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This is how America gets its vaccines

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This is how America gets its vaccines


Biden’s newly released pandemic strategy is organized around a central goal: to oversee administration of 100 million vaccines in 100 days. To do it, he’ll have to fix the mess.

Some critics have called his plan too ambitious; others have said it’s not ambitious enough. It’s guaranteed to be an uphill battle. But before we get to the solutions, we need to understand how the system operates at the moment—and which aspects of it should be ditched, replaced, or retained.

From manufacturer to patient

At the federal level, two core systems sit between the vaccine factories and the clinics that will administer the shots: Tiberius, the Department of Health and Human Services’ vaccine allocation planning system, and VTrckS, the Centers for Disease Control and Prevention’s vaccine ordering portal. 

Tiberius takes data from dozens of mismatched sources and turns it into usable information to help state and federal agencies plan distribution. VTrckS is where states actually order and distribute shots.

The two are eons apart technologically. Whereas Palantir built Tiberius last summer using the latest available technology, VTrckS is a legacy system that has passed through multiple vendors over its 10-year existence. The two are largely tied together by people downloading files from one and uploading them to the other.

Dozens of other private, local, state, and federal systems are involved in allocating, distributing, tracking, and administering vaccines. Here’s a step-by-step explanation of the process.

Step one: Manufacturers produce the vaccine

HHS receives regular production updates from Pfizer and Moderna. The manufacturers communicate estimated volumes in advance to help HHS plan before confirming real production numbers, which are piped into Tiberius.

Both vaccines are made of messenger RNA, a biotechnology that’s never been produced at scale before, and they need to be kept extremely cold until just before they go into a needle: Moderna’s must be kept at -25 to -15 °C, while Pfizer’s requires even lower temperatures of -80 to -60 °C. In the fall, it became clear that manufacturers had overestimated how quickly they could distribute doses, according to Deacon Maddox, Operation Warp Speed’s chief of plans, operations, and analytics and a former MIT fellow.

“Manufacturing, especially of a nascent biological product, is very difficult to predict,” he says. “You can try, and of course everybody wants to you try, because everybody wants to know exactly how much they’re going to get. But it’s impossible.”

PFIZER

This led to some of the first stumbles in the rollout. While training the states on how to use Tiberius, Operation Warp Speed entered those inflated estimates into a “sandbox” version of the software so states could model different distribution strategies for planning purposes. When those numbers didn’t pan out in reality, there was confusion and anger.

“At the end of December, people were saying, ‘We were told we were going to get this and they cut it back.’ That was all because we put notional numbers into the exercise side, and folks assumed that was what they were going to get,” says Maddox. “Allocation numbers are highly charged. People get very emotional.”

Step two: The federal government sets vaccine allocations

Every week, HHS officials look at production estimates and inventory numbers and decide on the “big number”—how many doses of each vaccine will go out to states and territories in total. Lately, they’ve been sticking to roughly 4.3 million per week, which they’ve found “allows us to get through lows in manufacturing, and save through highs,” Maddox says.

That number goes into Tiberius, which divvies up vaccines on the basis of Census data. Both HHS and media reports have sometimes described this step as using an algorithm in Tiberius. This should not be confused with any kind of machine learning. It’s just simple math based on the allocation policy, Maddox says.

Thus far, the policy has been to distribute vaccines according to each jurisdiction’s adult (18+) population. Maddox says the logic in Tiberius could easily be updated should Biden decide to do it on another basis, such as elderly (65+) population.

Once Operation Warp Speed analysts confirm the official allocation numbers, Tiberius pushes the figures to jurisdictions within their version of the software. An HHS employee then downloads the same numbers in a file and sends them to the CDC, where a technician manually uploads it to set order limits in VTrckS. (You can think of VTrckS as something like an online store: when health departments go to order vaccines, they can only add so many to their cart.)

Even that hasn’t been an exact science. Shortly before the inauguration, in a phone call with Connecticut governor Ned Lamont, outgoing HHS secretary Alex Azar promised to send the state 50,000 extra doses as a reward for administering vaccines efficiently. The doses arrived the next week.

The deal was representative of “the rather loose nature of the vaccine distribution process from the federal level,” Lamont’s press secretary, Max Reiss, told us in an email. 

Step three: States and territories distribute the vaccine locally

State and territory officials learn how many vaccines they’ve been allotted through their own version of Tiberius, where they can model different distribution strategies.

Tiberius lets officials put data overlays on a map of their jurisdiction to help them plan, including Census data on where elderly people and health-care workers are clustered; the CDC’s so-called social vulnerability index of different zip codes, which estimates disaster preparedness on the basis of factors like poverty and transportation access; and data on hospitalizations and other case metrics from Palantir’s covid surveillance system, HHS Protect. They can also enter and view their own data to see where vaccination clinics and ultra-cold freezers are located, how many doses different sites have requested, and where vaccines have already gone.

Once states decide how many doses of each vaccine they want to send to each site, they download a file with addresses and dose numbers. They upload it into VTrckS, which transmits it to the CDC, which sends it to manufacturers.

A Pfizer shipment

PFIZER

Last week, Palantir rolled out a new “marketplace exchange” feature, effectively giving states the option to barter vaccines. Since the feds divvy up both Moderna and Pfizer vaccines without regard to how many ultra-cold freezers states have, rural states may need to trade their Pfizer allotment for another state’s Moderna shots, Maddox says.

When thinking about the utility of the system, it’s worth noting that many health departments have a shallow bench of tech-savvy employees who can easily navigate data-heavy systems.

“It’s a rare person who knows technology and the health side,” says Craig Newman, who researches health system interoperability at the Altarum Institute. “Now you throw in large-scale epidemiology…it’s really hard to see the entire thing from A to Z.”

Step four: Manufacturers ship the vaccines

Somehow, shipping millions of vaccines to 64 different jurisdictions at -70 °C is the easy part.

The CDC sends states’ orders to Pfizer and to Moderna’s distribution partner McKesson. Pfizer ships orders directly to sites by FedEx and UPS; Moderna’s vaccines go first to McKesson hubs, which then hand them off to FedEx and UPS for shipping.

Tracking information is sent to Tiberius for every shipment so HHS can keep tabs on how deliveries are going.

Step five: Local pharmacies and clinics administer the vaccine

At this point, things really start to break down. 

With little federal guidance or money, jurisdictions are struggling with even the most basic requirements of mass immunization, including scheduling and keeping track of who’s been vaccinated.

Getting people into the clinic may intuitively seem easy, but it’s been a nightmare almost everywhere. Many hospital-based clinics are using their own systems; county and state clinics are using any number of public and private options, including Salesforce and Eventbrite. Online systems have become a huge stumbling block, especially for elderly people. Whenever jurisdictions set up hot lines for the technologically unsavvy, their call centers are immediately overwhelmed. 

Even within states, different vaccination sites are all piecing together their own hodgepodge solutions. To record who’s getting vaccines, many states have retrofitted existing systems for tracking children’s immunizations. Agencies managing those systems were already stretched thin trying to piece together messy data sources.

FedEx and UPS trucks depart from Pfizer.

PFIZER

It may not even be clear who’s in charge of allocating doses. Maddox described incidents when state officials contacted HHS to say their caps were too low in VTrckS, only to realize that someone else within their office had transferred doses to a federal program that distributes vaccines to long-term care homes, without telling other decision makers.

“Operation Warp Speed was an incredible effort to bring the vaccine to market quickly,” and get it to all 50 states, says Hana Schank, the director of strategy for public interest technology at the think tank New America. “All of that was done beautifully.” But, she says, the program paid little attention to how the vaccines would actually get to people.

Many doctors, frustrated by the rollout, agree with that sentiment. 

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How Twitter’s “Teacher Li” became the central hub of China protest information

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How Twitter’s “Teacher Li” became the central hub of China protest information


It’s hard to describe the feeling that came after. It’s like everyone is coming to you and all kinds of information from all over the world is converging toward you and [people are] telling you: Hey, what’s happening here; hey, what’s happening there; do you know, this is what’s happening in Guangzhou; I’m in Wuhan, Wuhan is doing this; I’m in Beijing, and I’m following the big group and walking together. Suddenly all the real-time information is being submitted to me, and I don’t know how to describe that feeling. But there was also no time to think about it. 

My heart was beating very fast, and my hands and my brain were constantly switching between several software programs—because you know, you can’t save a video with Twitter’s web version. So I was constantly switching software, editing the video, exporting it, and then posting it on Twitter. [Editor’s note: Li adds subtitles, blocks out account information, and compiles shorter videos into one.] By the end, there was no time to edit the videos anymore. If someone shot and sent over a 12-second WeChat video, I would just use it as is. That’s it. 

I got the largest amount of [private messages] around 6:00 p.m. on Sunday night. At that time, there were many people on the street in five major cities in China: Beijing, Shanghai, Chengdu, Wuhan, and Guangzhou. So I basically was receiving a dozen private messages every second. In the end, I couldn’t even screen the information anymore. I saw it, I clicked on it, and if it was worth posting, I posted it.

People all over the country are telling me about their real-time situations. In order for more people not to be in danger, they went to the [protest] sites themselves and sent me what was going on there. Like, some followers were riding bikes near the presidential palace in Nanjing, taking pictures, and telling me about the situation in the city. And then they asked me to inform everyone to be cautious. I think that’s a really moving thing.

It’s like I have gradually become an anchor sitting in a TV studio, getting endless information from reporters on the scene all over the country. For example, on Monday in Hangzhou, there were five or six people updating me on the latest news simultaneously. But there was a break because all of them were fleeing when the police cleared the venue. 

On the importance of staying objective 

There are a lot of tweets that embellish the truth. From their point of view, they think it’s the right thing to do. They think you have to maximize the outrage so that there can be a revolt. But for me, I think we need reliable information. We need to know what’s really going on, and that’s the most important thing. If we were doing it for the emotion, then in the end I really would have been part of the “foreign influence,” right? 

But if there is a news account outside China that can record what’s happening objectively, in real time, and accurately, then people inside the Great Firewall won’t have doubts anymore. At this moment, in this quite extreme situation of a continuous news blackout, to be able to have an account that can keep posting news from all over the country at a speed of almost one tweet every few seconds is actually a morale boost for everyone. 

Chinese people grow up with patriotism, so they become shy or don’t dare to say something directly or oppose something directly. That’s why the crowd was singing the national anthem and waving the red flag, the national flag [during protests]. You have to understand that the Chinese people are patriotic. Even when they are demanding things [from the government], they do it with that sentiment. 

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Your microbiome ages as you do—and that’s a problem

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Your microbiome ages as you do—and that’s a problem


These ecosystems appear to change as we age—and these changes can potentially put us at increased risk of age-related diseases. So how can we best look after them as we get old? And could an A-grade ecosystem help fend off diseases and help us lead longer, healthier lives?

It’s a question I’ve been pondering this week, partly because I know a few people who have been put on antibiotics for winter infections. These drugs—lifesaving though they can be—can cause mass destruction of gut microbes, wiping out the good along with the bad. How might people who take them best restore a healthy ecosystem afterwards?

I also came across a recent study in which scientists looked at thousands of samples of people’s gut microbe populations to see how they change with age. The standard approach to working out what microbes are living in a person’s gut is to look at feces. The idea is that when we have a bowel movement, we shed plenty of gut bacteria. Scientists can find out which species and strains of bacteria are present to get an estimate of what’s in your intestines.

In this study, a team based at University College Cork in Ireland analyzed data that had already been collected from 21,000 samples of human feces. These had come from people all over the world, including Europe, North and South America, Asia, and Africa. Nineteen nationalities were represented. The samples were all from adults between 18 and 100. 

The authors of this study wanted to get a better handle on what makes for a “good” microbiome, especially as we get older. It has been difficult for microbiologists to work this out. We do know that some bacteria can produce compounds that are good for our guts. Some seem to aid digestion, for example, while others lower inflammation.
 
But when it comes to the ecosystem as a whole, things get more complicated. At the moment, the accepted wisdom is that variety seems to be a good thing—the more microbial diversity, the better. Some scientists believe that unique microbiomes also have benefits, and that a collection of microbes that differs from the norm can keep you healthy.
 
The team looked at how the microbiomes of younger people compared with those of older people, and how they appeared to change with age. The scientists also looked at how the microbial ecosystems varied with signs of unhealthy aging, such as cognitive decline, frailty, and inflammation.
 
They found that the microbiome does seem to change with age, and that, on the whole, the ecosystems in our guts do tend to become more unique—it looks as though we lose aspects of a general “core” microbiome and stray toward a more individual one.
 
But this isn’t necessarily a good thing. In fact, this uniqueness seems to be linked to unhealthy aging and the development of those age-related symptoms listed above, which we’d all rather stave off for as long as possible. And measuring diversity alone doesn’t tell us much about whether the bugs in our guts are helpful or not in this regard.
 
The findings back up what these researchers and others have seen before, challenging the notion that uniqueness is a good thing. Another team has come up with a good analogy, which is known as the Anna Karenina principle of the microbiome: “All happy microbiomes look alike; each unhappy microbiome is unhappy in its own way.”
 
Of course, the big question is: What can we do to maintain a happy microbiome? And will it actually help us stave off age-related diseases?
 
There’s plenty of evidence to suggest that, on the whole, a diet with plenty of fruit, vegetables, and fiber is good for the gut. A couple of years ago, researchers found that after 12 months on a Mediterranean diet—one rich in olive oil, nuts, legumes, and fish, as well as fruit and veg—older people saw changes in their microbiomes that might benefit their health. These changes have been linked to a lowered risk of developing frailty and cognitive decline.
 
But at the individual level, we can’t really be sure of the impact that changes to our diets will have. Probiotics are a good example; you can chug down millions of microbes, but that doesn’t mean that they’ll survive the journey to your gut. Even if they do get there, we don’t know if they’ll be able to form niches in the existing ecosystem, or if they might cause some kind of unwelcome disruption. Some microbial ecosystems might respond really well to fermented foods like sauerkraut and kimchi, while others might not.
 
I personally love kimchi and sauerkraut. If they do turn out to support my microbiome in a way that protects me against age-related diseases, then that’s just the icing on the less-microbiome-friendly cake.

To read more, check out these stories from the Tech Review archive:
 
At-home microbiome tests can tell you which bugs are in your poo, but not much more than that, as Emily Mullin found.
 
Industrial-scale fermentation is one of the technologies transforming the way we produce and prepare our food, according to these experts.
 
Can restricting your calorie intake help you live longer? It seems to work for monkeys, as Katherine Bourzac wrote in 2009. 
 
Adam Piore bravely tried caloric restriction himself to find out if it might help people, too. Teaser: even if you live longer on the diet, you will be miserable doing so. 

From around the web:

Would you pay $15,000 to save your cat’s life? More people are turning to expensive surgery to extend the lives of their pets. (The Atlantic)
 
The World Health Organization will now start using the term “mpox” in place of “monkeypox,” which will be phased out over the next year. (WHO)
 
After three years in prison, He Jiankui—the scientist behind the infamous “CRISPR babies”—is attempting a comeback. (STAT)
 
Tech that allows scientists to listen in on the natural world is revealing some truly amazing discoveries. Who knew that Amazonian sea turtles make more than 200 distinct sounds? And that they start making sounds before they even hatch? (The Guardian)
 
These recordings provide plenty of inspiration for musicians. Whale song is particularly popular. (The New Yorker)
 
Scientists are using tiny worms to diagnose pancreatic cancer. The test, launched in Japan, could be available in the US next year. (Reuters)

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The Download: circumventing China’s firewall, and using AI to invent new drugs

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The Download: circumventing China’s firewall, and using AI to invent new drugs


As protests against rigid covid control measures in China engulfed social media in the past week, one Twitter account has emerged as the central source of information: @李老师不是你老师 (“Teacher Li Is Not Your Teacher”). 

People everywhere in China have sent protest footage and real-time updates to the account through private messages, and it has posted them, with the sender’s identity hidden, on their behalf.

The man behind the account, Li, is a Chinese painter based in Italy, who requested to be identified only by his last name in light of the security risks. He’s been tirelessly posting footage around the clock to help people within China get information, and also to inform the wider world.

The work has been taking its toll—he’s received death threats, and police have visited his family back in China. But it also comes with a sense of liberation, Li told Zeyi Yang, our China reporter. Read the full story.

Biotech labs are using AI inspired by DALL-E to invent new drugs

The news: Text-to-image AI models like OpenAI’s DALL-E 2—programs trained to generate pictures of almost anything you ask for—have sent ripples through the creative industries. Now, two biotech labs are using this type of generative AI, known as a diffusion model, to conjure up designs for new types of protein never seen in nature.

Why it matters: Proteins are the fundamental building blocks of living systems. These protein generators can be directed to produce designs for proteins with specific properties, such as shape or size or function. In effect, this makes it possible to come up with new proteins to do particular jobs on demand. Researchers hope that this will eventually lead to the development of new and more effective drugs. Read the full story.

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