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URL: https://dx.doi.org/DOI:10.17504/protocols.io.brcrm2v6

Authors: Chantal Vogels, Joseph Fauver, Nathan Grubaugh

Group: Coronavirus Method Development Community

Summary: As the B.1.1.7 "UK" variant continues to spread, there is a need for labs to screen COVID-19 samples for these viruses. While sequencing is the gold standard, it cannot always be scaled or implemented in some settings. The Applied Biosystems TaqPath COVID-19 assay (ThermoFisher), a PCR test, was discovered to have a distinct signature (spike gene target failure, [SGTF]) when testing viruses containing the Δ69/70 HV deletion, like the B.1.1.7 variant. Detecting the Δ69/70 HV deletion alone is not definitive for the B.1.1.7 variant, but tracking the frequencies of SGTFs helped the UK track the B.1.1.7 variant. In the US and other countries, screening samples for the SGTF helped to identify potential B.1.1.7 variants for sequencing prioritization. ThermoFisher, however, has not released their spike probe sequence, so the assay needs to be recreated to be used more broadly. Here, we designed a multiplexed PCR assay that recreates the SGTF signature using primer/probe set that targets the Δ69/70 HV deletion, the CDC N1 set as a positive control, and the CDC RNase P set as an extraction/sample control. Samples positive for the CDC N1 set but negative for the Δ69/70 HV deletion set can be tracked and prioritized for sequencing.

Affiliations: Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Department of Epidemiology of Microbial Diseases, Yale School of Public Health

Version: 1

Publication Date: 2021

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