New tools could catch disease outbreaks earlier - or predict them
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 tech helps people of all ages stay social
In March, Sonja Bauman, 39, used an online platform called Papa, which offers “family on demand,” to meet Mariela Florez, an 83-year-old retiree. Despite living with her adult children, Florez was bored and lonely when they left for work, and her recoveries from a stroke and broken hip were going slowly. That's when Bauman began visiting twice per week. They take walks, strengthening Florez’s hip, and play games like Connect Four for mental stimulation. “It’s very important for me so I don’t feel lonely all day long,” said Florez. Her memories, blurred by the stroke, are gradually returning.
Papa is one of a growing number of tech approaches that are bringing together people of all ages. In addition to platforms like Papa that connect people in real life, other startups use virtual reality and video, with some of them focusing especially on deepening social connections between the generations — relationships that support the health of older and younger people alike. “I enjoy seeing Mariela as much as she enjoys seeing me,” Bauman said.
Connecting in real life
Telehealth expert Andrew Parker founded Papa in 2017 to improve the health outcomes of older adults and families. Seniors can meet people — some their grandkids’ age — for healthy activities, while working parents find retirees to watch their children. These “Papa Pals” are provided as a benefit through Medicare, Medicaid and some employer health plans.
In 2020, Papa connected Bauman, the 39-year-old Floridian, with another woman in her mid-70s who lives alone and has very limited mobility. Bauman began driving her to doctor’s appointments and helping her with chores around the house. “When I’m not there, she doesn’t leave her apartment,” said Bauman. The two have gone to the gym together, and they walk slowly through the neighborhood, chatting so it feels less like exercise.
Parker was driven to start Papa by the problem of social isolation among seniors, exacerbated by the pandemic, but he believes users of all ages can benefit. “Many of our Pals feel more comfortable opening up with older members than their same-aged friends,” he said.
Other platforms aim for similar, in-person connections. Generation Tech unites teens with seniors for technology training. And Mon Ami, which provides case management software for aging and disability service providers, has an app that connects isolated older people with college-age volunteers.
Making new connections through video
Several new sites match you with strangers for real-time video chatting on various topics, such as finding common ground on political issues. Other video platforms focus on intergenerational connections.
S. Jay Olshansky, a gerontology professor at the University of Illinois-Chicago, recalls the first time he saw Hyunseung Lee, an 11-year-old from Seoul, through his computer screen. The kid was shy, but Olshansky, 67, encouraged him to ask questions. “Turns out, he was thirsting for this kind of interaction.”
They’d connected through Eldera, a platform that pairs mentors age 60 and up with mentees, using an algorithm, for video conversations. “The time and wisdom of older adults is the most important natural resource we can give future generations,” said Dana Griffin, Eldera's CEO. “Connecting through a screen is the opposite of social media.”
In weekly meetings, Olshansky noticed Lee’s unique interest in math. “There’s something special in you,” Olshansky told him. “How do we bring it to the surface?” He suggested Lee write a book on his favorite subject, and the preteen ran with it, cranking out 70 pages in two weeks. Lee has published his love letter to theorems on Amazon.
Hyunseung Lee, age 11, of Korea, and U.S. college professor Jay Olshanksy, 67, discuss math, strategy and Hyunsung's budding career as a book author during their video chats through a platform called Eldera. (Photo by Dana Palmer/Eldera)
Lee’s parents told Olshansky that their son has become more assertive — a recurring theme, Griffin said. “Confidence is the number one thing parents tell us about.” Since Eldera’s inception last year, the number of mentors has grown exponentially. Even so, Griffin said the waitlist for mentors typically numbers 200 kids.
Another site, Big and Mini, hosts video interactions between seniors and young adults; about 10,000 active users have joined since 2019, said co-founder Aditi Merchant.
Users often bring the benefits of their video interactions to their real-world relationships. Olshansky views Lee as an older version of his grandkids. “Eldera teaches me how to interact with them.” Lee, high on confidence, began instructing his classmates in math. Griffin noted that a group of Eldera mentors in Memphis, who met initially on Eldera, now take walks together in-person to trade ideas for helping each other’s Eldera kids solve problems in their schools and communities.
“We’ve evolved into a community for older adults who want to give back to the world,” said Griffin. Other new tools for connection take the form of virtual reality apps.
Connecting in virtual reality
During pandemic isolation, record numbers of people bought devices for virtual and augmented reality. Such gadgets can convince you that you’re hanging out with friends, even if they’re in another hemisphere. Lifelike simulations from miles away could be especially useful for meaningful interactions between people of different generations, since they’re often geographically segregated.
VR’s benefits require further study, but users report less social isolation and depression, according to MIT research. The immersive, 3-D experience is more compelling than FaceTime or Zoom. “It’s like the difference between a phone call and video call,” said Rick Robinson, Vice President of AARP’s Innovation Labs.
“When VR is designed right, the medium disappears,” said Jeremy Bailenson of Stanford.
Dana Pierce, a 56-year-old government employee in Indiana, got Meta's VR headset in May, 2021, thinking she’d enjoy it more than a new laptop. After many virtual group tours of exotic destinations, she has no regrets. Her adventures occur on Alcove, an app made by Robinson’s Innovation Labs. He co-created it with VR-company Rendever and sought input from people over age 50 to tailor it to their interests. “I’m an introvert,” said Pierce. “I’ve been more socially active since getting my headset than I am in real life.”
Tagging along with her to places like Paris are avatars representing real people around the world. She’s gotten to know VR users in their 70s, 80s and 90s, as well as younger people and some her own age. One is a new friend she plays chess with in relaxing nature settings. Another is her oldest son. He lives 90 minutes away but, earlier this year, Pierce welcomed him and his girlfriend to her virtual house on Alcove. They chatted in the living room decorated with family photos uploaded by Pierce. Then they took out a boat to go VR fishing — because why not — until 2 a.m.
“When VR is designed right, the medium disappears,” said Jeremy Bailenson, a communications professor who directs Stanford’s Virtual Human Interaction Lab. He’s teaching a class of 175 students entirely in VR. After months of covid isolation, the first time the class met, “there was a big catharsis. It really feels like you’re in a big crowd.” Like-minded people meet in VR for events such as comedy shows and creative writing meetups, while the Swedish pop group ABBA has performed this year as digital versions of themselves (“ABBA-tars”) during a virtual concert tour.
Karen Fingerman, a psychologist and director of the Texas Aging and Longevity Center at the University of Texas-Austin, supports the idea of VR for social connection, though she added that some people need it more than others. Hospitals and assisted-living facilities are using products such as Penumbra’s REAL I-Series and MyndVR to bring VR excursions to isolated patients and seniors. “If you’re in a bed or facility, this gives you something to talk about,” said Gita Barry, Penumbra’s executive vice president.
Pierce uses it on most days. She may see another adult son, who lives with her, less often as a result. But VR helps her manage real-world stressors, more than escaping them. After a long workday, she visits her back porch on Alcove, which overlooks a pond. “It’s my little retreat,” she said. “VR improves my mood. It’s added a lot to my life.”
Some seniors are using more than one technology. Olshansky and Lee discuss strategy while playing Internet chess. And Olshansky recently began using VR. He sees his sister, who lives far away, in a virtual beach house. “It’d be a great way to interact with Hyunseung,” he said. “I should get him a headset.”
A version of this article first appeared in The Washington Post on December 3, 2021.
Friday Five: These boots were made for walking, even for people who can't
The Friday Five covers important stories in health and science research that you may have missed - usually over the previous week but, today, we're doing a lookback on breakthrough research over the month of October. There are plenty of controversies and troubling ethical issues in science – and we get into many of them in our online magazine – but this news roundup focuses on scientific creativity and progress to give you a therapeutic dose of inspiration headed into the weekend.
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This Friday Five episode covers the following studies published and announced over the past month:
- New boots could have you moving like Iron Man
- The problem with bedtime munching
- The perfect recipe for tiny brains
- The best sports for kids to avoid lifelong health risks
- Can virtual reality reduce pain?