Ground Zero Kerala

Nipah death in Kerala | The other virus amid a raging pandemic

The road to the house of 12-year-old Mohammed Hashim, who succumbed to the Nipah virus, at Pazhoor in Kozhikode district, was closed as the area was declared a containment zone.   | Photo Credit: K. Ragesh

Mohammed Hashim was wheeled into the chaotic casualty ward of the Government Medical College Hospital in Kozhikode in north Kerala from a private hospital on August 31. “It was around 12.50 p.m.,” recalled Abdul Kareem (name changed), a healthcare volunteer. “Hashim (12) was on oxygen support, which was taken back by the private hospital staff. I fixed another oxygen mask on his face. Hashim was having seizures as if he was epileptic.”

Hashim’s mother, Wahida, who was beside herself with anxiety, kept telling Kareem that her son was scared of injections and that’s why he was getting seizures. Hashim was whisked off to the ‘red area’ earmarked for critical patients. An antigen test showed a negative result for COVID-19. The seizures continued, the cause undetected. Soon, he started vomiting profusely.

Nipah death in Kerala | The other virus amid a raging pandemic

Wahida and her husband, Vayoli Aboobacker, lost their only son in a private hospital on September 5. Barely a few hours before his death, Hashim had tested positive for the deadly Nipah virus.

Fear of the known

Kozhikode and the adjoining districts of Kannur and Malappuram were immediately put on high alert. Entry to Pazhoor, the village where Hashim lived, was barricaded. Nearby wards that fall in Mukkam Municipality and Kodiyathur Grama Panchayat were declared containment zones.

A familiar fear gripped the villagers. From September 4 night, TV news channels had started broadcasting reports about the infection recurring in Kozhikode for the second time after three years. While rushing to Kozhikode from the State capital, Health Minister Veena George confirmed the news about Hashim’s death at a brief stopover in Thrissur in the early hours of September 5. “The National Institute of Virology (NIV), Pune, informed us on Saturday night that the three body fluid samples of the boy have returned positive for Nipah,” she said.


It was a déjà vu moment for many who remembered the scary days of May-June 2018 when the Nipah infection was reported for the first time in Kozhikode. Of the 23 identified cases then, the virus had claimed the lives of 21 people in Kozhikode and Malappuram districts. Two of the infected persons had survived.

The family members of healthcare workers who attended to Hashim were equally alarmed. This provided a grim reminder of nurse Lini Puthussery, who succumbed to the virus while treating one of the infected persons during the first outbreak.


Classified by the World Health Organization (WHO) as a “zoonotic illness that is transmitted to people from animals”, the Nipah infection can also be passed on through contaminated food or from person to person. In infected people, it causes a range of illnesses. While some remain asymptomatic, others can have acute respiratory illness and fatal encephalitis. The virus can also cause severe disease in animals such as pigs. Fruit bats of the family Pteropodidae – particularly, species belonging to the Pteropus genus – are the natural hosts for the virus, says the WHO.

Symptoms include fever, headaches, muscle pain, vomiting and sore throat. This can be followed by dizziness, drowsiness, altered consciousness, and neurological signs that indicate acute encephalitis. The WHO says patients with severe infection get encephalitis and seizures and end up in coma in 24 to 48 hours. The mortality rate is as high as around 92%.

Editorial | Nipah amidst a pandemic

Following Hashim’s death, the National Centre for Disease Control deputed a special team to Kozhikode to assess the situation. A special lab under the aegis of the NIV was set up at the Kozhikode Medical College Hospital to test samples. A special control room was opened at the government guest house. Hashim’s parents, some of their relatives, and the healthcare workers who attended to him were all quarantined. By then, some of them had already developed mild fever.

Deserted roads stretched out in front of us when we visited the Munnur locality in Pazhoor two days after Hashim’s death. Only a few shops selling essential goods were open. Very few dared to venture out of their homes. COVID-19 rapid response team volunteers helped people, especially senior citizens, get medicines and grocery items, while other volunteers conducted a house-to-house survey to determine if there were unnatural fever deaths or unreported deaths in recent times. The road leading to Hashim’s house was blocked. Some of the local residents refused to talk. “He was a nice, calm boy. He used to roam around the area with his goats,” a neighbour later said on the phone.

Also read | Girl with Nipah symptoms dies in Kannur

Lack of a guideline

Kerala’s public health apparatus had won acclaim for its efforts to contain the virus when it was reported for the first time. A critically acclaimed movie was made on its handling of the crisis. In 2019, another case of the infection was reported: the patient was a 21-year-old youth in Ernakulam district. He recovered.

This time, as the days went by, questions emerged about the efficacy of the health system in diagnosing the infection at an early stage. Many asked why the Medical College Hospital did not follow a purported guideline, devised after the first outbreak to screen those with encephalitis, meningitis or Nipah-like symptoms.

Also read | ‘People should be informed about Nipah symptoms’

According to Vayoli Musthafa, one of Hashim’s relatives, the young boy had a fever from August 27. He was taken to a nearby doctor’s residence on August 29. He remained at home for two more days, but the symptoms did not subside. Wahida and Aboobacker rushed him to two private hospitals, at Mukkom and Omassery, on August 31 before approaching the Medical College Hospital.

Hashim remained in the casualty ward there for around 23 hours and was subjected to various scanning procedures. According to sources, initially only Hashim’s parents were there with him. The next morning, people from their neighbourhood reached the hospital too. Musthafa said that the hospital authorities advised them to shift Hashim to another hospital as the Medical College Hospital did not have a ventilator support for children then. Hashim was once again moved to another private hospital in the city, where doctors suspected something amiss after seeing his condition. Hashim’s body fluid samples were sent for a Nipah test, which returned out to be positive.


One of the doctors at the Medical College Hospital said on condition of anonymity that he was not sure if there was a definite guideline for Nipah. “That is a logically and scientifically accepted requirement in a place which has already documented an infection of a deadly nature like Nipah. When we make requests for such a guideline, it takes time at various levels within the institution and the government. It is quite possible that cases like this may have been missed because of the lack of a proper channelised system in government medical college hospitals,” he said. The doctor, however, claimed that in Hashim’s case, it wouldn’t have made a difference because he was already severely infected when taken to the Medical College Hospital. A sustainable mechanism should be put in place to ensure that the samples of all suspected cases are sent to labs so that no case is missed, another doctor said.

Soon after the first Nipah outbreak, the State government had announced its plan to set up a virology institute with international standards in Thiruvananthapuram, and a regional virology lab at the Kozhikode Medical College Hospital. The Institute of Virology set up at the Bio 360 Life Sciences Park at Thonnakkal in 2019 “as an institute of global standards networking Global Virology Institutes with most modern laboratories focusing research, diagnosis and management of emerging and re-emerging infectious viral diseases” is taking baby steps. The bio-safety level-III lab proposed at the Kozhikode Medical College Hospital, too, has not made much progress. This regional lab affiliated to the Indian Council of Medical Research (ICMR) was supposed to help detect infectious diseases such as Nipah, H1N1, West Nile fever, and Kyasanur Forest Disease.

Samples of rambutan fruits are collected from the area where Nipah victim Mohammed Hashim lived.

Samples of rambutan fruits are collected from the area where Nipah victim Mohammed Hashim lived.   | Photo Credit: K. Ragesh


According to sources, the Kozhikode Medical College Hospital had reported a couple of cases of Japanese Encephalitis in May 2018 in the same month the Nipah infection occurred. A public health expert said that those with Nipah would also show positive test results for Japanese Encephalitis. What was termed as Japanese Encephalitis could have been Nipah. There might not have been any follow-up study on the throat swab, cerebrospinal fluid, blood and urine samples of those infected persons, he said.

Althaf Ali, Associate Professor, Community Medicine, Government Medical College, Manjeri, who was part of an expert team that studied the first Nipah outbreak, stressed the need to strengthen the surveillance system in hospitals. “The body fluid samples of patients who are suspected to have symptoms of acute encephalitis syndrome, a notifiable condition by the WHO, should be subjected to mandatory lab tests. These tests should be made available for follow-up studies as well. Though the main attempt is to diagnose Japanese Encephalitis, infections such as Nipah and West Nile fever too can be detected this way,” he pointed out.

Tracing the source

The health authorities, however, highlighted how the healthcare system in the State is under strain. Soon after the first outbreak came the disastrous floods of 2018 and 2019. When it looked like the State was limping back from these jolts, the health system was shaken by the COVID-19 pandemic, which has been long-drawn, challenging and relentless. The news of a fresh case of Nipah infection emerged when Kerala was continuing to report the highest number of COVID-19 cases in the country.

Also read | Source of Nipah infection still elusive

They said that no effort would be wasted in tracing the source of the infection. The Department of Animal Husbandry collected throat swab samples of goats in the area as Hashim was reported to have the habit of rearing them. Body fluid samples of bats and some bat carcasses and bird droppings too were taken for tests at the National Institute of High Security Animal Diseases, Bhopal. However, all of them have returned negative for the virus along with the wild boar samples collected with the help of the Forest Department. After some of his neighbours said that Hashim had eaten rambutan, some of the half-eaten parts of the fruit too were taken to be tested. The results are awaited.

“One of the biggest challenges now will be to detect how the virus was transmitted from animals to humans. How it happened in 2018 is still unclear. Antibodies against the virus were found in 12 of the 52 samples of fruit bats collected from Changaroth Grama Panchayat and nearby areas in Kozhikode where the first outbreak occurred. There is no evidence other than that,” said Dr. Althaf. In 2019, after the infection recurred, the presence of antibodies was found in fruit bat samples in Ernakulam as well. These bats belonged to the species Flying Fox or Pteropus medius.

A public health expert, who did not wish to be named, said, “Some people try to compare the source of the Nipah infection with COVID-19, which is factually incorrect. For COVID-19, there has been only one index patient or zero patient, the person in whom the infection was detected first. But for Nipah, every one of the local occurrences so far has had an index case.” Detailed research has not been conducted as yet on the presence of the virus in bats in Kerala.

Also read | Nipah curbs in Chathamangalam and nearby wards lifted

According to reports, there are 48 species of bats in Kerala, of which seven are fruit bats. An international study titled ‘Prioritizing surveillance of Nipah virus in India’, published in the PLOS Neglected Tropical Diseases journal in June 2019, had claimed that at least 11 bat species in the country could carry the virus. “In addition to seven species in Kerala that were previously identified as Nipah virus seropositive, we identified at least four bat species that, on the basis of trait similarity with known Nipah virus-seropositive species, have a relatively high likelihood of exposure to Nipah or Nipah-like viruses in India,” said the study.

P.O. Nameer, Professor and Head of the Department of Wildlife Sciences and Centre for Wildlife Studies, College of Forestry, Kerala Agricultural University, Thrissur, was one of the co-authors of this study. “There are two important points. One, the samples collected for the study were not from India, but from other countries. Also, 10 of the 11 samples were subjected to only serological examination, which is suggestive of the presence of the virus, and not RT-PCR tests, which are more accurate. So, our study actually called for a detailed investigation into the presence of the virus in Indian bats,” he said.

An integrated approach

Public health experts have also called for an integrated approach to emerging infections, especially those zoonotic in nature. They don’t rule out the possibility of the Nipah infection recurring in the future.

M. Muraleedharan, State vice-president of the Indian Medical Association, said zoonotic diseases have been posing a challenge to our public health in the last few decades. “To address these infections, we need to coordinate the treatment methods and health surveillance of the people along with those for animals. Such an approach should also take into view ecological concerns, and a ‘One Health’ policy should be developed,” he said. He suggested that Kerala take steps to set up a research and study centre for animals on the lines of the national lab in Bhopal. The government should also set up bio-safety level-IV high security labs so that testing and diagnosis for infections such as Nipah can be done in the State itself, he said.


Dr. Muraleedharan said that it was high time that the State government implemented a Kerala Public Health Act as well. Now, an age-old Madras Public Health Act is in force in the Malabar region and a Travancore-Cochin Public Health Act is applicable to the rest of the State.

A doctor at the Kozhikode Medical College Hospital, a major healthcare institution in the Malabar region comprising six districts, underscored the problem of overcrowding in government medical college hospitals, which would have to be dealt with on an emergency basis. During the 2018 outbreak, many of the secondary contacts of the primary cases were in-hospital contacts due to lack of implementation of strict infection control practices. Crowding has to be minimised in casualty wards to prevent any cross infections, he said. There has to be a proper isolation system with the necessary infrastructure and manpower so that parallel medical services to other patients are not compromised during outbreaks like this, he said.

But it also looks like the existing COVID-19 protocol has come in handy in the fight against Nipah. “So far, we have seen that Nipah gets transmitted only after the infected person becomes terminally ill. The person is confined to a hospital, in intensive care units or wards. So, the chance of spreading the infection is confined to healthcare institutions and the people there — nearby patients, bystanders and healthcare workers,” Dr. Althaf said. Now COVID-19 protocols are in place — people are wearing face masks and are sanitising their hands frequently. All the hospitals have infection-control measures in place.


So far, 143 people on Hashim’s contact list, including 17 of those symptomatic for the infection, have tested negative for the virus. Restrictions on social life imposed on Chathamangalam Grama Panchayat and surrounding wards in other local bodies have been gradually eased. Life is slowly returning to normal. An NIV team has collected bat samples in a bid to study the source of the infection.

But a question still remains.

“Hashim’s parents were very particular about maintaining hygiene. We don’t believe that he had eaten a rambutan fruit bitten by a bat. He used to eat only freshly plucked ones from trees on his father’s property. So, how did he get infected,” Hashim’s neighbour wondered. We may have to wait for long for an answer.

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Printable version | Oct 17, 2021 3:58:47 AM |

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