Emerging Diseases in India: Trends and Challenges

India’s battle with infectious diseases has witnessed dramatic shifts over the past three decades. While the country celebrates victories against certain diseases, it simultaneously faces the emergence and re-emergence of infections that pose significant challenges to public health infrastructure. Understanding these patterns helps us prepare better responses and strengthen disease surveillance systems crucial for protecting millions of lives.

Historic outbreaks that shaped India’s disease surveillance
The 1994 Surat plague outbreak
Cholera O139: A new pandemic strain emerges
Diphtheria makes an unwelcome return
Zoonotic diseases: Threats from the animal-human interface
Nipah virus: Kerala’s recurring nightmare
Chikungunya: The painful comeback
Avian influenza H5N1: The bird flu threat
India’s surveillance backbone: IDSP and ongoing challenges
Persistent challenges in disease control

Historic outbreaks that shaped India’s disease surveillance

India has experienced several landmark disease outbreaks that fundamentally changed how the nation approaches infectious disease control. These episodes revealed both vulnerabilities and the resilience of the healthcare system.

The 1994 Surat plague outbreak

In September 1994, India witnessed one of its most dramatic public health emergencies when plague struck the industrial city of Surat in Gujarat. The outbreak, which lasted from August to October 1994, resulted in 693 suspected cases and 56 deaths across multiple states. What made this event particularly significant was the panic it generated-approximately 300,000 people fled Surat within two days, creating one of the largest post-partition migrations in India.

The outbreak likely stemmed from flooding in Surat, which had open sewers, bringing dead rats into contact with residents. The city’s congested conditions and poor sanitation infrastructure facilitated rapid spread. By the outbreak’s end, an estimated 78% of confirmed cases were in Surat’s slums. The economic impact was staggering, with losses estimated at ₹816 crore. However, the crisis prompted significant infrastructure improvements-the city tore down slums, covered sewers, constructed public toilets, and implemented strict littering fines, transforming Surat into one of India’s cleanest cities.

Cholera O139: A new pandemic strain emerges

In the early 1990s, a new cholera strain emerged that caught global health authorities by surprise. The Vibrio cholerae O139 serogroup first appeared in India and Bangladesh in 1992, causing major outbreaks. This was the first time a non-O1 strain had caused epidemic cholera, temporarily displacing the El Tor strain in southern Asia. Genetic analysis revealed that O139 was closely related to the pandemic O1 strain, suggesting evolution rather than an entirely new pathogen.

Diphtheria makes an unwelcome return

Despite decades of vaccination programs, diphtheria has resurged across India. In 2016, Kerala experienced a significant outbreak with over 533 reported cases concentrated in Malappuram, Kozhikode, and Kannur districts. The situation is particularly concerning because India represents 78% of globally reported diphtheria cases despite national immunization programs.

The resurgence stems from multiple factors: DPT vaccine coverage remains around 84%, booster dose coverage is even lower, and certain communities show vaccine hesitancy. Studies indicate that the disease, once common among children under five, now increasingly affects older children and adults, suggesting waning immunity. Outbreaks have been reported from multiple states including Jammu and Kashmir, Rajasthan, Haryana, Telangana, Gujarat, Assam, Maharashtra, and Andhra Pradesh in recent years.

Zoonotic diseases: Threats from the animal-human interface

Zoonotic diseases-infections transmitted from animals to humans-represent some of India’s most serious emerging disease threats. These pathogens constantly evolve and can spark outbreaks with little warning.

Nipah virus: Kerala’s recurring nightmare

Kerala has become India’s hotspot for Nipah virus, experiencing its first outbreak in 2018 with a devastating 91% case fatality rate among 23 infected individuals. Since then, the state has reported nine outbreaks by 2025. The 2018 outbreak was particularly tragic, claiming the life of nurse Lini Puthussery, who contracted the virus while treating infected patients.

The virus is transmitted through fruit bats and can spread through contaminated food or close contact with infected individuals. Recent 2025 outbreaks showed four cases across Malappuram and Palakkad districts, with no epidemiological links between patients, suggesting independent spillover events from bat populations. Kerala’s frequent outbreaks are attributed to large fruit bat populations harboring the virus. The lack of vaccines or specific treatments makes prevention through awareness and reducing human-bat contact crucial.

Chikungunya: The painful comeback

After 32 years of absence, chikungunya re-emerged in India in 2005-2006, affecting thousands across Andhra Pradesh, Karnataka, and Maharashtra. The disease, whose name means “to become contorted” in Kimakonde language, causes severe joint pain that can persist for months or years.

Since its re-emergence, chikungunya has become endemic, with almost 480 outbreaks recorded across 30 Indian states since 2015. The disease is now the third most common vector-borne illness in India. A major outbreak in 2016 recorded over 64,000 confirmed cases. The mosquito Aedes aegypti serves as the primary vector, and outbreaks tend to peak during summer months with high water storage, particularly affecting areas with better housing infrastructure where water storage is common.

Avian influenza H5N1: The bird flu threat

India reported its first avian influenza outbreak in February 2006 in Maharashtra, and since then, the country has experienced outbreaks almost every year in various states. Between 2006 and 2021, Maharashtra, West Bengal, Kerala, and Odisha reported the highest numbers of outbreaks, with over 25 episodes each state.

The situation intensified in December 2020 and early 2021 when outbreaks of H5N1 and H5N8 affected 15 states. India reported its first human H5N1 case in July 2021-an 11-year-old boy who died despite treatment. More recently, in 2025, India reported two fatal H5N1 infections among children with poultry exposure. While sustained human-to-human transmission hasn’t occurred, the virus’s ability to jump species and its high mortality rate in humans makes it a significant pandemic threat.

India’s surveillance backbone: IDSP and ongoing challenges

The Integrated Disease Surveillance Programme (IDSP) was launched in November 2004 with World Bank assistance to strengthen India’s disease monitoring capabilities. The program established a decentralized, laboratory-based, IT-enabled surveillance system spanning central, state, and district levels.

IDSP’s structure includes a Central Surveillance Unit at the National Centre for Disease Control in Delhi, State Surveillance Units at all state headquarters, and District Surveillance Units across India’s 741 districts. As of recent reports, over 90% of districts regularly submit weekly disease surveillance data. The program uses three reporting formats: ‘S’ for suspected cases from health workers, ‘P’ for presumptive cases from clinicians, and ‘L’ for laboratory-confirmed cases.

The Integrated Health Information Platform (IHIP), launched in 2019, modernized data collection with a web-enabled, real-time electronic system. This platform provides geospatial information for managing disease outbreaks and resources, offering decision-makers a comprehensive operational picture. IDSP has established 259 District Public Health Laboratories and a network of 108 referral laboratories across 23 states.

Persistent challenges in disease control

Despite robust surveillance infrastructure, India faces several ongoing challenges. Immunization coverage gaps remain critical-while DPT3 coverage reached 80% in 2015-2016, booster dose coverage is considerably lower, leaving populations vulnerable to vaccine-preventable diseases like diphtheria. Certain communities show vaccine hesitancy, creating pockets of susceptible individuals.

Laboratory capacity constraints limit rapid diagnosis during outbreaks, particularly in remote areas. Delays in diphtheria antitoxin administration and limited availability of specific treatments for emerging diseases like Nipah virus contribute to higher mortality rates. The rapid urbanization and environmental changes create conditions favorable for vector-borne diseases, while increased human-animal interactions at forest fringes heighten zoonotic spillover risks.

Healthcare worker awareness also needs strengthening. Many primary care physicians lack familiarity with rare or re-emerging diseases, leading to diagnostic delays. The COVID-19 pandemic revealed both strengths and weaknesses in India’s surveillance system-while data collection and reporting capabilities proved valuable, resource constraints and system overload highlighted areas needing improvement.

What do you think? How can India strengthen community participation in disease surveillance and prevention efforts? What role should technology play in improving real-time disease detection and response in rural areas?

References

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Table of Contents

Historic outbreaks that shaped India’s disease surveillance 🔗

The 1994 Surat plague outbreak 🔗

Cholera O139: A new pandemic strain emerges 🔗

Diphtheria makes an unwelcome return 🔗

Zoonotic diseases: Threats from the animal-human interface 🔗

Nipah virus: Kerala’s recurring nightmare 🔗

Chikungunya: The painful comeback 🔗

Avian influenza H5N1: The bird flu threat 🔗

India’s surveillance backbone: IDSP and ongoing challenges 🔗

Persistent challenges in disease control 🔗