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Thiruvananthapuram, November 27, 2025 – The Rajiv Gandhi Centre for Biotechnology (RGCB) in Kerala has been selected as one of four national Next-Generation Sequencing (NGS) hubs for the Metagenomic Syndromic Surveillance Programme, a key component of India’s National One Health Mission. This initiative, led by the Indian Council of Medical Research (ICMR) in collaboration with multiple institutions, targets undiagnosed infectious diseases like acute febrile illnesses (AFI), encephalitis, diarrhoeal conditions, and respiratory infections. By employing advanced metagenomic sequencing in RGCB’s Biosafety Level-3 (BSL-3) facility, the programme promises real-time detection of elusive pathogens, bolstering epidemic preparedness amid rising zoonotic threats and antimicrobial resistance (AMR).
Key Developments and RGCB’s Pivotal Role
RGCB, designated specifically for AFI surveillance, will process thousands of biological samples from sites nationwide, identifying known, rare, and novel pathogens missed by conventional tests. Dr. T.R. Santhosh Kumar, Director (Additional Charge) at RGCB, stated, “This selection underscores our expertise in viral genomics, host-pathogen interactions, and high-throughput sequencing.” The hub integrates clinical syndromic screening with unbiased metagenomics to map circulating pathogens and AMR patterns in real time.
The project partners include the Centre for Cellular and Molecular Biology (CCMB), Tata Institute for Genetics and Society (TIGS), Gujarat Biotechnology Research Centre (GBRC), ICMR-National Institute of Epidemiology (ICMR-NIE) Chennai, and ICMR Headquarters. Senior scientist Dr. Rajesh Chandramohanadas, faculty-in-charge of RGCB’s BSL-3 Lab, will lead efforts to generate genomic insights tailored to India’s diverse pathogen landscape. This multi-institutional approach exemplifies the One Health framework, linking human, animal, and environmental health.
The Burden of Undiagnosed Infectious Diseases in India
Acute febrile illness imposes a heavy toll, with studies revealing 14% to 47% undiagnosed cases among hospitalized patients in northern and southern India, respectively. Multicentre research highlights malaria and dengue as common culprits, yet overlaps in symptoms and low diagnostic accuracy leave many cases unresolved, complicating treatment. Syndromic surveillance data underscores the need for advanced tools, as traditional methods fail to capture the full spectrum of etiologies like scrub typhus (up to 47% in some central India cohorts) or emerging viruses.
In resource-limited settings, up to 80% of acute undifferentiated febrile illnesses (AUFI) evade diagnosis, fueling morbidity and mortality. The National One Health Mission, approved with ₹383.83 crores by the Prime Minister’s Science, Technology, and Innovation Advisory Council (PM-STIAC), addresses this gap through integrated protocols for emerging diseases at the human-animal-environment interface. Metagenomics fills critical voids, as demonstrated in global studies where it uncovered novel viruses in febrile patients, informing outbreak responses.
Expert Perspectives on Metagenomic Innovation
Dr. Nivedita Gupta, Scientist G and Head of ICMR’s Communicable Diseases Division, emphasized One Health’s urgency: “Mechanisms involve streamlining approvals for rapid response, as seen in past outbreaks.” While direct quotes from non-RGCB experts on this hub are emerging, international precedents affirm metagenomics’ value. Dr. Kristian Andersen, co-author of a Nigerian metagenomic study, noted its role in identifying 13 viruses, including a new dicistrovirus, and resolving outbreaks like yellow fever.
Indian experts echo this: Metagenomics transforms surveillance by detecting “hidden microbiomes” in water and patients, per Zoological Survey of India findings. Dr. Ankur Mutreja, CCMB Director, highlighted collaborative potential in similar ICMR projects, stressing unbiased sequencing for AMR tracking. These views position RGCB’s hub as a leap toward indigenous diagnostics amid climate-driven zoonoses.
Broader Context of One Health Mission
Launched under ICMR’s aegis, the Mission coordinates cross-sectoral efforts against pandemics, building on platforms like INSACOG for genomic surveillance. It responds to global calls for integrated ecosystems, as One Health prevents 75% of emerging diseases—mostly zoonotic. In India, where urbanization and climate change amplify risks, the programme supports protocol development for surveillance, plugging gaps in primary healthcare penetration.
Past initiatives, like the Department of Biotechnology’s One Health Consortium involving AIIMS and ICMR centres, laid groundwork. RGCB’s genomics facility, a long-standing NGS hub, now scales nationally, fostering data-sharing via repositories akin to GISAID. This ecosystem could preempt threats like Chandipura virus in encephalitis cases.
Public Health Implications and Practical Takeaways
For healthcare professionals, real-time genomic data enables targeted interventions, reducing empirical antibiotic use and curbing AMR. Consumers face fewer misdiagnoses; if fever persists beyond routine tests, clinicians may soon access metagenomic insights via networked hubs. Travellers and rural residents, prone to AFI, benefit from early warnings, like vector control for scrub typhus.
Communities should prioritize hygiene, vaccination, and reporting fevers promptly—metagenomics enhances, but doesn’t replace, basics. Policymakers gain epidemic intelligence for resource allocation, potentially averting pandemics. Daily decisions? Monitor symptoms, seek care early, and support One Health via awareness.
Limitations and Balanced Outlook
Challenges include high costs of NGS, data overload requiring analytics expertise, and equitable sample access from remote areas. Studies note metagenomics’ sensitivity to contamination, demanding BSL-3 rigor, which RGCB provides. Not all fevers are infectious—non-infectious mimics like pesticide poisoning require clinical correlation.
Sceptics question scalability in India’s vast terrain, but phased rollout with partners mitigates this. Ongoing evolution of protocols ensures adaptability. Overall, this hub advances evidence-based preparedness without overpromising cures.
Medical Disclaimer: This article is for informational purposes only and should not be considered medical advice. Always consult with qualified healthcare professionals before making any health-related decisions or changes to your treatment plan. The information presented here is based on current research and expert opinions, which may evolve as new evidence emerges.
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