The continuous evolution of SARS-CoV-2 poses challenges for current detection tools. Since the beginning of the pandemics, SARS-CoV-2 has featured distinct sets of genetic changes able to reduce diagnostics accuracy, but also eventually evade existing immunity and confer to the virus’s higher transmissibility.
With the paper entitled “New RT-PCR assay for the detection of current and future SARS-CoV-2 Variants” – published today in the special issue on “Wastewater-Based Epidemiology (WBE) in COVID-19 Pandemics” of the scientific journal “Viruses” – the Joint Research Centre (JRC) of the European Commission in collaboration with scientists of Luxembourg and The Netherlands, have achieved another milestone in the efforts to mitigate the COVID-19 pandemic.
Differently from other available assays, the JRC RT-PCR assay has been specifically conceived to detect genomic regions of the virus less prone to mutate. In this way, JRC scientists, with the help of partner laboratories, have developed a universal detection method so versatile that it is expected to detect all current and most likely all future SARS-CoV-2 variants. The method also drastically reduces the possibility to have false negative test results, i.e. a sample is tested negative whereas in reality it contains virus particles. The JRC has also produced the necessary control samples for wide, global distribution. All new variants like Gryphon - the XBB.1.5 variant currently circulating mainly in the US – and all other possible variants circulating in China are anticipated not to escape detection with this new method.
The new duplex real-time RT-PCR assay able to detect new variants
The new method developed by JRC scientists consists in a new duplex real-time RT-PCR assay able to detect two SARS-CoV-2 genomic regions that, after two years of virus evolution remained stable, (JRC scientists therefore called them ultra-conserved elements). 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 analytical high sensitivity and specificity. The assay also functions as a one-step droplet digital RT-PCR assay.
Positive results with this assay in conjunction with negative results from an lineage-specific assay (as for example the one developed earlier by the JRC for Omicron) may provide timely indication of the emergence of a potential novel SARS-CoV-2 variant of concern in a certain community and thereby aid public health interventions. 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.
Compatibility with the New Reference Material
The assay matches with a new reference material for the detection of SARS-CoV-2 by RT-PCR. The material consists of a synthetic ssRNA (EURM-014) covering a fraction of the viral genome. It will be particularly useful for clinical or environmental diagnostic laboratories seeking quality and trust in their SARS-CoV-2 measurements.
In 2020, the JRC issued a synthetic ssRNA molecule (EURM-019) that has been extensively used by numerous laboratories worldwide to control the reverse transcription and amplification steps of SARS-CoV-2 real-time RT-PCR assays.
The new material EURM-014 has an enhanced compatibility with existing PCR assays, is stable at room temperature and includes an internal control to verify the RNA extraction procedure and sample integrity.
Background
Tracking SARS-CoV-2 variants in communities is becoming pivotal to assure a rapid public health response. Following the opinion expressed by the Health Security Committee and the recommendation of the EU in the framework of the Integrated Political Crisis Response (IPCR) on the epidemiological situation in the EU/EEA and developments in China, the JRC provided technical guidance and tools in support to the testing and sequencing of wastewater from airports with international flights and aircraft arriving from China as well as the clinical testing of arriving passengers.
A common approach to screen and select wastewater samples for further characterization would be highly beneficial. The JRC assay coupled with other specific RT-PCR methods may therefore contribute to this aim and support the collaborating parties and entities of the EU Sewage Sentinel System for SARS-CoV-2.
Related links
JRC study: “New RT-PCR assay for the detection of current and future SARS-CoV-2 Variants”
Release of a new reference material for the detection of SARS-CoV-2 by RT-PCR
Decision of the Integrated Political Crisis Response (IPCR)
JRC Guidelines - Wastewater sampling of aircrafts for SARS-CoV-2 surveillance
EASA/ECDC guidelines for aviation as part of European response to COVID-19 developments in China