Chemical biomarkers as public health infrastructure: governing early detection of zoonotic threats

Detection and monitoring of chemical biomarkers represents an emerging chemistry-driven technology for public health infrastructure.¹ Molecular signatures of infection, such as metabolites produced by a pathogen or an immune response indicator of a host,² can be detected through analytical chemistry techniques such as mass spectrometry and biosensors, enabling proactive environmental surveillance and early warning of zoonotic threats.¹ ranging from facilitate non-invasive detection in wastewater, soil, air, and animal reservoirs, surpassing traditional PCR or serological methods by offering rapid, cost-effective, field-deployable monitoring without requiring viable pathogens or cold chains.³

In India, the high density of human–animal interfaces mean zoonotic diseases like leptospirosis, rabies and avian influenza impose a substantial morbidity and mortality burden on the population. Yet a critical policy gap persists in addressing this burden: fragmented surveillance systems lack integration of chemistry-based biomarker tools into national frameworks, resulting in delayed outbreak responses, siloed operations across health, veterinary and environmental ministries, insufficient funding for molecular diagnostics, and weak environmental monitoring despite initiatives like the Integrated Disease Surveillance Programme.^4,5 This deficiency is exacerbated by limited biosafety protocols, inadequate real-time data analytics and underutilisation of One Health approaches, leaving vulnerable populations in rural and peri-urban hotspots exposed to spillovers.^6,7

Despite nascent efforts, such as ICMR’s bird spillover studies and NCDC’s zoonotic prioritisation, no cohesive policy mandates chemistry-driven biomarkers for scalable early detection, hindering India’s preparedness against escalating threats from climate-driven habitat changes and antimicrobial resistance.^8,9 How can chemical biomarkers be institutionalised as core public health infrastructure to govern and enable early detection of zoonotic threats in India?

Context and rationale

Using chemical biomarkers as a tool of public health infrastructure holds profound relevance for India across economic, health, strategic and environmental dimensions, by offering early zoonotic threat detection that responds to the nation’s unique vulnerabilities.¹⁰

Economic: Zoonoses inflict direct losses exceeding $20 billion (£14.6 billion) globally every year, with indirect impacts surpassing $200 billion. In India, diseases like leptospirosis and rabies affect farming – a sector projected to be worth $20 billion in 2026 – by eroding livestock productivity. They also amplify healthcare costs in states like Punjab, where outbreaks disrupt rural livelihoods and national GDP.

Health: India grapples with high zoonotic burdens, including over 200,000 annual rabies deaths and surging leptospirosis cases in flood-prone regions, which is compounded by antimicrobial resistance and climate-altered spillovers from dense human-animal interfaces in peri-urban slums and agricultural belts.^11,12

Strategic: Integrating biomarkers into One Health frameworks like the National One Health Mission has the potential to bolster pandemic preparedness, aligning with ICMR’s real-time surveillance initiatives and NCDC’s hotspot mapping to counter geopolitical risks from transboundary threats, as evidenced by recent bird-to-human spillover studies.¹³

Environmental: Biomarker detection enables non-invasive monitoring of pathogen reservoirs in wastewater, soil and air. This helps to address issues of deforestation, wildlife trade and habitat loss that fuel 75% of emerging infections, while supporting sustainable land-use under India’s biodiversity policies.^10,14

International examples of biomarker policies

Globally, biomarker monitoring is already being used as a vital tool for public health. Wastewater-based epidemiology (WBE) has tracked SARS-CoV-2 weeks ahead of clinical surges in Europe and the US, with multi-biomarker panels quantifying 204 indicators, including oxidative stress metabolites and pharmaceuticals, for community health profiling (Table 1).^15,16 Case studies like Austria’s ‘zoonotic web’ network analysis integrate environmental sampling for tailored surveillance, while UK shellfish monitoring detects antimicrobial resistance via chemical residues, demonstrating scalable early-warning without viable pathogens. In LMICs, electrochemical biosensors democratise protein marker detection for neglected tropical diseases, mirroring needs for India’s resource-constrained settings.^17,18

Opportunities abound in anticipatory governance: biomarkers offer cost-effective, field-deployable tools (eg, mass spectrometry for volatile organics) to unify siloed ministries, expand BSL-3 networks, and leverage AI for predictive analytics, which could avert outbreaks via proactive hotspot interventions and filling voids in IDSP’s reactive model.^19,20

Risks include data silos, biosafety lapses in decentralised labs, ethical concerns over privacy in WBE and over-reliance without ground-truthing, alongside technical hurdles like biomarker specificity amid India’s diverse microbiomes. There is an urgent need to implement biomarker monitoring following the lessons learned from COVID in pandemic preparedness, as well climate-driven range expansions and 2025’s inter-ministerial pushes, demanding policy mandates for biomarker standardisation, workforce training in molecular diagnostics and public–private partnerships to preempt spillovers before they cascade into national crises.^21,22

The policy idea

We propose a National Chemical Biomarker Surveillance Framework (NCBSF) to establish chemical biomarkers – defined as pathogen-specific metabolites, volatile organic compounds and immune-response signatures detectable via mass spectrometry, electrochemical sensors, and biosensors¹⁹ – as a mandated pillar of India’s public health infrastructure for governing early detection of zoonotic threats.

This standards framework with institutional redesign and incentive schemes integrates biomarker-driven environmental surveillance into the National One Health Mission (NOHM), operationalised through a centralised Biomarker Early Warning Hub (BEWH) under the National Centre for Disease Control (NCDC), co-chaired by Ministries of Health and Family Welfare (MoHFW), Animal Husbandry and Dairying (MoAHD), and Environment, Forest and Climate Change (MoEFCC).^15,19

Implementation begins with a National Biomarker Panel: a multi-stakeholder body of chemists, epidemiologists and policymakers, prioritising 20 high-risk zoonoses (eg leptospirosis, avian influenza, rabies)^24,4 based on spillover potential, using validated markers like leptospiral lipopolysaccharides or H5N1 glycoproteins.²⁵ The framework mandates weekly sampling from 500 high-risk sites (wetlands, livestock markets, wastewater plants) identified via GIS-hotspot mapping, analysed in a networked 50 BSL-2/3 labs upgraded for chemistry analytics, with data feeding real-time dashboards linked to IDSP and IHIP portals for automated alerts.²⁶

How it works

Phase 1 (years 2026–27): deploy field kits for non-invasive sampling (air, soil, water and animal reservoirs), with processing via portable mass spectrometry yielding results in <24 hours. The results will trigger tiered responses: low-level signals prompt veterinary culls or quarantines; high signals activate inter-ministerial rapid response teams.²⁷

Phase 2 (years 2027–2028): scale up AI-driven predictive models correlating biomarkers with climate or wildlife data for 7-day forecasts. Incentives include INR500 crore (£40 million) seed funding for public-private partnerships (eg, CSIR-IIIM with startups for sensor indigenisation), tax breaks for biomarker R&D and performance grants to states (INR10 crore per 10% surveillance coverage). Training curricula for 5000 technicians via ICMR-NCDC academies ensures standardisation, with annual audits enforcing compliance.²⁸ Metrics track averted outbreaks, cost-savings (projected INR5,000 crore/year vs reactive responses) and equity in rural hotspots.

This distinguishes sharply from current Indian policies like IDSP and NOHM, which emphasise syndromic and PCR-based clinical surveillance with ad-hoc NGS pilots (eg, bird sanctuaries), lacking chemistry biomarkers or environmental mandates, resulting in 94% reactive responses and siloed data.

Unlike global wastewater epidemiology in the EU/US, focused on human viruses via RNA (eg, ArboNET for WNV, NZ’s HD frameworks), NCBSF pioneers chemistry-centric, pathogen-agnostic detection for LMIC contexts, integrating animal/environment sectors absent in WOAH/FAO Tripartite guides, and preempting AMR/neglected zoonoses via non-viable markers unlike genomic-heavy UK/EFSA systems.^21,14

Implementation strategy

The implementation strategy for the NCBSF²⁹ unfolds in a phased, pilot-driven rollout over 2026–2030, leveraging India’s National One Health Mission (NOHM) infrastructure to embed chemical biomarkers into zoonotic early detection.

Phase 1, pilot launch (year 2026): the policy is introduced via executive order under MoHFW, piloting in 5 high-risk states (Kerala, Gujarat, Maharashtra, Uttar Pradesh, Assam) with 50 sentinel sites each for wastewater/soil/air sampling of priority biomarkers (eg, leptospiral metabolites, H5N1 volatiles), co-funded by INR200 crore from NOHM and World Bank PHSPP; NCDC’s Biomarker Early Warning Hub (BEWH) prototypes real-time dashboards integrating IDSP data.

Phase 2, scale-up (years 2027–28): expansion to 500 sites nationwide post-pilot evaluation, mandating annual biomarker panels via Gazette notification, with ICMR certifying 20 portable mass spectrometry kits per state; inter-ministerial One Health Committees (OHCs) at state/district levels oversee via quarterly audits.

Phase 3, full integration (years 2029–30): 80% coverage is achieved, linking to IHIP for AI forecasts and triggering automated responses like veterinary alerts.^15,30 Key stakeholders include regulators (MoHFW/NCDC as lead, MoAHD/MoEFCC co-leads), research bodies (ICMR, CSIR-IIIM for validation), startups (biosensor firms like Strand Life Sciences), industry¹⁵ (Thermax for analytics, Biocon for reagents) and civil society (WWF-India, PHFI for community sampling) via public–private partnerships (PPPs) modeled on WOAH veterinary models.

Anticipated barriers and mitigation

Potential barriers to this proposal include Institutional inertia from siloed ministries, data gaps in baseline biomarkers and capacity shortages (only 30% labs are chemistry-ready). These can be addressed through: (i) legal frameworks amending IDSP guidelines for mandatory reporting (2026 ordinance); (ii) incentives like 150% tax deductions for R&D, INR50 crore PPP grants, and state performance bonuses (INR5 crore/10% coverage); (iii) training modules via NCDC’s 3-month Field Epidemiology Course expanded to ‘Biomarker One Health’ (5000 technicians by 2028, including hands-on mass spectrometry/biosensor sessions per Gujarat OHS model); (iv) timelines with milestones (eg, Q2 2026: stakeholder co-creation workshops; Q4 2027: interoperability protocols); and (v) gap-bridging via ICMR baseline studies and WHO/FAO technical aid, countering funding hurdles with ring-fenced NOHM budgets.^1,15,29

This pragmatic roadmap builds on Gujarat’s OHS pilots, ensuring equity by prioritising tribal and rural hotspots while fostering self-reliance through indigenised technology.³¹

Risks and ethics

The National Chemical Biomarker Surveillance Framework (NCBSF) confronts ethical dilemmas, including privacy erosion from aggregated wastewater or soil data potentially de-anonymising communities via biomarker patterns (eg, linking leptospiral signals to rural slums), stigmatisation of high-risk hotspots like livestock markets or tribal areas triggering disproportionate interventions, and equity gaps exacerbating urban–rural divides where under-resourced regions lack sampling access.^18,27

Unintended consequences encompass false positives from microbiome interference, inflating alerts and diverting resources, misuse for non-health surveillance²⁵ (eg, law enforcement on drug metabolites), animal welfare harms from preemptive culls without viable pathogen confirmation, and environmental justice issues where chemical sampling burdens marginalised farmers without benefits.

Social resistance may arise from distrust in government data use, cultural sensitivities around animal reservoirs, or fears of economic fallout in zoonotic-prone sectors like dairy.³² To embed public trust, equity and transparency, NCBSF mandates an Ethics Review Board under NCDC with civil society²⁷ (PHFI, WWF-India) veto power, enforcing aggregated reporting (>10,000 population thresholds), opt-out community consultations per IDSP models, and open-source dashboards with anonymised trends via NOHM portals.

Equity is integrated via affirmative funding (50% budget for Schedule V areas), indigenous biomarker validation with tribal input and benefit-sharing like free prophylaxis in alerted zones. This is further supported with transparency via annual audits, plain-language reports and grievance portals aligned with WHO One Health ethics, while training modules stress ‘do-no-harm’ protocols and precautionary principles to preempt misuse.¹¹

Conclusion

The National Chemical Biomarker Surveillance Framework (NCBSF) proposes a transformative standards framework embedding chemistry-driven biomarkers – such as pathogen metabolites and immune signatures detectable via mass spectrometry and biosensors – into India’s public health infrastructure, enabling proactive environmental surveillance for early zoonotic threat detection across wastewater, soil, and air matrices.

By piloting in high-risk states, scaling through inter-ministerial One Health hubs under NCDC, and incentivising public–private partnerships with INR500 crore funding and tax breaks, NCBSF bridges IDSP’s reactive gaps, averting outbreaks like leptospirosis surges that cost billions of dollars in livestock losses and healthcare burdens. Its value lies in cost-effective, field-deployable early warnings (projected INR5000 crore annual savings), AI-integrated forecasts unifying MoHFW, MoAHD and MoEFCC data silos, and equity-focused rollout prioritising rural hotspots, distinguishing it from global genomic-heavy models by pioneering pathogen-agnostic chemistry for LMICs.

Addressing ethics via review boards and transparent dashboards ensures trust amid privacy risks. For India’s clean growth, NCBSF aligns biomarker tech with sustainable development by monitoring AMR and climate-driven spillovers without ecological disruption. It also cements science leadership through ICMR-validated indigenous sensors, positioning India as a One Health innovator per NOHM, and bolsters governance via standardised protocols, real-time dashboards and anticipatory policy, fortifying resilience against zoonotic pandemics in a nation bearing 20% of global disease burden.