S-variant SARS-CoV-2 is associated with significantly higher viral loads in samples tested by ThermoFisher TaqPath RT-PCR

ABSTRACT

Birmingham University Turnkey laboratory is part of the Lighthouse network responsible for testing clinical samples under the UK government Test & Trace scheme. Samples are analysed for the presence of SARS-CoV-2 in respiratory samples using the Thermofisher TaqPath RT-QPCR test, which is designed to co-amplify sections of three SARS-CoV-2 viral genes. Since more recent information became available regarding the presence of SARS-CoV-2 variants of concern (S-VoC), which can show a suboptimal profile in RT-QPCR tests such as the ThermoFisher TaqPath used at the majority of Lighthouse laboratories, we analysed recently published data for trends and significance of the S-gene dropout variant. Results showed that O_LIthe population of S-gene dropout samples had significantly lower median Ct values of ORF and N-gene targets compared to samples where S-gene was detected C_LIO_LIon a population basis, S-gene dropout samples clustered around very low Ct values for ORF and N targets C_LIO_LIlinked Ct values for individual samples showed that a low Ct for ORF and N were clearly associated with an S-dropout characteristic C_LIO_LIwhen conservatively inferring relative viral load from Ct values, approximately 35% of S-dropout samples had high viral loads between 10 and 10,000-fold greater than 1 x 106, compared to 10% of S-positive samples. C_LI This analysis suggests that patients whose samples exhibit the S-dropout profile in the TaqPath test are more likely to have high viral loads at the time of sampling. The relevance of this to epidemiological reports of fast spread of the SARS-CoV-2 in regions of the UK is discussed.