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A French case report that has received widespread media attention suggests (actually stated in pretty strong terms in the paper) that Covid-19 was already spreading in France in December 2019. (In contrast, according to the received account/wisdom from the WHO, the first recorded case of Covid-19 outside China was on Jan 13 in Thailand.)

The retrospective PCR test for Covid-19 they did on the -86C frozen sample had an amplification curve like this:

enter preformatted text here

Fig. 2. Result of Charité protocol RT-PCR assay [11]: patient's curve in yellow; positive and negative test samples in purple.

A Ct of 30 seems pretty marginal to me, but I'm not really an expert. What does the Charité protocol research say about such a Ct figure, in terms of false positives, i.e. what's the probability that a Ct of 30 (or more) is a false positive using the Charité protocol/test for Covid-19?

(The ref/link [11] in the paper alas doesn't send to a useful page in that regard.)

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    According to FDA's published BGI (Chinese) protocol, a Ct below 37 is to be considered positive, but they don't give any probabilities. – Fizz May 7 '20 at 8:55
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    The Charity protocol is here eurosurveillance.org/content/10.2807/… – Graham Chiu May 9 '20 at 21:09
  • @GrahamChiu: alas I don't know how to interpret/transform their fig 3, which has the confidence bands expressed in c/r (copies per reaction) on the X-axis, in threshold cycle (Ct) terms, which is the usual stuff you see in daily use of PCR... – Fizz May 9 '20 at 21:21
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Well, interpreting the Charité numbers is still a bit of a mystery to me, but by analogy with a US case, having some tests close to the detection limit for Covid-19 is not so unusual in some circumstances.

For the first (well-investigated) US patient, the Ct was below 30 in some tests (but around 20 in others), albeit this is with the CDC tests of the time:

enter image description here

And from the CDC data they link/reference, the Ct in the 30s is somewhat close to the limits of detectability used in sensitivity evaluation of the CDC kits, but still comfortably positive, e.g. any Ct below 35.4 was 95% (or more) positive with the "advanced" kit. Even for the "mini kit" that 95% limit was around Ct of 32.8.

enter image description here

(Note that "2" is not a square there for Ct, it's a footnote.)

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