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

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

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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.

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.

) 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.

“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.

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.

Public health labs generally use genomics to expose otherwise-hidden information about outbreaks, or as part of track and trace efforts.

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.

‘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’.

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.

But many of those agencies are facing pressure to sequence as many covid genomes as possible.

“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.

Mark Pandori is director of the Nevada state public health laboratory, one of the programs OAMD supports.

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.

“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.


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