We Could Have Effective COVID-19 Genomic Surveillance, Even with the Crappy U.S. Healthcare System

I’ve been meaning to get to this Washington Post article about how genomic sequencing of COVID-19 is being used in the UK to assist in tracking outbreaks, and in the U.S…. not so much. What got me off my posterior was this comment over at Naked Capitalism, in one of their links roundups:

How the coronavirus’s genetic code can help control outbreaks WaPo. This sentence caught my eye: “While U.K. scientists, backed by their government, began work early to create a centralized tracking system that could benefit researchers around the country, the U.S. effort has remained more diffuse and disorganized.” Could that be — hear me out — because the U.K. has a national health service? (Hilariously, neither “National Health Service” nor “NHS” appear in the article.) This from a story that begins with a cute graphic that invites you to imagine “Scienceville”!

I’m not trying to drag good people (and they’re good people over there), but I don’t think this is correct. If we need massive healthcare overhaul to have effective genomic surveillance of COVID-19, then we’re not going to have it in time. Despite our shitty healthcare system and balkanized–to be charitable–public health system*, we still could do this.

How do I know that? Because we already do this for other pathogens. Every year, the U.S., as part of bacterial food-borne pathogen outbreak detection (E. coli, Salmonella, Campylobacter, and Listeria), sequences over 100,000 bacterial genomes and makes the data publicly available very rapidly.

Yes, there are differences in how to sequence these organisms, along with the other non-sequence data that need to be collected (‘metadata’) but these protocols had been worked out months ago. It’s now mid-October (boldface mine):

The tools are already in place in much of the country, where sequencing machines are prevalent and the cost of running the short coronavirus genome can run as low as $10, according to Francis deSouza, the CEO of Illumina, which dominates the market for sequencing machines. (That figure refers only to sequencing and does not include other costs, such as for collecting and testing coronavirus samples, or getting results to patients.)

We’ve got the sequencing horsepower,” said James Musser, a researcher at Houston Methodist Hospital who has presided over what appears to be the U.S.‘s largest single effort. “I think we should be doing this very extensively in the nation writ large, and I think it’s terrible that we are not.”

In the absence of federal support and coordination, the most successful sequencing efforts have occurred in a scattering of cities where the necessary resources already happened to be in place.

So what was/is missing? Federal leadership and resources:

Without federal funding, scientists say, even those who see the value of genomic epidemiology will be forced to give up on it.

In Pittsburgh, Cooper has reduced his efforts to small scale local sequencing, rather than trying to fully chart the city’s outbreak. Work at MacInnis’s lab nearly came to a standstill this summer as she filled out applications for NIH grants. A recent award from the CDC has allowed her to fill in some of the resulting data gaps. But she doesn’t expect to hear back from NIH until next year.

Slow the testing down, please.

An administration that doesn’t even want to record COVID-19 cases certainly isn’t going to push to do what needs to be done for providing more information about how outbreaks happen:

Unless the United States improves, “we just won’t be able to do that,” she said. “We won’t know where infections are coming from within the country, let alone how they’re being introduced when we open our borders.”

And it will be harder to decipher specific outbreaks, such as the high-profile coronavirus cluster within the White House, which has sickened dozens of people, including the president, the first lady and multiple administration officials.

We have the equipment and personnel in place, and with additional funding–a pittance compared to the size of the economic programs being bandied about–for supplies and training, we could do this. Yes, there would be gaps–we obviously don’t sequence every bacterial food-borne pathogen either–but we still have very useful and actionable information. The knowledge about COVID-19 we would gain even in our crappy system would still be extremely useful. Regular readers will know I follow D.C.’s COVID-19 data, and there are so many unanswered questions about spread that genomic sequencing could answer. That information would save lives.

The U.S. still could do widespread genomic sequencing, but there’s no way it really happens before late January. And we don’t need healthcare reform, just leadership that provides resources and motivation, and then stays the hell out of the way.

* I’ve pointed out numerous times over the years that we don’t have a public health system, but dozens of public health systems, as normies are now learning.

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