Original Article

Molecular detection and characterization of dengue isolates circulating in north India


Background and Objectives: In recent decades, the incidence of dengue has increased dramatically. In dengue-endemic countries, changes in dengue virus serotypes, genotypes, and lineages have been reported. This study was designed to detect and characterize the dengue virus isolates circulating in North India by serological and molecular techniques.
Materials and Methods: This study was conducted at the Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India. NS1 antigen and IgM antibody against dengue were detected by ELISA methods, viral RNA was extracted and amplified by conventional PCR and one-step single-tube multiplex PCR. The purified PCR products were cycle sequenced and a database search was implemented for the confirmation of the sequence product. Phylogenetic analysis was carried out with previously reported sequences.
Results: Among 1509 samples, 205 (13.6%) were found positive for IgM antibodies with the highest number (n=67) among the 21 to 30 years age group with peak positivity during post-monsoon months. Among acute samples, NS1 antigen was positive in 62.9%. Seven patients out of 13 had dengue viral RNA in PCR. It comprised six DENV-2 serotypes and one DENV-3 serotype. On phylogenetic analysis, DENV-2 strains grouped with genotype IV and DENV-3 with genotype III.
Conclusion: Dengue infection was found frequently during post-monsoon season. The positivity rate of the dengue NS1 antigen test was greater than that of the antibody test. The dengue isolates were characterized as genotype IV and genotype III of DENV-2 and DENV-3 respectively.

1. Wilder-Smith A, Rupali P. Estimating the dengue burden in India. Lancet Glob Health 2019;7(8):e988-989.
2. Guzman MG, Halstead SB, Artsob H, Buchy P, Farrar J, Gubler DJ, et al. Dengue : a continuing global threat. Nat Rev Microbiol 2010;8(12 Suppl):S7-16.
3. Waggoner JJ, Gresh L, Vargas MJ, Ballesteros G, Tellez Y, Soda KJ, et al. Viremia and clinical presentation in Nicaraguan patients infected with Zika virus, Chikungunya virus, and Dengue virus. Clin Infect Dis 2016;63:1584-1590.
4. Bhatt S, Gething PW, Brady OJ, Messina JP, Farlow AW, Moyes CL, et al. The global distribution and burden of dengue. Nature 2013;496:504-507.
5. Brady OJ, Gething PW, Bhatt S, Messina JP, Brownstein JS, Hoen AG, et al. Refining the global spatial limits of dengue virus transmission by evidence-based consensus. PLoS Negl Trop Dis 2012;6(8):e1760.
6. Murhekar MV, Kamaraj P, Kumar MS, Khan SA, Allam RR, Barde P, et al. Burden of dengue infection in India, 2017: a cross-sectional population based serosurvey. Lancet Glob Health 2019;7(8):e1065-e1073.
7. Zhang Y, Corver J, Chipman PR, Zhang W, Pletnev SV, Sedlak D, et al. Structures of immature flavivirus particles. EMBO J 2003;22:2604-2613.
8. Gupta N, Srivastava S, Jain A, Chaturvedi UC. Dengue in India. Indian J Med Res 2012;136:373-390.
9. Faridi MMA, Aggarwal A, Kumar M, Sarafrazul A. Clinical and biochemical profile of dengue haemorrhagic fever in children in Delhi. Trop Doct 2008;38:28-30.
10. Dash PK, Parida MM, Saxena P, Kumar M, Rai A, Pasha ST, et al. Emergence and continued circulation of dengue-2 (genotype IV) virus strains in northern India. J Med Virol 2004;74:314-322.
11. Tripathi SK, Gupta P, Khare V, Chatterjee A, Kumar R, Khan MY, et al. Emergence of new lineage of dengue virus 3 (genotype III) in Lucknow, India. Iran J Microbiol 2013;5:68-75.
12. 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;12:542-549.
13. Sathish N, Manayani DJ, Shankar V, Abraham M, Nithyanandam G, Sridharan G. Comparison of IgM capture ELISA with a commercial rapid immunochromatographic card test & IgM microwell ELISA for the detection of antibodies to dengue viruses. Indian J Med Res 2002;115:31-36.
14. Jasamai M, Yap WB, Sakulpanich A, Jaleel A. Current prevention and potential treatment options for dengue infection. J Pharm Pharm Sci 2019;22:440-456.
15. Pal S, Dauner AL, Mitra I, Forshey BM, Garcia P, Morrison AC, et al. Evaluation of dengue NS1 antigen rapid tests and ELISA kits using clinical samples. PLoS One 2014;9(11):e113411.
16. Lima Mda R, Nogueira RM, Bispo de Filippis AM, dos Santos FB. Comparison of two generations of the panbio dengue NS1 capture enzyme-linked immunosorbent assay. Clin Vaccine Immunol 2011;18:1031-1033.
17. Rahman M, Sharma A, Patgiri S, Hussain E, Borah AK, Saikia L. Serotyping of dengue viruses circulating during 2014-2015 in Assam, India. Indian J Med Microbiol 2018;36:429-431.
18. Tian JN, Yang CC, Chuang CK, Tsai MH, Wu RH, Chen CT, et al. A Dengue virus type 2 (DENV-2) NS4B-interacting host factor, SERP1, reduces DENV-2 production by suppressing viral RNA replication. Viruses 2019;11:787.
19. Klungthong C, Gibbons RV, Thaisomboonsuk B, Nisalak A, Kalayanarooj S, Thirawuth V, et al. Dengue virus detection using whole blood for reverse transcriptase PCR and virus isolation. J Clin Microbiol 2007;45:2480-2485.
20. Saxena P, Dash PK, Santhosh SR, Shrivastava A, Parida M, Rao PL. Development and evaluation of one step single tube multiplex RT-PCR for rapid detection and typing of dengue viruses. Virol J 2008;5:20.
21. Dengue fever climbs the social ladder. Nature 2007;448:734-735.
22. Fredericks AC, Fernandez-Sesma A. The burden of dengue and chikungunya worldwide: implications for the southern United States and California. Ann Glob Health 2014;80:466-475.
23. Murray NE, Quam MB, Wilder-Smith A. Epidemiology of dengue: past, present and future prospects. Clin Epidemiol 2013;5:299-309.
24. Kassim FM, Izati MN, TgRogayah TA, Apandi YM, Saat Z. Use of dengue NS1 antigen for early diagnosis of dengue virus infection. Southeast Asian J Trop Med Public Health 2011;42:562-569.
25. Singh MP, Majumdar M, Singh G, Goyal K, Preet K, Sarwal A, et al. NS1 antigen as an early diagnostic marker in dengue: report from India. Diagn Microbiol Infect Dis 2010;68:50-54.
26. Prakash O, Singh DD, Mishra G, Prakash S, Singh A, Gupta S, et al. Observation on dengue cases from a virus diagnostic laboratory of a tertiary care hospital in north India. Indian J Med Res 2015;142 Suppl(Suppl 1):S7-S11.
27. Ratho RK, Mishra B, Kaur J, Kakkar N, Sharma K. An outbreak of dengue fever in periurban slums of Chandigarh, India, with special reference to entomological and climatic factors. Indian J Med Sci 2005;59:518-526.
28. 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.
29. Ganeshkumar P, Murhekar MV, Poornima V, Saravanakumar V, Sukumaran K, Anandaselvasankar A, et al. Dengue infection in India: a systematic review and meta-analysis. PLoS Negl Trop Dis 2018;12(7):e0006618.
30. Ma M, Wu S, He Z, Yuan L, Bai Z, Jiang L, et al. New genotype invasion of dengue virus serotype 1 drove massive outbreak in Guangzhou, China. Parasit Vectors 2021;14:126.
IssueVol 14 No 1 (2022) QRcode
SectionOriginal Article(s)
DOI https://doi.org/10.18502/ijm.v14i1.8811
Dengue virus; Serotype; Genotype; Immunoglobulin M; Antigens

Rights and permissions
Creative Commons License This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
How to Cite
Mishra M, Yadav S, Mishra S, Ratho R. Molecular detection and characterization of dengue isolates circulating in north India. Iran J Microbiol. 2022;14(1):104-111.