A team at the Catalan Institution for Research and Advanced Studies is utilizing drones and weather stations to collect data on how mosquito breeding patterns are changing in response to climate shifts.
Every year, the villages which lie in the so-called ‘Nipah belt’— which stretches along the western border between Bangladesh and India, brace themselves for the latest outbreak. For since 1998, when Nipah virus—a form of hemorrhagic fever most common in Bangladesh—first spilled over into humans, it has been a grim annual visitor to the people of this region.
With a 70 percent fatality rate, no vaccine, and no known treatments, Nipah virus has been dubbed in the Western world as ‘the worst disease no one has ever heard of.’ Currently, outbreaks tend to be relatively contained because it is not very transmissible. The virus circulates throughout Asia in fruit eating bats, and only tends to be passed on to people who consume contaminated date palm sap, a sweet drink which is harvested across Bangladesh.
But as SARS-CoV-2 has shown the world, this can quickly change.
“Nipah virus is among what virologists call ‘the Big 10,’ along with things like Lassa fever and Crimean Congo hemorrhagic fever,” says Noam Ross, a disease ecologist at New York-based non-profit EcoHealth Alliance. “These are pretty dangerous viruses from a lethality perspective, which don’t currently have the capacity to spread into broader human populations. But that can evolve, and you could very well see a variant emerge that has human-human transmission capability.”
That’s not an overstatement. Surveys suggest that mammals harbour about 40,000 viruses, with roughly a quarter capable of infecting humans. The vast majority never get a chance to do so because we don’t encounter them, but climate change can alter that. Recent studies have found that as animals relocate to new habitats due to shifting environmental conditions, the coming decades will bring around 300,000 first encounters between species which normally don’t interact, especially in tropical Africa and southeast Asia. All these interactions will make it far more likely for hitherto unknown viruses to cross paths with humans.
That’s why for the last 16 years, EcoHealth Alliance has been conducting ongoing viral surveillance projects across Bangladesh. The goal is to understand why Nipah is so much more prevalent in the western part of the country, compared to the east, and keep a watchful eye out for new Nipah strains as well as other dangerous pathogens like Ebola.
"There are a lot of different infectious agents that are sensitive to climate change that don't have these sorts of software tools being developed for them," says Cat Lippi, medical geography researcher at the University of Florida.
Until very recently this kind of work has been hampered by the limitations of viral surveillance technology. The PREDICT project, a $200 million initiative funded by the United States Agency for International Development, which conducted surveillance across the Amazon Basin, Congo Basin and extensive parts of South and Southeast Asia, relied upon so-called nucleic acid assays which enabled scientists to search for the genetic material of viruses in animal samples.
However, the project came under criticism for being highly inefficient. “That approach requires a big sampling effort, because of the rarity of individual infections,” says Ross. “Any particular animal may be infected for a couple of weeks, maybe once or twice in its lifetime. So if you sample thousands and thousands of animals, you'll eventually get one that has an Ebola virus infection right now.”
Ross explains that there is now far more interest in serological sampling—the scientific term for the process of drawing blood for antibody testing. By searching for the presence of antibodies in the blood of humans and animals, scientists have a greater chance of detecting viruses which started circulating recently.
Despite the controversy surrounding EcoHealth Alliance’s involvement in so-called gain of function research—experiments that study whether viruses might mutate into deadlier strains—the organization’s separate efforts to stay one step ahead of pathogen evolution are key to stopping the next pandemic.
“Having really cheap and fast surveillance is really important,” says Ross. “Particularly in a place where there's persistent, low level, moderate infections that potentially have the ability to develop into more epidemic or pandemic situations. It means there’s a pathway that something more dangerous can come through."
Scientists are searching for the presence of antibodies in the blood of humans and animals in hopes to detect viruses that recently started circulating.
EcoHealth Alliance
In Bangladesh, EcoHealth Alliance is attempting to do this using a newer serological technology known as a multiplex Luminex assay, which tests samples against a panel of known antibodies against many different viruses. It collects what Ross describes as a ‘footprint of information,’ which allows scientists to tell whether the sample contains the presence of a known pathogen or something completely different and needs to be investigated further.
By using this technology to sample human and animal populations across the country, they hope to gain an idea of whether there are any novel Nipah virus variants or strains from the same family, as well as other deadly viral families like Ebola.
This is just one of several novel tools being used for viral discovery in surveillance projects around the globe. Multiple research groups are taking PREDICT’s approach of looking for novel viruses in animals in various hotspots. They collect environmental DNA—mucus, faeces or shed skin left behind in soil, sediment or water—which can then be genetically sequenced.
Five years ago, this would have been a painstaking work requiring bringing collected samples back to labs. Today, thanks to the vast amounts of money spent on new technologies during COVID-19, researchers now have portable sequencing tools they can take out into the field.
Christopher Jerde, a researcher at the UC Santa Barbara Marine Science Institute, points to the Oxford Nanopore MinION sequencer as one example. “I tried one of the early versions of it four years ago, and it was miserable,” he says. “But they’ve really improved, and what we’re going to be able to do in the next five to ten years will be amazing. Instead of having to carefully transport samples back to the lab, we're going to have cigar box-shaped sequencers that we take into the field, plug into a laptop, and do the whole sequencing of an organism.”
In the past, viral surveillance has had to be very targeted and focused on known families of viruses, potentially missing new, previously unknown zoonotic pathogens. Jerde says that the rise of portable sequencers will lead to what he describes as “true surveillance.”
“Before, this was just too complex,” he says. “It had to be very focused, for example, looking for SARS-type viruses. Now we’re able to say, ‘Tell us all the viruses that are here?’ And this will give us true surveillance – we’ll be able to see the diversity of all the pathogens which are in these spots and have an understanding of which ones are coming into the population and causing damage.”
But being able to discover more viruses also comes with certain challenges. Some scientists fear that the speed of viral discovery will soon outpace the human capacity to analyze them all and assess the threat that they pose to us.
“I think we're already there,” says Jason Ladner, assistant professor at Northern Arizona University’s Pathogen and Microbiome Institute. “If you look at all the papers on the expanding RNA virus sphere, there are all of these deposited partial or complete viral sequences in groups that we just don't know anything really about yet.” Bats, for example, carry a myriad of viruses, whose ability to infect human cells we understand very poorly.
Cultivating these viruses under laboratory conditions and testing them on organoids— miniature, simplified versions of organs created from stem cells—can help with these assessments, but it is a slow and painstaking work. One hope is that in the future, machine learning could help automate this process. The new SpillOver Viral Risk Ranking platform aims to assess the risk level of a given virus based on 31 different metrics, while other computer models have tried to do the same based on the similarity of a virus’s genomic sequence to known zoonotic threats.
However, Ladner says that these types of comparisons are still overly simplistic. For one thing, scientists are still only aware of a few hundred zoonotic viruses, which is a very limited data sample for accurately assessing a novel pathogen. Instead, he says that there is a need for virologists to develop models which can determine viral compatibility with human cells, based on genomic data.
“One thing which is really useful, but can be challenging to do, is understand the cell surface receptors that a given virus might use,” he says. “Understanding whether a virus is likely to be able to use proteins on the surface of human cells to gain entry can be very informative.”
As the Earth’s climate heats up, scientists also need to better model the so-called vector borne diseases such as dengue, Zika, chikungunya and yellow fever. Transmitted by the Aedes mosquito residing in humid climates, these blights currently disproportionally affect people in low-income nations. But predictions suggest that as the planet warms and the pests find new homes, an estimated one billion people who currently don’t encounter them might be threatened by their bites by 2080. “When it comes to mosquito-borne diseases we have to worry about shifts in suitable habitat,” says Cat Lippi, a medical geography researcher at the University of Florida. “As climate patterns change on these big scales, we expect to see shifts in where people will be at risk for contracting these diseases.”
Public health practitioners and government decision-makers need tools to make climate-informed decisions about the evolving threat of different infectious diseases. Some projects are already underway. An ongoing collaboration between the Catalan Institution for Research and Advanced Studies and researchers in Brazil and Peru is utilizing drones and weather stations to collect data on how mosquitoes change their breeding patterns in response to climate shifts. This information will then be fed into computer algorithms to predict the impact of mosquito-borne illnesses on different regions.
The team at the Catalan Institution for Research and Advanced Studies is using drones and weather stations to collect data on how mosquito breeding patterns change due to climate shifts.
Gabriel Carrasco
Lippi says that similar models are urgently needed to predict how changing climate patterns affect respiratory, foodborne, waterborne and soilborne illnesses. The UK-based Wellcome Trust has allocated significant assets to fund such projects, which should allow scientists to monitor the impact of climate on a much broader range of infections. “There are a lot of different infectious agents that are sensitive to climate change that don't have these sorts of software tools being developed for them,” she says.
COVID-19’s havoc boosted funding for infectious disease research, but as its threats begin to fade from policymakers’ focus, the money may dry up. Meanwhile, scientists warn that another major infectious disease outbreak is inevitable, potentially within the next decade, so combing the planet for pathogens is vital. “Surveillance is ultimately a really boring thing that a lot of people don't want to put money into, until we have a wide scale pandemic,” Jerde says, but that vigilance is key to thwarting the next deadly horror. “It takes a lot of patience and perseverance to keep looking.”
This article originally appeared in One Health/One Planet, a single-issue magazine that explores how climate change and other environmental shifts are increasing vulnerabilities to infectious diseases by land and by sea. The magazine probes how scientists are making progress with leaders in other fields toward solutions that embrace diverse perspectives and the interconnectedness of all lifeforms and the planet.
New research challenges the popular notion that all commercial breeding kennels are inhumane.
Candace Croney joined the faculty at Purdue University in 2011, thinking her job would focus on the welfare of livestock and poultry in Indiana. With bachelor's, master's, and doctoral degrees in animal sciences, her work until then had centered on sheep, cattle, and pigs. She'd even had the esteemed animal behaviorist Temple Grandin help shape her master's research project.
Croney's research has become the first of its kind in the world—and it's challenging our understanding of how dog breeding is being done.
Then came an email from a new colleague asking Croney to discuss animal welfare with some of Indiana's commercial dog breeders, the kind who produce large quantities of puppies for sale in pet stores.
"I didn't even know the term commercial breeders," Croney says. "I'd heard the term 'puppy millers.' That's pretty much what I knew."
She went to the first few kennels and braced herself for an upsetting experience. She's a dog lover who has fostered shelter mutts and owned one, and she'd seen the stories: large-scale breeders being called cruel and evil, lawmakers trying to ban the sale of commercially bred puppies, and constant encouragement to rescue a dog instead of paying into a greedy, heartless "puppy mill" industry.
But when she got to the kennels, she was surprised. While she encountered a number of things she didn't like about the infrastructure at the older facilities—a lack of ventilation, a lot of noise, bad smells—most of the dogs themselves were clean. The majority didn't have physical problems. No open sores. No battered bodies. Nothing like what she'd seen online.
But still, the way the dogs acted gave her pause.
"Things were, in many regards, better than I thought they would be," Croney says. "Google told me the dogs would be physically a mess, and they weren't, but behaviorally, things were jumping out at me."
While she did note that some of the breeders had play yards for their pups, a number of the dogs feared new people and things like leashes because they hadn't been exposed to enough of them. Some of the dogs also seemed to lack adequate toys, activities, and games to keep them mentally and physically stimulated.
But she was there strictly as a representative of the university to ask questions and offer feedback, no more or less. A few times, she says, she felt like the breeders wanted her to endorse what they were doing, "and I immediately got my back up about that. I did not want my name used to validate things that I could tell I didn't agree with. It was uncomfortable from that perspective."
After sharing the animal-welfare information her colleague had requested, Croney figured that was that. She never expected to be in a commercial kennel again. But six months later, her phone rang. Some of the people she'd met were involved in legislative lobbying, and they were trying to write welfare standards for Indiana's commercial breeders to follow.
In the continuing battle over what is, and is not, a "puppy mill," they wanted somebody with a strong research background to set a baseline standard, somebody who would actually bring objectivity to the breeder-activist conflict without being on one side or the other.
In other words, they wanted Croney's help to figure out not only appropriate enclosure sizes, but also requirements for socialization and enrichment activities—stimulation she knew the dogs desperately needed.
"I thought, crap, how am I not going to help?" she recalls. "And they said, 'Well how long will that take? A couple of weeks? A month?'"
Dr. Croney with Theo, whom she calls "a beloved family member of our research team."
(Photo credit: Purdue University/Vincent Walter)
Six years later, Croney's research remains ongoing. It has become the first of its kind in the world—and it's challenging our understanding of how dog breeding is being done, and how it could and should be done for years to come.
How We Got Here
Americans have been breeding pet dogs in large-scale kennels since World War II. The federal standard that regulates those kennels is the Animal Welfare Act, which President Johnson signed into law in 1966. Back then, people thought it was OK to treat dogs a lot differently than they do today. The law has been updated, but it still allows a dog the size of a Beagle to be kept in a cage the size of a dishwasher all day, every day because for some dogs, when the law was written, having a cage that size meant an improvement in living conditions.
Countless commercial breeders, who are regularly inspected under the Animal Welfare Act, have long believed that as long as they followed the law, they were doing things right. And they've seen sales for their puppies go up and up over the years. About 38 percent of U.S. households now own one or more dogs, the highest rate since the American Veterinary Medical Association began measuring the statistic in 1982.
Consumers now demand eight million dogs per year, which has reinforced breeders' beliefs that despite what activists shout at protests, the breeders are actually running businesses the public supports. As one Ohio commercial breeder—long decried by activists as a "puppy mill" owner—told The Washington Post in 2016, "This is a customer-driven industry. If we weren't satisfying the customer, we'd starve to death. I've never seen prices like the ones we're seeing now, in my whole career."
That breeder, though, is also among leading industry voices who say they understand that public perception of what's acceptable and what's not in a breeding kennel has changed. Regardless of what the laws are, they say, kennels must change along with the public's wishes if the commercial breeding industry is going to survive. The question is how, exactly, to move from the past to the future, at a time when demands for change have reached a fever pitch.
"The Animal Welfare Act, that was gospel. It meant you were taking care of dogs," says Bob Vetere, former head of the American Pet Products Association and now chairman of the Pet Leadership Council. "That was, what, 40 years ago? Things have evolved. People understand much more since then—and back then, there were maybe 20 million dogs in the country. Now, there's 90 million. It's that dramatic. People love their dogs, and everybody is going to get one."
Vetere became an early supporter of Croney's research, which, unbelievably, became the first ever to focus on what it actually means to run a good commercial breeding kennel. At the start of her research, Croney found that the scientific literature underpinning many existing laws and opinions was not just lacking, but outright nonexistent.
"We kept finding it over and over," she says of the literature gaps, citing common but uninformed beliefs about appropriate kennel size as just one example. "I can't find any research about how much space they're supposed to have. People said, 'Yeah, we had a meeting and a bunch of people made some recommendations.'"
She started filling in the research gaps with her team at Purdue, building relationships with dog breeders until she had more than 100 kennels letting her methodically figure out what was actually working for the dogs.
"The measurable successes in animal welfare over the past 50 years began from a foundation in science."
Creating Standards from Scratch
Other industry players soon took notice. One was Ed Sayres, who had served as CEO of the ASPCA for nearly a decade before turning his attention to lobbying efforts regarding the "puppy mill" issue. He recognized that what Croney was doing for commercial breeding mirrored the early work researchers started a half-century ago in the effort that led to better shelters all across America today.
"The measurable successes in animal welfare over the past 50 years began from a foundation in science," Sayres says. "Whether it was the transition to more humane euthanasia methods or how to manage dog and cat overpopulation, we found success from rigorous examination of facts and emerging science."
Sayres, Vetere, and others began pushing for the industry to support Croney's work, moving the goalposts beyond Indiana to the entire United States.
"If you don't have commercial breeding, you have people importing dogs from overseas with no restrictions, or farming in their backyards to make money," Vetere says. "You need commercial breeders with standards—and that's what Candace is trying to create, those standards."
Croney ended up with a $900,000 grant from three industry organizations: the World Pet Association, Pet Food Institute, and the Pet Industry Joint Advisory Council. With their support, she created a nationwide program called Canine Care Certified, like a Good Housekeeping Seal of Approval for a kennel. The program focuses on outcome-based standards, meaning she looks at what the dogs tell her about how well they are doing through their health and behavior. For the most part, beyond baseline requirements, the program lets a breeder achieve those goals in whatever ways work for the dogs.
The approach is different from many legislative efforts, with laws stating a cage must be made three feet larger to be considered humane. Instead, Croney walks through kennels with breeders and points out, for instance, which puppies in a litter seem to be shy or fearful, and then teaches the breeders how to give those puppies better socialization. She helps the breeders find ways to introduce dogs to strangers and objects like umbrellas that may not be part of regular kennel life, but will need to become familiar when the breeding dog retires and gets adopted into a home as a pet. She helps breeders understand that dogs need mental as well as physical stimulation, whether it comes from playing with balls and toys or running up and down slides.
The breeders can't learn fast enough, Croney says, and she remains stunned at how they constantly ask for more information—an attitude that made her stop using the term "puppy mill" to describe them at all.
"Now, full disclosure: Given that all of these kennels had volunteered, the odds were that we were seeing a skewed population, and that it skewed positive," she says. "But if you read what was in the media at the time, we shouldn't have been able to find any. We're told that all these kennels are terrible. Clearly, it was possible to get a positive outcome."
To Buy or Not to Buy?
Today, she says, she's shocked at how quickly some of the kennels have improved. Facilities that appalled her at first sight now have dogs greeting people with wagging tails.
"Not only would I get a dog from them, but would I put my dog there in that kennel temporarily? Yeah, I would."
"The most horrifying thing I learned was that some of these people weren't doing what I'd like to see, not because they didn't care or only wanted money, but because nobody had ever told them," she says. "As it turned out, they didn't know any different, and no one would help them."
For Americans who want to know whether it's OK to get a commercially bred puppy, Croney says she thinks about her own dogs. When she started working with the breeders, there were plenty of kennels that, she says, she would not have wanted to patronize. But now she's changing her mind about more and more of them.
"I'm just speaking as somebody who loves dogs and wants to make sure I'm not subsidizing anything inhumane or cruel," she says. "Not only would I get a dog from them, but would I put my dog there in that kennel temporarily? Yeah, I would."
She says the most important thing is for consumers to find out how a pup was raised, and how the pup's parents were raised. As with most industries, commercial breeders run the gamut, from barely legal to above and beyond.
Not everyone agrees with Croney's take on the situation, or with her approach to improving commercial breeding kennels. In its publication "Puppy Mills and the Animal Welfare Act," the Humane Society of the United States writes that while Croney's Canine Care Certified program supports "common areas of agreement" with animal-welfare lobbyists, her work has been funded by the pet industry—suggesting that it's impure—and a voluntary program is not enough to incentivize breeders to improve.
New laws, the Humane Society states, must be enacted to impose change: "Many commercial dog breeding operators will not raise their standards voluntarily, and even if they were to agree to do so it is not clear whether there would be any independent mechanism for enforcement or transparency for the public's sake. ... The logical conclusion is that improved standards must be codified."
Croney says that type of attitude has long created resentment between breeders and animal-welfare activists, as opposed to actual kennel improvements. Both sides have a point; for years, there have been examples of bottom-of-the-barrel kennels that changed their ways or shut down only after regulators smacked them with violations, or after lawmakers raised operating standards in ways that required improvements for the kennels to remain legally in business.
At the same time, though, powerful organizations including the Humane Society—which had revenue of more than $165 million in 2018 alone—have routinely pushed for bans on stores that sell commercially bred puppies, and have decried "puppy mills" in marketing and fund-raising literature, without offering financial grants or educational programs to kennels that are willing to improve.
Croney believes that the reflexive demonization of all commercial breeders is a mistake. Change is more effective, she says, when breeders "want to do better, want to learn, want to grow, and you treat them as advocates and allies in doing something good for animal welfare, as opposed to treating them like they're your enemies."
"If you're watching undercover videos about people treating animals in bad ways, I'm telling you, change is happening."
She adds that anyone who says all commercial breeders are "puppy mills" needs to take a look at the kennels she's seen and the changes her work has brought—and is continuing to bring.
"The ones we work with are working really, really hard to improve and open their doors so that if somebody wants to get a dog from them, they can be assured that those dogs were treated with a level of care and compassion that wasn't there five or 10 years ago, but that is there now and will be better in a year and will be much better in five years," she says. "If you're watching undercover videos about people treating animals in bad ways, I'm telling you, change is happening. It is so much better than people realize, and it continues to get even better yet."
