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.
Should egg and sperm donors reveal their identities? The debate pivots on genetics and medical history.
Until age 35, Cassandra Adams assumed her mother and father were her biological parents. Then she took saliva tests through two genealogy databases—23andMe and AncestryDNA—and discovered a discrepancy in her heritage. In bringing up the matter with her parents, she learned that fertility issues had led the couple to use a sperm donor.
“Most people my age were not told,” said Adams, now 40 and a stay-at-home mom in Jersey City, New Jersey, who is involved with donor-conception advocacy. “Even now, there’s still a lot of secrecy in the industry. There are still many parents who aren’t truthful or planning not to be truthful with their children.”
While some of those offspring may never know a significant part of their medical history, Adams is grateful that she does. Surprisingly, the DNA test revealed Jewish ancestry.
“There are a lot more genetic conditions that run in Jewish families, so it was really important that I get my medical history, because it’s very different from my dad who raised me,” said Adams, who has met her biological father and two of three known half-siblings. As a result of this experience, she converted to Judaism. “It has been a big journey,” she said.
In an era of advancing assisted reproduction technologies, genetics and medical history have become front and center of the debate as to whether or not egg and sperm donations should be anonymous – and whether secrecy is even possible in many cases.
Obstacles to staying anonymous
People looking to become parents can choose what’s called an “identity-release donor,” meaning their child can receive information about the donor when he or she turns 18. There’s no way to ensure that the donor will consent to a relationship at that time. Instead, if a relationship between the donor and child is a priority, parents may decide to use a known donor.
The majority of donors want to remain anonymous, said reproductive endocrinologist Robert Kiltz, founder and director of CNY Fertility in Syracuse, New York. “In general, egg and sperm donation is mostly anonymous, meaning the recipient doesn’t know the donor and the donor doesn’t know the recipient.”
Even if the donor isn’t disclosed, though, the mystery may become unraveled when a donor-conceived person undergoes direct-to-consumer genetic testing through ancestry databases, which are growing in number and popularity. These services offer DNA testing and links to relatives with identifiable information.
In the future, another obstacle to anonymity could be laws that prohibit anonymous sperm and egg donations, if they catch on. In June, Colorado became the first state in the nation to ban anonymous sperm and egg donations. The law, which takes effect in 2025, will give donor-conceived adults the legal authority to obtain their donor’s identity and medical history. It also requires banks that provide sperm and egg collection to keep current medical records and contact information for all donors. Meanwhile, it prohibits donations from those who won’t consent to identity disclosures.
“The tradition of anonymous sperm or egg donation has created a vast array of problems, most significantly that the people thus created want to know who their mommy and daddy are,” said Kenneth W. Goodman, professor and director of the Institute for Bioethics and Health Policy at the University of Miami Miller School of Medicine.
“There are counter arguments on both sides. But the current situation has led to great uncertainty and, in many cases, grief,” Goodman said.
Donors should bear some moral responsibility for their role in reproduction by allowing their identity to be disclosed to donor-conceived individuals when they turn 18, Goodman added, noting that “there are counter arguments on both sides. But the current situation has led to great uncertainty and, in many cases, grief.”
Adams, the Jersey City woman who learned she was Jewish, has channeled these feelings into several works of art and performances on stage at venues such as the Jersey City Theater Center. During these performances, she describes the trauma of “not knowing where we come from [or] who we look like.”
In the last five years, Kathleen “Casey” DiPaola, a lawyer in Albany, New York, who focuses her practice on adoption, assisted reproduction and surrogacy, has observed a big shift toward would-be parents looking to use known sperm donors. On the other hand, with egg donation, “I’m not seeing a whole lot of change,” she said. Compared to sperm donation, more medical screening is involved with egg donation, so donors are primarily found through fertility clinics and egg donor agencies that prefer anonymity. This leads to fewer options for prospective parents seeking an egg donor with disclosed identity, DiPaola said.
Some donors want to keep in touch
Rachel Lemmons, 32, who lives in Denver, grew interested in becoming an egg donor when, as a graduate student in environmental sciences, she saw an online advertisement. “It seemed like a good way to help pay off my student loan debt,” said Lemmons, who is married and has a daughter who will turn 2-years-old in December. She didn’t end up donating until many years later, after she’d paid off the debt. “The primary motivation at that point wasn’t financial,” she said. “Instead, it felt like a really wonderful way to help someone else have a family in a few weeks’ time.”
Lemmons originally donated anonymously because she didn’t know open donations existed. She was content with that until she became aware of donor-conceived individuals’ struggles. “It concerned me that I could potentially be contributing to this,” she said, adding that the egg donor and surrogacy agency and fertility clinic wouldn’t allow her to disclose her identity retroactively.
Since then, she has donated as an open donor, and kept in touch with the recipients through email and video calls. Knowing that they were finally able to have children is “incredibly rewarding,” Lemmons said.
When to tell the kids
Stanton Honig, professor of urology and division chief of sexual and reproductive medicine at Yale School of Medicine, said for years his team has recommended that couples using donor sperm inform children about the role of the donor and their identity. “Honesty is always the best policy, and it is likely that when they become of age, they might or will be able to find out about their biological sperm donor,” he said. “Hiding it creates more of a complicated situation for children in the long run.”
Amy Jones, a 45-year-old resident of Syracuse, N.Y., has three children, including twins, who know they were conceived with anonymous donor eggs from the same individual, so they share the same genetics. Jones, who is a registered nurse and asked for her real name not to be published, told them around age seven.
“The thought of using a known donor brought more concerns—what if she wanted my babies after they were born, or how would I feel if she treated them as her own every time I saw her?” said Jones.
“I did a lot of reading, and all psychologists said that it is best to start the conversation early,” she recalled. “They understood very little of what I was telling them, but through the years, I have brought it up in discussion and encouraged them to ask questions. To this day, they don't seem to be all that interested, but I expect that later on in life they may have more questions.”
Jones and her husband opted to use a donor because premature ovarian failure at age 27 had rendered her infertile. “The decision to use an egg donor was hard enough,” she said. “The thought of using a known donor brought more concerns—what if she wanted my babies after they were born, or how would I feel if she treated them as her own every time I saw her?”
Susan C. Klock, a clinical psychologist in the section of fertility and reproductive medicine at Northwestern University Feinberg School of Medicine, said, “Anonymity is virtually impossible in the age of direct-to-consumer genetic testing.” In addition, “selecting an identity-release donor is typically not the first thing parents are looking at when they select a donor. First and foremost, they are looking for a donor with a healthy medical background. Then they may consider donor characteristics that resemble the parents.”
The donor’s medical history can be critical
Donor agencies rely on the self-reported medical history of egg and sperm donors, which can lead to gaps in learning important information. Knowing a donor’s medical history may have led some families to make different or more well-informed choices.
After Steven Gunner, a donor-conceived adult, suffered from schizophrenia and died of a drug overdose at age 27 in 2020, his parents, who live in New York, learned of a potential genetic link to his mental illness. A website, Donor Sibling Registry, revealed that the sperm donor the couple had used, a college student at the time of donation, had been hospitalized during childhood for schizophrenia and died of a drug overdose at age 46. Gunner’s story inspired Steven’s Law, a bill that was introduced in Congress in July. If passed, it would mandate sperm banks to collect information on donors’ medical conditions, and donors would have to disclose medical information the banks weren’t able to find.
With limited exceptions, the U.S. Food and Drug Administration requires donors to be screened and tested for relevant communicable disease agents and diseases such as HIV, hepatitis viruses B and C, the Zika virus and several STDs. With current technology, it is also impossible to screen for thousands of rare genetic diseases. “If a couple is using IVF (in vitro fertilization) to conceive with the donor gamete, some may opt for pre-implantation genetic testing to assess for chromosomal abnormalities,” Klock said.
Even these precautions wouldn't cover every disease, and some would-be parents don't get the genetic screening. In a situation where one donor has a large number of offspring, it is concerning that he or she can spread a rare disease to multiple people, said Nick Isel, 37, of Yorkville, Illinois, who was conceived with donor sperm due to his parents’ fertility issues. They told him the truth when he was a teenager, and he found his biological father with a journalist’s help.
Since 2016, Isel, who owns a roofing company, has been petitioning the FDA to extend the retention of medical records, requiring the fertility establishment to maintain information on sperm and egg donors for 50 years instead of the current 10-year mandate.
“The lack of family health information,” he said, “is an ongoing, slow-motion public health crisis since donor conception began being regulated by the FDA as a practice.”
Saliva May Help Diagnose PTSD in Veterans
As a bioinformatician and young veteran, Guy Shapira welcomed the opportunity to help with conducting a study to determine if saliva can reveal if war veterans have post-traumatic stress disorder, or PTSD.
The research team, which drew mostly from Tel Aviv University’s Sackler Faculty of Medicine and Sagol School of Neuroscience, collected saliva samples from approximately 200 veterans who suffered psychological trauma stemming from the years they spent fighting in the First Lebanon War in 1982. The researchers also characterized the participants’ psychological, social and medical conditions, including a detailed analysis of their microbiomes.
They found that the former soldiers with PTSD have a certain set of bacteria in their saliva, a distinct microbiotic signature that is believed to be the first biological marker for PTSD. The finding suggests that, in the future, saliva tests could be used to help identify this disorder. As of now, PTSD is often challenging to diagnose.
Shapira, a Ph.D. student at Tel Aviv University, was responsible for examining genetic and health-related data of the veterans who participated – information that had been compiled steadily over four decades. The veterans provided this data voluntarily, Shapira says, at least partly because the study carries important implications for their own psychological health.
The research was led by Illana Gozes, professor emerita of clinical biochemistry. “We looked at the bacteria in their blood and their saliva,” Gozes explains. To discover the microbial signatures, they analyzed the biometric data for each soldier individually and as a group. Comparing the results of the participants’ microbial distribution to the results of their psychological examinations and their responses to personal welfare questionnaires, the researchers learned that veterans with PTSD – and, more generally, those with significant mental health issues – have the same bacterial content in their saliva.
“Having empirical metrics to assess whether or not someone has PTSD can help veterans who make their case to the Army to get reparations,” Shapira says.
More research is required to support this finding, published in July in Nature’s prestigious Molecular Psychiatry, but it could have important implications for identifying people with PTSD. Currently, it can be diagnosed only through psychological and behavioral symptoms such as flashbacks, nightmares, sleep disorders, increased irritability and physical aggressiveness. Veterans sometimes don’t report these symptoms to health providers or realize they’re related to the trauma they experienced during combat.
The researchers also identified a correlation that indicates people with a higher level of education show a lower occurrence of the microbiotic signature linked to PTSD, while people who experienced greater exposure to air pollution show a higher occurrence of this signature. That confirms their finding that the veterans’ health is dependent on their individual biology combined with the conditions of their environment.
“Thanks to this study, it may be possible in the future to use objective molecular and biological characteristics to distinguish PTSD sufferers, taking into account environmental influences,” Gozes said in an article in Israel21c. “We hope that this new discovery and the microbial signatures described in this study might promote easier diagnosis of post-traumatic stress in soldiers so they can receive appropriate treatment.”
Gozes added that roughly a third of the subjects in their study hadn’t been diagnosed with PTSD previously. That meant they had never received any support from Israel’s Ministry of Defense or other officials for treatment and reparations, the payments to compensate for injuries sustained during war.
Shapira’s motivation to participate in this study is personal as well as professional: in addition to being veteran himself, his father served in the First Lebanon War. “Fortunately, he did not develop any PTSD, despite being shot in the foot...some of his friends died, so it wasn’t easy on him,” says Shapira.
“Having empirical metrics to assess whether or not someone has PTSD can help veterans who make their case to the Army to get reparations,” Shapira says. “It is a very difficult and demanding process, so the more empirical metrics we have to assess PTSD, the less people will have to suffer in these committees and unending examinations that are mostly pitched against the veterans because the state is trying to avoid spending too much money.”