An Analysis of PCR Ct Scores and Distributions from the ONS Community Infection Survey during the COVID-19 Second Wave in the UK

This work presents an analysis of PCR cycle threshold (Ct) scores and their distributions, i.e. the probabilities that a test is positive with a score Ct, P(Ct), derived from the survey during the second COVID wave in the UK. Their relation to gene target breakdown is exemplified. Thus a significant parameter for tracking the course of COVID in the second wave is the percentage of positive tests with Ct < 25, %Ct <25, which is obtained by plotting weekly percentiles from the survey against Ct to construct the ogive or cumulative frequency curve (CMF). The biological basis for studying this parameter is the strong correlation between %Ct < 25 and the percentage of positive tests comprising target genes ORF1ab+N and ORF1ab+N+S, or %Inf. Furthermore, the probability distributions, obtained by differentiating the ogives, were found to be predominantly bimodal with a hot peak at Ct = 20.31+/- 4.65 and a cold peak with Ct = 32.95+/-1.11. These closely match the peaks found for the target genes ORF1ab+N, viz. Ct=18.54+/-2.31 and Ct=32.02+/-0.49 as well as in Walker et al [12]. Similar results were found in [13] and [14]. The cold peak seems likely to be associated with residue from a previous infection. The distributions for gene targets in cfvroc Pillar 2 [15,16] are also bimodal but the peaks occur at lower values of Ct. This suggests the results are machine/sample dependent and emphasises the need for calibration, if quality control in PCR testing is to be improved.