The Abbot RealTime SARS-CoV-2 Assay that used in this paper says in its package insert that it is "intended for the qualitative detection of nucleic acid from SARS-CoV-2". I understand that one would expect the CT values to be lower with higher viral loads but the assay is not really designed to draw quantitative conclusions. I get that this is potentially interesting preliminary data but shouldn't this be confirmed with an assay that is designed to quantify viral RNA before we draw the conclusion that "young children can potentially be important drivers of SARS-CoV-2 spread in the general population"?
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Your data seem plausible, however the qPCR data are not performed how they should.
- The Abbott test is only validated for qualitative purposes. A quantitative validation with a standard curve should have been included. Furthermore, this is a multiplex, which makes quantitation even harder. Cycle quantification values (Cqs) from different targets do influence each other.
- Getting quantitative data from such early PCR amplification cycle thresholds (Cts) is hard. Did you validate your linear range with a standard curve? I mean, at a Cq = 5 f.e. it gets really hard to correctly subtract your baseline. /> - Thirdly, Cq is not a quantitative measure. If you took a calibrator sample, you should use the values or you should work with (d)dCq taking into account efficiencies from your standard curve.
- An analysis with normalized qPCR data would be more correct. Normalization for volume/internal control is a minimum, as extraction can be a variable factor. Even better is a human control, to assess for RT efficiency and for swabbing efficiency.
In summary, you cannot take a quantitative assay and use in in a qualitative way.
Kind Regards