At one point, the stench from the rotting carcasses was so intense the primary school was forced to close. In a bid to curb a “terrifying” virus spreading among farmers, the Malaysian army was deployed to kill close to one million pigs in this sleepy region, 50 miles south of Kuala Lumpur.
Soldiers shot the animals until they ran out of bullets; they then used wooden sticks to “destroy the pigs”, according to local newspaper reports of the slaughter. The corpses were scooped up by diggers and unceremoniously dumped into deep, muddy pits.
“The village was very smelly,” says Hoon Keong Goh, who lost 4,000 pigs when the virus hit. “It became very empty too, almost everyone left. Very empty, very smelly… I couldn’t recognise my home anymore. It was like a hell.”
In 1999, Sungai Nipah village was ground zero in an infectious disease outbreak that killed 105 people, infected a further 160, and destroyed a billion-dollar pig-farming industry.
“It was a big tragedy,” says Prof Dato CT Tan, a neurologist who treated many of the patients at the University of Malaya Medical Centre (UMMC). “You look at a family, two or three people were sick – some died, some [were] in a vegetative state. And it’s not just their health, they’d lost everything, because [they had been] pig farming for three generations.”
Initially misdiagnosed as Japanese encephalitis – prompting a mosquito-spraying strategy that did nothing to prevent fatalities – scientists eventually discovered in March 1999 that they were dealing with a dangerous new zoonotic pathogen. They called it Nipah.
More than two decades later, and despite repeated outbreaks, there are still no vaccines or drugs to specifically target the virus, which is deemed by the World Health Organization (WHO) and others to have “serious epidemic potential”.
The virus, which inspired the film Contagion about a global pandemic, attacks the brain and has a fatality rate as high as 70 per cent.
Now, survivors from the first outbreak are giving their blood to scientists racing to develop vaccines, in a push to prevent a similar scenario ever unfolding again.
Scarred for life
Last year Mr Goh blacked out while on his motorbike. It was a close call – though he careened into the back of a lorry, he avoided any serious injuries. But the incident was a sign that the epileptic fits he’s experienced since he recovered from Nipah virus are getting worse.
“The doctors have had to double my medication, and I’ve been banned from driving,” he says, looking away from the needle as a medic takes blood. Later, researchers will analyse these samples, searching for clues about how the virus operates.
Mr Goh was just 27 when he was among the first cluster of cases in Sungai Nipah and a handful of neighbouring villages. His memories of what happened remain confused – he knows he collapsed and was rushed to hospital with a high fever, but his recollection of the ward and the doctors who treated him are hazy.
But he does remember the terror of his first blackout – it happened just after he was eventually discharged. Nipah attacks the brain, causing encephalitis or swelling of the tissue, and the virus had left a permanent scar.
“I was very scared, I didn’t know what was happening,” he says. “Epilepsy has changed my life, it’s hard to work. But I still think I’m lucky – my business partner died.”
Jian Jie Lee, who was 28 at the time, was also Mr Goh’s best friend. “Sometimes I think about the life he would have had. I think about that more than I think about the life I would have had [without epilepsy]. I still really miss him.”
Of those who survive Nipah, roughly 20 per cent are left with long-term neurological conditions, including personality changes or seizure disorders.
The pathogen can also linger in the body, sometimes causing problems much later – in the two years following the Sungai Nipah outbreak, 10 people developed late-onset encephalitis while another 12 relapsed. Scientists have also documented how a 35-year-old-woman suffered late-onset brain inflammation in 2010 – 11 years after she had an asymptomatic infection.
In Kong Chong Wong’s case, the pathogen attacked his eyesight. The 47-year-old pig farmer turned temple caretaker – who’s mother and sister died during the outbreak – has had double vision since he was hospitalised with Nipah. He was one of the last people in the area to catch the virus in 1999.
“They weren’t like this before,” he says, pointing to his eyes. “They’re not aligned… if there’s one person in front of me, I see two. Also I can only write slowly, and I dare not drive.”
“Sometimes what happened here feels like a dream,” Mr Wong adds. “But whenever I pass by the area where we used to keep our pigs, it reminds me of what happened.”
Endless spillover possibilities
Nipah virus is regularly described as a terrifying disease due to its high fatality rate, the speed at which patients deteriorate, and the long-lasting impacts.
Listed by the World Health Organization as a “priority pathogen” with pandemic potential, it can rapidly attack the respiratory and central nervous systems. The United States deems the virus a Category C bioterrorism threat, as it “could be engineered for mass dissemination in the future”.
Symptoms of the respiratory disease vary – it often starts with a fever, headache or myalgia before developing into dizziness or confusion, which signals brain inflammation. In severe cases, people can become comatose within 24 hours.
“It’s one the deadliest pathogens known to infect humans,” says Dr Gabrielle Breugelmans, director of epidemiology at the Coalition for Epidemic Preparedness Innovations (Cepi).
“[The] reason it’s so scary… is that it’s very pathogenic across a broad range of mammals, including humans, and so it has what we call high pandemic potential, because there’s a high likelihood of a spillover… from animals to humans,” she adds.
In Malaysia, scientists eventually traced the virus from humans to pigs to fruit bats. While Sungai Nipah and the surrounding villages were hardest hit, it later emerged that the pathogen initially jumped to pigs and a handful of people 160 miles north in Ipoh, where bats are common.
But it was in Sungai Nipah – where people lived in close proximity to their pigs and farms were tightly packed together – that the virus found the ideal conditions to thrive, sparking what remains the world’s biggest, and Malaysia’s only, Nipah outbreak.
“My memory of Nipah is the fever, the body aching, the panic,” says Jeou Ching Pau, who caught the virus when he was 14 – his father was one of the first to die in UMMC. “As the virus spread, everyone in the village was scared. I knew so many people who got sick.”
In the years since, the pathogen has predominantly affected Bangladesh, where a slightly different – and potentially more lethal – strain circulates. The country has seen almost annual outbreaks in the ‘Nipah belt’ since the virus was first detected there in 2001. This year alone, 11 people have so far contracted the disease and eight have died – the highest annual toll since 2015.
Unlike Malaysia, Nipah generally jumps directly from bats to people in Bangladesh and parts of India, which has also seen sporadic outbreaks. Many of these cases have been linked to raw date juice – a sap that’s popular among bats and humans alike. The flying mammal’s contaminated saliva has turned the delicacy into a potential poison.
“There is also person to person transmission, but that’s much, much less [common] – you really need to be in contact with bodily fluids from [an infected] human being to get that,” says Dr Breugelmans.
“But the possibilities for the virus to spillover from bats or other animals to us is pretty much endless – these fruit bats, they live in close proximity to markets, places of worship, schools. You name it,” she adds. “It’s also used as fertiliser in fields, meaning agricultural workers can also be in frequent contact with the virus – so there’s endless possibilities.
“Add not just in southeast Asia, where currently Nipah outbreaks predominantly happen. [Fruit bats] are all over the world – so if something were to change in the ecosystem, the vector is there.”
But with no tools to combat the disease, the prognosis for those infected is poor. Bangladesh has reported an overall fatality rate of 71 per cent – since 2001, 231 of the 330 known cases have died. In the southern Indian state of Kerala in 2018, Nipah killed 17 out of the 18 people who were infected.
Vaccine urgency
At a lab in Kuala Lumpur, tucked away behind a warren of key-card access points, a small team of female scientists are part of a growing effort to unlock new clues about how the body responds to a Nipah virus infection for the first time.
By analysing the blood of 24 survivors in Sungai Nipah – and comparing that to samples from 24 people in the community unaffected by the virus – the researchers aim to gather critical data which could guide the development of much-needed vaccines, as well as the assays used to test their performance.
“There is a need for a vaccine for prevention and protection,” says Prof Li-Yen Chang, associate professor of medical microbiology at the University of Malaya (UM) and head of the Nipah virus work.
“But before a vaccine can be established, it is important to know how a person responds to an infection – whether they get an antibody response or any other immune response. So this project looks to characterise that, so vaccine developers can use that data,” she adds.
At least eight groups, including the team behind the Oxford/AstraZeneca jab, are currently working on vaccine candidates that could benefit from the UM’s work.
The ‘survivors project’, which has also been launched at icddr,b research institute in Bangladesh, is funded by Cepi. The initiative is a major backer of Nipah vaccine development and the “enabling” research considered critical to reach that goal.
“I’m very excited about the work currently ongoing – I think it has a lot of potential,” says Dr Breugelmans. “It’s critical – particularly as it’s such a deadly disease… but I think we also need to think about it in terms of pandemic preparedness. We’re always one step behind nature – outbreaks, epidemics, pandemics are occurring more frequently… so preparedness needs to be at the forefront of everything we do.”
In Malaysia, Prof Chang’s team looks set to publish a paper describing the antibody response later this year. Characterising the second part of the immune response, T cells, is taking a little longer – they’re currently in a “troubleshooting” phase and may adjust their methods.
“Nipah is really very scary, and I hope that we see no more outbreaks,” says Dr Hui Ming Ong, project manager of the UM survivors project. “But if we do, at least the work is taking place to help respond, at least something is in progress.”
Back in Sungai Nipah, thousands of palm trees have replaced the pig sheds that once surrounded the village – farming swine remains banned here.
While some people switched to rear chickens or produce palm oil, the community has also shrunk as many left to find work elsewhere or avoid painful memories, says Mr Pau.
But for the 38-year-old, taking part in the UM research is just another part of his drive to mark the events of 1999 – he helped set up a small museum in Sungai Nipah, which recounts how the virus devastated the village it was named after.
“In the beginning, most people had an objection to the virus being called Nipah, they felt that it was not a good memory [and had] bad associations,” Mr Pau says. “But today, after so many years, I think it’s good – we can let people know what happened here 24 years ago… we want a new generation to be aware.”
Mr Goh, too, believes the world must not forget those that died. And he’s hopeful that the blood he’s provided may help others avoid a similar fate.
“I wanted to help scientists check, what is this virus and what does it do to us?” he says. “I hope they make a vaccine, and if they do I want my children to take it.”
