Spending billions on covid sequencing won’t tell us how to stop the variants

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

“Some states are very good and want to know a lot about the variants that are circulating in their state,” says Brian Krueger of Labcorp. “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, the fact that each jurisdiction only analyzes a small portion of the dataset reduces the amount of knowledge that can be gleaned about real-world behavior.

However, getting around these problems – making it easier to connect large-scale clinical sequences and metadata – would require more than just basic and branch reform of privacy regulations. It would require a reorganization of all health and public health systems in the United States, where each of the 64 public health agencies functions as fiefdoms, and there is no centralization of information or power. .

“Metadata is the biggest uncracked nut,” says Jonathan Quick, general manager of pandemic response, preparedness and prevention at the Rockefeller Foundation. (The Rockefeller Foundation helps finance coverage at MIT Technology Review, although it has no editorial control.) Because it is so difficult for public health to put together datasets large enough to truly understand the behavior of variants in the real world, our understanding must come from vaccine makers and hospitals adding sequencing to own clinical trials, he says.

It is frustrating for him that so many huge data sets of useful information already exist in electronic medical records, immunization registers and other sources, but cannot be easily used.

“There is a lot more to learn, and to learn faster, without the barriers we place on the use of this data,” says Quick. “We can’t just rely on vaccine manufacturers for surveillance.”

Boosting bioinformatics at the state level

If public health laboratories are to focus more on tracking and understanding variants on their own, they will need all the help they can get. Doing something about variations on a case-by-case basis, after all, is public health work, while doing something about variations at the political level is political work.

Public health laboratories typically use genomics to expose otherwise hidden information about epidemics, or as part of tracking and traceability efforts. In the past, sequencing has been used to link outbreaks of E. Coli on specific farms, identify and interrupt chains of HIV transmission, isolate Ebola cases in the United States, and monitor annual influenza patterns.

Even those with well-established agendas tend to use genomics sparingly. The cost of sequencing has dropped precipitously over the past decade, but the process still isn’t cheap, especially for cash-strapped state and local health services. The machines themselves cost hundreds of thousands of dollars to buy, and more to run: Illumina, one of the largest manufacturers of sequencing equipment, says labs spend on average $ 1.2 million annually on the supplies of each of its machines.

“We’re going to miss out on a ton of opportunities if we just give money to health departments to put programs in place without having a federal strategy so everyone knows what they’re doing.”

Health agencies don’t just need money; they also need expertise. Surveillance requires highly skilled bioinformaticians to turn long chain letters in a sequence into useful information, as well as people to explain the findings to officials and convince them to turn the lessons learned into policy.

Fortunately, the OAMD has worked to support state and local health departments as they attempt to understand their sequencing data, employing regional bioinformaticians to consult with public health officials, and facilitating agency efforts to share. their experiences.

It also invests hundreds of millions of people in building and supporting these agencies’ sequencing programs – not just for covid, but for all pathogens.

But many of these agencies face pressure to sequence as many covid genomes as possible. Without a coherent data collection and analysis strategy, it is not clear how useful these programs will be.

“We’re going to be missing out on a ton of opportunities if we just give money to health departments to put programs in place without having a federal strategy so everyone knows what they’re doing,” Warmbrod says.

Initial visions, usurped

Mark Pandori is director of the Nevada State Public Health Laboratory, one of the programs supported by the OAMD. He has been a strong supporter of genomic surveillance for years. Before moving to Reno, he ran the Alameda County, Calif., Public health laboratory where he helped set up a program using sequencing to track the transmission of infections in hospitals.

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

“The CDC can say, ‘go buy a bunch of sequencing equipment, do a bunch of sequencing.’ But it doesn’t matter until the consumers of that data know how to use it and how to apply it, ”he says. “I’m telling you about the robotics we need to sequence things every day, but healthcare just needs a simple way to tell if cases are related.”

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

Pandori launched its covid sequencing program in hopes of reducing the work required to investigate potential covid outbreaks, by quickly identifying whether cases caught near each other were related or by chance.

His lab was the first in North America to identify a patient reinfected with covid-19, and then found variant B.1.351 in a hospitalized man who had just returned from South Africa. Thanks to a quick contact tracing, the health service was able to prevent its spread.

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