Pandemic prevention consortium announces new leadership team

STOP Spillover is strengthening our capacity to reduce the risks of emerging pathogens

Business Announcement

TUFTS UNIVERSITY

 

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HELLEN AMUGUNI, ASSOCIATE PROFESSOR OF INFECTIOUS DISEASE AND GLOBAL HEALTH AT THE CUMMINGS SCHOOL OF VETERINARY MEDICINE AT TUFTS UNIVERSITY, IS NAMED PROJECT DIRECTOR FOR STOP SPILLOVER.

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CREDIT: ALONSO NICHOLS/TUFTS UNIVERSITY

Recognizing the many milestones it has reached in recent months, Strategies to Prevent Spillover, or STOP Spillover, a project funded by the U.S. Agency for International Development (USAID) and led by Tufts University, has announced that the interim leadership team that was put in place in March 2023 will take on a permanent role for the next two years of the project.

Hellen Amuguni, an associate professor in the Department of Infectious Disease and Global Health at Cummings School of Veterinary Medicine, is the new project director. The co-deputy directors are Felicia Nutter, director of the International Veterinary Medicine Program at Cummings School, and Jonathon Gass, an assistant professor of infectious disease epidemiology at the School of Medicine. (Amuguni and Nutter have secondary appointments at Tufts University School of Medicine, and Gass has a secondary appointment at Cummings School.)

“We are entering the fourth year of STOP Spillover on a high note, and our vision for the project remains clear,” says Amuguni. “Our focus is to build capacity and prepare countries to identify high-risk interfaces, control zoonotic diseases at their source before they become epidemics or pandemics, and develop interventions that reduce risks of exposure in human populations. We are privileged to work closely with amazing country teams and government counterparts as well as our consortium partners who bring expertise in wildlife health, infectious diseases, social and behavior change.”

At least 75 percent of emerging and re-emerging infectious diseases of humans—including Ebola, Nipah virus, and zoonotic avian flu—have an animal origin. Chances are that when the next illness like COVID-19 emerges to threaten global health, it will originate in animals before it passes to humans, a process known as spillover. STOP Spillover aims to keep that tipping point from happening, or at least mitigate the dangerous effects.

“STOP Spillover has achieved so much in its third year thanks to these directors, who have been working with stakeholders in key countries in Africa and Asia to find ways to decrease the risks of harmful viral pathogens that jump—or spill over—from animals to humans,” said Caroline Genco, Tufts’ provost and senior vice president, who is also an immunologist. “Through this important work, our expert researchers and community partners demonstrate our shared commitment to One Health as a way of mitigating the significant global risk represented by zoonotic disease spillover.”

Leading a Global Consortium of Regional Partners

Begun in late 2020, STOP Spillover has so far partnered with colleagues in Bangladesh, Cambodia, Côte d’Ivoire, Liberia, Uganda, Viet Nam, and Sierra Leone to strengthen country capacities to reduce the risks of zoonotic diseases, or those that move between animals and humans. Teams of experts collaborate to develop country- and locality-specific research studies and interventions to reduce risks associated with selected viral zoonotic pathogens and to prevent their spread.

USAID administers the U.S. foreign assistance program providing economic and humanitarian assistance in more than 80 countries worldwide. For this project, Tufts leads a global consortium of partners with cross-disciplinary experience and regional knowledge.

From the outset, this consortium of experts in human, animal, and environmental health has been heavily focused on engagement, working with stakeholders at the national, regional, and local levels to reduce risks of exposure to and mitigate the spread of selected zoonotic viral pathogens, including coronaviruses, filoviruses (Ebola and Marburg viruses), avian influenza, and Lassa virus, among others.

Protecting Health and Providing Financial Stability

On the ground at the local level—in places such as wildlife farms in Dong Nai province, Vietnam, and wild animal meat markets in Kenema, Sierra Leone—community-led workshops have provided important data about the interactions humans have with wild and domestic animals in these settings, as well as the barriers they see to behavior changes that reduce spillover risk.

Gass, who recently visited wildlife farms in Viet Nam with its in-country team, said that STOP Spillover is filling major gaps in understanding the spillover ecosystem, which will improve conditions for both animals and humans.

Gass noted that wildlife farmers, government officials, and other stakeholders are very interested in working together to increase biosafety. “Farming practices are critical for the financial livelihoods of farmers and their families,” he said. “When outbreaks occur on farms and the animals either die or need to be culled, this has serious financial repercussions. STOP Spillover’s interventions will not only protect health but also provide increased financial stability via risk reduction.”

The program has formed local expert working groups to identify places where spillover is most likely to occur and to design risk-reduction interventions. In Liberia, for example, STOP Spillover is conducting research to understand Lassa virus distribution in rodent reservoir hosts both within what is considered the “Lassa belt” and beyond. Working with the Ministry of Health, National Public Health Lab, the Ministry of Agriculture, and local communities, teams are collecting and testing samples from the African soft-furred mouse and other rodents for the presence of Lassa virus RNA (an indication of infection) within and outside of the Lassa belt.

The documentation of the true distribution of Lassa virus in reservoir hosts will allow the country to better understand the risks to humans, develop more effective rodent control strategies, and inform future research, policy, and public health measures.

Technology and Space Redesign for Biosafety

At live bird markets in Dhaka, Bangladesh, where the threat of highly pathogenic avian influenza is a concern, efforts are underway to develop a coordinated and sustainable platform for pathogen surveillance and data sharing. A mobile application has been developed, enabling the public to report sick and dead poultry as well as sudden febrile illness among market vendors. Moreover, the STOP Spillover team is working with public health experts and engineers to redesign market spaces so that biosafety is optimized, and consumer and vendor health protected.

In Côte d’Ivoire, Cambodia, and Liberia, teams have been trained to safely collect samples for surveillance of wastewater and liquid waste effluent, with potential testing for multiple zoonotic viruses. The aim is to create a surveillance system that can act as an “early warning system” for potential spillover events.

The program exemplifies the One Health concept: the interconnection of human, animal, and environmental health. “STOP Spillover continues the longstanding work of Tufts University, mainstreaming One Health approaches to address complex, globally important health problems, including zoonotic diseases,” said Felicia Nutter.

“Humans make choices every day that impact our health, the health of other animals, and the ecosystems and environments that we all share. Our current work empowers people to make more informed choices that safeguard our shared health,” said Nutter.

 

New report from Harvard and global experts shows investments in nature needed to stop the next pandemic

Protecting forests and changing agricultural practices are essential, cost-effective actions to prevent pandemics

Reports and Proceedings

HARVARD T.H. CHAN SCHOOL OF PUBLIC HEALTH

Boston, Mass. - As the world struggles to contain COVID-19, a group of leading, scientific experts from the U.S., Latin America, Africa and South Asia released a report today outlining the strong scientific foundations for taking actions to stop the next pandemic by preventing the spillover of pathogens from animals to people. The report provides recommendations for research and actions to forestall new pandemics that have largely been absent from high-level discussions about prevention, including a novel call to integrate conservation actions with strengthening healthcare systems globally. 

The report from the International Scientific Task Force to Prevent Pandemics at the Source makes the case that investments in outbreak control, such as diagnostic tests, drugs and vaccines, are critical but inadequate to address pandemic risk. These findings come as COVID-19 vaccinations availability in many low- and middle-income countries remains inadequate—and even in wealthier nations vaccine coverage is far from reaching levels needed to control the Delta variant. 

“To manage COVID-19, we have already spent more than $6 trillion dollars on what may turn out to be the most expensive band aids ever bought, and no matter how much we spend on vaccines, they can never fully inoculate us from future pandemics,” said Dr. Aaron Bernstein, interim director of the Center for Climate, Health, and the Global Environment at Harvard T.H. Chan School of Public Health and leader of the Scientific Task Force for Preventing Pandemics at the Source. “We must take actions that prevent pandemics from starting by stopping the spillover of diseases from animals to humans. When we do, we can also help stabilize the planet’s climate and revitalize its biosphere, each of which is essential to our health and economic welfare.”

Previous research by Dr. Bernstein and colleagues found that the costs of preventing the next pandemic—by reducing deforestation and regulating the wildlife trade—are as little as $22 billion a year, 2% of the economic and mortality costs of responding to COVID-19.

The task force found that spillover of possible pandemic pathogens occurs from livestock operations; wildlife hunting and trade; land use change—and the destruction of tropical forests in particular; expansion of agricultural lands, especially near human settlements; and rapid, unplanned urbanization. Climate change is also shrinking habitats and pushing animals on land and sea to move to new places, creating opportunities for pathogens to enter new hosts.

Agriculture is associated with greater than 50% of zoonotic infectious diseases that have emerged in humans since 1940. With human population growing, and food insecurity on the rise because of the pandemic, investments in sustainable agriculture and in the prevention of crop and food waste are critical to reduce biodiversity losses, conserve water resources, and prevent further land use change while promoting food security and economic welfare.

A key recommendation from the task force calls for leveraging investments in healthcare system strengthening and One Health to jointly advance conservation, animal and human health, and spillover prevention. A successful example of this integrated model comes from Borneo where a decade of work resulted in ∼70% reduction in deforestation and provided health care access to more than 28,400 patients and substantial decreases in diseases like malaria, tuberculosis and common diseases of childhood.

Additional recommendations for investments and research include:

Investment priorities:

• Conserve tropical forests, especially in relatively intact forests as well as those that have been fragmented.
• Improve biosecurity for livestock and farmed wild animals, especially when animal husbandry occurs near large or rapidly expanding human populations.
• Establish an intergovernmental partnership to address spillover risk from wild animals to livestock and people from aligned organizations such as FAO, WHO, OIE, UNEP, and Wildlife Enforcement Networks.
• In low- and middle-income countries, leverage investments to strengthen healthcare systems and One Health platforms to jointly advance conservation, animal and human health, and spillover prevention.

Research priorities:

• Establish which interventions, including those focused on forest conservation, wildlife hunting and trade, and biosecurity around farms, are most effective at spillover prevention.
• Assess the economic, ecological, long term viability and social welfare impacts of interventions aimed at reducing spillover. Include cost-benefit analysis that considers the full scope of benefits that can come from spillover prevention in economic analyses.
• Refine our understanding of where pandemics are likely to emerge, including assessments of pandemic drivers like governance, travel, and population density. 
• Continue viral discovery in wildlife to ascertain the breadth of potential pathogens and improve genotype-phenotype associations that can enable spillover risk and virulence assessments.

The task force was convened by Harvard Chan C-CHANGE and the Harvard Global Health Institute (HGHI). The findings laid out in their inaugural report will be translated into international policy recommendations to inform the G20 summit in October and the 26th United Nations Climate Change Conference (COP26) in November.

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About Harvard Chan C-CHANGE

The Center for Climate, Health, and the Global Environment at Harvard T. H. Chan School of Public Health (Harvard Chan C-CHANGE) increases public awareness of the health impacts of climate change and uses science to make it personal, actionable, and urgent. Led by Dr. Aaron Bernstein, the Center leverages Harvard’s cutting-edge research to inform policies, technologies, and products that reduce air pollution and other causes of climate change. By making climate change personal, highlighting solutions, and emphasizing the important role we all play in driving change, Harvard Chan C-CHANGE puts health outcomes at the center of climate actions. To learn more visit https://www.hsph.harvard.edu/c-change/. 

About Harvard Global Health Institute

The Harvard Global Health Institute is committed to surfacing and addressing some of the most persistent challenges in human health. We believe that the solutions to these problems will be drawn from within and beyond the medicine and public health spheres to encompass design, law, policy, business, and other fields. At HGHI, we harness the unique breadth of excellence within Harvard and are a dedicated partner to organizations, governments, scholars, and committed citizens around the globe. We convene diverse perspectives, identify gaps, design new learning opportunities, and advise policy makers to advance health equity for all. You can learn more at globalhealth.harvard.edu. 

 

 

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ARTICLE TITLE

Report of the Scientific Task Force on Preventing Pandemics

ARTICLE PUBLICATION DATE

18-Aug-2021

Warming climate may boost Arctic 

"virus spillover" risk, research shows

CBSNews

Wed, October 19, 2022 

A warming climate could bring viruses in the Arctic into contact with new environments and hosts, increasing the risk of "viral spillover," according to research published Wednesday. Viruses need hosts like humans, animals, plants or fungi to replicate and spread, and occasionally they can jump to a new one that lacks immunity, as seen during the COVID-19 pandemic.

Scientists in Canada wanted to investigate how climate change might affect spillover risk by examining samples from the Arctic landscape of Lake Hazen.

It is the largest lake in the world entirely north of the Arctic Circle, and "was truly unlike any other place I've been," researcher Graham Colby, now a medical student at University of Toronto, told AFP.

This handout picture taken on May 29, 2017 and made available by Graham Colby on October 17, 2022 shows researchers drilling holes to collect sediment at the Lake Hazen in Nunavut, to investigate how climate change might increase the risk of

The team sampled soil that becomes a riverbed for melted glacier water in the summer, as well as the lakebed itself -- which required clearing snow and drilling through two meters of ice, even in May when the research was carried out.

They used ropes and a snowmobile to lift the lake sediment through almost 300 meters of water, and samples were then sequenced for DNA and RNA, the genetic blueprints and messengers of life.

"This enabled us to know what viruses are in a given environment, and what potential hosts are also present," said Stephane Aris-Brosou, an associate professor in the University of Ottawa's biology department, who led the work.

But to find out how likely they were to jump hosts, the team needed to examine the equivalent of each virus and host's family tree.

"Basically what we tried to do is measure how similar these trees are," said Audree Lemieux, first author of the research.

Similar genealogies suggest a virus has evolved along with its host, but differences suggest spillover.

And if a virus has jumped hosts once, it is more likely to do so again.

"Should climate change also shift species range of potential viral vectors and reservoirs northwards, the High Arctic could become fertile ground for emerging pandemics," the researchers wrote in Proceedings B, the Royal Society's biological research journal.

Scientists Wake Up Ancient Viruses Unknown to Medicine

Feb 24, 2020

The Infographics Show

Scientists uncover ancient prehistoric viruses hidden for centuries inside Tibetan glaciers that could be potentially life threatening for all humanity. These viruses laid dormant inside the ice but scientists were able to wake them up and they are unlike any virus humanity has ever seen. 

"It's really unpredictable"

The analysis found pronounced differences between viruses and hosts in the lakebed, "which is directly correlated to the risk of spillover," said Aris-Brosou.

The difference was less stark in the riverbeds, which the researchers theorize is because water erodes the topsoil, removing organisms and limiting interactions between viruses and potential new hosts.

Those instead wash into the lake, which has seen "dramatic change" in recent years, the study says, as increased water from melting glaciers deposits more sediment.

"That's going to bring together hosts and viruses that would not normally encounter each other," Lemieux said.

The authors of the research, published in the Proceedings of the Royal Society B: Biological Sciences journal, caution they are neither forecasting an actual spillover nor a pandemic.

"The likelihood of dramatic events remains very low," Lemieux said.

They also warn more work is needed to clarify how big the difference between viruses and hosts needs to be to create serious spillover risk.

"Disentangling this risk from actual spillovers and pandemics will be a critical endeavour to pursue in parallel with surveillance activities, in order to mitigate the impact of spillovers on economy and health-related aspects of human life, or on other species," the researchers wrote.

They argue that warming weather could increase risks further if new potential hosts move into previously inhospitable regions.

"It could be anything from ticks to mosquitoes to certain animals, to bacteria and viruses themselves," said Lemieux.

"It's really unpredictable... and the effect of spillover itself is very unpredictable, it can range from benign to an actual pandemic."

The team wants more research and surveillance work in the region to understand the risks.

"Obviously we've seen in the past two years what the effects of spillover can be," said Lemieux.

SPILLOVER: ANIMAL INFECTIONS AND THE NEXT HUMAN PANDEMIC

(PDF) Spillover: Animal Infections and the Next Human ...

https://www.researchgate.net › publication › 279755005_Spillover_Anima...

These diseases can't be well understood. until the principles of zoonotic spillover are. understood. Secondly, a large part of my book is de-. voted to these big ...

AUTHOR INTERVIEW 

THE AUTHOR OF SPILLOVER IS A SCIENCE JOURNALIST
“Intrepid disease ecologists are hiking into forests, climbing through caves,… and sleuthing the mysteries of reservoir host and spillover.” David Quammen
THE ROYAL SCOTTISH GEOGRAPHICAL SOCIETY JOURNAL
Winter 2013 -14 Zoonoses Reservoirs, reasons and the role of viruses • RSGS’s First ‘Explorer-in Residence’ • Zoonotic Geographies – A Multi-Faceted Issue • Viruses, Evolution & Spillover • Living Patterns, Vaccines & Vermin •

Book
 A journey of zoonotic discovery
 Many of the students I teach will no doubt enjoy David Quammen’s Spillover: Animal Infections and the Next Human Pandemic; they are always excited about patients haemorrhaging blood everywhere, there being no cure, and the arguments about what happens next. Quammen’s fast-paced book tracks various zoonotic pathogens across the globe as he tells the contrasting stories of, among others, Hendra virus infection, the viral haemorrhagic fevers caused by Marburg or Ebola virus, severe acute respiratory syndrome (SARS), and HIV/AIDS. Quammen makes it clear from the outset that if we are to halt this epidemic of zoonotic cases we must stop destroying natural ecosystems at a “cataclysmic rate”. And it’s from this perspective that Quammen relates his account of these viruses, making the point that “It’s not that they target us especially. It’s just that we are so obtrusively, abundantly available.” Readers will be enthralled by his tales of tramping into caves looking for bats and pythons and even the odd cobra, or feeding gorillas in central Africa. Quammen does this well, keeping back from the action and documenting his encounters with the experts. We follow the author as he interviews scientists, survivors, and local people in horse farms, jungles, and high-biosecurity laboratories in such countries as Bangladesh, the Congo, and China. As we travel alongside him, we realise that each chapter is essentially a mixture of news and research fi ndings, with interviews and travelogue thrown in.

Disease spillover risk poorly communicated, oversimplified during COVID-19 pandemic

Peer-Reviewed Publication

AMERICAN INSTITUTE OF BIOLOGICAL SCIENCES

COVID-19 has been the first pandemic that has taken place alongside the interconnectivity of the Internet. Consequently, the spread of ideas and information about the disease has been unprecedented—but not always accurate.. One of the widely circulated headlines was that of the relationship between land change and the spillover of diseases from wildlife to humans. Writing in BioScience, Andre D. Mader of the Institute for Global Environmental Strategies and colleagues survey primary and secondary literature, as well as webpage content on the subject of land change and zoonotic disease risk. Based on the patterns picked up from this literature and media coverage, Mader and colleagues describe what amounts to a case study in improper science communication and its possible consequences.

According to the authors, media messaging consistently described direct causality between zoonotic disease spread and land use change, despite the fact that only 53% of the surveyed peer-reviewed literature made this association. The authors delve into theoretical scenarios that would demonstrate the difficulty of tracing the real risk of zoonotic spillover, emphasizing that the “complexity of pathogen responses to land change cannot be reduced to one-size-fits-all proclamations.”

The authors found that as the literature moves from primary research to review articles and commentaries, and finally to webpages, the “overstating of the evidence” increases, with 78% of secondary papers implying the land use–zoonotic spillover association and all but one of the sampled webpages making this association. The authors also noted that secondary sources and webpages often failed to mention the uncertainty associated with their conclusions.

The potential consequences of simplistic messaging and a lack of proper communication regarding zoonotic spillover can erode credibility, neglect local community’s specific needs when it comes to policy making, and detract attention from other factors that can lead to zoonotic spillover, say Mader and colleagues. The authors recommend more accurate, nuanced, and explanatory dissemination of the studies on zoonotic spillover risk, arguing that such an approach would also benefit science more broadly. As the authors conclude, “if the goal of science communication is to improve understanding, it must strike a balance: sufficient simplicity to be grasped by as broad an audience as possible but sufficient nuance to capture the complexity of an issue and contribute meaningfully to the discussion around it, especially when it goes viral.”

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JOURNAL

BioScience

DOI

10.1093/biosci/biac075 

METHOD OF RESEARCH

Literature review

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

Messaging Should Reflect the Nuanced Relationship between Land Change and Zoonotic Disease Risk

ARTICLE PUBLICATION DATE

16-Sep-2022

NONFICTION

Scientists Knew More About Covid-19 Than We Think. And They Still Do.

In “Breathless,” David Quammen explores the predictable lead-up to the global Covid pandemic, and the frantic, belated attempts to stop it.

New Jersey first responder Robert Sabia being decontaminated after answering a call in March, 2020.

Credit...Chang W. Lee/The New York Times

By Michael Sims
Oct. 1, 2022

BREATHLESS: The Scientific Race to Defeat a Deadly Virus, by David Quammen

“Nobody,” Donald Trump claimed in a March 2020 address, “had any idea.” He was talking about the Covid virus — which had, seemingly overnight, sparked a global pandemic. In his compelling and terrifying new book, “Breathless: The Scientific Race to Defeat a Deadly Virus,” the veteran science journalist David Quammen demonstrates just how much was known — and expected — by infectious disease scientists long before patrons of the Huanan Seafood Wholesale Market fell ill in December 2019 with a pneumonia-like virus.

“Soothsayer” isn’t on Quammen’s extensive résumé, but he was among those who had long predicted this kind of catastrophe. In 2012 he provided a field guide to the future, “Spillover,” whose subtitle — “Animal Infections and the Next Human Pandemic” — explains exactly what the scientific community had long been expecting.

“This is a book about the science of SARS-CoV-2,” he specifies in his new book. “The medical crisis of Covid-19, the heroism of health care workers and other people performing essential services, the unjustly distributed human suffering, and the egregious political malfeasance that made it all worse — those are topics for other books.” Instead, he focuses his informed attention on the unsung heroes who dare to wrestle with viruses, those strange entities he calls “the dark angels of evolution.” Human beings are part of a sprawling family of interconnected species who can share illness because they all grew up together. It is our common ancestry and related bodily ecology that makes spillover possible between, say, bats and Earth’s (currently) dominant mammal.

Covid is, after all, as natural as a wolf cub or David Attenborough, and its thriller-level rate of evolution is part of its danger. “A virus is a parasite, yes,” writes Quammen, “a genetic parasite, to be more precise, using the resources of other organisms to replicate its own genome.” He demonstrates the sheer weirdness of viruses when he explains how difficult it is to even define them.

Quammen follows the story of Covid from scientists’ first awareness of the outbreak in Wuhan through reports of Omicron in late 2021. Alongside the human story, spillover between humans and other animals is a persistent theme. Early in 2020, a dog in Hong Kong tested positive. There were positive cats in Minnesota, two positive hippos in Antwerp, a positive tiger in Knoxville. An outbreak spread through mink farms in the Netherlands. Last year, of the many white-tailed deer sampled in Pennsylvania, 44 percent tested positive. The persistent danger of spillover between species informs arguments over the virtues and the flaws of both approaches to pandemics: “prediction and prevention versus surveillance and response.”

“Breathless” is so good that I was slow to realize that it lacks the vivid you-are-there details of “Spillover.” That’s because he wasn’t there. In “Breathless,” there are no scenes of an intrepid author helping trap macaques at a Sufi shrine or examining a white-footed mouse for Lyme-infested larval ticks. Among its other virtues, “Spillover” was something of a nightmare travel book, but “Breathless” is a different species of tour de force. Quammen’s research methods have mutated. “I avoided airports for more than two years after Covid-19 exploded,” he says up front, “and I got through the year 2020 on one tank of gas.” Yet these barriers didn’t prevent him from writing a luminous, passionate account of the defining crisis of our time — and the unprecedented international response to it. While many people were begging for mercy from the motley of gods that they also credit with designing this Eden for viruses, epidemiologists and vaccine scientists all over the world raced to save the lives of people they would never meet.

Citing Faulkner’s multiple narrators, Quammen says, “The discernment of truth — let’s make that ‘truth,’ because it’s such an imperious and suspect word — comes from listening to many voices.” He read a library’s worth of books and Zoomed with some 95 sources — epidemiologists, geneticists and public health officials who were closely involved in research and decision-making. He smoothly weaves not only their facts, but their way of speaking, into his story. “Spoken words are data, in nonfiction,” he says, “and I share scientists’ respect for the sanctity of data.” He provides a mini-biography of each interviewee. Backstage outtakes humanize the participants, as when Quammen asks Anthony Fauci whether Brad Pitt or Kate McKinnon did a better job of satirizing him. These glimpses undergird his assertion that science is “a rational process leading toward ever-clearer understanding of the material world, but it’s also an activity performed by humans.”

Quammen marries an old-fashioned love of colorful language to his passion for detail — an odd coupling that results not just in a lucid book about an important topic, but also in a book that’s a pleasure to read. “What nature of bug seethed in this dollop of liquid human distress?” he asks of a private genome-sequencing company in Guangzhou. Sometimes his Chandleresque metaphors distract. (When the rate of infection among the deer spikes, it’s “like popcorn in a hot pan.”) Usually, however, his imagery vividly reinforces a point. He explains that a laboratory sample from bat feces “is not a virus, just as the text of ‘Hamlet, Prince of Denmark’ is not a performed play” — that the sample is, instead, “the script of a virus.”

Quammen can’t resist snarking that Trump, “as you may have heard, is not a scientific sophisticate,” but he doesn’t waste much time shooting at such an easy target. He describes Elon Musk as an “entrepreneur and spaceman,” and Alex Azar, the secretary of health and human services, as “pliable.” The “Intelligence Community” is “a bodacious aggregation of intelligences” that includes Space Delta 7 — “within the United States Space Force, whatever that is.” Didier Raoult, the French physician who promoted hydroxychloroquine, Quammen terms a “prideful contrarian.” Hydroxychloroquine did indeed have a history of prescription for malaria, and, he deduces, presumably, “Trump listened to people who listened to people who listened to Didier Raoult.”

While staying on mission, Quammen allows himself room for context. The importance of the February 2020 announcement that scientists had found in pangolins a close match to the virus infecting humans makes more sense — both scientific and narrative — because Quammen begins with a brief survey course on these armored-looking, anteater-like creatures. He smoothly interweaves their evolution, the ecological sin of animal trafficking, the imaginary pharmacological virtues of pangolin scales (which are actually mostly keratin) and the contemporary “vogue in urban China for ye wei, or ‘wild tastes.’”

“This virus is going to be with us forever,” Quammen warns, with a wealth of data and precedent to support him. We haven’t eradicated polio or measles. “And those viruses have nowhere to hide except within humans.” This one could be cleared from every living human, and still exist in other animals. “Covid-19 won’t be our last pandemic of the 21st century. It probably won’t be our worst.” In our international world, as one scientist tells Quammen, “A disease anywhere is a disease everywhere.”

Michael Sims’s books include “Adam’s Navel” and a companion volume to the National Geographic Channel series “In the Womb: Animals.”

BREATHLESS: The Scientific Race to Defeat a Deadly Virus | By David Quammen | 406 pp. | Simon & Schuster | $28.99

Read More on the Coronavirus PandemicA Persistent Variant: Ten months have passed since Omicron’s debut. Since then it has displayed a remarkable capacity to evolve new tricks.

A Blunted Response: Major data gaps, the result of decades of underinvestment in public health, have undercut the U.S. government’s response to Covid — and now to monkeypox.

Biden’s Comments: In an interview that aired on CBS’s “60 Minutes,” President Biden said that “the pandemic is over.” But 400 to 500 Americans are still dying every day of Covid-19.

Menstrual Cycle: A new study adds to a growing body of research suggesting that the Covid vaccine can indeed affect the length of a person’s menstrual cycle.

THE BAT LANDS | PART 2

HOW A DEADLY BAT VIRUS FOUND NEW WAYS TO INFECT PEOPLE

First it jumped from bats to pigs. Then pigs gave it to people. Now the brain-damaging Nipah virus has found a way to leap from bats to humans without an intermediary host.

By Deborah J. Nelson, Ryan McNeill, Sreekanth Sivadasan, Allison Martell, Ruma Paul, Andrew R.C. Marshall, and Adolfo Arranz

Filed May 16, 2023
CHANGAROTH, INDIA

On May 3, 2018, Muhammad Sabith awoke with a fever while staying with his parents in this village near the southwest coast of India.

The 26-year-old electrician assistant went to a community hospital and was placed in a ward with other patients for observation. Over the next 24 hours, his symptoms quickly worsened: vomiting, delirium, tremors and violent coughing. The staff directed him to a medical center where he was tested for mosquito-borne illnesses like dengue and malaria.

All came back negative. Doctors treated him with antibiotic and antiviral medications, to no avail. His lungs filled with fluid, his oxygen levels plunged and, on May 5, Sabith “was no more,” his grieving younger brother, Muthalib, told Reuters.

Medical staff recorded his cause of death as viral encephalitis, but they really didn’t know what killed him. It would be nearly two weeks before doctors realized that Sabith had contracted a virus from bats, an event known as zoonotic spillover, when a pathogen jumps from one species to another.

By then, another 22 people – including his father, an older brother, an aunt, healthcare workers and patients who had shared his room – had been infected, according to scientific studies published after the outbreak. Of those who fell sick, only two people survived.

HOW THE NIPAH VIRUS SPREAD

Muhammad Sabith, a 26-year-old electrician’s assistant suffering from fever, went to a community hospital in 2018 in Perambra, India. Sabith, whom epidemiologists call “the index case,” died two days later. It took doctors almost two weeks to figure out he had succumbed to the Nipah virus. By then, 22 others had been infected. All but two died. This is how the virus spread.

Source: The Journal of Infectious Disease

Sabith’s story is a study in the rapid evolution of disease and risk, a problem exacerbated by runaway development in ecologically sensitive areas. As more and more people across the globe live close to bats and other animals that host deadly viruses, those pathogens are finding easier pathways to infect people, often with lethal consequences.

Nipah virus, the disease that killed Sabith, has proven particularly adept at finding new routes to infection. It is carried by some Asian fruit bats, and was responsible for previous outbreaks in Malaysia and Bangladesh. Nipah is considered one of the most dangerous pathogens circulating in the wild. There is no vaccine to prevent infection and no treatment to cure it.

After Sabith died and his relatives fell ill, a doctor who had recently read about Nipah suggested testing for it on a hunch. One test after another came back positive, as did samples from a colony of bats roosting near Sabith’s home, according to scientists who studied the outbreak.

Once authorities here were aware of the Nipah diagnosis, they quickly isolated everyone they could find who had been near him or other known contacts. While those precautions stopped that particular outbreak, the case also underscored the fast and aggressive path the pathogen can take.

A Reuters analysis of conditions that make such outbreaks possible shows that by the time Sabith fell ill, this corner of India had become one of the likeliest places on Earth for a spillover to people from bats, a leading wildlife source of new diseases in humans. Reuters has dubbed these areas “jump zones.”

Deforestation and development bring humans ever closer into contact with once-remote breeding grounds for bats and the viruses they carry. In Kerala, a tropical state surrounding Sabith’s hometown, extensive tree loss and rapid urbanization in recent decades created ideal conditions for a virus like Nipah to emerge.

The 2018 outbreak was Nipah’s first known appearance in this part of India. But there have been at least two Nipah spillovers in Kerala since then – to a 21-year-old college student who survived in 2019 and a 13-year-old boy who died in 2021.

Pragya Yadav, the lead scientist on Nipah research at India’s National Institute of Virology, said the expansion of human settlement in Kerala and worldwide has led to habitat loss, declining biodiversity and migration of animals closer to people, “which eventually helps the virus to jump from bats to humans.”

COMMON CARRIER: Outbreaks of the Nipah virus have been traced back to flying foxes, a fruit bat found across tropical Asia. Above, the animals hang from a tree in the Indian state of Kerala. 

REUTERS/Sivaram V


The Reuters jump-zone analysis highlights a global trend that world leaders need to address “for the future of humanity,” Yadav said. “Nobody is safe…It will take no time for a disease outbreak to reach anywhere in the world because of international travel and trade.”

The analysis is based on an examination of 95 spillovers in the past two decades of viruses found in bats, including Ebola, SARS, Marburg and Nipah. The news agency identified more than 9 million sq km in 113 countries where human alteration of sensitive landscapes has created conditions that closely match those around past spillovers.

Kerala, on the eastern shore of the Arabian Sea, has some of the leading jump zones identified by Reuters. It is home to more than 40 species of bats and 35 million people. Its mountain forests and wooded hillocks, prime bat habitat, have been progressively cleared to make way for homes, agriculture, businesses, and industry, with major rail and highway projects still on the agenda.

Quick growth, the Reuters analysis shows, made conditions ripe for spillover across 83% of Kerala at the time of the Nipah outbreak, up from 58% in 2002.

India’s national government didn’t respond to phone queries or emails by Reuters to the country’s Ministry of Health and Family Welfare, the National Centre for Disease Control, the Ministry of External Affairs and other agencies.

Kerala Chief Minister Pinarayi Vijayan, elected in 2016, has sought to speed up growth with major infrastructure projects, industrial development and increased tourism. His press secretary emailed Reuters a statement that said: “All steps will be taken to mitigate the risk of spillover of Nipah virus and other emerging infections from their reservoir hosts to humans while planning development activities in the State.”

The statement cited ongoing efforts by the state to map ecologically vulnerable areas and a planned initiative by two Indian universities, funded by the U.S. government, to improve surveillance of animals and people for Nipah and other zoonotic viruses.

The Reuters analysis found the risk of spillover in the 25 sq km area around Sabith’s family home rose precipitously in the two years before his illness, placing the area in the top 1.5% of locales worldwide most conducive to a bat-borne virus infecting humans.

TREE LOSS IN BAT TERRITORY

A 2002 satellite image of Muhammad Sabith’s neighborhood shows dense foliage surrounding a sprinkling of rooftops. By 2018, when Sabith died of Nipah, new buildings and laterite quarries had consumed chunks of forest. Scientists found bats with Nipah virus roosting near Sabith’s home.

Bat roost

Sabith’s

family home

400 ft

100 m

2002

Laterite quarries

Bat roost

Sabith’s

family home

2018

2018 bulidings

2002 buildings

Bat roost

Sabith’s

family home

400 ft

100 m

CHANGE

Source: satellite images by Maxar Technologies

While scientists are certain the virus that infected Sabith came from bats, it’s not clear exactly how he came into contact with the pathogen. Nipah can infect people when their eyes, nose or mouth come into contact with fluids containing the virus – saliva, urine, blood and nasal or respiratory droplets.

In the weeks after doctors learned Sabith had died from Nipah, researchers explored the area. They found bat bite marks on guava, mangoes and berries collected from the area around the family’s home and places he had been working when he fell ill.

Muthalib, now 23, told Reuters that he and Sabith would often pick up fruits beneath area trees and eat them. “We didn’t eat mangoes if they had bite marks, but guavas we’d eat after removing that part.” Their mother, Mariyam umma, said that eating fruit off the ground had been common practice in the village and that Sabith had done so in the weeks leading up to his illness.

MULTIPLE VICTIMS: Muhammad Sabith’s brother, Muthalib, says his family used to eat fruit outside their home that had already been foraged by bats. In addition to Muhammad, Nipah killed his father, another brother and an aunt. 

REUTERS/Sivaram V

“We used to eat every fruit we got,” she said. “I didn’t have any fears.”

Scientists tested the fruit from around the home and Sabith’s worksites. But they found no evidence of Nipah. Rain may have washed away residue of the virus, they speculated, or Sabith may have been infected elsewhere.

A search of the neighborhood led to a colony, near their house, of flying foxes, a common fruit bat. A so-called megabat, the flying fox has a five-foot wingspan and a canine face. It is found throughout the Asian tropics.

THE FLYING FOX

Testing by Yadav’s lab at the National Institute of Virology found Nipah in 13 of 52 flying foxes the scientists captured near Sabith’s house. Human and bat strains of the viruses were 97.7% to 100% identical, her study reported, “indicating bats were the source of the outbreak.”

“If you are sitting under a tree, and a huge number of bats are there, and they’re dropping urine, and fecal material, it could be direct exposure,” Yadav told Reuters.

Compared with prior known spillovers elsewhere in Asia, the outbreak was particularly deadly, killing 90% of those infected. A 1998 outbreak in Malaysia killed nearly 40% of its victims. Outbreaks in Bangladesh starting in 2001 have had an overall mortality rate of about 70%.

The Nipah outbreak cost Mariyam umma two sons, her husband and a sister-in-law. Her losses are still too much to fathom, she said: “It’s painful for me to even remember their names.”

Scientists who have studied the virus told Reuters they don’t know why more recent outbreaks have been more lethal. The Kerala strain is different from those that appeared in Bangladesh and Malaysia, Yadav said, but it’s not clear yet how that affects the virus’s infectiousness, deadliness or clinical course.

Its high death rate, its infectiousness and the lack of a cure have put Nipah on the World Health Organization’s short list of high-priority pathogens with epidemic potential.

Scientists who study Nipah fear the virus will mutate, and a more highly transmissible strain will emerge from bats.

“I'd say, even more likely, is that it's out there already," said Raina Plowright, a scientist based at Cornell University, who has co-authored more than 100 studies on bat viruses and spillover. “The more that we pressure these environments, the more likely these events are going to happen.”

As development in risky areas continues apace, Nipah has found new places to spill over. To learn more, Reuters visited six spillover sites, reviewed hundreds of research papers, and interviewed dozens of doctors, scientists, and grieving relatives of Nipah victims. Around each outbreak, runaway development of the local economy had paved a pathway for a spillover. In each case, the virus found it.

COUGHING PIGS

Scientists suspect Nipah has lived among flying foxes for millennia.

But the spillovers of recent decades have illustrated a versatility the virus wields as a pathogen: its ability to infect cells that possess so-called ephrin-B receptors. These receptors regulate what gets in or out of cells that line vital organs and the central nervous system. Because all mammals have similar receptors, Nipah is able to infect many of them, including humans.




NETTING NIPAH: Researchers in Bangladesh use nets to catch bats and collect samples to find the Nipah virus in the wild. REUTERS/Mohammad Ponir Hossain

Whether Sabith ate contaminated fruit or somehow came into direct contact with a bat, the virus entered his cells. From there, it would have replicated and moved through the organs of his body, eventually infecting his brain and respiratory tract, according to descriptions by Nipah experts of how the disease progresses. Once he began coughing, it easily spread from Sabith to others through droplets.

In earlier outbreaks, the mechanism was less direct.

In 1998, pig production in Malaysia was at an all-time high. Driven by growing demand for pork, the pig population that year swelled to 3 million head, according to one study, a 50% increase in less than a decade. For extra income, many pig farmers also planted fruit orchards.

In the Kinta Valley, about 200 km north of Kuala Lumpur, the concentration of pigs and mango trees was particularly high. Flying foxes once roosted in tall forest, living off wild fruit and the nectar of flowering trees. But later, as their habitat diminished, the dog-faced megabats sought out farmed fruit instead.

One colony established itself near a farm with 30,000 pigs and groves of mango. Farm workers there later told scientists that flying foxes at night would raid the fruit trees, some of whose branches overhung pigpens.

“They’re very messy eaters,” said Juliet Pulliam, an epidemiologist at Stellenbosch University in South Africa, who authored a reconstruction of the outbreak. “They tend to slobber everywhere and drop things as they’re eating. They also tend to urinate and defecate and lighten the load before they take off.”

At some point, the virus infected the pigs. The animals began coughing.

Initially unalarmed, the farm sold piglets to other farms and sent mature pigs for slaughter. Soon, some of the farm workers and the drivers who transported the animals sickened. Slaughterhouse workers also fell ill. Unlike the pigs, the workers’ main symptom was fever, not cough.

Because many victims died of brain inflammation, public health officials initially suspected Japanese encephalitis, a mosquito-borne disease with similar symptoms. They fogged the region with insecticides, but the virus continued to spread.

In March 1999, scientists analyzed the spinal fluid of a victim from the town of Kampung Sungai Nipah. Kaw Bing Chua, a Malaysian virologist, identified the pathogen, later named Nipah after the village. The Malaysian government soon after ordered the slaughter of a million pigs, ending the outbreak that infected nearly 300 people and killed more than 100.





NEW STRAINS: Scientists don’t know why recent outbreaks of Nipah have been more lethal than initial infections by the virus. Researchers, like those testing bats in Bangladesh above, seek strains of the virus for answers. REUTERS/Mohammad Ponir Hossain

A year later, Chua’s team found the same strain of Nipah virus in flying foxes. The cause of the epidemic became clear, Chua said: deforestation followed by the integration of pig-farming and fruit orchards. Malaysia’s government placed restrictions on orchards near pig farms. The country hasn’t documented an outbreak since.

In 2001, Nipah found another path, 4,000 km away, once again abetted by close proximity between bats and people. Starting in northeast India, then in Bangladesh, patients appeared in hospitals with fevers. This time, many had coughs.

The outbreak in India and two more in Bangladesh killed 62 of 91 people infected before the U.S. Centers for Disease Control detected a new strain of Nipah, studies and public health data show. Scientists found antibodies to the virus in animals nearby – flying foxes.

Unlike in Malaysia, where most victims had direct contact with infected pigs, this strain was passing from person to person. It caused coughs and also spread via droplets.

“Pathogens that could concern us have two tricks,” said Emily Gurley, an epidemiologist at Johns Hopkins University, in Baltimore, who studied the outbreaks in Bangladesh. “One is the ability to cross species and infect people. The other is to be efficient at spreading between people.”

Doctors were still unsure how the virus had spilled over, though.

In 2005, an outbreak in Tangail, a central district of Bangladesh, killed 11 of 12 victims. Gurley and colleagues hurried to the region and sifted for clues in the victims’ daily routines. They were struck by one common element: Seven of those sickened had consumed raw date palm sap, a sweet, local delicacy tapped from area trees.

A MYSTERY SOLVED
Scientists discovered sap from date palm trees serves as a vehicle for the Nipah virus, enabling it to leap from bats to humans.
Date palm tree
Licking
Bats lick syrup that flows to collection pots from cuts in the trunk.
Contamination
Bats’ saliva mixes with the sap, and their urine and feces dribble into the pots. People get Nipah from drinking the contaminated sap.

A man whose young son was one of the victims said he often heard bats in the trees above taps he set around his home and sometimes found feces in the sap he collected, Gurley and colleagues wrote in their research. In addition to home tree taps, date palm juice is collected on plantations. With infrared cameras, the scientists filmed flying foxes at area plantations licking syrup with their long, pink tongues – and their saliva and urine dripping into the buckets beneath.

Through the sap, studies showed, the virus was infecting people directly, without passing through another animal. “Case fatality if you’re infected through date palm sap,” Gurley told Reuters: “90% or higher.”

Despite warnings by public health officials to avoid drinking raw date palm sap, more than 160 have died since then.

In the city of Ishwardi, doctors this year patrolled with megaphones and broadcast warnings from loudspeakers at mosques after Soad Hossain, a 7-year-old boy, died of Nipah on Jan. 23. He had drunk sap from a tree in his yard. His parents told Reuters they had never heard of Nipah. “Nothing could make up for or console this loss,” said his father, Mohammad Sanwar Hossain, a 33-year-old day laborer.

F.A. Asma Khan, a physician and regional official for Bangladesh’s Ministry of Health and Family Welfare, told Reuters that some Bangladeshis, especially some who are illiterate, remain hard to reach despite the government’s public awareness campaigns.

“BIOLOGICAL DISASTER”

A study Gurley co-authored found evidence suggesting that bats had adapted to the fragmented forests and dense population of western Bangladesh. They split into smaller colonies scattered throughout villages, where they fed on human food sources.

Few places had more potential for spillover than Kerala. In the past half century, the Indian state changed dramatically.
HIGH RISK: Rapid development has altered ecosystems and increased the risk of viral spillover in portions of the Indian subcontinent, including the fast-growing state of Kerala and parts of Bangladesh. REUTERS

Lush forest in the early 1970s carpeted nearly 25,000 of Kerala’s 38,000 sq km, according to a report by the Indian Institute of Science’s Centre for Ecological Sciences. From 1973 to 2016, more than a third of that woodland disappeared, with rapid urbanization and expansion of plantations. Kerala is one of India’s leading producers of rubber, coffee, coconut and spices.

“In the name of development, we degraded the landscapes which are ecologically fragile,” report co-author T.V. Ramachandra told Reuters. “We made the region more vulnerable.”

Urban areas, meanwhile, ballooned from 95 sq km to more than 4,000. Three of the world’s 50 fastest-growing metropolitan areas are in Kerala, according to UN urban population estimates for large cities.

A study by an international team of scientists, based on 2000-2018 data, listed Kerala among the top seven “global hotspots” for the potential emergence of a new, SARS-related coronavirus. The authors cited deforestation, high livestock density and human encroachment on bat habitat as “major factors contributing to the spillover of zoonotic infectious diseases.”

But Nipah emerged first.

Flying foxes abound in coastal areas of Kerala and in the midlands, wooded hills running north and south between the sea and mountains to the east. The open terrain accommodates the bats’ large wingspan. A 2022 study that mapped the distribution of bat species in Kerala found 90% of flying fox territory there is unprotected, vulnerable to development.

DIMINISHING HABITAT: The ecosystem around flying foxes in Kerala is changing quickly, as development and economic growth transform the southern Indian state. 

REUTERS/Sivaram V


The coast and midlands are where most of Kerala’s growth has occurred. It’s also where three recent spillovers happened: the 2018 outbreak that began with Sabith and two individual cases since.

Malik Fasil Madala, a wildlife ecologist who studies flying foxes at Kerala Agricultural University, has observed destruction of the animals’ habitat for mining and construction. He cited studies that found evidence that stress from such disturbances weakens bats’ ability to fend off viruses. “And virus spillover tends to happen more,” Madala said.

After the 2018 spillover, public health officials began a campaign to dissuade residents from eating fruit with bite marks or doing anything that could disturb flying fox colonies. But residents say the bats have become increasingly difficult to avoid.

Gokul Krishna, a telecommunications student, couldn’t leave the house in the evening without encountering flying foxes. The bats flocked to a mango tree just outside the door of the home where he and other family members lived.

The Reuters analysis found that nearly 90% of the roughly 200 sq km around the home – outside the city of Kochi, Kerala’s largest – was at high risk for spillover.

RAPID EXPANSION OF RISK

In India, more people than any other country live in areas with high spillover risk. Population in those parts of India grew dramatically from 2002 to 2020, to nearly half a billion people.

Source: Reuters analysis

TREE LOSS IN BAT TERRITORY

A 2002 satellite image of Muhammad Sabith’s neighborhood shows dense foliage surrounding a sprinkling of rooftops. By 2018, when Sabith died of Nipah, new buildings and laterite quarries had consumed chunks of forest. Scientists found bats with Nipah virus roosting near Sabith’s home.

Bat roost

Sabith’s

family home

400 ft

100 m

2002

Laterite quarries

Bat roost

Sabith’s

family home

2018

2018 bulidings

2002 buildings

Bat roost

Sabith’s

family home

400 ft

100 m

CHANGE

Source: satellite images by Maxar Technologies

The bats’ presence had increased noticeably in recent years, Gokul told Reuters.

“If we walked below the tree, they would shower mango leaves upon us, and I used to cover my head with my hands to prevent mangoes from falling on me,” he said. “I saw their toothprints on the mangoes that fell down. Sometimes I would take those mangoes and throw them away to clear the pathway and leave my hands unwashed.”

On May 23, 2019, Gokul developed a fever. Doctors at local clinics prescribed antibiotics, but his condition worsened, he said.

Over the next week, he began hallucinating and shaking so violently that his entire bed trembled. He told Reuters he remembers nothing between May 27, four days after his first symptoms, and June 9, the day he awoke in intensive care. It was his birthday.

Weeks later, before he was discharged from the hospital, a local health official told Gokul he had tested positive for Nipah.

Alarmed, public health officials by then had fanned out, traced his contacts, and isolated anyone who could have been infected. They had a lucky break: He didn’t develop a cough, limiting the virus’s ability to spread to others. No one else caught it. A study led by Gurley of 248 Nipah victims in Bangladesh found one in 10 infected others, she said.

GETTING CROWDED: Kerala residents, including some affected by Nipah outbreaks, say flying foxes, their roosts altered by encroaching development, increasingly settle near homes and villages. REUTERS/Sivaram V

A search for Nipah in flying foxes near the family’s home did little to allay fears about future spillover. Thirty percent of the bats scientists captured around Gokul’s house and in nearby plantations tested positive. About 60 km to the east, around the college Gokul attended, scientists found more than 10,000 flying foxes in a single half-acre fragment of forest. Nearly 20% of the bats tested there were positive.

Gokul survived, but suffered memory loss and depression, long-lasting neurological problems shared by other Nipah survivors. He couldn’t finish school or find work. Now 25 years old, he has slowly nursed himself back to health through meditation and diet, he said.

Recently, his home and those of neighbors were demolished to make way for the widening of a national highway. The highway project, overseen by the national government, runs nearly the entire length of Kerala and passes within 20 km of the other two Nipah outbreak sites to the north. A planned high-speed rail project parallel to the highway will bring additional tree loss and development.

The environmental assessment for the railway includes one paragraph, in a section entitled “biological disaster,” acknowledging the risk of spillover and spread of a zoonotic virus. Vinod T.R., one of the authors of the report, said the assessment was expedited and the analysts didn’t have the time or resources to do a more in-depth examination. “The State is already a hotspot of Zoonotic diseases and any further development may increase the spread,” he wrote in an email to Reuters.

India’s Ministry of Road Transport and Highways didn’t respond to emails or phone calls from Reuters. The Ministry of Railways declined to comment, referring Reuters to the project website.

The statement from Chief Minister Vijayan’s office described outbreak readiness as a high priority. His administration set up Nipah monitoring stations at medical centers after the 2018 spillover and launched a campaign to improve hospital preparedness after the outbreak a year later.

Nevertheless, a third spillover took medical authorities by surprise in August 2021. It occurred just 40 km from the site of the first outbreak. Over five days, 13-year-old Hashim Vayoli, feverish and vomiting, was taken by his parents to a clinic, two small hospitals and the Government Medical College Hospital, where Sabith had died three years earlier.

Doctors were stumped.

GRIEVING PARENTS: Aboobacker Vayoli holds a photo of his late son, Hashim Vayoli, as Wafeeda, the boy’s mother, weeps. The 13-year-old died from a Nipah infection in September 2021. REUTERS/Sivaram V

Chandni Radhakrishnan, the doctor in charge of the college hospital’s emergency medicine department, said timing had played a factor. The previous Nipah outbreaks had occurred during the spring fruit season. Doctors, focused on the COVID-19 pandemic, weren’t expecting Nipah in late summer.

Hashim began convulsing. As he grew weaker and struggled to breathe, the hospital transferred him to a facility with a child-sized ventilator. Medical staff ordered an MRI. On September 4, the doctors told his parents Hashim had Nipah.

He died the next day.

By then, at least 64 people had come into close contact with Hashim, public health investigators found. Many were masked because of the pandemic.

Family members had tended to him at the Government Medical College Hospital, wiping foam from his mouth with their clothing.

“He would put his tongue out and bite it. So we helped him put his tongue inside with our hands,” said his mother, Wafeedah. “There was not even a wash basin there to wash our hands.”

But, once again, health authorities dodged a bullet: Hashim, like Gokul, didn’t develop a cough or spread the virus to anyone else.

Within weeks of his death, scientists found Nipah in flying fox colonies near Hashim’s home in the village of Pazhoor. Twenty percent of the bats they tested in a roost a kilometer away, and more than half of those tested in a roost 18 km away, were positive.

Investigators, though, couldn’t determine how Hashim became infected.

POSITIVE TESTS: After recent outbreaks of Nipah in Kerala, scientists have taken lab samples from flying foxes in the vicinity of victims’ homes. Many of the results show the animals carried the virus. REUTERS/Sivaram V

Reuters visited his home last year. It sits in a wooded area between a recently expanded mosque and a river. A betel nut orchard and mango, jackfruit and date-palm trees grow nearby. Those foods and the water attract flying foxes.

His father, Aboobacker, said bats multiplied in their neighborhood several years ago, after a stand of trees across the river was cleared for a banana plantation. Wafeeda struggles to accept that her son died from a virus carried by bats. Some people in Kerala want to eradicate the flying foxes, but she doesn’t think they should be harmed.

“We can’t kill living beings, right?” she said.

The Bat Lands

By Deborah J. Nelson, Ryan McNeill, Sreekanth Sivadasan, Allison Martell, Ruma Paul, Andrew R.C. Marshall and Adolfo Arranz

Contributor: Rupam Nair

Data: Ryan McNeill and Allison Martell

Additional graphics: Daisy Chung and Sam Hart

Illustration and animation: Adolfo Arranz and Matthew Weber

Photo editing: Simon Newman

Video: Sreekanth Sivadasan, Rafiqur Rahman, Sivaram V, Rosanna Philpott, Lucy Ha and Matthew Stock

Edited by Feilding Cage, Paulo Prada, Janet Roberts and Blake Morrison

METHODOLOGY
Guided by scientists and statisticians, Reuters created an original method for assessing where deadly viruses are most likely to spill over from bats to humans. Click here for a detailed explanation of how we did it.

MULTI MEDIA

Bat habitat destruction could spark next pandemic (reuters.com)

The Bat Lands

PART 1: WEST AFRICA
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The world's bat lands are under attack, seeding risk of a new pandemic. Here's where.
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PART 3: LAOS
CHINA, BIRTHPLACE OF THE COVID PANDEMIC, IS LAYING TRACKS FOR ANOTHER GLOBAL HEALTH CRISIS

China, birthplace of the COVID pandemic, is laying tracks for another global health crisis

PART 4: BRAZIL
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Deep in the Amazon, scientists race against time to identify unknown pathogens


PART 5: SOLUTIONS
BATS CARRY KILLER VIRUSES. SCIENTISTS SUGGEST WAYS TO COPE

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