I used to set up and run a large plate of qPCR (we didn't use the RT step in our particular use case) in an hour or so. Mind you this was for something like 200 samples. It took 2-3h to run the actual machine. If I was setting up such an assay, I'd order a bunch of different primers (you need DNA to make DNA) and run a bunch of plates with as many samples as I could to see what primers worked best. You'd include a bunch of negative controls, ideally some controls from patients/cultures infected with similar but not identical virus (for example a different coronavirus). To develop an RT-qPCR assay would take a week or two (rough guess), I think it took about a week to develop the WHO assay.

From what I can tell (mostly anecdotal and other data from friends I trust) the CDC assay used bad primers, they were noisy, showing a bunch of false positives. They also used a potentially dodgy fluorescence readout. I used to use the same readout, but our scenario was full of internal controls and the input sample was far more consistent. For human sample data a different fluorescent method that is more reliable should have been used.

Important ways this can be screwed up: it's helpful to use the same machine, the same protocol every time. This is because qPCR is an exponential assay, which means small errors can have big repercussions.

TLDR: Scale of fuckup here is massive. This really isn't that hard, and we could just have used what the WHO/others were using. I have no idea why they decided to go their own way.

more info: https://www.propublica.org/article/cdc-coronavirus-covid-19-...