Implementation of an in-house real-time reverse transcription-PCR assay to detect the emerging SARS-CoV-2 N501Y variants

ABSTRACT

The real-time detection of emerging SARS-CoV-2 variants is critical to manage patients appropriately, and monitor and assess their epidemiological and clinical features. Sequencing is not a feasible comprehensive detection strategy considering the very large number of SARS-CoV-2 cases in our current setting. SARS-CoV-2 variants currently of greatest concern carry the N501Y substitution within the spike receptor binding domain. They have become predominant in England (20I/501Y.V1) and were detected in South Africa (20H/501Y.V2), Brazil and dozens of other countries worldwide. The 20I/501Y.V1 variant has started to spread worldwide including in France. It has been reported as 50-74% more transmissible than preexisting strains, suspected to evade anti-spike antibodies, and it caused a reinfection. We have implemented an in-house one-step real-time reverse transcription-PCR (qPCR) assay that specifically detects SARS-CoV-2 N501Y. It was found reliable to detect specifically the N501Y substitution and preliminarily allowed estimating 20I/501Y.V1 variant prevalence to 4% among our current SARS-CoV-2 diagnoses since January.