‘VIRUS HUNTERS’: Filipino Scientists Explore Phl Hotspots In Search Of Coronaviruses In Bats

Bat ecologist Dr. Phillip Alviola spent his childhood scaling the mystical Mount Makiling in Laguna, where his father, Pedro Alviola III, was also a known wildlife biologist from the University of the Philippine Los Baños.

Because of this, the ecologist knows the mountain well – both as a sanctuary for wild animals as well as a legendary abode of a goddess believed to be guarding the forest from poachers.

Now, he is hiking not just Makiling that happens to be nearby when he was a child, but other mountains as well to document the endemic fauna in these areas. Despite following his father’s footsteps, he said he did not feel like living under his shadows. He chose to focus on a mammal known for stirring both fear and wonder among locals: bats, a natural reservoir of coronaviruses.

Alviola’s team called themselves “bat virus hunters,” an idea they got from watching nature documentaries on television.

Bats are among the animals widely seen to be the source of severe acute respiratory syndrome coronavirus 2 or SARS-CoV-2, the virus that causes COVID-19, although experts said the virus may have jumped to an intermediary animal before spilling over to humans.

It is this zoonotic scenario that Alviola and his team of ecologists at the Biological Sciences Institute of the University of the Philippines Los Baños hope to prevent - by identifying coronavirus-carrying bats in the country and mapping out possible hotspots.

For this particular research,  Alviola and three fellow ecologists take a 30-minute car ride up a road flanked by towering trees to the “Agila” base or the jump-off point of a trail in Mount Makiling.

From there, his team scales a steep muddy slope for another half an hour. As they climb, they have to avoid moss-covered stones and spiky rattan branches to reach a limestone crevice, which serves as a roost for thousands of bats during the day.

They set up two mist nets – one directly below the mouth of the bat cave and another away from it. And there, they wait for the dark, when the bats come out at night to look for food.

Wearing face masks, protective suits and gloves, Alviola said his team would document their encounter with the bats, hoping to predict the next zoonotic spillover, or a scenario of animal viruses jumping to humans, triggering a pandemic.

“(The pandemic) created a renewed interest or fervor in studying the bats as a reservoir of the viruses,” Alviola said. “(Our study) can serve as a surveillance of places where there are a huge percentage of bats…These places could be a potential ground zero for another pandemic.”

According to Alviola, his previous studies to detect pathogens from bats sometimes involve mercy killing the mammals to bring to the laboratory, where they are then dissected to take viral samples from their inner organs.

In biology, a pathogen is any organism that can produce disease, an infectious agent, or simply a germ. Zoonotic spillover is the transmission of a pathogen from an animal to a human, often through an intermediary species. For such an event to happen, zoonotic pathogens must overcome a series of barriers that would otherwise prevent spillover infections into humans.

In this pandemic study, Alviola noted he is aware of the need to conserve these virus-carrying bats or keep them alive.

In the country’s experience with swine and bird flu, the infected intermediary animals, mostly livestock, are culled just to prevent the outbreak from spreading. Alviola said the killing of animals to prevent a spillover can be avoided.

He wouldn’t want bats to be culled out of discrimination due to their natural capacity to harbor coronavirus. It is not their fault, the ecologist said as human activities triggered the spillover.

“We err on the side of caution. We don’t want to be destructive in our sampling,” Alviola said, noting that if humans can be swabbed for coronaviruses, why not bats?

“We release the bats after one or two hours. It’s more of a conservation, animal care point of view,” Alviola said.

Since the first COVID-19 case was detected at a wet animal market in Wuhan, China, the scientific community has been on the hunt for the origin of the virus that may have jumped to humans through the illegal wildlife trade.

A recent study (under consideration for publication in the Nature Portfolio Journal) suggested that relatives of the SARS-CoV-2 were detected in bats living in the caves of Northern Laos, just nearby China’s Yunnan province where another related bat coronavirus was detected. Several studies have also suggested pangolin – a highly trafficked animal in the illegal wildlife trade – as a possible intermediary host before spilling over to humans.

The research being done by Alviola’s team is the country’s contribution to this worldwide hunt for the pandemic’s origins.

His team sends out the animal samples they collected to Japan for sequencing. The detected genetic sequences are then added to the GenBank, an “annotated collection of all publicly available DNA sequences” according to the National Center for Biotechnology Information.

Alviola’s ultimate aim is to develop a simulation model to predict the next bat-derived coronavirus infection for humans by locating possible hotspots.

Since 2007, Alviola’s team has visited 11 provinces and islands across the Philippines, documented over 30 species of bats, and detected 12 that are positive for different viruses. These viruses that have the potential of jumping to humans include the gamma herpes virus, the Reston ebolavirus, and coronaviruses, a virus strain that causes COVID-19.

But the pandemic restrictions forced them to focus their fieldwork in nearby Mount Makiling. Since January this year, Alviola’s team has sent 315 tube samples containing oral and anal or rectal bat swabs, covering 10 species caught in the Makiling forest reserve.

By sequencing the virus samples, the bat coronaviruses can be compared with coronaviruses capable of infecting humans like the SARS-CoV-2.

“If the match is almost similar to each other, and the viral protein, we would take that as having a potential to infect humans as well,” Alviola said.

With his extensive background on viruses and bats, Alviola was recently admitted to the World Health Organization’s (WHO) Scientific Advisory Group for the Origins of Novel Pathogens like SARS-CoV-2. Alviola pointed out it is most crucial to look into the roots of the pandemic, which he considers the “most significant existential threat to the human species” yet.

While bats are natural reservoirs of viruses and have been known as “super immune” to them, the WHO and experts have noted that no strong evidence exists to directly link the mammals to the raging pandemic.

“There is no smoking gun yet that proves the direct transfer of viruses from bats to humans. For the two pandemics, it always involved an intermediate host,” Alviola said, adding that viruses can even evolve through “recombination,” a process that makes viruses more infectious as it jumps from animals to humans.

In mentioning the two pandemics, Alviola was referring to two virus spillovers in recent history – the COVID-19 pandemic and the 2002 to 2003 SARS outbreak, which was called by the World Wildlife Fund (WWF) as the "averted pandemic'' that infected over 8,000 people and killed 774.

In its 2020 report entitled “Pandora’s box: A report on the human zoonotic disease risk in Southeast Asia with a focus on wildlife markets,” the WWF said SARS that reached epidemic proportions may have been caused by a bat coronavirus that jumped to palm civets, which were sold at live animal markets in Guangdong, China. The outbreak did not reach pandemic scale due to a low infection rate among humans, according to WWF.

The COVID-19 pandemic, which was also believed to have originated from a wet market in Wuhan, proved to be more infectious than its predecessor.

Addressing misconceptions

Rights groups warned there had been possible discrimination against bats borne out of misinformation and irrational fear that the winged mammals are to be blamed for the pandemic.

During the early months of the pandemic, social media platforms were flooded with memes falsely suggesting that Chinese citizens caused the disease by eating bats as a delicacy.

Lisa Paguntalan, executive director of the Philippines Biodiversity Conservation Foundation Inc., said the pandemic stirred the misconception that all bats can trigger a pandemic. While massive culling of bats – except for bushmeat in the illegal meat trade – has not yet been reported in the Philippines, the group hopes to educate the public about the role of bats in ecology.

“Even before the pandemic, it has been part of our bat conservation program to raise awareness on the importance and ecological services of bats,” Paguntalan said.

With the scientific research for the SARS-CoV-2 focused on bats, the group expressed worry that all bat species could be generalized as coronavirus carriers. She emphasized that bat species actually promote life and are not a threat to it.

Bats are beneficial because their species contribute to the preservation of the environment, according to the Department of Environment and Natural Resources’ (DENR) Biodiversity Management Bureau.

Despite their role in the emergence of zoonotic diseases, bats are crucial in reviving the forest by dispersing the seeds of fruits that they eat, the DENR added. Insect-eating bats control pests, while fruit-eating ones pollinate plants and trees, making them a crucial link in the ecological cycle of life. The bats’ feces also offer fertilizer to the forest floor, promoting flora.

The Philippines has over 78 species of bats - 25 are fruit-eating and 53 are insectivorous, according to the DENR.

“When the pandemic hit, there was a lot of misconception and negative perception of bats. The pandemic offered the recipe to put a lot of hate on all bats. It’s never been about the positive light,” Paguntalan said.

Like Alviola, Paguntalan stressed bats are not to blame for being natural carriers of viruses. Spillovers happen because of human activities like hunting, animal farming and wildlife trading or trafficking that encroach on animal habitats and bring humans and animals closer than ever to trigger a pathogenic transfer, Paguntalan said.

She said these human activities close the gap between people and wildlife, and only speed up the inevitable scenario of humans contracting diseases caused by zoonotic viruses.

Before the COVID-19 pandemic, the Philippines has had several virus outbreaks related to bats, according to the World Health Organization. In 2008, Reston ebolavirus infected pig workers in Bulacan and Pangasinan after exposure to sick pigs, and from 1989 to 1996, animal handlers exposed to infected monkeys in Calamba, Laguna also fell ill due to the virus. Experts said the infected animals were kept at a facility located near fruit-bearing trees, which may have attracted the bats to the animals triggering a virus spillover. Bats are also known reservoirs of the ebola virus.

“An environment – which promotes the crossing of that virus to an animal host and then to the human population – poses the risk of having zoonosis,” Paguntalan said. “Human behavior has contributed to the emergence of zoonotic diseases in the last century.”

Alviola agreed that ultimately, the best way to prevent a pandemic is to keep the animals at peace from human encroachment.

“The pandemic is happening because of the narrowing interface between human population and the wild,” Alviola said. “We are encroaching on their habitat. It’s a matter of time when people will encounter these viruses that they did not know before.”

With increasing human activity – like deforestation to give way to more residential areas, or illegal trading linked to the demand for wild meat – “it was inevitable that the pandemic would happen,” Alviola said.

“The fault lies with the people, for destroying their habitat, for the shrinking of the forest, for disturbing their caves for trading and hunting,” he added.

With over five million people killed worldwide because of the pandemic, the scientist hoped their research would lead to a “major rewiring of mindset” to prepare for the next pandemic.

“It was bound to happen. It was not a matter of if, but when,” Alviola stated.

Virus laboratory

Alviola’s team hopes to develop the country’s first pathogenic database to determine bacteria, parasites, and viruses found in animals that could jump to humans. His efforts may just be realized with the construction of the Philippines’ own Virology Institute (VIP).

Several bills have been filed in Congress seeking to create the country’s first virus laboratory as the country’s central research hub on pathogens. The laboratory will include a virus gene bank, alongside the virus genome and reference laboratory, and virus reference laboratory, the first of its kind in the country. The laboratory will include a virus gene bank, and a virus genome and reference laboratory, the first of its kind in the country.

“One of the objectives or goals of the VIP is to establish a repository of all the known and unknown viruses, be it human plant or animal origin,” said Jaime Montoya, executive director of the Philippine Council for Health Research and Development under the Department of Science and Technology (DOST).

Alviola’s work may be part of the VIP’s pathogen genome database, which will be housed in the VIP for its research on treating diseases caused by these viruses.

The VIP will further develop the ongoing research on Zika virus, the African swine fever virus, even the so-called tomato yellow leaf curl virus for plants.

“While you are fixated on bats, it can really be any other animal that can serve as host from which a virus can cross to humans,” DOST Undersecretary for Research and Development Rowena Guevara said of the VIP’s mandate.

“With its genome bank, the VIP aims to create a vaccine to treat the diseases caused by these pathogens.We cannot stop at characterizing pathogens, we need to be able to develop the vaccines for that,” Guevara added.

Guevara said despite the delays before Congress, they are optimistic about its speedy approval with the support of President Duterte, who touted the need for a virus laboratory in his last State of the Nation Address.

The VIP will be composed of the beneficiaries of the DOST’s “Balik Scientist” program, which encourages Filipino scientists working abroad to go back to the country and help in the implementation of the virology institute.

The DOST recently inaugurated its Level 2 biosafety laboratory, but the proposed VIP building in New Clark City in Tarlac, a province north of Metro Manila, will house up to Level 3 or 5. Biological safety levels refer to the series of protections that take place in particular biological laboratories. These are individual safeguards designed to protect laboratory personnel, as well as the surrounding environment and community.

The Department of Public Works and Highways was given P50 million to design the building. Meanwhile, the VIP was promised the following budgetary allocation in the next five years, according to figures uploaded on the government’s freedom of information portal – P762.8 million in 2022, P810 million in 2023, P881 million in 2024, P955 million in 2025, and P1.03 billion in 2026. For 2021, the DOST was given a P284 million budget for research and development on eight zoonotic projects.

Montoya touted the need to have a “One Health” approach in finding solutions to the pandemic.

By this, Montoya meant that the studies on human, animal, and plant pathogens should be interconnected, in order to find a more holistic solution to diseases that could reach pandemic scale.

“We are adopting the One Health approach… The health sector should not just focus on human diseases. You also look at the animals, which really are the sources of the viruses that eventually infect humans, and the environment that facilitates the transmission of the virus from animal to human hosts,” Montoya said.

“Among others, we have to look at all these disciplines to come up with a holistic view. It’s not just inter-, but transdisciplinary. It is of a higher level because it means that we are involving many disciplines, and integrating them into a whole,” he added, noting the importance of relating people with their environment in the study of pathogens.

Educating the public about the importance of research on zoonotic viruses may help in dispelling misconceptions about the pandemic’s origins, such as conspiracy theories that the SARS-CoV-2 was a laboratory experiment that leaked or was a biowarfare weapon, DOST’s Guevara said.

Filipino scientists need to be better communicators too about the science behind the pandemics to put a stop on the “infodemic” of false information, especially those found online, she added.

“The ‘infodemic’ is here to stay, especially with the way people eat up (false information) on social media. What we found as a strategy that works is… we train our scientists to be good communicators. That’s the only way to clear the ‘infodemic,’” Guevara emphasized.

With the VIP’s genome bank underway, Alviola said his team would be willing to offer their field surveillance experience as the VIP’s “foot soldiers” to collect samples from animals for sequencing. He said he has had initial discussion with those from the “Balik Scientist Program” involved with the project.

With their yearslong work to detect viruses in the wild, Filipino ecologists like Alviola have paved the way for the country’s own virus database.

Back in Mount Makiling, Alviola’s team waited for over an hour in darkness for the bats to arrive. Their mist nets only snagged two little bats of the Rhinolophus macrotis species, which are insect-eating big-eared horseshoe bats roosting in the small crevice above them. At past 7 p.m., Alviola decided to call it a night.

It was better than nothing, Alviola’s assistant ecologist Kirk Taray explained, because there were visits when they packed up empty-handed.

The number of bats depends on their mating season, Taray said, noting that the crevice where they caught the bats for swabbing was a mating roost.

Preparing for descent, Alviola and his assistant ecologists kept on their protective attire. They carefully slid down the slippery slope cradling the cloth sacks that contain the mammals.

Upon arriving at the jump-off point, Alviola and Taray settled down and used the plastic storage box that carried their swabbing equipment as a makeshift table.

Perched on a nearby tree, a hive was buzzing with bees, which swooped down and flew around Alviola and Taray as they measured the bat’s wingspan and identified the species.

They were undeterred by the dangers of bee stings, as they swabbed saliva and fecal samples using cotton buds, which they then dipped in reagent test tubes.

Alviola explained that the test tube contained the reagent "RNAlater" to preserve the sample DNA for sequencing in the laboratory.

The bat was bound with a piece of cloth as Alviola swabbed samples. It was actually the sock of his five-year-old son, Pedro, that he used to bind the bat, Alviola said with a smile, noting that the sock was a perfect fit for the small mammal. Alviola named his son after his father, as his way of passing on a tradition in the family.

True to his word, Alviola held the bat carefully between his gloved fingers to give it its freedom. He pinched the bat’s feet, taking extra caution not to be bitten, so that the bat hung from his hand as it would from a tree.

The ecologist then let go. The little mammal flitted out of his hand, free to go back to its roosting cave once more.

This story is supported by the Earth Journalism Network’s Asia-Pacific project, as part of its story production grant on Zoonotic Diseases and One Health in the region. The Philippine STAR reporters Romina Cabrera and Marc Jayson Cayabyab, photographer Michael Varcas and commissioned videographer Kathleen Lei Limayo joined the team of ecologist Dr. Phillip Alviola in the search for bats that are possible carriers of coronaviruses in Mount Makiling in October.

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