Ok, listing out my issues with this article for non-scientists here:

1. Virus load in a nasal swab is very variable. Flu studies have even found differences in virus loads depending on whether the sample was taken from R or L nostril, the collection volume of the swab etc. https://twitter.com/apoorva_nyc/status/1299705092178956288

2. Given this variability, it is obviously safer to use a reasonably low bar for positivity (i.e Ct <40) because the virus load in the body is > than the load in the swab which is > than the load in the collection tube which can be > than the load actually tested.

3. Ct values aren't a really measure of virus load in the patient in a test like this where there's no comparison with a host gene possible. (RNaseP levels are very variable)
4. Plus the load changes as infection progresses so you really can't be too stringent with thresholds.

4. This is why the tests for H1N1 also use a high Ct (37-38) for positivity. Something the journalist could've easily looked up.
5. My point: scientists who come up with these tests aren't stupid. They just have to deal with different challenges from academic scientists.

6. Yes, in an academic setting you'd probably ignore/re-test a Ct of 40. But the stakes are different.
7. Caveat: I'm not an immunologist or diagnostician (I have done virology research in and 1000s of RT PCRs)

8. It took me no time to think of these questions, and it's worrying that neither the journalist or the scientists interviewed brought up these issues.
In any case to go from this article and conclude that "90% (!!!) of positives are not contagious" seems laughable.

To the extent that the article suggests we need to more periodic testing with less sensitive rapid test kits, sure, let's talk about that once we have capacity to swab everyone at least just once!

Also, I'll happily delete any of these if someone shows me my take is wrong as this is just a bit far from my expertise.