A thread about the delayed #coronavirus/#COVID19 testing, and more broadly, about the process of science: 1/
One of the many questions of the past week in the US has been: "WHY AREN'T WE TESTING ALL SUSPECTED CASES?" This is a very fair and natural question if you do not work in a clinical laboratory or, more broadly, in R&D as applied to human health. 2/
To set the stage, imagine if there would be mass disruption to everyday life by the triggering of containment policies on a grand scale, not to mention lives on the line, if absolutely everything at your work was not reliably perfect every time. Those are the stakes. 3/
I especially wanted to write this thread in response to @ChrisCuomo's comments on his @SIRIUSXM show, which I listen to and enjoy regularly. He has been asking why labs cannot simply run the tests, even if some are falsely positive. Let's say the order is issued to do so 4/
@ChrisCuomo @SIRIUSXM (Azar's recent announcement notwithstanding) If I were holding BAL fluid from a suspected patient, what shelf would I go to to find the reagents to test it? I wouldn't have them handy. This is NOT a critique of @ChrisCuomo, as his question was a very fair one if you've never.. 5/
@ChrisCuomo @SIRIUSXM ..worked in a laboratory. Testing for #COVID19 works by detecting the virus' genetic material. To do that, custom reagents called primers have to be synthesized. There is no company I can call that makes #SARSCoV2 primers at this moment (though @CepheidNews will soon). 6/
@ChrisCuomo @SIRIUSXM @CepheidNews So here I am, holding a specimen cup of BAL fluid or a NP swab, needing it to be tested. I would have to design (or pull published sequences) primers and then order them. Once they arrive, I would have to reconstitute them and run a quick test to make sure they were made 7/
@ChrisCuomo @SIRIUSXM @CepheidNews correctly, that they work reliably with my other reagents, and that there is nothing in BAL fluid, NP swabs, OP swabs, or anything else that will interfere with the reaction. Here is where we run into another GIANT hurdle. I would need some SARVCoV2 RNA or cDNA as a + control. 8/
@ChrisCuomo @SIRIUSXM @CepheidNews This is not widely available in the US at this moment. PEople are scrambling and working around the clock on it, but at this moment, it is simply not widely available because enough quantities to distribute widely do not exist. You may be wondering why the + control is so... 9/
@ChrisCuomo @SIRIUSXM @CepheidNews ...important here. I would ask you to think about a home pregnancy test. The basic point that all tests, every time, have one line appear, and a positive test has two lines appear. The one line is the +control. If that line didn't appear, but the "pregnant/non pregnant" line..10/
@ChrisCuomo @SIRIUSXM @CepheidNews ..didn't either, would you believe that it was a negative test and go have a vodka&tonic and a cigarette? PRobably not. The same instinct applies here. By accounts, the problem with the majority of CDC kits was the opposite- the negative controls were giving +results. Imagine 11/
@ChrisCuomo @SIRIUSXM @CepheidNews Moving on.... for context, onboarding a new molecular dx test in a clinical laboratory often takes weeks to months, and these are tests that have been through standard FDA-required clinical trials, where ll the major kinks have been worked out. We know exactly how long swabs..14/
@ChrisCuomo @SIRIUSXM @CepheidNews ...need to be circled in the nose, or passed across the tonsils. We know whether the test can be run straight from BAL fluid or sputum, or whether initial extraction is needed. IT STILL TAKES WEEKS to get it reliably operational on site. 15/
@ChrisCuomo @SIRIUSXM @CepheidNews REmember how this thread started - the stakes of accuracy could not be higher. 16/
@ChrisCuomo @SIRIUSXM @CepheidNews What is the consequence of a false result, you may ask? Stories like this, for starters:
cidrap.umn.edu/news-perspecti… 17/
cidrap.umn.edu/news-perspecti… 17/
@ChrisCuomo @SIRIUSXM @CepheidNews I do not bring this up to blame people for asking about immediate reinfection, of course. It is a natural question to ask if the laboratory world is not your world. Occam's razor would suggest that these positives followed by negatives followed by positives are a result of..18/
@ChrisCuomo @SIRIUSXM @CepheidNews ..natural inconsistencies in a very, very new test that still has kinks to work out, rather than a failure of immunity. If people take away the impression that we cannot become immune to #COVID19, that is a major problem for subsequent #vaccine efforts. 19/
@ChrisCuomo @SIRIUSXM @CepheidNews Implementing this type of testing is fundamentally different from assessing a cluster of 20 patients for a potential unknown novel pathogen. A big hospital can, and will, do deep sequencing on those 20 patients to assess the situation and try to contain it. These techniques 20/
@ChrisCuomo @SIRIUSXM @CepheidNews are extremely accurate and reliable, but they are extremely laborious and require specialized expertise and equipment. The average community hospital or outpatient clinic, which is where we are at now in the US, cannot do this. This is why we could get this information early..21/
@ChrisCuomo @SIRIUSXM @CepheidNews ..from the first US cases, but it isn't a practical reality now. Could CDC do this technically for all of these patients? TEchnically. But the personnel needed is in short supply. If there are not enough humans to run deep sequencing, it can't be done even if asked. 22/
@ChrisCuomo @SIRIUSXM @CepheidNews The question may then be asked, "why bother throwing more money at this?" This was asked during the #HIV epidemic in the 80s (for film of it, see the terrific @frontlinepbs Frontline documentary from 2006, "The Age of AIDS" - required watching for new students in my lab) 23/
@ChrisCuomo @SIRIUSXM @CepheidNews @frontlinepbs Money buys things, but it also hires people. This is why it is a critical measure. But I digress~ 24/
@ChrisCuomo @SIRIUSXM @CepheidNews @frontlinepbs I wanted to explore this with you all because there has been a somewhat conspiratorial tone around the limiting of testing. I can only speak for my scientific colleagues when I say- no one goes into this line of work for any reason other than to help people, as much as we can 25/
@ChrisCuomo @SIRIUSXM @CepheidNews @frontlinepbs and as fast as we can. IT is a grueling line of work. It is stressful. You can never turn it off. There is no punching out at 5. I can't speak for anyone else's motivations or guiding principles, but these are ours. 26/
@ChrisCuomo @SIRIUSXM @CepheidNews @frontlinepbs I'll end by reiterating that these are completely natural questions, and if I were not a scientist I would have been asking them too. I think a popular press book about the process of science would be a terrific endeavor so that insight into how discoveries are made 27/
@ChrisCuomo @SIRIUSXM @CepheidNews @frontlinepbs can be accessible to everyone, but once again, I digress. Testing will be available soon, but it isn't as simple as we all might hope. That is the unfortunate reality. /end
@ChrisCuomo @SIRIUSXM @CepheidNews @frontlinepbs P.S. And my apologies to @ChrisCuomo - I would have called in to talk with you about this, as I know you appreciate being edified and challenged by your listeners, but alas, I was driving.
@ChrisCuomo @SIRIUSXM @CepheidNews @frontlinepbs P.S.2 To be clear, I am NOT defending the coordination or current state of the testing situation. I am simply hoping to provide insight into the question of "why can all labs just start testing?"
