ThermoFisher RT-PCR COVID-19 Test Detects B.1.1.7 Variant

An available RT-PCR assay has shown capability to detect prevalent UK SARS-CoV-2 variant strain B.1.1.7, according to an assessment of 100-plus samples collected in the first half of 2021.

The findings, presented at the American Society of Microbiology (ASM) 2021 World Microbe Forum this week, provide assurance that the ThermoFisher TaqPath COVID-19 RT-PCR assay—granted Emergency Use Authorization (EUA) by the US Food and Drug Administration (FDA)—is a device able to assist tracking the more transmissible SARS-CoV-2 variant, originally observed in southeast England in Fall 2020.

Led by Derek Moates, MBS, of the UAB Fungal Reference Lab, Department of Pathology and Laboratory Medicine at the University of Alabama at Birmingham, investigators sought to observe the clinical utility of the RT-PCR assay in detecting B.1.1.7 through remnant nasopharyngeal swab sequencing.

As they noted, identifying SARS-CoV-2 variants of concern and significance require whole genome sequencing (WGS), a process generally hindered by costs, skilled personnel availability, limited resourcing, and time constraints.

“However, once a variant of public health significance is known, targeted RT-PCR assays may enable accurate, high throughput, and cost-effective detection to help guide epidemiologic interventions,” they wrote.

Moates and colleagues conducted testing of symptomatic patients who tested positive for all gene targets except the SARS-CoV-2 spike gene, or “S gene dropout.”

Samples with cycle threshold (Ct) value <30 were sequenced via a WGS panel. Preliminary SARS-CoV-2 variant calls and genome assemblies were obtained via relevant software, as were lineage calls.

The investigators attempted WGS on 79 samples with Ct <30 that also exhibited S gene dropout. They obtained sufficient coverage and read depth for variant calls and genome assembly in 92.5% (n = 111) of 120 overall samples.

Among 3 repeated samples, all maintained success. All 111 (100%) S gene dropout samples successfully read were identified as UK SARS-CoV-2 variant B.1.1.7.

Hands on time and mean time to result per run were 4 hours and 24 hours, respectively.

Moates and colleagues concluded the findings support the use of the ThermoFisher RT-PCR COVID-19 assay for detecting and screening for the B.1.1.7 variant of SARS-CoV-2.

“Although WGS is the gold standard and is essential to identify novel variants, RT-PCR screens for the UK and other known variants of public health significance may enable high throughput and cost-effective variant detection to help guide epidemiologic interventions,” they wrote.