• Allan Dyen-Shapiro

My Perspective on the Revelations from the CDC

The investigation, reported in this Washington Post article, has revealed what went wrong with testing for the coronavirus in the US. The key issue was cross-contamination of kit components with viral DNA--a noninfectious form used within CDC labs. This happens. Ideally, the manufacturing facility should not have been used by anyone working with SARS-CoV-2 nucleic acid of any sort.

Rather than rehash what will soon be everywhere, I'm going to draw on personal experience from my scientist days to try to give a perspective that won't be found in the mainstream media. I would argue that the CDC scientists were not stupid, there was no conspiracy, and the errors were understandable, albeit tragic.

Experience #1: In my first research project, done at a research hospital in the summer after my sophomore undergraduate year, I worked with artificial skin. It had just become possible to grow sheets of keratinocytes—the cells of the visible, outer layer of skin—in tissue culture. It took four weeks to grow enough to wrap them as sheets on the body of patients with >80% of their bodies burned in an accident. The average patient in this condition died in three weeks. Nonetheless, there was a lot of variation around that average. This treatment saved lives.

I was working with the next generation of materials, using both keratinocytes and fibroblasts. The work was ultimately published and said some interesting things about wound healing. However, I had to use the same laminar flow hood as the two technicians growing the keratinocyte sheets to use with patients. If I ever got anything contaminated, I knew people would die. That was a pretty good incentive to learn sterile culture technique very well.

Nobody died due to my incompetence.

So, why in the world would a major research hospital risk patient's lives in this fashion? Money and space. There was one hood in that lab. Three people had to share it.

These limitations explain why every university and biotech company in the country couldn't make their own in-house test for the coronavirus. These places are set up for research, not production.

Experience #2: One of my colleagues at the last university where I was full-time faculty was hired, in part, to work on a project using DNA from human bones. She had the expertise to do the project. She had plenty of money. She tried to use the freezers already in the department, because even if she spent the money to buy new -80-degree-Celsius freezers, there was no completely isolated space in which to put them.

She experienced miserable failure from contamination to the point where she abandoned the project.

The CDC does a lot of enormously important work. There are lots of people working there. I am certain the pressures to share space are unavoidable.

In this case, it proved unwise, and people died. And are still dying.

The other issue—the decision to use an additional test in the kits to also detect other related coronaviruses—likely made sense at the time. False positives are the bane of PCR-based tests. If you can tell me that many different coronavirus controls cannot show a positive signal in your test, I am much more confident that you are detecting SARS-CoV-2.

The CDC had no way to know that false positives wouldn't be such a big issue with tests for this virus. Every other nation in the world bet differently. They were right; the CDC was wrong. But if the CDC had been right, the narrative would have been the Americans saving the world.

Bad luck and near-unavoidable facilities utilization issues shouldn't get anyone fired. Nobody is to blame.

However, the CDC's silence on what went wrong may not be as defensible. I'll bet anything that a lot of scientists there guessed what went wrong based on the available data. I'll also bet that lawyers told them to shut up. Hubris on the part of higher-ups may have also played a role. Had the first scientist with reasonable suspicion gone on TV and said that viral material was used in the production facility, probably leading to the contamination, the moving of production to a different lab might have taken place earlier. Time was lost.

Correcting the problem did not need certainty as to what went wrong, just reasonable suspicion. A "we think things are in bad shape at the CDC, move production elsewhere" message didn't require a lot of details. Protection of higher-ups from a witch hunt did. Limitation of liability did.

Fault the system: with the anti-science and generally anti-intellectual attitude prevalent in some parts of the US government today, CYA is an understandable mantra.

To avoid this problem recurring with future pandemics (and trust me, they will come), I'd argue that the US needs a lot more than one production facility for viral test kits the size of what CDC now has in Atlanta. I'd also argue for surplus capacity—one of them left unused and pristine until just this sort of emergency happens and then sterilized and left vacant after the crisis passes.

That takes money. In the era where a trillion here, a trillion there is considered chump change, you'd think this wouldn't be a problem. If so, you've never done science in an atmosphere of government antipathy. Trump wasn't the first anti-science president. The years in which federal budget cuts were one of the causes of my science career ending came under Bush II.

Voters should take note: it's not a good idea to vote for politicians who disdain science. People die when you elect those folks.

And the deaths from the climate catastrophe are only beginning.

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© 2016 by Allan Dyen-Shapiro

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