New RT-PCR Assay for the detection of current and future SARS-CoV-2 variants

Multiple lineages of SARS-CoV-2 have been identified containing mutations in their viral genome that enhance infectivity and ability to evade existing immunity. SARS-CoV-2 will continue to evolve and new lineages are expected to emerge in the future further lessening the efficacy of current therapeutics and/or vaccination measures. The evolution of SARS-CoV-2 is also challenging diagnostic methods developed to identify the presence of the virus in clinical and environmental samples. In this study, we have first evaluated the performance of the 14 WHO recommended real-time RT-PCR assays currently in use for the detection of SARS-CoV-2 and found that only one assay has reduced performance against Omicron. We then developed a new duplex real-time RT-PCR assay based on the amplification of two ultra-conserved elements present within the SARS-CoV-2 genome. We show that the assay recognizes all of the main SARS-CoV-2 variants described thus far with high sensitivity, in both clinical and environmental samples, including the currently dominant Omicron BA.4 and BA.5 descendent lineages. Furthermore, we describe the development of a synthetic single strand RNA, which includes 5 non-overlapping sequences of the SARS-CoV-2 genome, to be used as a positive control in our and other commonly used SARS-CoV-2 RT-PCR assays.

MARCHINI Antonio;  PETRILLO Mauro;  PARRISH Amy;  BUTTINGER Gerhard;  TAVAZZI Simona;  QUERCI Maddalena;  BETSOU Fay;  ELSINGA Goffe;  MEDEMA Gertjan;  ABDELRAHMAN Tamir;  GAWLIK Bernd;  CORBISIER Philippe; 

2023-05-19

MDPI

JRC130941

1999-4915 (online),   

https://www.mdpi.com/1999-4915/15/1/206,    https://publications.jrc.ec.europa.eu/repository/handle/JRC130941,   

10.3390/v15010206 (online),