Showing posts sorted by relevance for query SPILLOVER. Sort by date Show all posts
Showing posts sorted by relevance for query SPILLOVER. Sort by date Show all posts

Saturday, September 17, 2022

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.”

Saturday, July 20, 2024

 

Global study by Hawaiʻi Institute of Marine Biology demonstrates benefit of marine protected areas to recreational fisheries




UNIVERSITY OF HAWAII AT MANOA
Global Marine Protected Areas 

IMAGE: 

A GLOBAL MAP OF MARINE PROTECTED AREAS

 

view more 

CREDIT: MARINE CONSERVATION INSTITUTE & MARINE PROTECTION ATLAS




Marine Protected Areas (MPAs) are having a positive spillover effect, producing more “trophy-size” fish just outside of the fully protected areas, and the effect is growing stronger over time. That’s according to research led by University of Hawaiʻi at Mānoa scientists at the Hawaiʻi Institute of Marine Biology (HIMB) published today in Science Advances. The research provides the first global assessment of the benefits of MPAs. “Trophy-size” refers to fish that are exceptionally long or heavy and are considered a rare, prized catch.

“This standardized global assessment illustrates the benefits that MPAs provide for recreational anglers, confirming the effectiveness of MPAs in enhancing fish biomass and local fisheries,” shares Simone Franceschini, Principal Investigator of the study and a Postdoctoral Researcher at HIMB. “Our study found that MPAs may take more than 20 years to show tangible spillover effects in the adjacent areas, which helps to set realistic expectations about the timeframe over which a marine reserve can be expected to have this type of effect on surrounding fisheries.”

The Hawaiian archipelago has 13 state and federal MPAs (complete list below). The state protected areas, called Marine Life Conservation Districts, are managed by the State of Hawaiʻi Division of Aquatic Resources. 

Marine protected areas have been identified as one of the most effective tools for securing marine biodiversity, but until now the global impact of MPAs on local, recreational fisheries has been unclear. This study provides globally-relevant guidance for what management agencies, conservation practitioners, and, importantly, recreational fishers can expect over the long term from the establishment of MPAs.

The research builds on the work of Callum Roberts et al., a team of scientists who twenty years ago conducted a study in Florida and discovered that the cumulative number of trophy fish caught near an MPA (within 100km of its boundary) rises rapidly between 12-30 years after MPA establishment. 

“In this paper, we test whether the results of one of the most well-known studies of MPA impacts on recreational fishers can be replicated at a global scale,” explains Elizabeth Madin, co-author of the paper and Associate Professor at HIMB. “We show that, on average, highly-protected marine ecosystems produce tangible, real-world, long-term benefits for recreational fishers, resulting in a win-win situation for nature and people alike. Nonetheless, it’s important to realize that not every MPA will have the same spillover effects, and that successful MPAs have been shown to depend on community support, enforcement, and effective fisheries management.” 

The findings of this study hold important implications for the future of MPAs and the global “30x30” marine conservation initiative, which aims to protect 30% of the world’s oceans by 2030. 

“These results provide evidence-based guidance that can help ensure the successful implementation and long-term support of MPAs worldwide,” says co-author John Lynham, who is a Professor of Economics at University of Hawaiʻi at Mānoa. “It's intriguing to note that various MPAs around the world, despite their differing sizes and characteristics, have demonstrated a similar positive spillover effect and a similar ‘wait time:’ roughly 20 years.”

The study also underscores the importance of setting practical expectations about the benefits of marine reserves for local fisheries. While MPAs can lead to substantial increases in the abundance of large fish, these benefits often require decades to materialize. This requires patience and long-term commitment from policymakers and local communities to maintain support for conservation efforts. Nonetheless, as Callum Roberts, lead author of the original 2001 study upon which the current study was built, points out, “Local fishers will see benefits to their catches from spillover of smaller fish long before that spillover becomes detectable in the form of large trophy fish, which take longer to reach record breaking sizes. So, well protected MPAs can help support local livelihoods within a decade of creation.”

Saltwater recreational fishing holds cultural significance and is a key  economic driver throughout the world. In the United States in 2017, 8.6 million saltwater anglers took 202 million fishing trips generating $73.8 billion in sales impacts, $41.5 billion in value-added impacts, $24.7 billion in income impacts, and supporting 487,000 jobs (NOAA). 

CREDIT

Tri Nguyen

This graph illustrates the cumulative records of trophy-size fish catches over time in five different Marine Protected Areas (MPAs). The open (white) circles represent records within 0-100km from the MPA boundary, while the dark (black) circles represent records between 100-200km from the MPA boundary. The vertical dark-blue dashed lines indicate when fishing protection was implemented within the MPAs. After the MPAs were established, there is a noticeable increase in the number of record-sized fish caught near the MPAs. This is consistent with the MPA providing a spillover of record-sized fish into adjacent, fished areas.

CREDIT

Franceschini et al. and Nancy Hulbirt, SOEST Illustrations, University of Hawaiʻi at Mānoa



Marine Protected Areas in Hawaiʻi

Federally protected marine areas

  • Hawaiian Islands Humpback Whale National Marine Sanctuary
  • Papahānaumokuākea Marine National Monument

State protected marine areas

  • Hanauma Bay Marine Life Conservation District, Oʻahu
  • Pūpūkeaahu Marine Life Conservation District, Oʻahu
  • Waikīkī Marine Life Conservation District, Oʻahu
  • Kealakekua Bay Marine Life Conservation District, Hawai'i
  • Lapakahi Marine Life Conservation District, Hawai'i
  • Old Kona Airport Marine Life Conservation District, Hawai'i
  • Waialea Bay Marine Life Conservation District, Hawai'i
  • Wai'ōpae Tidepools Marine Life Conservation District, Hawaii
  • Honolua–Mokulē'ia Marine Life Conservation District, Maui
  • Mānele–Hulopo'e Marine Life Conservation District, Maui
  • Molokini Shoal Marine Life Conservation District, Maui

 

Thursday, September 19, 2024

FROM THE MARKET NOT THE LAB

Scientists again link covid pandemic origin to Wuhan market animals

Genetic evidence from a new report suggests the coronavirus pandemic most likely spilled over from animals in the Wuhan market.


By Joel Achenbach
September 19, 2024

An international team of scientists published a peer-reviewed paper Thursday saying genetic evidence indicates the coronavirus pandemic most likely originated with a natural spillover from an animal or animals sold in a market in Wuhan, China, where many of the first human cases of covid-19 were identified.

The paper, which appears in the journal Cell, does not claim to prove conclusively that the pandemic began in the Huanan Seafood Wholesale Market, and it is unlikely to end the acrimonious and politicized debate over the coronavirus’s origin.

For more than four years, researchers, intelligence agencies, journalists and amateur sleuths have tussled over the two main scenarios for the pandemic’s origin: a natural spillover from animals or some kind of leak from a laboratory experimenting on coronaviruses.

The new report bolsters the natural spillover theory, but it does not rule out other origins. A key limitation of the research is that the genetic data, obtained by Chinese investigators in the early days of the pandemic after the market was closed, cannot reveal whether any animal was actually infected with the virus.

“The results we see are consistent with infected animals, but we cannot prove that they were,” said Florence Débarre, an evolutionary biologist at the French National Center for Scientific Research and a co-author of the new paper.

Much of the report is familiar territory. Many of the 23 authors of the paper are known to have long supported a market origin for the virus. In an informal report in March 2023, they presented a central feature of the genetic data — the confirmation that animals potentially capable of triggering a pandemic were in the market.

That early report, which was not peer-reviewed or published in a journal, had a scientifically awkward provenance. It was written over the course of about 10 days, Débarre said, after she noticed that Chinese researchers had posted some of their genetic data from the market on GISAID, a public database regularly scanned by pandemic researchers.

The Chinese researchers had submitted a report to the journal Nature, and, after peer review, it was published in April 2023. The Nature paper from the Chinese scientists describes the genetic data as inconclusive about the origin of the pandemic, including that there is no proof any animals were infected with the virus.

“Furthermore, even if the animals were infected, our study does not rule out human-to-animal transmission, as the sampling was carried out after the human infection within the market,” the Nature paper states. “Thus, the possibility of potential introduction of the virus to the market through infected humans, or cold-chain products, cannot yet be ruled out.”

The new paper in Cell is longer, more comprehensive, probes a broader range of questions, and includes more data from the market and early-patient cases than the international team’s informal 2023 report, Débarre said.

Both the earlier and the new reports document that traces of the virus were found clustered in a section of the Huanan Seafood Wholesale Market where genetic traces of animals were also found. Several of those species — raccoon dogs, rabbits and dogs — are known to be susceptible to infection with SARS-CoV-2, the virus that causes covid. Raccoon dogs have also been shown experimentally to be capable of transmitting the virus.

A significant element of the new paper is an analysis of when the pandemic began. Scientists can study mutations of the coronavirus, which evolves at a relatively steady rate, to estimate when the millions of genomes deposited in databases had the most recent common ancestor. That genetic evidence points to mid-November 2019 as the most likely time the virus spilled into humans and began spreading, and there could have been two or more spillover events, the researchers said.

“The timing of the origin of the market outbreak is genetically indistinguishable from the timing of the origin of the pandemic as a whole,” the report states.


There are many independent lines of evidence pointing to the market as the epicenter of the pandemic, said Kristian Andersen, an infectious-disease researcher at Scripps Research in La Jolla, Calif., and a co-author of the report in Cell. No previous virus spillover has been so well-documented, he said.

“Of any previous outbreak, pandemic, you name it, we don’t have this level of granularity,” he said. “We can narrow it down to a single market, and narrow it down to a section in that market, and maybe even narrow it down to a single stall in that market. That is mind-boggling.”

Early in the outbreak, as word spread of an unusual respiratory illness in Wuhan, officials closed the Huanan market. It was cleaned and all animals were removed.

Finding the specific animals that could have caused a spillover of the virus may be impossible, said Michael Worobey, a University of Arizona evolutionary biologist and co-author of the report.

“Immediately, you have a needle-in-a-haystack situation, but then you incinerate all the haystacks and burn up all the needles,” Worobey said.

The genetic evidence, the new report contends, supports the hypothesis that SARS-CoV-2 emerged in the same way that SARS-CoV-1 — which sickened people in 2002-2003 but was extinguished before it could cause a full-blown pandemic — is widely believed to have started, from animals sold in a market. The authors contend the world needs to take more aggressive action to shut down the illegal trade in wildlife to lower the risk of another catastrophic pandemic.

“All the data [on the origin of the pandemic] currently available point in the same direction, which is the wildlife trade in the Huanan market. Will it put the debate to an end? I’m afraid it’s unlikely,” Débarre said.

The natural spillover hypothesis has been challenged by proponents of the “lab leak theory,” an umbrella term for a suite of scenarios, many of them involving the Wuhan Institute of Virology. The sprawling institute conducted extensive research on coronaviruses, including SARS-CoV-1. Proponents of the lab leak theory argue the institute conducted research with lax biosafety protocols.

The debate over covid’s origins continues to be contentious and politicized. It is also entangled with geopolitical tensions and with a broader debate about biosafety practices and the regulatory oversight of laboratory experiments that seek to assess and understand the threat pathogens could pose.

The lab leak theory emerged early in 2020 and was embraced by President Donald Trump. It gained momentum in May 2021 when 18 scientists, including Worobey, wrote a letter to the journal Science saying all possible origins of the pandemic, including a lab leak, deserve investigation. President Joe Biden then asked his intelligence agencies to investigate.

They were unable to reach a consensus. Most favored a natural origin, but two agencies favored a lab origin. None claimed high confidence in their conclusions.

report from Senate Republicans in 2022 said a “research-related accident” was the “most likely” origin of the pandemic, although it did not rule out a natural origin. “Critical corroborating evidence of a natural zoonotic spillover is missing,” the report said.

There is no evidence that the virus, or its progenitor, was inside a laboratory before the outbreak. Chinese officials have denied the virus came from a lab. But the Chinese government has limited outside investigations, and the lack of transparency has been an obstacle in the search to understand the origin of the virus.

Chinese officials have also dismissed the market origin, instead floating conjectures, generally dismissed by the global scientific community, that the virus came from outside China, possibly via packages of frozen seafood or from a military research facility in Maryland.

“To the question — Did it come from a lab or come from a market? — I think we already knew the answer to that,” Andersen said. “Yep, it’s the market. It’s natural, as we’ve previously seen happen.”


Sunday, October 02, 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.

Wednesday, May 17, 2023

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.


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

The Bat Lands

PART 1: WEST AFRICA
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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
DEEP IN THE AMAZON, SCIENTISTS RACE AGAINST TIME TO IDENTIFY UNKNOWN PATHOGENS