Thread by @MackayIM

COVID-19 testing and correlation with infectious virus, cycle thresholds, and analytical sensitivity cebm.net/study/covid-19… via @cebmoxford

Upfront-how one interprets late PCR results DOES MATTER. No argument. I am very much aware that late Cts mean less RNA (and by extrapolation based on history and experience, less virus) is typically present.
How does that relate to "false positives" & PCR cycle numbers?

A false-positive PCR result typically means that the PCR was positive when no virus had ever been present.
This is different from an infected person's sample not having any *infectious* virus, yet still returning a PCR-positive because of "dead virus"/RNA fragments being shed.

The latter isn't a false positive. It's a true positive, indicating that the person was infected and for a time was infectious. They may not be now.
PCR false positives are generally very rare (virologydownunder.com/the-false-posi…)

False positives rates are <<1% but will depend on how professional the particular lab is & what quality processes are in place. Really importantly-how overwhelmed the lab is by samples. This impacts how well processes *can be* adhered to. That's not the test's fault though.

What you see in the paper at the top of the thread is a single example.
I posted a slightly different single example recently (virologydownunder.com/the-false-posi…).
There is clearly a range of maximum Cts that yield infectious virus, exemplified by these 2 examples.

Using a single Ct value like 30 or 35 as the cut-off is not even attempting to accommodate that variability. I think that's largely just down to a limited understanding of some things, & overwhelmed systems.
People may not know that culturing virus in cells ('virus culture')...

.. is an art form.
Virus culture is much more subject to biological variability than PCR. It's impacted by
😣poor quality sample collection
😣bad choice of tissue site for sample collection
😣poor specimen transport
😣bad specimen handling (e.g. sitting around)
😣freeze-thawing

PCR is barely affected by most of that. That's good if you want to know if a person is infected but *can* be bad if you only want to know if infectious virus is being produced from that specifically sampled tissue site (who knows about the other tissues?) right now.

To throw a spanner in the 'RNA fragments lead to long/late PCR results' works.
Don't forget we know of persistence in the gut epithelium. Could this be happening in the airways? Could late Cts be uncultivable levels of virus? Would that be a risk if so?

https://twitter.com/MackayIM/status/1324932175821561857?s=20

Now, we scientists are supposed to talk about uncertainty so if all 👆isn't enough so far...
The expertise to *perform* virus isolation & cell culture also sits across a spectrum. I know people whose culture skills are crap. I'd frankly fear for the wellbeing of their pets!

And the expertise of labs conducting PCR can sit across a similar spectrum. Although as I've highlighted, PCR can be more forgiving.
To belabour this-PCR is a very good tool when wielded by people who understand it (12 months ago I thought more did than clearly do)

How you act on PCR *results* does matter.
If Ct values are the sole tool for diagnosis then you have a problem. Lab shouldn't have that much power; clinical oversight & epidemiological context are need for diagnosis. As I said👆, the process may be overwhelmed; yet still needed

PCR used without the collaborative process means that you will struggle to ever evolve your response, something we should be doing now that we know much more about what works, what doesn't and what is unnecessary.
/end