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Global Health Security is a research thematic we continue to pursue here at OODALoop, including the role of cybersecurity and emerging and exponential technologies in the areas of:
Featured here: promising innovations in global and U.S.-based pandemic preparedness and response by way of Artificial Intelligence-based Predictive Analytics and open-source participatory science.
New AI tool can predict viral variants, ID most dangerous, help make vaccines ‘future-proof’
As reported by the Harvard Gazzette:
…what if there were a way to make predictions about new viral variants before they actually emerge? A new artificial intelligence tool named EVEscape, developed by researchers at Harvard Medical School and the University of Oxford, can do just that. The tool has two elements:
Together, they allow EVEscape to make predictions about the variants most likely to occur as the virus evolves. In a study published Wednesday in Nature, the researchers show that had it been deployed at the start of the COVID-19 pandemic, EVEscape would have predicted the most frequent mutations and identified the most concerning variants for SARS-CoV-2. The tool also made accurate predictions about other viruses, including HIV and influenza. The researchers are now using EVEscape to look ahead at SARS-CoV-2 and predict future variants of concern; every two weeks, they release a ranking of new variants. Eventually, this information could help scientists develop more effective vaccines and therapies. The team is also broadening the work to include more viruses.
Designing mutation-proof vaccines and therapies
“We want to figure out how we can actually design vaccines and therapies that are future-proof.”
The team is now applying EVEscape to SARS-CoV-2 in real time, using all of the information available to make predictions about how it might evolve next. The researchers publish a biweekly ranking of new SARS-CoV-2 variants on their website and share this information with entities such as the World Health Organization. The complete code for EVEscape is also freely available online. They are also testing EVEscape on understudied viruses such as Lassa and Nipah, two pathogens of pandemic potential for which relatively little information exists.
Such less-studied viruses can have a huge impact on human health across the globe, the researchers noted. Another important application of EVEscape would be to evaluate vaccines and therapies against current and future viral variants. The ability to do so can help scientists design treatments that are able to withstand the escape mechanisms a virus acquires. “Historically, vaccine and therapeutic design has been retrospective, slow, and tied to the exact sequences known about a given virus,” Thadani said. Noor Youssef, a research fellow in the Marks lab, added, “We want to figure out how we can actually design vaccines and therapies that are future-proof.”
A tool called metagenomic sequencing can help detect unknown pathogens.
This article reports on a project in which an early warning radar system is being developed to detect the emergence of new pandemics before they become widespread. The proposed system would use data from sources like air travel, climate and weather patterns, and public health monitoring to identify potential pandemic outbreaks as soon as they occur. By tracking these events and providing early warnings to public health officials, the system could help prevent the spread of infectious diseases and save lives. The project is being developed by the European Commission in collaboration with IBM, and it is expected to be operational within the next few years.
The project has the potential to make a huge difference in the ability to detect and contain future pandemics. It could also provide invaluable information about how pandemics emerge and spread, allowing for more effective strategies to prevent them. If successful, the early warning radar system could be a powerful tool for helping to protect populations from the devastating effects of pandemics.
Crowdsourcing/Participatory Science
The Covid Moonshot effort to develop antivirals began in 2020 with a tweet. Three and a half years later, the team has a leading drug candidate.
The MIT Technoloy Review provides a really compelling overview of the recently released report by the Covid Moonshot – an open-science initiative to develop antivirals against the coronavirus:
“…the researchers behind the project published their results in Science. The effort, which relied on more than 200 volunteer scientists from 25 countries, produced 18,000 compound designs that led to the synthesis of 2,400 compounds. One of those became the basis for what is now the project’s lead candidate: a compound that targets the coronavirus’s main viral enzyme. The enzyme, known as Mpro, snips long viral proteins into short chunks, a key step in viral replication. The compound stops this enzyme from working. Paxlovid, an antiviral developed by Pfizer after the pandemic began, hits the same target.” Maybe that doesn’t feel like a huge win. Even if the compound works, it will likely take many more years to develop it into a drug. But “it’s still gone remarkably quickly if you were to compare that with most drug discovery stories,” says Charles Mowbray, discovery director of the nonprofit Drugs for Neglected Diseases Initiative (DNDi), a Moonshot participant.
What happens next? DNDi will be taking the lead on developing the lead candidate, called DNDI-6501, shepherding it through preclinical development. And the Covid Moonshot team will continue its work too. Last year, the US National Institutes of Health awarded the consortium nearly $69 million to continue developing oral antivirals. They’ll be developing drugs to treat not only the coronavirus but also West Nile, Zika, dengue, and enteroviruses. No medicine has ever made it to market through an entirely open-source process. But that doesn’t mean that the model can’t make a difference in drug development. The pharma company Shionogi used data from the Covid Moonshot to help develop its antiviral ensitrelvir, which is already approved for emergency use in Japan. “Contrary to what is often assumed, openness is not a barrier to translation of impactful molecules, either directly or by pharma,” says Matthew Todd, a chemist at University College London and the founder of Open Source Pharma.
Mowbray would like to see more sharing in drug research and development. We don’t know what virus will spark the next pandemic. Will it be a variant of something we’ve seen before, or an entirely new virus? The idea that a single entity would have enough antiviral drugs ready to manage the risks seems unrealistic, he says. “If we’re prepared to share what we’re doing between us, we probably have a much better chance of having the right drug candidates ready.”
At the end of their coverage of the release of the report by the Covid Moonshot team, almost as a coda, The MIT Technology Review also provided an update on the CDC’s effort focused on Traveler-based Genomic Surveillance: Preparing for the next pandemic requires more than a drug development overhaul. We also need to beef up our early warning system. In 2021, the Centers for DIsease Control and Prevention launched a surveillance project at a handful of major US airports to detect emerging SARS-CoV-2 variants. Now the agency plans to expand that program to cover 30 new pathogens, including influenza and RSV. For now, the additional testing will take place at just four airports: San Francisco International, JFK, Logan, and Dulles.
Here’s how it works:International travelers flying into airports where the surveillance program operates can volunteer to collect their own nasal swab samples. Those samples go to a lab for PCR testing. Positive samples undergo whole-genome sequencing. The program also collects samples of wastewater from individual planes and from the common drain into which all plane wastewater gets dumped. “One sample from an aircraft coming from a geographic destination afar can give us information potentially about 200 to 300 people that were on that plane,” Cindy Friedman, who leads the CDC’s traveler genomic surveillance program, told CNN. As of last month, the surveillance program had tested more than 370,000 travelers from more than 135 countries and sequenced more than 14,000 samples.
Planning for a Continuous Pandemic Landscape: COVID-19’s geopolitical repercussions are evident, with recent assessments pointing to China’s role in its spread. Regardless of the exact origins, the same conditions that allowed COVID-19 to become a pandemic persist today. Therefore, businesses must be prepared for consistent health disruptions, implying that a substantial portion of the workforce might always operate remotely, even though face-to-face interactions remain vital for critical decisions. See: COVID Sensemaking
The New Tech Trinity: Artificial Intelligence, BioTech, Quantum Tech: Will make monumental shifts in the world. This new Tech Trinity will redefine our economy, both threaten and fortify our national security, and revolutionize our intelligence community. None of us are ready for this. This convergence requires a deepened commitment to foresight and preparation and planning on a level that is not occurring anywhere. The New Tech Trinity.
The Revolution in Biology: This post provides an overview of key thrusts of the transformation underway in biology and offers seven topics business leaders should consider when updating business strategy to optimize opportunity because of these changes. For more see: The Executive’s Guide To The Revolution in Biology
About the Author
Daniel Pereira is research director at OODA. He is a foresight strategist, creative technologist, and an information communication technology (ICT) and digital media researcher with 20+ years of experience directing public/private partnerships and strategic innovation initiatives.
Informing your decisions with actionable intelligence
Informing your decisions with actionable intelligence