2007 81 4753 4765 10.1128/JVI.02283-06 17301146
24. Dengue virus serotype 2 from a sylvatic lineage isolated from a patient with dengue hemorrhagic fever. Cardosa J, Ooi MH, Tio PH, Perera D, Holmes EC, Bibi K, Abdul Manap Z, PLoS Negl Trop Dis 2009 3 423 10.1371/journal.pntd. 0000423 19399166
25. Evolutionary processes among sylvatic dengue type 2 viruses. Vasilakis N, Holmes EC, Fokam EB, Faye O, Diallo M, Sall AA, Weaver SC, J Virol 2007 81 9591 9595 10.1128/JVI.02776-06 17553878
26. Comparison of a dengue-2 virus and its candidate vaccine derivative: sequence relationships with the flaviviruses and other viruses. Blok J, McWilliam SM, Butler HC, Gibbs AJ, Weiller G, Herring BL, Hemsley AC, Aaskov JG, Yoksan S, Bhamarapravati N, Virology 1992 187 573 590 10.1016/0042-6822(92) 90460-7 1312269
27. Not so different after all: a comparison of methods for detecting amino acid sites under selection. Kosakovsky Pond SL, Frost SD, Mol Biol Evol 2005 22 1208 1222 10.1093/molbev/msi105 15703242
28. Adaptation to different human populations by HIV-1 revealed by codon-based analyses. Pond SL, Frost SD, Grossman Z, Gravenor MB, Richman DD, Brown AJ, PLoS Comput Biol 2006 2 62 10.1371/journal.pcbi.0020062 16789820
29. HyPhy: hypothesis testing using phylogenies. Pond SL, Frost SD, Muse SV, Bioinformatics 2005 21 676 679 10.1093/bioinformatics/bti079 15509596
30. Detecting individual sites subject to episodic diversifying selection. Murrell B, Wertheim JO, Moola S, Weighill T, Scheffler K, Kosakovsky Pond SL, PLoS Genet 2012 8 1002764 10.1371/journal.pgen.1002764 22807683
31. Suppressors of RNAi from plant viruses are subject to episodic positive selection. Murray GG, Kosakovsky Pond SL, Obbard DJ, Proc Biol Sci 2013 280 20130965 10.1098/rspb.2013.0965 23804618
32. Reemergence of dengue virus type-3 (subtype-III) in India: implications for increased incidence of DHF & DSS. Dash PK, Parida MM, Saxena P, Abhyankar A, Singh CP, Tewari KN, Jana AM, Sekhar K, Rao PV, Virol J 2013 3 55
33. Comparative complete genome analysis of dengue virus type 3 circulating in India between 2003 and. Sharma S, Dash PK, Agarwal S, Shukla J, Parida MM, Rao PV, J Gen Virol 2008 92 1595 1600
34. The flavivirus NS1 protein: molecular and structural biology, immunology, role in pathogenesis and application as a diagnostic biomarker. Muller DA, Young PR, Antiviral Res 2013 98 192 208 10.1016/j.antiviral.2013.03.008 23523765
35. The effects of site-directed mutagenesis on the dimerization and secretion of the NS1 protein specified by dengue virus. Pryor MJ, Wright PJ, Virology 1993 194 769 780 10.1006/viro.1993.1318 8389081
36. Structure of the Flavivirus helicase: implications for catalytic activity, protein interactions, and proteolytic processing. Wu J, Bera AK, Kuhn RJ, Smith JL, J Virol 2005 79 10268 10277 10.1128/JVI.79.16.10268-10277.2005 16051820
37. Crystal structure and activity of Kunjin virus NS3 helicase; protease and helicase domain assembly in the full length NS3 protein. Mastrangelo E, Milani M, Bollati M, Selisko B, Peyrane F, Pandini V, Sorrentino G, Canard B, Konarev PV, Svergun DI, et al. J Mol Biol 2007 372 444 455 10.1016/j.jmb.2007.06.055 17658551
38. Towards the design of antiviral inhibitors against flaviviruses: the case for the multifunctional NS3 protein from Dengue virus as a target. Lescar J, Luo D, Xu T, Sampath A, Lim SP, Canard B, Vasudevan SG, Antiviral Res 2008 80 94 101 10.1016/j.antiviral.2008.07.001 18674567
39. Insights into RNA unwinding and ATP hydrolysis by the flavivirus NS3 protein. Luo D, Xu T, Watson RP, Scherer-Becker D, Sampath A, Jahnke W, Yeong SS, Wang CH, Lim SP, Strongin A, et al. EMBO J 2008 27 3209 3219 10.1038/emboj.2008.232 19008861
40. Multiple dengue serotypes and high frequency of dengue hemorrhagic fever at two tertiary care hospitals in Lahore during the 2008 dengue virus outbreak in Punjab, Pakistan. Humayoun MA, Waseem T, Jawa AA, Hashmi MS, Akram J, Int J Infect Dis 2013 14 Suppl 3 54 59
41. Molecular characterization and phylogenetic analysis of dengue viruses imported into Taiwan during 2008-2010. Huang JH, Su CL, Yang CF, Liao TL, Hsu TC, Chang SF, Lin CC, Shu PY, Am J Trop Med Hyg 87 349 358
42. Emergence of dengue virus type 4 (genotype I) in India. Dash PK, Sharma S, Srivastava A, Santhosh SR, Parida MM, Neeraja M, Subbalaxmi MV, Lakshmi V, Rao PV, Epidemiol Infect 139 857 861
43. Rapid detection and typing of dengue viruses from clinical samples by using reverse transcriptase-polymerase chain reaction. Lanciotti RS, Calisher CH, Gubler DJ, Chang GJ, Vorndam AV, J Clin Microbiol 1992 30 545 551 1372617
44. Clustal W and Clustal X version 2.0. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, et al. Bioinformatics 2007 23 2947 2948 10.1093/bioinformatics/btm404 17846036
45. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S, Mol Biol Evol 2011 28 2731 2739 10.1093/molbev/msr121 21546353
46. BEAST: Bayesian evolutionary analysis by sampling trees. Drummond AJ, Rambaut A, BMC Evol Biol 2007 7 214 10.1186/1471-2148-7-214 17996036
47. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Drummond AJ, Suchard MA, Xie D, Rambaut A, Mol Biol Evol 2012 29 1969 1973 10.1093/molbev/mss075 22367748