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America’s sequencing boom may be throwing money at the wrong problem

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America's sequencing boom may be throwing money at the wrong problem


Instead of trying to work through these issues at the national level, the sequencing contracts allow individual public health agencies to request the names and contact information of people who have tested positive for variants of concern. But that just pushes the same problems of data ownership down the chain.

“Some states are very good and want to know a lot about variants that are circulating in their state,” says Labcorp’s Brian Krueger. “The other states are not.” 

Public health epidemiologists often have little experience with bioinformatics, using software to analyze large datasets like genomic sequences. Only a few agencies have pre-existing sequencing programs; even if they did, having each jurisdiction to analyze just a small slice of the dataset undercuts how much knowledge can be gleaned about real-world behavior.

Getting around those issues—making it easier to connect sequences and clinical metadata on a large scale—would require more than just root and branch reform of privacy regulations, however. It would need a reorganization of the entire healthcare and public health systems in the US, where each of the 64 public health agencies operate as fiefdoms, and there is no centralization of information or power. 

“Metadata is the single biggest uncracked nut,” says Jonathan Quick, managing director of pandemic response, preparedness, and prevention at the Rockefeller Foundation. (The Rockefeller Foundation helps fund coverage at MIT Technology Review,, although it has no editorial oversight.) Because it’s so hard for public health to put together big enough datasets to really understand real-world variant behavior, our understanding has to come from vaccine manufacturers and hospitals adding sequencing to their own clinical trials, he says. 

It’s frustrating to him that so many huge datasets of useful information already exist in electronic medical records, immunization registries, and other sources, but can’t easily be used. 

“There’s a whole lot more that could be learned, and learned faster, without the shackles we put on the use of that data,” says Quick. “We can’t just rely on the vaccine companies to do surveillance.”

Boosting state-level bioinformatics

If public health labs are expected to focus more on tracking and understanding variants on their own, they’ll need all the help they can get. Doing something about variants case-by-case, after all, is a public health job, while doing something about variants on a policy level is a political one. 

Public health labs generally use genomics to expose otherwise-hidden information about outbreaks, or as part of track and trace efforts. In the past, sequencing has been used to connect E. coli outbreaks to specific farms, identify and interrupt chains of HIV transmission, isolate US Ebola cases, and follow annual flu patterns. 

Even those with well-established programs tend to use genomics sparingly. The cost of sequencing has dropped precipitously over the last decade, but the process is still not cheap, particularly for cash-strapped state and local health departments. The machines themselves cost hundreds of thousands of dollars to buy, and more to run: Illumina, one of the biggest makers of sequencing equipment, says labs spend an average of $1.2 million annually on supplies for each of its machines. 

“We’ll miss a ton of opportunities if we just give health departments money to set up programs without having a federal strategy so that everyone knows what they’re doing”

Health agencies don’t just need money; they also need expertise. Surveillance requires highly trained bioinformaticians to turn a sequence’s long strings of letters into useful information, as well as people to explain the results to officials, and convince them to turn any lessons learned into policy. 

Fortunately, the OAMD has been working to support state and local health departments as they try to understand their sequencing data, employing regional bioinformaticians to consult with public health officers and facilitating agencies’ efforts to share their experiences.

It is also pouring hundreds of millions into building and supporting those agencies’ own sequencing programs—not just for covid, but for all pathogens.

But many of those agencies are facing pressure to sequence as many covid genomes as possible. Without a cohesive strategy for collecting and analyzing data, it’s unclear how much utility those programs will have. 

“We’ll miss a ton of opportunities if we just give health departments money to set up programs without having a federal strategy so that everyone knows what they’re doing,” says Warmbrod.

Initial visions, usurped

Mark Pandori is director of the Nevada state public health laboratory, one of the programs OAMD supports. He has been a strong proponent of genomic surveillance for years. Before moving to Reno, he ran the public health lab in Alameda County, California, where he helped pioneer a program using sequencing to track how infections were being passed around hospitals. 

Turning sequences into usable data is the biggest challenge for public health genomics programs, he says.

“The CDC can say, ‘go buy a bunch of sequencing equipment, do a whole bunch of sequencing.’ But it doesn’t do anything unless the consumers of that data know how to use it, and know how to apply it,” he says. “I’m talking to you about the robotics we need to get things sequenced every day, but health departments just need a simple way to know if cases are related.”

When it comes to variants, public health labs are under many of the same pressures the CDC faces: everyone wants to know what variants are circulating, whether or not they can do anything with the information.

Pandori launched his covid sequencing program hoping to cut down on the labor needed to investigate potential covid outbreaks, quickly identifying whether cases caught near each other were related or coincidental. 

His lab was the first in North America to identify a patient reinfected with covid-19, and later found the B.1.351 variant in a hospitalized man who had just come back from South Africa. With rapid contact tracing, the health department was able to prevent it from spreading.

Tech

Investing in women pays off

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Investing in women pays off


“Starting a business is a privilege,” says Burton O’Toole, who worked at various startups before launching and later selling AdMass, her own marketing technology company. The company gave her access to the HearstLab program in 2016, but she soon discovered that she preferred the investment aspect and became a vice president at HearstLab a year later. “To empower some of the smartest women to do what they love is great,” she says. But in addition to rooting for women, Burton O’Toole loves the work because it’s a great market opportunity. 

“Research shows female-led teams see two and a half times higher returns compared to male-led teams,” she says, adding that women and people of color tend to build more diverse teams and therefore benefit from varied viewpoints and perspectives. She also explains that companies with women on their founding teams are likely to get acquired or go public sooner. “Despite results like this, just 2.3% of venture capital funding goes to teams founded by women. It’s still amazing to me that more investors aren’t taking this data more seriously,” she says. 

Burton O’Toole—who earned a BS from Duke in 2007 before getting an MS and PhD from MIT, all in mechanical engineering—has been a “data nerd” since she can remember. In high school she wanted to become an actuary. “Ten years ago, I never could have imagined this work; I like the idea of doing something in 10 more years I couldn’t imagine now,” she says. 

When starting a business, Burton O’Toole says, “women tend to want all their ducks in a row before they act. They say, ‘I’ll do it when I get this promotion, have enough money, finish this project.’ But there’s only one good way. Make the jump.”

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Preparing for disasters, before it’s too late

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Preparing for disasters, before it’s too late


All too often, the work of developing global disaster and climate resiliency happens when disaster—such as a hurricane, earthquake, or tsunami—has already ravaged entire cities and torn communities apart. But Elizabeth Petheo, MBA ’14, says that recently her work has been focused on preparedness. 

It’s hard to get attention for preparedness efforts, explains Petheo, a principal at Miyamoto International, an engineering and disaster risk reduction consulting firm. “You can always get a lot of attention when there’s a disaster event, but at that point it’s too late,” she adds. 

Petheo leads the firm’s projects and partnerships in the Asia-Pacific region and advises globally on international development and humanitarian assistance. She also works on preparedness in the Asia-Pacific region with the United States Agency for International Development. 

“We’re doing programming on the engagement of the private sector in disaster risk management in Indonesia, which is a very disaster-prone country,” she says. “Smaller and medium-sized businesses are important contributors to job creation and economic development. When they go down, the impact on lives, livelihoods, and the community’s ability to respond and recover effectively is extreme. We work to strengthen their own understanding of their risk and that of their surrounding community, lead them through an action-planning process to build resilience, and link that with larger policy initiatives at the national level.”

Petheo came to MIT with international leadership experience, having managed high-profile global development and risk mitigation initiatives at the World Bank in Washington, DC, as well as with US government agencies and international organizations leading major global humanitarian responses and teams in Sri Lanka and Haiti. But she says her time at Sloan helped her become prepared for this next phase in her career. “Sloan was the experience that put all the pieces together,” she says.

Petheo has maintained strong connections with MIT. In 2018, she received the Margaret L.A. MacVicar ’65, ScD ’67, Award in recognition of her role starting and leading the MIT Sloan Club in Washington, DC, and her work as an inaugural member of the Graduate Alumni Council (GAC). She is also a member of the Friends of the MIT Priscilla King Gray Public Service Center.

“I believe deeply in the power and impact of the Institute’s work and people,” she says. “The moment I graduated, my thought process was, ‘How can I give back, and how can I continue to strengthen the experience of those who will come after me?’”

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The Download: a curb on climate action, and post-Roe period tracking

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The US Supreme Court just gutted the EPA’s power to regulate emissions


Why’s it so controversial?: Geoengineering was long a taboo topic among scientists, and some argue it should remain one. There are questions about its potential environmental side effects, and concerns that the impacts will be felt unevenly across the globe. Some feel it’s too dangerous to ever try or even to investigate, arguing that just talking about the possibility could weaken the need to address the underlying causes of climate change.

But it’s going ahead?: Despite the concerns, as the threat of climate change grows and major nations fail to make rapid progress on emissions, growing numbers of experts are seriously exploring the potential effects of these approaches. Read the full story.

—James Temple

The must-reads

I’ve combed the internet to find you today’s most fun/important/scary/fascinating stories about technology.

1 The belief that AI is alive refuses to die
People want to believe the models are sentient, even when their creators deny it. (Reuters)
+ It’s unsurprising wild religious beliefs find a home in Silicon Valley. (Vox)
+ AI systems are being trained twice as quickly as they were just last year. (Spectrum IEEE)

2 The FBI added the missing cryptoqueen to its most-wanted list
It’s offering a $100,000 reward for information leading to Ruja Ignatova, whose crypto scheme defrauded victims out of more than $4 billion. (BBC)
+ A new documentary on the crypto Ponzi scheme is in the works. (Variety)

3 Social media platforms turn a blind eye to dodgy telehealth ads
Which has played a part in the prescription drugs abuse boom. (Protocol)
+ The doctor will Zoom you now. (MIT Technology Review)

4 We’re addicted to China’s lithium batteries
Which isn’t great news for other countries building electric cars. (Wired $)
+ This battery uses a new anode that lasts 20 times longer than lithium. (Spectrum IEEE)
+ Quantum batteries could, in theory, allow us to drive a million miles between charges. (The Next Web)

5 Far-right extremists are communicating over radio to avoid detection
Making it harder to monitor them and their violent activities. (Slate $)
+ Many of the rioters who stormed the Capitol were carrying radio equipment. (The Guardian)

6 Bro culture has no place in space 🚀
So says NASA’s former deputy administrator, who’s sick and tired of misogyny in the sector. (CNN)

7 A US crypto exchange is gaining traction in Venezuela
It’s helping its growing community battle hyperinflation, but isn’t as decentralized as they believe it to be. (Rest of World)
+ The vast majority of NFT players won’t be around in a decade. (Vox)
+ Exchange Coinbase is working with ICE to track and identify crypto users. (The Intercept)
+ If RadioShack’s edgy tweets shock you, don’t forget it’s a crypto firm now. (NY Mag)

8 It’s time we learned to love our swamps
Draining them prevents them from absorbing CO2 and filtering out our waste. (New Yorker $)
+ The architect making friends with flooding. (MIT Technology Review) 

9 Robots love drawing too 🖍️
Though I’ll bet they don’t get as frustrated as we do when they mess up. (Input)

10 The risky world of teenage brains
Making potentially dangerous decisions is an important part of adolescence, and our brains reflect that. (Knowable Magazine)

Quote of the day

“They shamelessly celebrate an all-inclusive pool party while we can’t even pay our rent!”

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