On Friday 14 January 2022, Luxembourg's national laboratory (Laboratoire National de Santé, LNS) confirmed 316 new cases of the SARS-CoV-2 Omicron variant of concern (VOC) representing 74.9% of all circulating variants in Luxembourg in week 52 (27 December 2021 to 2 January 2022).
Due to the emergence of the new Omicron VOC, as well as the high incidence rates in the European context, LNS is carrying out targeted PCR tests for potential Omicron cases within 24h from reception of the specimen. The targeted PCR tests specifically look at the 9/70del, K417N and N501Y mutations which are hallmark for Omicron. Once identified, these specimens are then prioritised for confirmation by sequencing.
(Note: it is not possible to determine the variant from a positive PCR or antigen test. The positive samples are sent to the LNS for detailed analysis from which they can then determine the variant and other genomic information: this additional process takes a couple of weeks and therefore the delay in reporting variants, etc.)
In week 52, 5,641 new COVID-19 cases were registered in Luxembourg of which 1,409 national specimens were screened by targeted PCR.
458 resident specimens from week 52 were further sequenced at LNS of which 422 were assigned to lineages. For the remaining, the data quality was not sufficient to determine lineage with confidence. Of the 422 specimens with confirmed lineages, 316 (74.9%) were Omicron and the rest 106 were Delta and Delta subtypes. No other VOC was detected in the sequenced samples.
Week 52 also represents the first week for Omicron VOC as the dominant lineage in Luxembourg, in just four weeks since the first case was detected in week 49.
The week before, week 51, Omicron represented 34.9% of all circulating lineages in Luxembourg.