New RT-PCR Assay for the Detection of Current and Future SARS-CoV-2 Variants

• Published in: Viruses Vol. 15; no. 1; p. 206
• Main Authors: Marchini, Antonio, Petrillo, Mauro, Parrish, Amy, Buttinger, Gerhard, Tavazzi, Simona, Querci, Maddalena, Betsou, Fay, Elsinga, Goffe, Medema, Gertjan, Abdelrahman, Tamir, Gawlik, Bernd, Corbisier, Philippe
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 11.01.2023; MDPI
• Subjects: Coronaviruses; COVID-19; COVID-19 - diagnosis; COVID-19 Testing; Genomes; Humans; Mutation; Pandemics; Polymerase chain reaction; Public health; Real-Time Polymerase Chain Reaction; Reverse Transcriptase Polymerase Chain Reaction; Reverse Transcription; RT-PCR diagnostic assays; SARS-CoV-2; SARS-CoV-2 - genetics; SARS-CoV-2 ultra-conserved genomic elements; Severe acute respiratory syndrome coronavirus 2; Wastewater; wastewater surveillance; WHO recommended assays; South Korea; Luxembourg; SARS-CoV-2 ultra-conserved genomic elements; SARS-CoV-2; RT-PCR diagnostic assays; WHO recommended assays; wastewater surveillance
• ISSN: 1999-4915; 1999-4915
• DOI: 10.3390/v15010206

Multiple lineages of SARS-CoV-2 have been identified featuring distinct sets of genetic changes that confer to the virus higher transmissibility and ability to evade existing immunity. The continuous evolution of SARS-CoV-2 may pose challenges for current treatment options and diagnostic tools. In this study, we have first evaluated the performance of the 14 WHO-recommended real-time reverse transcription (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. The new duplex assay successfully detects all of the tested SARS-CoV-2 variants of concern (including Omicron sub-lineages BA.4 and BA.5) from both clinical and wastewater samples with high sensitivity and specificity. The assay also functions as a one-step droplet digital RT-PCR assay. This new assay, in addition to clinical testing, could be adopted in surveillance programs for the routine monitoring of SARS-CoV-2's presence in a population in wastewater samples. Positive results with our assay in conjunction with negative results from an Omicron-specific assay may provide timely indication of the emergence of a novel SARS-CoV-2 variant in a certain community and thereby aid public health interventions.