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The CDC’s $ 1.75 billion sequencing boom could throw money on the wrong problem

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Rather than attempting to address these issues at the national level, the sequencing contracts allow individual public health authorities to request the names and contact information of people who have tested positive for worrying variants. However, this leads to the same problems with data ownership in the chain.

“Some states are very good and want to know a lot about variants that are in circulation in their state,” says Brian Krüger of Labcorp. “The other states aren’t.”

Public health epidemiologists often have little experience with bioinformatics and use software to analyze large data sets such as genome sequences. Few agencies already have sequencing programs. Even if it were, analyzing each individual jurisdiction only undermines a small fraction of the dataset of how much knowledge can be gained about behavior in the real world.

However, to circumvent these issues and make it easier to connect sequences and clinical metadata on a large scale would require more than just a reform of data protection regulations. It would require a reorganization of the entire health and health system in the US, where each of the 64 public health agencies act as a fief and there is no centralization of information or power.

“Metadata is the biggest unsolved nut,” said Jonathan Quick, chief executive officer, pandemic, preparedness and prevention at the Rockefeller Foundation. (The Rockefeller Foundation helps fund the coverage of MIT Technology Review, although it has no editorial control.) Because it is so difficult for public health to compile data sets large enough to really understand variant behavior in practice To understand, our understanding must come from vaccine manufacturers and hospitals adding sequencing to their own clinical trials, he says.

It is frustrating for him that so much huge dataset of useful information is already in electronic medical records, vaccination registers, and other sources but cannot be easily used.

“Without the shackles we use to use this data, a lot more can be learned and learned faster,” says Quick. “We can’t just rely on the vaccine companies to do the surveillance.”

Promotion of bioinformatics at the state level

If public health laboratories are expected to focus more on tracking and understanding variants on their own, they need all the help they can get. After all, it is a public health responsibility to take action against variants on a case-by-case basis, while it is a political task to do something against variants at a political level.

Public health laboratories generally use genomics to uncover otherwise hidden information about outbreaks or as part of track and trace efforts. In the past, sequencing has been used to link E. coli outbreaks to specific farms, identify and disrupt 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 sharply over the past decade, but the process is still not cheap, especially for state and local health departments struggling with cash. The machines themselves cost hundreds of thousands of dollars to buy and more to run: According to Illumina, one of the largest sequencing equipment manufacturers, laboratories spend an average of $ 1.2 million a year on delivering each machine.

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

Health authorities don’t just need money; You also need expertise. For monitoring, highly qualified bioinformaticians need to convert the long strings of letters in a sequence into useful information and inform officials of the results and convince them to translate the knowledge gained into policy action.

Fortunately, the OAMD has worked to help state and local health departments attempt to understand their sequencing data, consult regional bioinformaticians to advise with public health officials, and facilitate efforts by authorities to share their experiences.

Hundreds of millions are also pouring into building and supporting these agencies’ own sequencing programs – not just for Covid, but for all pathogens.

However, many of these agencies are under pressure to sequence as many Covid genomes as possible. Without a coherent strategy for collecting and analyzing data, it is unclear what use these programs will be.

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

First visions, usurped

Mark Pandori is the director of the Nevada State Health Laboratory, one of the OAMD-supported programs. He has been a strong advocate of genomic surveillance for years. Before moving to Reno, he ran the Public Health Laboratory in Alameda County, California, where he pioneered a program that used sequencing to track how infections were transmitted in hospitals.

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

“The CDC can say, ‘Buy a set of sequencers, get a set of sequencers.’ But it doesn’t do anything unless the consumers of that data know how to use it and how to apply it, “he says.” I’m talking to you about the robotics we need to sequence things every day, but the health departments just need an easy way to know if cases are related. “

When it comes to variants, the public health laboratories are under the same pressure as the CDC: everyone wants to know which variants are in circulation, whether they can do something with the information or not.

Pandori launched its Covid sequencing program in hopes to reduce the amount of work involved in investigating potential Covid outbreaks and quickly determining whether cases caught close together were related or random.

His laboratory was the first in North America to identify a patient re-infected with covid-19 and later found variant B.1.351 in a hospital man who had just returned from South Africa. By quickly tracing contacts, the health department was able to prevent the spread.

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Steven Gregory