Genomic surveillance of SARS-CoV-2

Updated: 24.6.2024

The evolution of SARS-CoV-2 viruses has been monitored in Finland through whole genome sequencing since December 2020. Whole genome sequencing is applied for timely identification of the viruslineages circulating in the population and the mutations occurring in them.

THL is responsible for the national genomic surveillance of SARS-CoV-2 in Finland. Wellbeing service counties and laboratories conducting coronavirus diagnostics provide a weekly sample of PCR positive SARS-CoV-2 samples for sequencing. The sequence data produced for viral genomic surveillance purposes does not contain any identifying information.

The genomic surveillance data is reported to the National Infectious Diseases Register with an approximately 2-week delay from sample collection. Based on the sequence data, viruses are also selected for further laboratory investigations at THL, for example for studies assessing the ability of the viruses to evade immunity.

The sequence data produced in Finland is combined with global SARS-CoV-2 datasets which are used to identify emerging and potentially pandemic variants and to monitor regional changes in sublineage prevalence.

Information based on the sequencing results and on the national infectious diseases register may differ slightly due to registry reporting delays. Results for the last reporting week are often based on a relatively small number of samples and are therefore less reliable than data for the previous weeks.

Detected coronavirus variants in wastewater
WHO and ECDC maintain lists of variants of interest (VOI) and variants under monitoring (VUM) with the objective to investigate if these lineages may pose an additional threat to global public health as compared to other circulating viruses.
Tracking SARS-CoV-2 variants (WHO)
SARS-CoV-2 variants of concern (ECDC)
You can view global data on SARS-CoV-2 sublineages around the world on the Nextstrain website.
Genomic epidemiology of SARS-CoV-2 (Nextrain.org)

Overview, June 2024

In May-June, the majority of sequenced viruses were descendants of the BA.2.86-JN.1 sublineage and so-called FLiRT-variants. While numerous variants circulate in parallel, the most commonly observed sublineages were JN.1.18, KP.3 and KP.2.

JN.1 became the dominant sublineage in Finland and elsewhere in Europe in the beginning of the year. Currently, JN.1 and descendant lineages count for over 90 percent of reported sequences globally.

FLiRT-variants are a family of current variants that share a set of spike protein mutations. These mutations have also been observed in some previous variants. According to WHO's assessment, the currently circulating variants do not significantly differ in their public health impact compared to previous variants.

The results from the Finnish SARS-CoV-2 genomic surveillance are in line with variant trends observed elsewhere in Europe. The evolution of SARS-CoV-2 lineages is expected to continue through mutations that confer improved evasion of the population immunity.

The number of reported SARS-CoV-2 cases is currently very low and therefore, the genomic surveillance data is based on a relatively small number of samples.

WHO's risk assessment on JN.1, 09.02.2024