The focus of research in our lab has been on understanding the RNA virus replication, in particular the Japanese encephalitis virus, and the development of viral vaccine candidates.

Japanese Encephalitis virus (JEV) is a member of the Flaviviridae family of animal viruses that contains several other medically important viruses such as Dengue and Yellow fever. JEV is a major cause of human encephalitis and is responsible for considerable mortality and morbidity in India. Frequent epidemics of Japanese encephalitis (JE) are being reported from various parts of India and JEV has become endemic in several parts of the country. We are studying the replication of JEV and investigating the role of the cellular proteins in virus replication. We are also examining the potential of small nucleic acid molecules such as siRNA and DNAzymes for inhibiting JEV replication.

Our group also focuses on key aspects of the JEV life-cycle like receptor-binding and entry mechanisms, molecular mechanisms of virus replication, assembly and egress. The virus infectious-cycle involves a complex interaction between virus and host proteins. We are employing JEV- recombinant proteins and infectious viruses as exploratory systems in combination with molecular biology, cell biology and proteomic approaches. These studies provide insight into JEV pathogenesis, and have the potential to offer therapeutic interventions.

In the recent years, we have focused our efforts on understanding the biology of Chikungunya virus with a view to develop novel antivirals. Our laboratory has also been involved in the clinical development an oral rotavirus vaccine for children. Besides, we are interested in developing novel adenoviral vectors useful for vaccine delivery.

• Dr. Anshula Sharma (Project Scientist)
• Dr. Shweta Duggal (Project Scientist)
• Ms. Khashpathika Ganesh (Research Assistant)
• Mr. Shauri K (Research Assistant)
• Ms. Arundhati Deb (PhD candidate)
• Mr. Brohmomoy Basu (PhD candidate)
• Ms. Shivani Balyan (PhD candidate)
• Mr. Harsh Thakur (PhD candidate)
• Mr. Gaurav Lukhar (Lab Assistant)
• Mr. Hemant (Lab Assistant)

• FNA (Fellow of the Indian National Science Academy)
• FNASc (Fellow of the National Academy of Sciences, India)
• FASc (Fellow of the Indian Academy of Sciences)
• J.C. Bose National fellow (SERB, Department of Science & Technology)
• Elected Member, Guha Research Conference
• Distinguished Alumni Award, G. B. Pant University of Agric. & Technol., Pantnagar
• Australian Alumni Excellence Award, Australian High Commission, India
• Tata Innovation Fellowship, Dept. of Biotechnology (DBT), Govt. of India
• NASI-Reliance Industries Platinum Jubilee Award, Natl. Academy of Sciences, India
• Alembic Award, Association of Microbiologists of India
• Professor K. P. Bhargava Memorial Medal, Indian National Science Academy
• Outstanding scientific achievement award, National Institute of Immunology
• National Bioscience Award, DBT, Govt. of India
• Dr. J. B. Srivastava Oration award, Indian Council of Medical Research
• Vasvik Industrial Research Award, Vividhlaxi Audhyogik Sams. Vikas Kendra, Mumbai
• National Scholarship, Govt. of India

• Patent No. 686844; DNA encoding ovine adenovirus (OAV287) and its use as a viral vector; Australian Patent
• Patent No. 289785; DNA encoding ovine adenovirus (OAV287) and its use as a viral vector; New Zealand Patent
• Patent No. 243547; Recombinant vaccine against Japanese encephalitis virus (JEV) infection and a method thereof; Indian Patent
• Patent No. 2004312444; Recombinant vaccine against Japanese encephalitis virus (JEV) infection and a method thereof; Australian Patent
• Patent No. 2005315141; DNAzymes for inhibition of Japanese encephalitis virus; Australian Patent
• Patent No. 7037712; DNA encoding ovine adenovirus (OAV287) and its use as a viral vector; US Patent
• Patent No. EP1708746; Recombinant vaccine against Japanese encephalitis virus (JEV) infection and a method thereof; European Patent
• Patent No. 123824; Recombinant vaccine against Japanese encephalitis virus (JEV) infection and a method thereof; Singapore Patent
• Patent No. 133150; DNAzymes for inhibition of Japanese encephalitis virus; Singapore Patent

1. Duggal S, Rawat R, Siddqui G, Vishwakarma P, Samal S, Banerjee A, Vrati S (2024) Dengue virus infection in mice induces bone marrow myeloid cell differentiation and generates Ly6Glow immature neutrophils with modulated functions. Journal of Leukocyte Biology 115:130-148.
2. Prajapat SK, Mishra L, Khera S, Owusu SD, Ahuja K, Sharma P, Choudhary E, Chhabra S, Kumar N, Singh R, Kaushal PS, Mahajan D, Banerjee A, Motiani RK, Vrati S, Kalia M (2024) Methotrimeprazine is a neuroprotective antiviral in JEV infection via adaptive ER stress and autophagy. EMBO Molecular Medicine 16:185-217.
3. Chaudhary M, Kumar A, Sharma KB, Vrati S and Sehgal D (2024) In silico identification of Chikungunya virus replication inhibitor validated using biochemical and cell-based approaches. FEBS Journal (in press).
4. Saini J, Thapa U, Bandyopadhyay B, Vrati S, Banerjee A (2023) Knockdown of NEAT1 restricts dengue virus replication by augmenting interferon alpha-inducible protein 27 via the RIG-I pathway. Journal of General Virology 104(1). doi: 10.1099/jgv.0.001823.
5. Agarwal S, Kaur S, Asuru TR, Joshi G, Shrimali N, Singh A, Singh ON, Srivastva P, Shrivastava T, Vrati S, Surjit M, Guchhait P (2022) Dietary αKG inhibits SARS CoV-2 infection and rescues inflamed lungs to restore normal O2 saturation in animals. Clinical and Translational Medicine 12 (9):e1041. doi: 10.1002/ctm2.1041.
6. Bhardwaj K, Garg A, Pandey AD, Sharma H, Kumar M, Vrati S (2022) Insights into the Human Gut Virome by Sampling a Population from the Indian Subcontinent. Journal of General Virology 103 (8). doi: 10.1099/jgv.0.001774.
7. Agarwal A, Alam MF, Basu B, Pattanayak S, Asthana S, Syed GH, Kalia M, Vrati S (2022) Japanese Encephalitis Virus NS4A Protein Interacts with PTEN-Induced Kinase 1 (PINK1) and Promotes Mitophagy in Infected Cells. Microbiology Spectrum 10 (3) : e0083022.
8. Thiruvengadam R, Awasthi A, Medigeshi G, Bhattacharya S, Mani S, Sivasubbu S, Shrivastava T, Samal S, Murugesan DR, Desiraju BK, Kshetrapal P, Pandey R, Scaria V, Malik PK, Taneja J, Ahmed S, Kumar R, Bhattacharya J, Subramani C, Wadhwa N, Gupta N, Pandey AK, Agrawal A, Vrati S, Bhatnagar S, Garg PK (2021) Effectiveness of ChAdOx1 nCoV-19 vaccine against SARS-CoV-2 infection during the delta (B.1.617.2) variant surge in India: a test-negative case-control study and a Mechanistic Study of Post-Vaccination Immune Responses. The Lancet Infectious Diseases 22 (4) : 473-482.
9. Tripathi A, Banerjee A, Vrati S (2021) Development and characterisation of an animal model of Japanese Encephalitis Virus infection in adolescent C57VL/6 mice. Disease models and mechanisms doi call: 10. 1242/DMM. 049176
10. Sehrawat S, Khasa R, Deb A, Prajapat SK, Mallick S, Basu A, Surjit M, Kalia M, Vrati S (2021) Valosin-containing protein/p97 plays critical roles in the Japanese encephalitis virus life cycle. Journal of Virology 95 (11) : e02336-20 PMID: 33731458.
11. Banerjee A, Tripathi A, Duggal S, Banerjee A, Vrati S (2020) Dengue virus infection impedes megakaryopoiesis in MEG-01 cells where the virus envelope protein interacts with the transcription factor TAL-1. Scientific Reports 10(1):19587.
12. Saini J, Bandyopadhyay B, Pandey AD, Ramachandran VG, Das S, Sood V, Banerjee A, Vrati S (2020) High-Throughput RNA Sequencing Analysis of Plasma Samples Reveals Circulating microRNA Signatures with Biomarker Potential in Dengue Disease Progression. mSystems 5(5):e00724-20.
13. Levine MM, Abdullah S, Arabi YM, Darko DM, Durbin AP, Estrada V, Jamrozik E, Kremsner PG, Lagos R, Pitisuttithum P, Plotkin SA, Sauerwein R, Shi SL, Sommerfelt H, Subbarao K, Treanor JJ, Vrati S, King D, Balasingam S, Weller C, Aguilar AO, Cassetti MC, Krause PR, Restrepo AMH (2020) Viewpoint of a WHO Advisory Group Tasked to Consider Establishing a Closely-Monitored Challenge Model of COVID-19 in Healthy Volunteers. Clinical Infectious Diseases 28:ciaa1290.
14. Mukherjee S, Akbar I, Kumari B, Vrati S, Basu A, Banerjee A (2018) Japanese Encephalitis Virus-induced let-7a/b interacted with the NOTCH-TLR7 pathway in microglia and facilitated neuronal death via caspase activation. Journal of Neurochemistry doi: 10.1111/ jnc.14645.
15. Nain M, Mukherjee S, Karmakar SP, Paton AW, Paton JC, Abdin MZ, Basu A, Kalia M, Vrati S (2017) GRP78 Is an Important Host Factor for Japanese Encephalitis Virus Entry and Replication in Mammalian Cells. Journal of Virology 91(6): e02274-16
16. Sharma M, Bhattacharyya S, Sharma KB, Chauhan S, Asthana S, Abdin MZ, Vrati S, Kalia M (2017) Japanese encephalitis virus activates autophagy through XBP1 and ATF6 ER stress sensors in neuronal cells. J Gen Virol 98(5): 1027
17. Goswami S, Banerjee A, Kumari B, Bandopadhyay B, Bhattacharya N, Basu N, Vrati S, Banerjee A (2017) Differential Expression and Significance of Circulating microRNAs in Cerebrospinal Fluid of Acute Encephalitis Patients Infected with Japanese Encephalitis Virus. Molecular Neurobiology 54(2) : 1541-1551
18. Kumari B, Jain P, Das S, Ghosal S, Hazra B, Trivedi AC, Basu A, Chakrabarti J, Vrati S, Banerjee A (2016) Dynamic changes in global microRNAome and transcriptome reveal complex miRNA-mRNA regulated host response to Japanese Encephalitis Virus in microglial cells. Scientific Reports 6: 20263
19. Sharma D, Priyadarshini P and Vrati S (2015) Unraveling the web of viroinformatics: computational tools and databases in viral research. Journal of Virology 89: 1489
20. Bhullar D, Jalodia R, Kalia M, Vrati S (2014) Cytoplasmic translocation of polypyrimidine tract-binding protein and its binding to viral RNA during Japanese encephalitis virus infection inhibits virus replication. PLoS ONE 9 (12): e114931.
21. Pareek S, Roy S, Kumari B, Jain P, Banerjee A, Vrati S (2014) miR-155 induction in microglial cells suppresses Japanese encephalitis virus replication and negatively modulates innate immune responses. Journal of Neuroinflammation 11: 97 doi: 10.1186/1742-2094-11-97
22. Sharma M, Bhattacharya S, Nain M, Kaur M, Sood V, Gupta V, Khasa R, Abdin MZ, Vrati S, Kalia M (2014) Japanese encephalitis virus replication is negatively regulated by autophagy and occurs on LC3-I and EDEM1 containing membranes. Autophagy 10: 1637
23. Bhandari N, Rongsen-Chandola T, Bavdekar A, John J, Antony K, Taneja S, Goyal N, Kawade A, Kang G, Rathore SS, Juvekar S, Muliyil J, Arya A, Shaikh H, Abraham V, Vrati S, Proschan M, Kohberger R, Thiry G, Glass R, Greenberg HB, Curlin G, Mohan K, Harshavardhan GV, Prasad S, Rao TS, Boslego J, Bhan MK (2014) Efficacy of a monovalent human-bovine (116E) rotavirus vaccine in Indian infants: a randomised, double-blind, placebo-controlled trial. Lancet S0140-6736 : 62630
24. Appaiahgari MB, Glass R, Singh S, Taneja S, Rongsen-Chandola T, Bhandari N, Mishra S, Vrati S. (2014) Transplacental rotavirus IgG interferes with immune response to live oral rotavirus vaccine ORV-116E in Indian infants. Vaccine 3; 32(6): 656.
25. Bhattacharyya S, Sen U, Vrati S. (2014) Regulated IRE1-dependent decay pathway is activated during Japanese encephalitis virus-induced unfolded protein response and benefits viral replication. J Gen Virol. 95: 79.
26. Kalia M, Khasa R, Sharma M, Nain M, Vrati S. (2013) Japanese encephalitis virus infects neuronal cells through a clathrin-independent endocytic mechanism. J Virol87(1): 162.
27. Appaiahgari MB, Vrati S. (2012) Clinical development of IMOJEV ®--a recombinant Japanese encephalitis chimeric vaccine (JE-CV). Expert Opin Biol Ther. 12(9): 1263.
28. Anantpadma, M. and Vrati, S. (2012) siRNA-mediated suppression of Japanese encephalitis virus replication in cultured cells and mice. Journal of Antimicrobial Chemotherpay 67: 451.
29. Vashist, S., Bhullar, D., and Vrati, S. (2011) La protein can simultaneously bind to both 3' and 5'-noncoding regions of Japanese encephalitis virus genome. DNA and Cell Biology: 30: 346
30. Appaiahgari M.B., and Vrati, S. (2010) IMOJEV® : a Yellow Fever virus-based novel Japanese encephalitis vaccine. Expert Review of Vaccines 9: 1384.
31. Anantpadma, M., Stein, D.A., Vrati, S. (2010) Inhibition of Japanese encephalitis virus replication in cultured cells and mice by a peptide-conjugated morpholino oligomer. Journal of Antimicrobial Chemotherpay 65: 961.
32. Bhandari, N., Sharma, P., Taneja, S., Kumar, T., Rongsen-Chandola, T., Appaiahgari, M.B., Mishra, A., Singh, S., Vrati, S.; Rotavirus Vaccine Development Group (2009) A Dose-Escalation Safety and Immunogenicity Study of Live Attenuated Oral Rotavirus Vaccine 116E in Infants: A Randomized, Double-Blind, Placebo-Controlled Trial. Journal of Infectious Diseases 200: 429.
33. Vashist, S., Anantpadma, M., Sharma, H., Vrati S. (2009) La protein binds the predicted loop structures in the 3' non-coding region of Japanese encephalitis virus genome: role in virus replication. Journal of General Virology 90: 1343
34. Bharati, K., Rani, R. and Vrati, S. (2009) Evaluation of Japanese encephalitis virus DNA vaccine candidates in rhesus monkeys [Macaca mulatta]. Vaccine 27: 16.
35. Appaiahgari, M.B. and Vrati, S. (2007) DNAzyme-mediated inhibition of Japanese encephalitis virus replication in mouse brain. Molecular Therapy 15: 1593
36. Appaiahgari, M.B., Saini, M., Rauthan, M., Jyoti, Vrati, S. (2006) Immunization with recombinant adenovirus synthesizing the secretory form of Japanese encephalitis virus envelope protein protects adenovirus-exposed mice against lethal encephalitis. Microbes & Infection 8: 104.
37. Appaiahgari, M.B. and Vrati, S. (2004) Immunogenicity and protective efficacy in mice of a formaldehyde-inactivated Indian strain of Japanese encephalitis virus grown in Vero cells.Vaccine 22: 3675.
38. Saini, M. andVrati, S. (2003) A Japanese encephalitis virus peptide present on Johnson grass mosaic virus-like particles induces virus-neutralizing antibodies and protects mice against lethal challenge. Journal of Virology 77: 33494.
39. Kaur R., Sachdeva, G. and Vrati, S. (2002) Plasmid DNA immunization against Japanese encephalitis virus : Immunogenicity of membrane-anchored and secretary envelope protein.Journal of Infectious Diseases 185: 12.
40. Ta, M. and Vrati, S.(2000) Mov34 protein from mouse brain interacts with the 3' noncoding region of Japanese Encephalitis virus. Journal of Virology 74: 5115.
41. Vrati, S., Giri R.K., Razdan, A., and Malik, P. (1999) Complete nucleotide sequence of an Indian strain of Japanese Encephalitis virus : sequence comparison with other strains and phylogenetic analysis. American Journal of Tropical Medicine and Hygiene 61: 680.
42. Vrati, S., Agarwal, V., Malik, P., Wani, S. A. and Saini, M. (1999) Molecular characterization of an Indian isolate of Japanese Encephalitis virus that shows an extended lag phase during growth. Journal of General Virology 80: 1671.