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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 preexisting sequencing programs; even if they did, having each jurisdiction analyze just a small slice of the data set 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 mean a reorganization of the entire health care system 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 experts to put together big enough data sets to really understand real-world variant behavior, our understanding has to come from vaccine manufacturers and hospitals that add sequencing to their own clinical trials, he says. 

It’s frustrating to him that so many huge data sets 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 dramatically 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.

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The world had a chance to avoid the pandemic—but blew it

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The world had a chance to avoid the pandemic—but blew it


The covid-19 pandemic is a catastrophe that could have been averted, say a panel of 13 independent experts tasked with assessing the global response to the crisis. 

Their report, released May 12 and commissioned by the WHO, lambasts global leaders who failed to heed repeated warnings, wasted time, hoarded information and desperately needed supplies, and failed to take the crisis seriously. While some countries took aggressive steps to curb the spread of the virus, “many countries, including some of the wealthiest, devalued the emerging science, denied the disease’s severity, delayed responding, and ended up sowing distrust among citizens with literally deadly consequences,” said Helen Clark, cochair of the Independent Panel for Pandemic Preparedness and Response and former prime minister of New Zealand, on Wednesday. 

The report —COVID-19: Make It the Last Pandemic  takes a hard look at why we failed to curb the spread of the coronavirus. It also looks to the future, highlighting strategies for ending the current crisis and avoiding future ones. 

Here are five key takeaways: 

  1. We had an opportunity to avoid disaster in early 2020, and we squandered it. “The combination of poor strategic choices, unwillingness to tackle inequalities, and an uncoordinated system created a toxic cocktail which allowed the pandemic to turn into a catastrophic human crisis,” the authors write. 
  2. Vaccine supply must be boosted and shots redistributed. The report calls on rich countries to provide a billion vaccine doses to low- and middle-income countries by September 2021 and another billion by the middle of next year. It also pushes for vaccine makers to offer up licensing and technology transfer agreements. And if those agreements don’t come within three months, it calls for an automatic waiver so that production can begin where the shots are most needed.  
  3. The World Health Organization needs more power and more money. The WHO should have the authority to investigate pathogens with pandemic potential in any country on short notice, and to publish information about outbreaks without approval from national governments.  
  4. A new organization is needed to help the WHO. The report calls for the formation of a Global Health Threats Council composed of heads of state to ensure that countries stay committed to pandemic preparedness and to hold countries accountable if they fail to curb outbreaks.  
  5. The pandemic’s impact on nearly every aspect of daily life is hard to overstate. More than 3 million people have died of covid-19, including at least 17,000 health workers. The crisis provided “the deepest shock to the global economy since the Second World War and the largest simultaneous contraction of national economies since the Great Depression,” the panel writes. The crisis pushed more than a hundred million people into extreme poverty. “Most dispiriting is that those who had least before the pandemic have even less now,” they add.  

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A nonprofit promised to preserve wildlife. Then it made millions claiming it could cut down trees

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A nonprofit promised to preserve wildlife. Then it made millions claiming it could cut down trees


Clegern said the program’s safeguards prevent the problems identified by CarbonPlan.   

California’s offsets are considered additional carbon reductions because the floor serves “as a conservative backstop,” Clegern said. Without it, he explained, many landowners could have logged to even lower levels in the absence of offsets.

Clegern added that the agency’s rules were adopted as a result of a lengthy process of debate and were upheld by the courts. A California Court of Appeal found the Air Resources Board had the discretion to use a standardized approach to evaluate whether projects were additional.

But the court did not make an independent determination about the effectiveness of the standard, and was “quite deferential to the agency’s judgment,” said Alice Kaswan, a law professor at the University of San Francisco School of Law, in an email.

California law requires the state’s cap-and-trade regulations to ensure that emissions reductions are “real, permanent, quantifiable, verifiable” and “in addition to any other greenhouse gas emission reduction that otherwise would occur.”

“If there’s new scientific information that suggests serious questions about the integrity of offsets, then, arguably, CARB has an ongoing duty to consider that information and revise their protocols accordingly,” Kaswan said. “The agency’s obligation is to implement the law, and the law requires additionality.”

The recipe

On an early spring day, Lautzenheiser, the Audubon scientist, brought a reporter to a forest protected by the offset project. The trees here were mainly tall white pines mixed with hemlocks, maples and oaks. Lautzenheiser is usually the only human in this part of the woods, where he spends hours looking for rare plants or surveying stream salamanders.

The nonprofit’s planning documents acknowledge that the forests enrolled in California’s program were protected long before they began generating offsets: “A majority of the project area has been conserved and designated as high conservation value forest for many years with deliberate management focused on long-term natural resource conservation values.”

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Meet Jennifer Daniel, the woman who decides what emoji we get to use

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Meet Jennifer Daniel, the woman who decides what emoji we get to use


Emoji are now part of our language. If you’re like most people, you pepper your texts, Instagram posts, and TikTok videos with various little images to augment your words—maybe the syringe with a bit of blood dripping from it when you got your vaccination, the prayer (or high-fiving?) hands as a shortcut to “thank you,” a rosy-cheeked smiley face with jazz hands for a covid-safe hug from afar. Today’s emoji catalogue includes nearly 3,000 illustrations representing everything from emotions to food, natural phenomena, flags, and people at various stages of life.

Behind all those symbols is the Unicode Consortium, a nonprofit group of hardware and software companies aiming to make text and emoji readable and accessible to everyone. Part of their goal is to make languages look the same on all devices; a Japanese character should be typographically consistent across all media, for example. But Unicode is probably best known for being the gatekeeper of emoji: releasing them, standardizing them, and approving or rejecting new ones.

Jennifer Daniel is the first woman at the helm of the Emoji Subcommittee for the Unicode Consortium and a fierce advocate for inclusive, thoughtful emoji. She initially rose to prominence for introducing Mx. Claus, a gender-inclusive alternative to Santa and Mrs. Claus; a non-gendered person breastfeeding a non-gendered baby; and a masculine face wearing a bridal veil. 

Now she’s on a mission to bring emoji to a post-pandemic future in which they are as broadly representative as possible. That means taking on an increasingly public role, whether it’s with her popular and delightfully nerdy Substack newsletter, What Would Jennifer Do? (in which she analyzes the design process for upcoming emoji), or inviting the general public to submit concerns about emoji and speak up if they aren’t representative or accurate.

“There isn’t a precedent here,” Daniel says of her job. And to Daniel, that’s exciting not just for her but for the future of human communication.

I spoke to her about how she sees her role and the future of emoji. The interview has been lightly edited and condensed. 

What does it mean to chair the subcommittee on emoji? What do you do?

It’s not sexy. [laughs] A lot of it is managing volunteers [the committee is composed of volunteers who review applications and help in approval and design]. There’s a lot of paperwork. A lot of meetings. We meet twice a week.

I read a lot and talk to a lot of people. I recently talked to a gesture linguist to learn how people use their hands in different cultures. How do we make better hand-gesture emoji? If the image is no good or isn’t clear, it’s a dealbreaker. I’m constantly doing lots of research and consulting with different experts. I’ll be on the phone with a botanical garden about flowers, or a whale expert to get the whale emoji right, or a cardiovascular surgeon so we have the anatomy of the heart down. 

There’s an old essay by Beatrice Warde about typography. She asked if a good typeface is a bedazzled crystal goblet or a transparent one. Some would say the ornate one because it’s so fancy, and others would say the crystal goblet because you can see and appreciate the wine. With emoji, I lend myself more to the “transparent crystal goblet” philosophy. 

Why should we care about how our emoji are designed?

My understanding is that 80% of communication is nonverbal. There’s a parallel in how we communicate. We text how we talk. It’s informal, it’s loose. You’re pausing to take a breath. Emoji are shared alongside words.

When emoji first came around, we had the misconception that they were ruining language. Learning a new language is really hard, and emoji is kind of like a new language. It works with how you already communicate. It evolves as you evolve. How you communicate and present yourself evolves, just like yourself. You can look at the nearly 3,000 emoji and it [their interpretation] changes by age or gender or geographic area. When we talk to someone and are making eye contact, you shift your body language, and that’s an emotional contagion. It builds empathy and connection. It gives you permission to reveal that about yourself. Emoji can do that, all in an image.

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