Phylogenetic and molecular clock analysis of dengue serotype 1 and 3 from New Delhi, India

PLoS ONE

Volumn 10, Issue 11, 2015, Pages

  Afreen, Nazia ^a   Naqvi, Irshad H ^a   Broor, Shobha ^b   Ahmed, Anwar ^c   Parveen, Shama ^a  

^a JAMIA MILLIA ISLAMIA CENTRAL UNIVERSITY   (India)

^b SGT UNIVERSITY   (India)

^c KING SAUD UNIVERSITY   (Saudi Arabia)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; ARTICLE; DENGUE VIRUS 1; DENGUE VIRUS 2; DENGUE VIRUS 3; DENGUE VIRUS 4; ENVELOPE GENE; FEMALE; HUMAN; INDIA; MAJOR CLINICAL STUDY; MALE; MIXED INFECTION; MOLECULAR CLOCK; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; NUCLEOTIDE SEQUENCE; PHYLOGENY; POPULATION DYNAMICS; POPULATION SIZE; PREVALENCE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEROTYPING; VIRUS DETECTION; VIRUS STRAIN; BAYES THEOREM; CLASSIFICATION; DENGUE; DENGUE VIRUS; GENETICS; GENOTYPE; ISOLATION AND PURIFICATION; MOLECULAR EVOLUTION; PROSPECTIVE STUDY; SEROTYPE; TRANSMISSION; VIROLOGY; YOUNG ADULT;

VIRUS RNA;

ADULT; BAYES THEOREM; DENGUE; DENGUE VIRUS; EVOLUTION, MOLECULAR; FEMALE; GENOTYPE; HUMANS; INDIA; MALE; PHYLOGENY; PROSPECTIVE STUDIES; RNA, VIRAL; SEROGROUP; SEROTYPING; YOUNG ADULT;

EID: 84951185311     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0141628     Document Type: Article

References (31)

1. WHO. Dengue: guidelines for diagnosis, treatment, prevention, and control. Special Programme for Research and Training in Tropical Diseases. 2009.
2. Wright WF, Pritt BS. Update: The diagnosis and management of dengue virus infection in North America. Diagn Microbiol Infect Dis 2012; 73(3):215-20. doi: 10.1016/j.diagmicrobio.2012.03.021 PMID: 22541792
3. Kukreti H, Dash PK, Parida M, Chaudhary A, Saxena P, Rautela RS, et al. Phylogenetic studies reveal existence of multiple lineages of a single genotype of DENV-1 (genotype III) in India during 1956-2007. Virol J. 2009; 6:1. doi: 10.1186/1743-422X-6-1 PMID: 19126194
4. Kumar SRP, Patil J a, Cecilia D, Cherian SS, Barde P V, Walimbe AM, et al. Evolution, dispersal and replacement of American genotype dengue type 2 viruses in India (1956-2005): selection pressure and molecular clock analyses. J Gen Virol. 2010; 91(Pt 3):707-20. doi: 10.1099/vir.0.017954-0 PMID: 19923266
5. Patil J, Cherian S, Walimbe M, Bhagat, Vallentyne J, Kakade M, et al. Influence of evolutionary events on the Indian subcontinent on the phylogeography of dengue type 3 and 4 viruses. Infect Genet Evol. 2012; 12(8):1759-69. doi: 10.1016/j.meegid.2012.07.009 PMID: 22890284
6. Lanciotti RS, Calisher CH, Gubler DJ, Chang GJ, Vorndam A V. Rapid detection and typing of dengue viruses from clinical samples by using reverse transcriptase-polymerase chain reaction. J Clin Microbiol. 1992; 30(3):545-51. PMID: 1372617
7. Afreen N, Deeba F, Naqvi I, Shareef M, Ahmed A, Broor S, et al. Molecular Investigation of 2013 Dengue Fever Outbreak from Delhi, India. plos Curr outbreaks. 2014;Sep 2.
8. Afreen N, Deeba F, Khan WH, Haider SH, Kazim SN, Ishrat R, et al. Molecular characterization of dengue and chikungunya virus strains circulating in New Delhi, India. Microbiol Immunol. 2014; 58:688-96. doi: 10.1111/1348-0421.12209 PMID: 25346397
9. Wu W, Bai Z, Zhou H, Tu Z, Fang M, Tang B, et al. Molecular epidemiology of dengue viruses in southern China from 1978 to 2006. Virol J.2011; 8(1):322.
10. Huang JH, Liao TL, Chang SF, Su CL, Chien LJ, Kuo YC, et al. Laboratory-based dengue surveillance in Taiwan, 2005: A molecular epidemiologic study. Am J Trop Med Hyg. 2007; 77(5):903-9. PMID: 17984351
11. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994; 22(22):4673-80. PMID: 7984417
12. Hall T. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser. 1999; 41:95-8.
13. Posada D and Crandall K A. MODELTEST: testing the model of DNA substitution. Bioinformatics. 1998; 14(9):817-8. PMID: 9918953
14. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013; 30(12):2725-9. doi: 10.1093/molbev/mst197 PMID: 24132122
15. Drummond AJ, Suchard M a., Xie D, Rambaut A Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. 2012; 29(8):1969-73. doi: 10.1093/molbev/mss075 PMID: 22367748
16. Drummond AJ, Ho SYW, Phillips MJ, Rambaut A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 2006; 4(5):699-710.
17. Patil J, Cherian S, Walimbe M, Patil BR, Sathe PS, Shah PS, et al. Evolutionary dynamics of the American African genotype of dengue type 1 virus in India (1962-2005). Infect Genet Evol. 2011; 11 (6):1443-8. doi: 10.1016/j.meegid.2011.05.011 PMID: 21632029
18. Huang JH, Su CL, Yang CF, Liao TL, Hsu TC, Chang SF, et al. Molecular characterization and phylogenetic analysis of dengue viruses imported into Taiwan during 2008-2010. Am J Trop Med Hyg. 2012; 87(2):349-58. doi: 10.4269/ajtmh.2012.11-0666 PMID: 22855770
19. Sharma S, Dash PK, Agarwal S, Shukla J, Parida MM, Rao PVL. Comparative complete genome analysis of dengue virus type 3 circulating in India between 2003 and 2008. J Gen Virol. 2011; 92(Pt 7):1595-600. doi: 10.1099/vir.0.030437-0 PMID: 21411675
20. Mishra G, Jain A, Prakash O, Prakash S, Kumar R, Garg RK, et al. Molecular characterization of dengue viruses circulating during 2009-2012 in Uttar Pradesh, India. J Med Virol. 2014 2;2:1-8.
21. Das B, Das M, Dwibedi B, Kar SK, Hazra RK. Molecular investigations of dengue virus during outbreaks in Orissa state, Eastern India from 2010 to 2011. Infect Genet Evol. 2013; 16:401-10. doi: 10.1016/j. meegid.2013.03.016 PMID: 23523598
22. Pandey Nidhi, Nagar Rachna, Gupta Shikha, Omprakash, Khan Danish, Singh Desh Deepak, Mishra Gitika, Shantanu Prakash, Singh K.P., Singh Mastan JA. Trend of dengue virus infection at Lucknow, north India (2008-2010): A hospital based study. Indian J Med Res. 2012;
23. Kukreti H, Chaudhary A, Rautela RS, Anand R, Mittal V, Chhabra M, et al. Emergence of an independent lineage of dengue virus type 1 (DENV-1) and its co-circulation with predominant DENV-3 during the 2006 dengue fever outbreak in Delhi. Int J Infect Dis. 2008; 12(5):542-9. doi: 10.1016/j.ijid.2008.02. 009 PMID: 18495513
24. Chakravarti A, Chauhan MS, Kumar S, Ashraf A. Genotypic characterization of dengue virus strains circulating during 2007-2009 in New Delhi. Arch Virol. 2013; 158(3):571-81. doi: 10.1007/s00705-012-1522-5 PMID: 23129129
25. Singh P, Mittal V, Rizvi MM a, Chhabra M, Sharma P, Rawat DS, et al. The first dominant co-circulation of both dengue and chikungunya viruses during the post-monsoon period of 2010 in Delhi, India. Epidemiol Infect. 2012; 140(7):1337-42. doi: 10.1017/S0950268811001671 PMID: 21906409
26. Bharaj P, Chahar HS, Pandey A, Diddi K, Dar L, Guleria R, et al. Concurrent infections by all four dengue virus serotypes during an outbreak of dengue in 2006 in Delhi, India. Virol J. 2008; 5:1. doi: 10. 1186/1743-422X-5-1 PMID: 18182120
27. Anoop M, Issac A, Mathew T, Philip S, Kareem NA, Unnikrishnan R, et al. Genetic characterization of dengue virus serotypes causing concurrent infection in an outbreak in Ernakulam, Kerala, South India. Indian J Exp Biol. 2010 Aug; 48(8):849-57. PMID: 21341545
28. Dash PK, Sharma S, Soni M, Agarwal A, Sahni AK, Parida M. Complete genome sequencing and evolutionary phylogeography analysis of Indian isolates of Dengue virus type 1. Virus Res; 2014; 195:124-134. doi: 10.1016/j.virusres.2014.08.018 PMID: 25197040
29. Ho S. Y. W. and Shapiro B. Skyline-plot methods for estimating demographic history from nucleotide sequences. Mol Ecol Resour. 2011; 11:423-34. doi: 10.1111/j.1755-0998.2011.02988.x PMID: 21481200
30. Araújo JMG, Nogueira RMR, Schatzmayr HG, Zanotto PMD a, Bello G. Phylogeography and evolutionary history of dengue virus type 3. Infect Genet Evol. 2009; 9(4):716-25. doi: 10.1016/j.meegid.2008. 10.005 PMID: 19010450
31. Pandey A, Diddi K, Dar L, Bharaj P, Chahar HS, Guleria R, et al. The evolution of dengue over a decade in Delhi, India. J Clin Virol. 2007; 40(1):87-8. PMID: 17631046