Estimating infectiousness throughout SARS-CoV-2 infection course jones2021estimating

The reference event is symtom onset. Viral load is semiquantitative, estimating RNA copies per entire swab sample, whereas only a fraction of the volume can reach the test tube. The quantification is based on a standard curve and derive a formula in which RT-PCR cycle threshold values are converted to viral loads. Viral load is estimated from the cycle threshold (Ct) value using the empirical formulae 14.159 - (Ct x 0.297) for the Roche Light Cycler 480 system and 15.043 - (Ct x 0.296) for the Roche cobas 6800/8800 systems. An estimated 3 percent of our samples were from the lower respiratory tract. These were not removed from the dataset because of their low frequency and the fact that the first samples for patients are almost universally swab samples. Samples from the lower respiratory tract are generally taken from patients only after intubation, by which point viral loads have typically fallen.

The reference event is confirmation date. Viral load is semiquantitative, estimating RNA copies per entire swab sample, whereas only a fraction of the volume can reach the test tube. The quantification is based on a standard curve and derive a formula in which RT-PCR cycle threshold values are converted to viral loads. Viral load is estimated from the cycle threshold (Ct) value using the empirical formulae 14.159 - (Ct x 0.297) for the Roche Light Cycler 480 system and 15.043 - (Ct x 0.296) for the Roche cobas 6800/8800 systems. An estimated 3 percent of our samples were from the lower respiratory tract. These were not removed from the dataset because of their low frequency and the fact that the first samples for patients are almost universally swab samples. Samples from the lower respiratory tract are generally taken from patients only after intubation, by which point viral loads have typically fallen.