We would like to bring to your attention an important development in the JRC’s work related to the detection of SARS-CoV-2 variants including Omicron that can be used by the health authorities in your country.

The SARS-CoV-2 virus is constantly evolving and the new variants, such as Omicron, may slip through the detection net and lead to “false negative” results because most testing methods focus on the original variant. For instance, out of 17 standard PCR protocols recommended by WHO to detect SARS-CoV-2, 11 still work perfectly, but 4 have a decreased efficacy and will not detect the virus in low concentration, whereas 2 do not work at all.

The key step towards the detection of new variants is based on the knowledge of its genetic sequence. JRC designed an Omicron-specific method using sophisticated bioinformatics tools, which has been tested on hospital samples. This method can be readily used with routine equipment to confirm presence of Omicron without the need of expensive and time-consuming sequencing. This allows for better and quicker tracing of the variant spread and, consequently, leads to better health interventions. As of January 2022, the protocol presenting the method has been downloaded over 3.500 times. This method is uploaded on the Zenodo platform where the scientific community can download and implement it.

Also, as variant evolution does not stop with Omicron. JRC developed a dashboard, where laboratories can check if the method they use is still valid against specific variants.

Moreover, JRC is developing novel “universal” methods that should help detect any SARS-CoV-2 variant: those present today and those that may come up in the future. These methods could be applied to both human, as well as environmental samples.

We remain available to provide in-depth information to relevant services, as well as hold dedicated meetings presenting these new methods.

Kind regards,
Emanuela Bellan
Head of Unit
European Commission, Joint Research Centre