A state renowned for being the model of public health in the country and one which has consistently recorded some of the best health indicators nationwide, is now battling three simultaneous disease outbreaks. A Nipah case was confirmed in Kozhikode on June 11 — the state's sixth outbreak of the virus since 2018. At the same time, Shigella, a waterborne bacterial infection, had spread to seven districts, with 266 confirmed cases and six deaths by the end of the month. Twelve confirmed West Nile virus cases were recorded across Malappuram, Kozhikode and Thrissur.
Every year, as rains arrive, Kerala's disease calendar activates — dengue, leptospirosis, hepatitis A, cholera, and, in the forests, Kyasanur Forest Disease. The state recorded 31,536 hepatitis A cases and 82 deaths in 2025 alone. Dengue has been classified as endemic rather than episodic, with 20,674 cases and 128 deaths in 2024.
The monsoon does most of the work
Kerala's tropical climate and prolonged monsoon season remain the single biggest driver of infectious disease outbreaks.
Kerala receives two monsoons: the South-West system from June to September and the North-East from October to December, with almost no dry window in between. Heavy rain fills tyres, construction debris and blocked drains with stagnant water, creating breeding sites for Aedes aegypti and Aedes albopictus mosquitoes, the mosquitoes responsible for transmitting dengue and chikungunya.
Flooding does a second kind of damage. It overwhelms sanitation systems, contaminates wells and overhead tanks, and sends Shigella, hepatitis A, leptospirosis and cholera into the water supply together. The consequences have been visible after major flooding events. Following the devastating 2018 floods, leptospirosis cases jumped to 372 in a single month, with 54 deaths, as people waded through contaminated water with open cuts. The 2026 Shigella outbreak also emerged under the same environmental conditions, intensifying rain and compromised water sources leading to rapid spread.
Ecological changes are increasing zoonotic spillover
Kerala's second driver is ecological. The state borders the Western Ghats, one of the world's 36 biodiversity hotspots. As forests have been cleared and converted to monoculture plantations, the animals that carried pathogens in the wild have moved closer to human settlements.
A 2022 study of Wayanad found that natural forest cover in the district fell 62% between 1950 and 2018, replaced largely by plantation agriculture. Dengue and leptospirosis cases clustered along plantation edges. Kyasanur Forest Disease (KFD), a tick-borne haemorrhagic fever historically confined to Karnataka, appeared in Wayanad and Malappuram in 2014-15 and has not left. The Kattunayakan tribal community in Wayanad, who carry out forest floor labour, and the Cholanaickan tribe in Malappuram, who hunt monkeys, bear the highest burden. Roughly 500 KFD cases are reported annually across the Western Ghats, with a 10 percent fatality rate.
Nipah follows the same displacement logic. Pteropus fruit bats, roost in orchards and gardens adjacent to homes. Their activity peaks between April and September, overlapping with fruiting season. Most Kerala spillover events have involved humans consuming bat-contaminated fruit or coming into contact with bat secretions, including the June 2026 Kozhikode case, where the patient had been cleaning a bat-infested building.
West Nile virus, recurring in Kerala since 2011, is transmitted by Culex mosquitoes and cycles through birds. Kerala's bird sanctuaries, water bodies and tropical ecology provide, as ICMR researchers describe it, "an ideal ecological niche" for its transmission.
Urbanisation and 859 people per square kilometre
Once a pathogen enters the human population, Kerala's density of 859 people per sq km, more than double the national average (2011 Census of India), accelerates its spread. Dense housing, shared water sources and close contact do what monsoon flooding starts.
Migration compounds this. Kerala hosts millions of migrant workers from other Indian states. Researchers have identified this workforce as a recurring source of "seeded" infections, malaria and cholera cases periodically reappearing in the state, introduced by workers from endemic regions. Tourism and the large expatriate community returning home add further exposure pathways.
The paradox of good surveillance
Paradoxically, Kerala's strong public health system is also one of the reasons it appears to experience more outbreaks than other states, because the state finds diseases because it looks for them.
Kerala has one of India's most sensitive disease surveillance systems. It logs an estimated 130 to 140 outbreak signals a year. Small clusters that would go undiagnosed in states with weaker laboratory capacity get confirmed, sequenced and reported in Kerala. WHO has noted that Nipah likely circulates enzootically across a wider area of India than the outbreak map suggests. Kerala's infrastructure converts that silent circulation into confirmed cases.
