In response to the exhaustive need to accommodate COVID-19 testing demands, the NHS and the Public Health England Laboratories have set up a new test and trace program with their partner, Lighthouse Laboratories, to process COVID-19 swab samples. Test and Trace is now the largest diagnostic network in British history, processing around 2 million tests per week. Data generated from Lighthouse Laboratories reveals a high proportion of the S gene dropout. Consequently, a significant proportion of S-gene dropout is associated with higher viral loads and faster transmissibility.
B.1.1.7 (S-VoC) viral load and impact on transmissibility
The population of S-gene dropout samples had significantly lower median Ct values of ORF and N in the same sample, inferring relative high viral loads, which leads to increased infection and transmissibility. Consequently, results from qPCR median Ct values dictates delta in viral titers. This analysis suggests that patients whose samples exhibit the S-dropout profile in the TaqPath RT-PCR test are more likely to have high viral loads at the time of testing.
How much higher are the viral loads?
The observed cluster of S-dropout samples corresponds to a conservative estimate of a significantly larger population of infectious subjects that have an increased viral load up to 10,000-fold higher. Thus, the study explains transmissibility but not how the increased viral load occurs.
Identify Potential Variants
Identify Potential Variants Early to Help Curb the Spread Because the detection patterns of the TaqPath COVID-19 tests can differ among variants, test results from these kits can provide initial insight into developments in SARS-CoV-2’s evolution. Being able to distinguish between different, potentially more transmissible SARS-CoV-2 variants is of value for gathering preliminary data on the appearance and spread of SARS-CoV-2 variants and lineages.
Data from TaqPath RT-QPCR
Lighthouse Laboratories reveals the S-variant of SARS-CoV-2 shows a suboptimal profile in TaqPath RT-PCR test. Following an analysis of the trends and significance of the S-gene ‘dropout’ variant, it was discovered that the population of S-gene dropout samples had significantly lower median Ct values (the lower the Ct value, the greater the amount of nucleic acid).
Furthermore, 35% of samples infected with a variant with the 69-70del mutation (the cause of S gene drop out) showed significantly higher viral load. This seems to support preliminary evidence that some variants (like B.1.1.7 – UK variant) show an increased viral load, which supports the theory of higher transmissibility.
 “S-variant SARS-CoV-2 is associated with significantly higher viral loads in samples tested by ThermoFisher TaqPath RT-QPCR,” M Kidd et al, medRxiv 2020.12.24.20248834; doi:https://doi.org/10.1101/2020.12.24.20248834
Learn More about emerging variants of SARS-CoV-2 at https://www.thermofisher.com/covid19mutations
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