It was 3 January 2020, and Supaporn Wacharapluesadee was standing by, awaiting a delivery. Word had spread that there was some kind of respiratory disease affecting people in Wuhan, China, and with the Lunar New Year approaching, many Chinese tourists were headed to neighbouring Thailand to celebrate. Cautiously, the Thai government began screening passengers arriving from Wuhan at the airport, and a few select labs – including Wacharapluesadee's – were chosen to process the samples to try to detect the problem.
Wacharapluesadee is an expert virus hunter. She runs the Thai Red Cross Emerging Infectious Disease-Health Science Centre in Bangkok. Over the past 10 years, she's been part of Predict, a worldwide effort to detect and stop diseases that can jump from non-human animals to humans.
She and her team have sampled many species. But their main focus has been on bats, which are known to harbour many coronaviruses.
She and her team were able to understand the disease in just a matter of days, detecting the first case of Covid-19 outside of China. They found that – as well as being a novel virus that didn't originate in humans – it was most closely linked to coronaviruses they had already found in bats. Thanks to the early information, the government was able to act quickly to quarantine patients and advise citizens. Despite being a country of nearly 70 million people, as of 3 January 2021 Thailand had recorded 8,955 cases and 65 deaths.
The next threat
But even as the world grapples with Covid-19, Wacharapluesadee is already looking to the next pandemic.
Asia has a high number of emerging infectious diseases. Tropical regions have a rich array of biodiversity, which means they are also home to a large pool of pathogens, increasing the chances that a novel virus could emerge. Growing human populations and increasing contact between people and wild animals in these regions also ups the risk factor.
Over the course of a career sampling thousands of bats, Wacharapluesadee and her colleagues have discovered many novel viruses. They've mostly found coronaviruses, but also other deadly diseases that can spill over to humans. (Watch a short film about the viruses that pose the greatest threat of causing a pandemic on BBC Reel.)
These include the Nipah virus. Fruit bats are its natural host. "It's a major concern because there's no treatment… and a high mortality rate [is] caused by this virus," says Wacharapluesadee. The death rate for Nipah ranges from 40% up to 75%, depending on where the outbreak occurs.
She isn't alone in her worry. Each year, the World Health Organization (WHO) reviews the large list of pathogens that could cause a public health emergency to decide how to prioritise their research and development funds. They focus on those that pose the greatest risk to human health, those that have epidemic potential, and those for which there are no vaccines.
Nipah virus is in their top 10. And, with a number of outbreaks having happened in Asia already, it is likely we haven't seen the last of it.
There are several reasons the Nipah virus is so sinister. The disease's long incubation period (reportedly as long as 45 days, in one case) means there is ample opportunity for an infected host, unaware they are even ill, to spread it. It can infect a wide range of animals, making the possibility of it spreading more likely. And it can be caught either through direct contact or by consuming contaminated food.
Someone with Nipah virus may experience respiratory symptoms including a cough, sore throat, aches and fatigue, and encephalitis, a swelling of the brain that can cause seizures and death. Safe to say, it's a disease that the WHO would like to prevent from spreading.
Exposure is everywhere
It's first light in Battambang, a city on the Sangkae River in north-west Cambodia. At the morning market, which starts at 05:00, motorbikes weave past shoppers, kicking up dust in their wake. Carts piled high with goods and covered in colourful sheets are perched next to makeshift stalls selling misshapen fruits. Locals wander in and out of the stands, plastic bags bulging with their purchases. Elderly ladies in wide-brimmed hats crouch over blankets covered with vegetables for sale.
In other words, it's a fairly normal morning market. That is, until you crane your neck to the sky.
Hanging quietly in the trees above are thousands of fruit bats, defecating and urinating on anything that passes below them. On closer inspection the roofs of the market stalls are covered in bat faeces. "People and stray dogs walk under the roosts exposed to bat urine every day," says Veasna Duong, head of the virology unit at the scientific research lab Institut Pasteur in Phnom Penh and a colleague and collaborator of Wacharapluesadee's.
The Battambang market is one of many locations where Duong has identified fruit bats and other animals coming into contact with humans on a daily basis in Cambodia. Any opportunity for humans and fruit bats to get near to one another is considered a "high risk interface" by his team, meaning a spillover is highly possible. "This kind of exposure might allow the virus to mutate, which might cause a pandemic," says Duong.
Despite the dangers, the examples of close proximity are endless. "We observe [fruit bats] here and in Thailand, in markets, worship areas, schools and tourist locations like Angkor Wat – there's a big roost of bats there," he says. In a normal year, Angkor Wat hosts 2.6 million visitors: that's 2.6 million opportunities for Nipah virus to jump from bats to humans annually in just one location.
From 2013 to 2016, Duong and his team launched a GPS tracking programme to understand more about fruit bats and Nipah virus, and to compare the activities of Cambodian bats to bats in other hotspot regions.
Two of these are Bangladesh and India. Both countries have experienced Nipah virus outbreaks in the past, both of which are likely linked to drinking date palm juice.
At night, infected bats would fly to date palm plantations and lap up the juice as it poured out of the tree. As they feasted, they would urinate in the collection pot. Innocent locals would pick up a juice the next day from their street vendor, slurp away and become infected with the disease.
Across 11 different outbreaks of Nipah in Bangladesh from 2001 to 2011, 196 people were detected to have Nipah – 150 died.
Date palm juice is also popular in Cambodia, where Duong and his team have found that fruit bats in Cambodia fly far – up to 100km each night – to find fruit. That means humans in these regions need to be concerned not just about being too close to bats, but also about consuming products that bats might have contaminated.
Duong and his team identified other high-risk situations, too. Bat faeces (called guano) make for popular fertiliser in Cambodia and Thailand and in rural areas with few work opportunities, selling bat droppings can be a vital way to make a living. Duong identified many locations where locals were encouraging the fruit bats, also known as flying foxes, to roost nearby their homes so they could collect and sell their guano.
But many guano harvesters have no idea what risks they face in doing so. "Sixty percent of people we interviewed didn't know that bats transmit disease. There is still a lack of knowledge," says Duong.
Back at the Battambang market, Sophorn Deun is selling duck eggs. Asked if she had heard of Nipah virus, one of the many risky diseases the bats could be carrying, she says, "Never. The villagers are not bothered by the flying foxes, I have never gotten sick from them."
Educating locals about the threats faced by bats should be a major initiative, Duong believes.
Changing the world
Avoiding bats may have been simple at one point in human history, but as our population expands, humans are changing the planet and destroying wild habitats to meet the increasing demand for resources. Doing so is driving up the spread of disease. "The spread of these [zoonotic] pathogens and risk of transmission accelerate with … land-use changes such as deforestation, urbanisation, and agricultural intensification," write authors Rebekah J. White and Orly Razgour in a 2020 University of Exeter review about emerging zoonotic diseases.
Sixty percent of the world's population already lives in Asia and the Pacific regions, and rapid urbanisation is still taking place. According to the World Bank, almost 200 million people moved to urban areas in East Asia between the years 2000 and 2010.
The destruction of bat habitats has caused Nipah infections in the past. In 1998, a Nipah virus outbreak in Malaysia killed more than 100 people. Researchers concluded that forest fires and local drought had dislodged the bats from their natural habitat and forced them towards fruit trees – trees grown on the same farms as pigs. Under stress, bats have been shown to shed more viruses. The combination of being forced to relocate and being in close contact with a species they would not normally interact with allowed the virus to jump from bats to pigs, and onwards to the farmers.
Meanwhile, Asia is home to nearly 15% of the world's tropical forests, but the region is also a deforestation hotspot. The continent ranks among the highest in the world for biodiversity loss. Much of it is due to the destruction of forests into plantations for products like palm oil, but also to create residential areas and space for livestock.
Fruit bats tend to live in thick forest regions with lots of fruit trees for them to feed on. When their habitat is destroyed or damaged, they find new solutions – like the roost of a house, or the creviced turrets of Angkor Wat. "The destruction of bat habitat and the interference of humans through hunting drives flying foxes to search for alternative roosts," says Duong. It's likely the bats that Duong's team have monitored travelling up to 100km per night for fruit are doing so because their natural habitat no longer exists.
But bats, we now know, harbour a number of nasty diseases – Nipah and Covid-19, but also Ebola and Sars.
Should we just eradicate bats? Not unless we want to make things much worse, says Tracey Goldstein, institute director at the One Health Institute Laboratory and lab director of the Predict Project.
"Bats play hugely important ecological roles,” says Goldstein. They pollinate more than 500 plant species. They also help to keep insects in check – playing a hugely important role in disease control in humans by, for example, reducing malaria by eating mosquitoes, says Goldstein.
"They play a hugely important role in human health."
She also points out that culling bats has been shown to be detrimental from a disease perspective. "What a population does when you decrease numbers is to have more babies – that would make [a human] more susceptible. By killing animals you increase the risk, because you increase the number of animals shedding virus," she says.
Finding answers, creating questions
For as many answers as Duong and his team find, more questions are always cropping up. One is: why hasn't Cambodia experienced a Nipah virus outbreak yet, given all the risk factors? Is it a matter of time, or are Cambodian fruit bats slightly different to Malaysian fruit bats, for example? Is the virus in Cambodia different to Malaysia? Is the way humans are interacting with bats different in each country?
Duong's team is working to find out the answers, but they don't know yet.
Of course, Duong's team isn't alone in looking at these questions. Virus hunting is a massive global collaborative effort, with scientists, veterinarians, conservationists and even citizen scientists teaming up to understand what diseases we face and how to avoid an outbreak.
When Duong samples a bat and finds Nipah virus, he sends it to David Williams, head of the Emergency Disease Laboratory Diagnosis Group at the Australian Centre for Disease Preparedness.
Because Nipah virus is so dangerous – it is considered by governments across the globe to have bioterrorism potential – only a handful of laboratories across the world are allowed to culture, grow and store it.
Williams's lab is one of them. His team are some of the world's leading experts on Nipah virus, with access to a huge range of diagnostic tools not available in most labs. Wearing airtight containment suits, they are able to grow more of the highly dangerous virus from a tiny sample and then, working with a bigger load, to run tests to understand how it is replicated, transmitted and how it causes disease.
It's quite the operation to get to this point: first, Duong collects bat urine by spreading a plastic sheet under a bat roost in Cambodia. This avoids having to catch the bats, which can be traumatising for them. He takes his samples back to the lab, decants them into tubes, labels them and packs them safely into cool boxes. These are collected by a special courier who is approved to ship dangerous goods and flown to Australia, where the virus samples pass through customs to have the accompanying licenses and permits approved.
Eventually they arrive at Williams's lab. After testing, he'll share the results with Duong back in Cambodia. I ask Williams if building more high-security labs like his across the globe might speed up the detection of harmful diseases. "Potentially yes, by putting more [biosecure] labs in places like Cambodia that could speed up characterisation and diagnosis of these viruses," he says. "However, they're expensive to build and maintain. Often that's the limiting element."
Funding for the work that Duong and Wacharapluesadee are carrying out has been patchy in the past. The 10-year Predict programme was allowed to expire by the Trump administration, although US President-elect Joe Biden has promised to restore it. Meanwhile, Wacharapluesadee has funding for a new initiative called the Thai Virome Project, a collaboration between her team and the government's Department of National Parks, Wildlife and Plant Conservation in Thailand. This will allow her to sample more bats and a wider range of wildlife to understand the diseases they harbour and the threats to human health.
Duong and his team are searching for funding for their next pathogen detection trip – one to support the continuous surveillance of bats in Cambodia and to understand if there have been so-far-unreported infections in humans.
They have not yet managed to secure the money to continue their Nipah virus work. Without it, they say, a potentially catastrophic outbreak is more likely.
"The long-term surveillance helps us … inform authorities [to enact] preventive measures and to prevent undetected spillover which would cause bigger outbreak," says Duong. And without continued training, scientists might not be able to identify and characterise new viruses rapidly, as Wacharapluesadee did with Covid-19 in Thailand. This information is needed to start working on a vaccine.
When we spoke in June 2020 via video call, I asked if Wacharapluesadee was proud of her team's remarkable achievement. "Proud?" she said. "Yes, I am proud.
"But the Predict project was an exercise on how to diagnose novel viruses from wild animals. So when me and my team found the genome of the [coronavirus pathogen] it's not too much [of a] surprise, because of the research project. It gave us a lot of experience. It strengthened our capacity," she said.
Duong and Wacharapluesadee hope to continue collaborating to fight Nipah virus in South East Asia, and the pair have drafted a proposal for Nipah virus surveillance in the region together. They plan to submit it to the Defense Threat Reduction Agency, a US governmental organisation that funds work aimed at reducing the threats posed by infectious disease agents, once the Covid-19 crisis subsides.
In September 2020 I asked Wacharapluesadee if she thinks she can stop the next pandemic. She was sitting in her office in her white lab coat, having processed hundreds of thousands of samples to test for Covid-19 in the past months – far beyond the usual capacity of her lab in any more usual year.
Despite it all, a smile broke across her face. "I will try!" she said.
With additional reporting by Mora Piseth in Cambodia.