The three-year-old was in agony. Her body was convulsed with seizures, she was running a high temperature and she could not stop vomiting.

On September 16, when Gayatri Madkami was brought to the district hospital of Malkangiri in Odisha, the only large government hospital in 5,791 square kilometres, Dr Santosh Mishra, the sole paediatrician at the hospital, was reminded of November 2014. That month, 12 children had been admitted to the hospital with symptoms similar to Madkami’s. He could only save one. The others died within hours.

Mishra shifted Madkami in an ambulance to the Maharaja Krishna Chandra Gajapati Medical College and Hospital in Berhampur in Ganjam district. It was 320 kilometers away but was the nearest speciality hospital. Tucked away in the southernmost corner of Odisha, Malkangiri is one of India’s poorest and worst-connected districts.

“It took us 12 hours to reach there,” recalled Gayatri’s mother Ungi Madkami. About 24 hours later, the child died.

In 2014, the cause of child deaths could not be determined, even though Mishra suspected they were cases of Japanese encephalitis, a viral disease that was first documented in Japan in 1871. This year, however, laboratory tests have confirmed the presence of antibodies to the Japanese encephalitis virus in Madkami’s blood, and that of 32 other children who died.

Dr Santosh Mishra examining a child at Malkangiri's district headquarters hospital. Photo: Priyanka Vora.

In South Asia, not just in India, the Japanese encephalitis virus is responsible for most cases of Acute Encephalitis Syndrome, which is colloquially called brain fever. Those infected with the virus have inflammation of the brain, which results in fever, headaches, seizures, disorientation and vomiting. The condition can rapidly cause death.

Since September, 93 children admitted to the district hospital have died of encephalitis. Blood tests have confirmed that 32 of the deaths were caused by the Japanese encephalitis virus. The other deaths are still being investigated.

“We are running tests to screen the blood samples for other agents that can trigger a similar outcome in patients,” said Bhagirath Dwibedi, scientist at the Regional Medical Research centre in Bhubaneswar, a laboratory under the Indian Council of Medical Research, India’s apex body on biomedical research.

Dwibedi did not rule out the possibility that some of these deaths could have been caused by the Japanese encephalitis virus even though the tests were not positive. “It is not necessary that all blood samples will test positive for antibodies against the Japanese encephalitis virus as the probability of positivity also depends on the time of illness during which the sample was collected,” he explained.

This is because the Japanese encephalitis virus shows up through existing tests only at certain stages of infection. If blood samples are collected at other times, the virus may be undetectable even though it is present and causing sickness.

The state government has sent a team of experts headed by Dr T Jacob John, an epidemiologist working with Christian Medical College in Vellore, to determine the cause of the deaths of the unconfirmed cases. John had previously identified the toxin in litchi fruit to be responsible for an outbreak of Acute Encephalitis Syndrome in Muzaffapur district in Bihar in 2014 and 2015.

A preventable outbreak

The reason the central government is placing such an emphasis on determining the cause of this round of encephalitis, and isolating cases of Japanese encephalitis, is because the outbreak was preventable. The Japanese encephalitis virus is transmitted by the Culex mosquito from pigs to humans, and better mosquito-control can prevent its spread. In addition, there is a vaccine that can protect children from the infection, which is administered by the central health agencies in areas in which the disease is endemic.

Some experts say Malkangiri should have been placed on the vaccination programme years ago. In addition to 2014, the district had seen an encephalitis outbreak in 2012. Mishra remembers spending nights in the district hospital that year, treating children with symptoms similar to Madkami’s. As many as 38 children died of what he suspected was encephalitis caused by the Japanese encephalitis virus.

Mishra’s suspicions were confirmed by a team of scientists from the Regional Medical Research Centre in Bhubaneswar. Dwibedi led the team which visited several villages in Malkangiri and collected blood samples of 55 children who had the symptoms of encephalitis. The laboratory tests found antibodies against the Japanese encephalitis virus in 11 blood samples. The team also isolated the virus from cerebrospinal fluid – the fluid that surrounds the brain and spinal cord – of children who Mishra had clinically classified as “classical cases of Japanese encephalitis”.

“We established that the Japanese encephalitis virus was in circulation in Malkangiri,” said Dwibedi. A report was submitted to both the state and the central governments in December 2012. But nothing happened.

Two years later, in November 2014, another wave of near-identical child deaths swept through the wards of Malkangiri district hospital. Among those who died was two-and-a-half-year-old Shalini Khora of Potrel village – one of the villages where Dwibedi’s team had detected the Japanese encephalitis virus in 2012.

This time, the team from the Regional Medical Research Centre in Bhubaneswar did not come to Malkangiri. The blood and cerebrospinal fluid samples of Khora and 11 other children were sent to them. The results were negative.

Mishra does not find that surprising. “It was bound to happen,” he said. “Children were dying quickly. There wasn’t much of a chance that their bodies would have developed the antibodies against the virus which the laboratory tests could pick.”

Another challenge was transporting the samples to Bhubaneshwar which is more than 600 kilometers away. “We had to maintain a cold chain to keep the sample intact for testing,” Mishra explained. Scientists at the laboratory confirmed that the long distance could have contaminated the samples, making it “nearly impossible” to detect the virus.

A poster outside a school in Malkangiri explaining Japanese encephalitis transmission. Photo: Priyanka Vora.

Vacillating over a vaccine

A senior official from the central government involved with the working of the health department in Odisha blamed the state government’s complacency for this year’s outbreak.

“If the government had fought hard to get vaccination to the affected districts earlier we would have perhaps not seen such a big outbreak,” he said. “But the state was already grappling with malaria and filariasis and didn’t want one more disease to worry about.”

Malkangiri is not the only district in Odisha that is considered vulnerable to Japanese encephalitis. A report of the Ministry of Health and Family Welfare shows that in 2014 the state recorded the highest incidence of encephalitis in the country – 1,849 cases and 116 deaths. Doctors suspect that the Japanese encephalitis virus accounted for a large number of these deaths. Even before the 2012 study, a group of doctors at MKCG Medical College in Berhampur found the presence of the Japanese encephalitis virus in Cuttack district of Odisha. As many as 45% of the samples tested for the virus were positive.

Principal secretary of Odisha’s health department Arti Ahuja claimed the state had asked the centre for vaccines for four districts – Malkangiri, Keonjar, Mayurbanj and Jajpur – as far back as 2012.

Email communication from 2012 between Ahuja and Dr Madan Pradhan, the joint director of the National Vector Borne Disease Control Programme, acknowledged that 38 children had died in Malkangiri of what was suspected to be Japanese encephalitis.

Director of the National Vector Borne Disease Control Programme Dr AC Dhariwal said the programme had informed the technical advisory committee of the union health ministry of the situation in Odisha in 2012. “My work is to present the facts to the committee, they decide when to start vaccination,” said Dhariwal.

Dr Soumya Swaminathan, director of the Indian Council of Medical Research and co-chair of the technical advisory committee, said that the committee’s role was limited to selecting the Japanese encephalitis vaccine. “The union health ministry decides on the districts where the vaccine is to be provided.”

The health ministry said that it can offer the vaccine to a particular district in the country only after the National Vector Borne Disease Control Programme classifies it as endemic. “For a district to be classified as endemic, it should report five confirmed cases of Japanese encephalitis for three consecutive years,” said Dhariwal.

When asked about the Bhubaneswar institute’s study which confirmed 11 cases of the Japanese Encephalitis virus in 2012, Dhariwal said that there was a difference of opinion among scientists about the results of the study. “The cases did not fit the clinical definition of Japanese encephalitis,” he said.

Dr PK Sen, additional director at National Vector Borne Disease Control who specialises in Acute Encephalitis Syndrome, said that the 2012 study was indicative and not conclusive. An health ministry official who requested anonymity said the study did not use testing kits approved by the centre. The researchers denied this. “We used the kits supplied by the central government,” said Dwibedi, the lead author of the study.

The only hospital in Malkangiri where children with Japanese encephalitis are undergoing treatment. The hospital got a padeiatric intensive care unit only after children with Japanese encephalitis started dying. Photo: Priyanka Vora

Delayed action

Some argue the National Vector Borne Disease Control Programme’s guidelines for declaring that a Japanese encephalitis is endemic to a particular district are narrow and restrictive. International protocols do not necessitate confirmatory tests for the introduction of the vaccine. The World Health Organisation’s position paper on the disease states:

“Japanese encephalitis vaccination should be integrated into national immunisation schedules in all areas where JE is recognized as a public health priority. Even if the number of JE-confirmed cases is low, vaccination should be considered where there is a suitable environment for JEV transmission, i.e. presence of animal reservoirs, ecological conditions supportive of virus transmission, and proximity to other countries or regions with known JEV transmission.”

Going by the position paper, Malkangiri fits the bill for vaccination. It has a large presence of pigs, which are known to host the Japanese encephalitis virus, and of the Culex mosquito which transmits the virus from pigs to humans.

The National Vector Borne Disease Control Programme “decided to stick to the textbook and chose the wait and watch approach,” said a scientist from Indian Council of Medical Research, who requested anonymity. “A programme like this need to be dynamic. If we had offered vaccine, the burden of cases would have been less.”

This year’s outbreak has ended the debate over the vaccine.

At least 93 children have died in Malkangiri since September, of which 32 cases have been confirmed as caused by the Japanese encephalitis virus. The actual number of deaths could be higher, since only those cases that have come to the district hospital have been counted.

Abandoning its earlier approach, the National Vector Borne Disease Control Programme has made fresh recommendations to the technical advisory committee of the union health ministry. “The committee has decided to offer the vaccine to four districts of Odisha,” said Dhariwal.

He described the current outbreak as “unusual” because the district has suddenly reported so many cases in a short span of time. “The committee feels that Malkangiri is prone to another outbreak and its best to offer vaccination.”

Vaccination was not the only safeguard available to protect Malkangiris children from Japanese encephalitis. Better mosquito-control measures could have helped contain the outbreak. The next story in the series looks at how and why the district failed on this account.

This reporting project has been made possible partly by funding from the New Venture Fund for Communications project, which receives support from the Bill & Melinda Gates Foundation.