Qualitative and quantitative effects of thermal treatment of naso-oropharyngeal samples before cobas SARS-CoV-2 testing

Pryce, Todd M.; Boan, Peter A.; Kay, Ian D.; Flexman, James P.

To improve laboratory safety we thermally treated naso-oropharyngeal samples before testing with the cobas SARS-CoV-2 assay. This study aimed to determine if thermal treatment significantly affects the qualitative detection of SARS-CoV-2 and the quantitative measurement of cobas SARS-CoV-2 ORF1a and E-gene target copy number using an in-house quantitative method. A collection of positive (n=238) and negative samples (n=196) was tested in parallel comparing thermal treatment (75°C for 15 minutes) to room-temperature. There were no significant differences in the final qualitative outcomes for thermal treatment versus room-temperature (99.8% agreement) despite a statistically significant reduction (p<0.05) in target copy number following thermal treatment. The median ORF1a and E-gene reduction in target copy number was ­0.07 (1.6%) and ­0.22 (4.2%) log(10) copies/mL respectively. The standard curves for both ORF1a and E-gene targets were highly linear (r(2)=0.99). Good correlation was observed for ORF1a (r(2)=0.96) and E-gene (r(2)=0.98) comparing thermal treatment to room-temperature control.