Virology Biotechnology

Key areas of research

Biomarker Discovery: Identification and evaluation of novel diagnostic biomarkers for early and accurate diagnosis of TB using non-sputum-based specimens, predictive biomarkers for early identification of individuals at high risk for progression from infection to active TB disease, and prognostic biomarkers for monitoring treatment response and predicting treatment outcomes.

Host–pathogen Interactions and Immunopathogenesis: Dissecting the molecular and cellular interplay between the host immune system and Mycobacterium tuberculosis with particular emphasis on neutrophil extracellular traps (NETs), comprehensive cataloguing of host and pathogen transcriptomic signatures in different forms of extrapulmonary tuberculosis to elucidate disease-specific molecular pathways and to identify potential therapeutic targets.and their role in tuberculosis–diabetes and tuberculosis-HIV.

HIV/TB Co-infection: Elucidating the pathogenesis and molecular dynamics of HIV/TB co-infection, identifying factors that drive disease severity and progression, and supporting the discovery of novel broadly neutralizing antibodies and anti-HIV compounds with translational potential.

Emerging and Zoonotic Viral Diseases: Expanding research efforts into zoonotic respiratory viral infections under the One Health framework, addressing the interface between human, animal, and environmental health.

Vector-Borne Viral Surveillance: Conducting pan-India antigenic characterization of dengue viruses to monitor viral evolution, diversity, and its implications for vaccine design and disease control strategies.

List of ongoing projects

An integrative biomarker discovery and validation approach to aid the development of point-of-care tests for tuberculosis (Funded by ICMR Intramural, 2023-26, Total grant: 4,50,00,000/-)

Role of persistent immune activation and systemic inflammation on accelerated immune senescence and increased risk of mortality in successfully treated and cured TB patients (Funded by ICMR under the Ad-hoc Scheme, 2022-2025, Total grant: Rs. 67,68,000/-)

Central Biorepository for TB Specimens – Phase II (Funded by DBT, 2022-26, Total grant: Rs.3,50,00,000/-)

Setting up of Nation-wide Network of Laboratories for Managing Epidemics and National Calamities – Medical College Level VRDL (Funded by DHR, 2021-26, Total grant: Rs.2,43,50,000/-)

Pan-India antigenic characterization of dengue viruses: early warning signal for a potential pandemic (Funded by ICMR under PM-ABHIM scheme, 2024-27, Multicentric, Total grant: Rs.2,30,00,000/-)

Surveillance of zoonotic respiratory viral infections in animal farms from Thiruvallur District, Tamil Nadu: a model project with a focus on One Health approach (Funded by ICMR under PM-ABHIM scheme, 2024-27, Total grant: Rs.3,00,00,000/-)

Harnessing T cell repertoires and metrics of diversity and clonality for HIV vaccine development (Funded by ICMR & IAVI, 2024-27, Total grant: Rs. 1,78,00,000/-)

Prospective multicenter evaluation of feasibility and performance of blood-based triage test for tuberculosis in intended setting of use (Funded by ICMR under the Task Force Scheme, 2025-27, Multicentric, Total grant: Rs. 3,88,00,020/-)

Development of therapeutic broadly neutralizing antibodies against circulating HIV-1 clade C in children and adults (Funded by DBT, 2023-2026, Multicentric, Total grant: Rs. 7,13,57,104/-)

The Department has a Diagnostic Serology Laboratory, Tissue Culture and Cellular Immunology Laboratory, Molecular Biology Laboratory, Virology Laboratory, BSL-II Plus Laboratory and a Bioinformatics Laboratory. Some of the key facilities and assets of the Department are showcased below.

Since the tuberculosis (TB) cases among HIV infected population result from the reactivation of latent bacilli, development of LRPs capable of detecting dormant bacteria would be useful.

TB Biorepository

The Department has a large, state-of-the-art TB Biorepository, that is well-equipped with essential infrastructure to undertake storage of different types of biological specimens, and is provided with all safety devices like access control, CCTV surveillance, carbon dioxide monitors, fire alarms and fire extinguishers to ensure the safety of the stored specimens. All storage equipment are connected to real-time temperature monitoring devices to ensure sample integrity. Chain of custody and sample inventory management at the Biorepository are implemented through the cloud-based Freezer Pro Specimen Management System.

Virus Research and Diagnostic Laboratory (VRDL)

A Medical College Level VRDL was established by the Department in 2023 with funding from the Department of Health Research, GOI, under the scheme called ‘Establishment of Network of Laboratories for Managing Epidemics and Natural Calamities’. The VRDL participates in National External Quality Assurance Programs and engages itself in the public health initiatives of the GOI by offering diagnostic support for viral infections, providing training for health professionals and undertaking research in relevant viral infections.

Flow Cytometry Facility

The Department has a high-end flow cytometer cum sorter (FACS ARIA III SORP) which is capable of detecting 11 different fluorochromes in a single tube. It can also sort the cells of interest with high purity. The facility has contributed extensively to various immunological studies of NIRT, and supported several TB and HIV vaccine trials. The facility is also widely accessed by researchers from various academic and research institutions in the city for an unlimited breadth of applications.

Sanger Sequencing Facility

The Department has a 3500 Genetic Analyzer from Applied Biosystems which is used extensively for HIV-1 drug resistance testing and pharmacogenomic studies aimed at identifying genetic polymorphisms in anti-TB and anti-HIV drug metabolizing genes. The Laboratory is accredited by WHO for HIV-1 drug resistance genotyping and has been identified as a National Reference Laboratory for HIV-1 drug resistance testing.

Droplet Digital PCR System

The Department recently acquired a Droplet Digital PCR system (BioRad QX200) for ultrasensitive detection, multiplexing and absolute quantification of target DNA or RNA molecules. The system comprises of a QX200 Droplet Generator, QX200 Droplet Reader, C1000 Touch Thermal Cycler and PX1 PCR Plate Sealer. Data acquisition is managed through Bio-Rad’s QuantaSoft™ software, which discriminates between PCR-positive and PCR-negative droplets based on fluorescence intensity and calculates the absolute number of target copies per input volume.

i. Eden MIST, Vetrivel U. (2025). Optimal Dual RNA-Seq Mapping for Accurate Pathogen Detection in Complex Eukaryotic Hosts. Bio Protocols, Feb 5;15(3): e5182. doi: 10.21769/BioProtoc.5182.

ii. Nogueira BMF, Rangel F, Andrade AMS, Daniel EA, Figueiredo MC, Staats C, Rolla VC, Kritski AL, Cordeiro-Santos M, Gupta A, Hanna LE, Sterling TR, Araújo-Pereira M, Andrade BB, RePORT Brazil and RePORT India Consortia (2025). Predictive Markers of Incident Tuberculosis in Close Contacts in Brazil and India. The Journal of Infectious Diseases, jiae642. Advance online publication. https://doi.org/10.1093/infdis/jiae642.

iii. Daniel EA, Upadhyay S, Selvachithiram M, Pattabiraman S., Bhanu B, Sivaprakasam A, Kulkarni V, Karyakarte R, Gaikwad S, Paradkar M, Yogendra Shivakumar SVB, Mave V, Gupta A, Prasad K, Hanna LE. (2025). Predictive metabolite signatures for risk of progression to active TB from QuantiFERON supernatants of household contacts of TB patients. Emerging Microbes & Infections, 14(1), 2437242. https://doi.org/10.1080/22221751.2024.2437242.

iv. Rajamanickam A, Ann Daniel E, Dasan B, Thiruvengadam K, Chandrasekaran P, Gaikwad S, Pattabiraman S, Bhanu B, Sivaprakasam A, Kulkarni V, Karyakarte R, Paradkar M, Shivakumar SVBY, Mave V, Gupta A, Hanna LE, Babu S. (2025). Plasma Immune Biomarkers Predictive of Progression to Active Tuberculosis in Household Contacts of Patients with Tuberculosis. The Journal of Infectious Diseases, 231(3), 696–705. https://doi.org/10.1093/infdis/jiae365.

v. Joseph NH, Natarajan AP, Natarajan S, Ponnuraja C, A M, I G, P H, S R, Jayabal L, Ayyamperumal M, P M R, Hanna LE. (2025). Previous COVID-19 infection significantly reduces elastase levels in newly diagnosed pulmonary tuberculosis patients. Frontiers in Immunology, 16, 1586789. https://doi.org/10.3389/fimmu.2025.1586789.

vi. Babu H, Rachel G, Neogi U, Palaniappan AN, Narayanan A, Ponnuraja C, Sundaraj V, Viswanathan VK, Kumar CPG, Tripathy SP, Hanna LE. (2024). Accelerated cognitive aging in chronically infected HIV-1 positive individuals despite effective long-term antiretroviral therapy. Metabolic Brain Disease, 40(1), 32. https://doi.org/10.1007/s11011-024-01458-w.

vii. Angamuthu D, Vivekanandan S, Hanna LE. (2023). Experimental models for HIV latency and molecular tools for reservoir quantification-an update. Clinical microbiology reviews, 36(4), e0001323. https://doi.org/10.1128/cmr.00013-23.

viii. Daniel EA, Thiruvengadam K, Rajamanickam A, Chandrasekaran P, Pattabiraman S, Bhanu B, Sivaprakasam A, Paradkar M, Kulkarni V, Karyakarte R, Shivakumar SVBY, Mave V, Gupta A, Babu S, Hanna LE. (2023). QuantiFERON Supernatant-Based Host Biomarkers Predicting Progression to Active Tuberculosis Disease Among Household Contacts of Tuberculosis Patients. Clinical Infectious Diseases, 76(10), 1802–1813. https://doi.org/10.1093/cid/ciac979.

ix. Mikaeloff F, Svensson Akusjärvi S, Ikomey GM, Krishnan S, Sperk M, Gupta S, Magdaleno GDV, Escós A, Lyonga E, Okomo MC, Tagne CT, Babu H, Lorson CL, Végvári Á, Banerjea AC, Kele J, Hanna LE, Singh K, de Magalhães JP, Benfeitas R, Neogi U. Trans cohort metabolic reprogramming towards glutaminolysis in long-term successfully treated HIV-infection. Commun Biol. 2022 Jan 11;5(1):27. doi: 10.1038/s42003-021-02985-3.

x. Daniel EA, Sathiyamani B, Thiruvengadam K, Vivekanandan S, Vembuli H, Hanna LE. MicroRNAs as diagnostic biomarkers for Tuberculosis: A systematic review and meta- analysis. Front Immunol. 2022 Sep 27; 13:954396. doi: 10.3389/fimmu.2022.954396.

The Department has been serving as a Regional Reference Laboratory for the National AIDS Control Organization for two National Programs viz. Early Infant Diagnosis Program and National ART Program.

The Department has been recognized as a National Reference Laboratory for HIV-1 Drug Resistance Genotyping by WHO to support HIV drug resistance surveillance in the country.

The Department established a Medical College Level VRDL under the GOI scheme of Setting up of Nation-wide Network of Laboratories for Managing Epidemics and National Calamities to support viral diagnosis and kit validation.

The Department has been implementing a Proficiency Testing Program for Isolation and Cryopreservation of Peripheral Blood Mononuclear Cells, which is the first and only PBMC PT Program available in the country.

The Department manages a large Biorepository that serves as Central Biorepository for the RePORT India Consortium and Regional Biorepository for the National HIV Cohorts Program.