How Scientists Detect and Prevent the Spread of Viruses with Pandemic Potential22 April 2020
In this webinar, part of a series on zoonotic diseases and their links to environmental change, we discuss how scientists are working to detect and prevent the emergence of viruses with pandemic potential.
Held on Earth Day, April 22, 2020, we were joined by an expert team of researchers working in Asia and Africa to strengthen virus surveillance in animals and humans and identify strategies and countermeasures to prevent and control diseases, such as Covid-19. (See complete bios at the end of this resource).
Their projects – PREDICT, supported by the U.S. Agency for International Development, and PREEMPT – are aimed at identifying hotspots for emerging viruses.
Some factors driving the spread of disease are high levels of human interaction with wildlife, population density and landscape change, said David Wolking, who currently manages the projects. When they come together, it can create a “perfect storm,” he said, allowing for a virus or disease to “spill over” from wildlife to humans or domestic animals.
How does it work?
Understanding community behaviors is key to PREDICT, which is safely and humanely collecting samples from wildlife populations and then partnering with health centers and clinics and hospitals to collect samples from people.
The team takes those samples and tests them using a relatively cost-effective disease-detection platform that can be deployed in laboratories around the world. This platform can detect both known and newly emerging viral threats by looking more broadly at the family a virus belongs to, such as coronaviruses, rather than a specific virus itself, such as SARS-CoV-2, Wolking said.
Over the past six years, PREDICT’s laboratory partners tested samples for five viral families considered high priorities for surveillance: coronaviruses (including MERS and SARS-related viruses), filoviruses (Ebola and Marburg), flaviviruses (Yellow Fever, Zika, Dengue, and West Nile), paramyxoviruses (Nipah and Hendra), and influenza viruses.
They also partner with behavioral and social scientists to understand what factors in human communities could be linked to a spillover event. Guano harvesting and the bushmeat trade are some examples. And once they’ve compiled virus findings, they put together ways to communicate the risks those behaviors pose to the spread of disease and help identify potential strategies for disease prevention.
What has it achieved?
Over the last 10 years, the PREDICT project has sampled more than 100,000 individual wild animals and about 16,500 people, according to Dr. Pranav Pandit, a veterinary epidemiologist at the University of California Davis. They’ve detected more than 900 completely new viruses, including zoonotic diseases of public health concern, such as Zaire Ebola virus and MERS- and SARS-related coronaviruses, Wolking said.
They’ve determined that emerging threats can be detected before spillover into human populations, such as with the Bombali ebolavirus in Sierra Leone, and have developed some financial projections to understand the cost-benefit to preventing a pandemic outbreak.
The models are also helping them develop targeted wildlife surveillance for emerging infectious diseases, said Dr. Pandit, and helping to identify species and regions where more sampling and studies are needed.
Before the modeling, for example, the team knew of roughly 14 species that could carry Zika and Yellow Fever viruses. Now they have a list of 112 species that could potentially harbor those viruses, indicating a need for further sampling and testing.
Below is a Q&A that followed the presentation. Answers were offered live or in the chat box and have been edited for length and clarity.
Q: How can journalists constructively communicate the urgency and severity of pandemics without contributing to panic or fear of viruses?
Answer from James Fahn: Check out the EJN website, where we have posted a tip sheet on how to communicate about zoonotic diseases. As journalists, … look for local scientists you can talk to regularly, get their advice and especially talk to medical experts to make sure you’re giving good tips.
Q: Could COVID-19 have been detected earlier? Are any of the panelists surprised by its far-reaching spread?
A: “Within the epidemiology field, people are not really surprised with how far the coronavirus has reached globally,” Dr. Pandit said. That may have something to do with the expansion of air travel globally from China, which was far lower when the SARS1 and MERS outbreaks occurred in 2002 and 2013, respectively, he noted.
Q: Did we need to be checking in wildlife markets in Asia, for instance, which you identified as an at-risk interface? And is that being done by your team or someone else?
A: A lot of research groups are doing work in wildlife markets around the world, and these wet markets, wildlife markets are not unique to Asia; they’re also prevalent in West, Central and East Africa and beyond, Wolking said. PREDICT did collect samples in those markets and worked to understand the value chain – from the source animal in its natural habitat, through the trade system and the network, and into the market itself.
“It’s something that requires ongoing monitoring,” Wolking continued. “Everyone needs to understand that viruses evolve and things change and it’s not a static landscape.”
Wolking said a lot of work was done in China to monitor bats after SARS, but the risks remained. What needs to be addressed, he said, is the way humans are interacting with wildlife and the impact and the footprint of our species on the planet and how that’s responsible for causing some of these events.
“We really need to work on how to live safely with wildlife and how to live together and how to protect habitats, work with conservation groups and work with health experts and work with communities to really address some of the drivers of these things,” Wolking said.
Q: How much are climate change and encroachment on natural spaces factors in driving disease outbreaks
A: It definitely plays an important role, said Dr. Pandit. Flaviviruses, for example, are all transmitted by vectors – such as mosquitos and ticks – and their populations are heavily regulated by temperature and other climatic behaviors. There is a fear that these vectors will [become] more prevalent in temperate regions because of global warming.
Q: Have we identified beforehand the types of genes that are vulnerable to mutations leading to spillover into a new species? Is it possible to determine which viruses in the wild we might be immune to and which present more of a threat?
A: “This is what our lab teams are doing once we’ve detected a new virus,” said Dr. Pandit. For example, his lab at the University of California, Davis’ One Health Institute identified a new species of ebolavirus (Bombali virus) in Sierra Leone and is working together with partners to understand the specific genes and proteins used by the virus to infect bat cells and if the virus can infect human cells and cause disease. These studies are critical for understanding public health risks from a newly discovered virus and for informing the development of potential treatments and countermeasures if a new virus is determined to be a threat, he said.
Q: What are the potentially overlooked areas for spillover? Are there any other at-risk interfaces we should be aware of?
A: Livestock farming is definitely an important source of emerging zoonotic diseases – far higher than the wildlife trade, Dr. Pandit said. Mitigating those risks involves improving biosafety and reducing contact with wildlife and the contact interface between livestock and wildlife.
Q: You’ve identified more than 900 new viruses, along with the metadata about them. How do you determine which are the most threatening?
A: “That’s why we have a whole team working on modeling and analytics,” Dr. Pandit said. “We try to look at viruses that we already know are zoonotic and compare them with viruses that are not zoonotic or at least have yet to spillover into humans. And then we try to understand, what are the factors within zoonotic viruses that are making them zoonotic?”
They could be either ecological or virologic factors. On the ecological footprint, the team tries to ascertain whether the virus can get in contact with humans so that it can spillover. And then on the virologic footprint, they try to understand the specific genes that can help [the virus] get into humans.
Q: Can you provide practical advice for people who have to live with bats? Should we avoid eating them? What about people who collect guano?
A: There are ways to renovate houses so that bats cannot roost in them, said Dr. Grace Mwangoka, a research scientist based at the Ifakara Health Institute in Tanzania. If there is a chance it happens and people have to clean up their guano, they need to use protective gear, such as gloves and masks. People shouldn’t touch dead bats or feed them to their animals, but [rather] bury or burn them immediately.
It’s better also not to use bat guano, especially if you can get fertilized manure from other animals. “We have to try to protect ourselves. We have to live with them yes, but we have to make sure we live safely with them because they are carrying a lot of viruses and we don’t know at what time the virus will spill over,” Dr. Mwangoka said. [NB: It should also be noted that in addition to posing threats of viral spillover, bats play a very important and positive ecological role by eating insect pests and as pollinators.]
Q: Is there anything we can do to help build immunity in advance of future outbreaks? We’ve heard a lot about building herd immunity, for instance. So is there any way we can do that short of just letting the virus run through the human population or developing a vaccine?
A: As we know, the virus is quite fatal and has significant health impacts on certain groups of people, said Dr. Pandit. So the best approach, eventually, could be to develop a vaccine and develop herd immunity through vaccine. When it comes to emerging viruses, to avoid what’s really happening with COVID-19 we should think of reducing contact with wildlife and animals and target those specific interfaces where there is quite a lot of human-animal contact happening, which is giving viruses a lot of opportunity to jump into humans.
Q: There’s been a lot of talk about how we need to better monitor our interaction with wild animals and a lot of attention on these wildlife markets. Do you provide specific advice for how these markets should be regulated or monitored? Or do you think they should be closed down altogether?
A: Regulating of markets is a very complex issue, involving a lot of social factors as well, and some equity considerations, said Wolking. Often livelihoods are dependent on some of these activities. So there’s a lot of factors to consider there – culture, livelihoods, income – beyond just the simple blanket, ‘we can shut down a market and stop the risk.’
“We need to be aware that regulating markets is great, creating safer markets might be an option,” Wolking said. PREDICT has some partners in Southeast Asia working with governments on policy ideas and strategies around this issue. But it’s not a simple context to work through, he noted, and it’s hard to say whether regulating a market is going to stop the risk since there’s still the risk of contact with wildlife outside the market and continuation of the wildlife trade in underground markets where regulation is more challenging.
“That’s why we’ve taken, as researchers, the more value-chain approach to really understand the risk along the entire stream from the wild animal in its natural habitat into the market where it’s finally sold or consumed.”
The following questions and answers were asked and addressed via text during the webinar.
Q: When collecting data or monitoring wildlife, is there any point in that process where volunteers could be implemented to scale up data collection? Or is all data collection and monitoring high-risk for exposure to viruses?
A: Citizen science approaches would be really valuable. Sampling wildlife is indeed high-risk but data on interfaces, human behaviors, habitats, ecology, etc., are open avenues for further cooperation.
Q: One after-effect of virus spillover could be a vilification of animal species. In India for instance, bats are being killed (their roosts cut down) after Covid-19 came in. Does One Health also include dissemination of information and creating awareness of such issues -- and the ramifications of what such knee-jerk reactions could be?
A: Yes, One Health is critical in communicating the correct mitigation strategies, said Dr. Pandit. “We have developed material that we share with communities for living safely with wildlife. And that could be a great start. ” (See Living Safely with Bats, a communication campaign developed for West Africa)
Q: You guys have been working for the past decade, and still this spillover of COVID-19 happened. At which point have your projects contributed to alerting governments [of threats]?
A: Our teams communicate all findings and their associated risks with government partners. We detected more than 160 coronaviruses, but no research groups detected SARS-CoV-2 prior to the outbreak. This shows the complexity and diversity of viral threats and the need to work on preventing spillover at large for the diversity of disease threats.
Q: Could the design of PREDICT have picked-up this COVID-19 virus before clinical cases appeared? Or is the program designed to detect only known pathogens?
A: By design yes, we detected both known and new viruses and we have detected hundreds of coronaviruses and other viruses in bats, including SARS and MERS-related viruses, said Wolking. But, Dr. Pandit added, the surveillance was planned to collect samples only until March 2019, a few months before the virus emerged. PREDICT and partners have detected coronaviruses that are similar to SARS-CoV-2 and now are planning additional, though limited, work in the Asia region to re-test bat samples for SARS-CoV-2.
Q: Why did African countries struggle initially to test COVID-19 cases? Do we really not have the equipment or know-how? Or was it a plan to reduce panic or cover up its spread?
A: All countries, including the United States, have struggled with the launch of widespread testing, said Wolking. In Africa, there are many amazing labs and they are coming online as quickly as they can with testing given the global challenges.
Q: How long does a study of the kind Dr. Pandit ran last? Can some of the viruses we know about help us to be protected against COVID-19?
A: Developing models can take a long time, which also includes the validation of models with real data. It can be anywhere from a year to a few years. These known viruses help us identify the ecological drivers behind the emergence of viruses such as SARS-CoV-2. Hence studies like these will help avoid future emergence of viruses that can cause pandemics.
Q: What other factors are there to consider in assessing behavior risk?
A: Behavioral risk analysis includes looking into factors such as behavior related to animal contact, perception of people about health risks from animals and special behaviors, such as guano farming/hunting that tend to increase the chances of spillover from animals to humans, Dr. Pandit said.
Q: Can you please specifically cite one example of capacity building at the local level that is now active in responding to the COVID-19 pandemic?
A: As COVID was emerging from China, our partners successfully detected COVID-19 in the Southeast Asia region before there were specific assays available. Locally, we have many successes in partner countries where teams are engaged in response from the lab side to supporting community surveillance. Learn more here.
Q: What precautions are taken to ensure that the very act of virus hunting and the handling of viral material does not in itself cause a spillover?
A: Teams are trained to do the high-risk work of sampling and testing these samples from wildlife. All of our PREDICT teams take great precautions donning PPE [personal protective equipment] during sampling and testing, as you can see in some of the field photos shown here in today's presentation. Prior to engaging in any project activities, our staff and partners were trained and certified as proficient in biosafety, in the safe and humane handling of wildlife, as well as safe transport and storage of all biological materials. Our labs also have robust biosafety and biosecurity measures in place for sample storage, handing, and testing.
- David Wolking currently manages the PREDICT and PREEMPT projects. He is also the senior manager for global programs at the UC Davis One Health Institute. For the past 10 years he has worked with teams of scientists around the world to investigate emerging disease threats and identify solutions to prevent the spillover and spread of dangerous viruses.
- Dr. Pranav Pandit, a veterinary epidemiologist at UC Davis with a research interest in the ecology of emerging infectious diseases. His expertise lies in the mathematical modeling of infectious diseases in wildlife, livestock and humans. Pranav's recent research investigates environmental factors associated with the distribution of zoonotic pathogens in animal populations using innovative machine learning approaches.
- Dr. Grace Mwangoka, a research scientist based at the Ifakara Health Institute in Tanzania. As a veterinarian and public health expert, Grace is uniquely qualified as a leader in One Health research in Tanzania and recently led the PREDICT project's surveillance for emerging viral threats in at-risk human communities in Tanzania's Lake Zone.
- James Bangura, a project coordinator with UC Davis based in Freetown, Sierra Leone. James led the PREDICT project in Sierra Leone and also coordinates the PREEMPT project. A public health professional, he is a technical expert in outbreak response and is currently supporting national COVID-19 response efforts.
- USAID PREDICT Project - Stories and insights from 10 years of investigations into virus spillover and spread
- Link between virus spillover, wildlife extinction, and the environment
- Pandemic: How to prevent an outbreak (Netflix series featuring PREDICT team members)
- Spillover: Zika, Ebola, and Beyond (PBS film exploring the rise of spillover of viruses that can make the leap from animals to humans, how human behaviors spread diseases, and what science can do to anticipate and prevent epidemics around the world)
- COVID-19 Chapter 7: Spillover (Link to podcast exploring virus spillover with PREDICT project director Dr. Jonna Mazet)
- Emerging technologies to reduce catastrophic biologic risk (John Hopkins report on emerging technologies to reduce pandemic risk, including those in development by the PREEMPT project)
- How Climate Change Is Contributing to Skyrocketing Rates of Infectious Disease (ProPublica story that mentions PREDICT's work in China)
Banner image created by Lívia Koreeda for United Nations Global Call Out To Creatives - help stop the spread of COVID-19 - via Unsplash.