Genomic surveillance of SARS-CoV-2
Updated: 20.3.2024
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.
- For more information on the evolution and lineages of SARS-CoV-2 viruses, see the Coronavirus variants page.
Coronavirus variants - 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, March 2024
The omicron variant BA.2.86 and descendant lineages are the dominant variants during the winter. The most prevalent sublineage is JN.1. Descendant lineages of the omicron variant XBB, which dominated the variant landscape last autumn, continue to circulate with a low prevalence.
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
Contents
- Table 1. Sequencing results, proportion of variants of interest (VOI) and variants under monitoring (VUM)
- Figure 1. Weekly proportions of SARS-CoV-2 sublineages recorded in the national infectious diseases register
- Figure 2. Monthly proportions of SARS-CoV-2 sublineages in Uusimaa and other parts of the country, recorded in the national infectious diseases register
- Figure 3. Weekly distribution of observed SARS-CoV-2 sublineages
- Figure 4. Weekly number of variants of concern recorded in the national infectious diseases register, from December 2020 onwards
Table 1. Sequencing results, proportion of variants of interest (VOI) and variants under monitoring (VUM)
Click on the image to enlarge (png, 83 KB). The temporal change of variants of interest (VOI) and variants under monitoring (VUM). The table presents the proportion (%) of sublineages among the sequenced surveillance samples by week of sample collection.
Table 1 in an accessible table format (csv, 1 KB)
Figure 1. Weekly proportions of SARS-CoV-2 sublineages recorded in the national infectious diseases register
Click on the image to enlarge (png, 155 KB). The graph shows the proportions (%) of sublineages under monitoring, recorded among sequenced surveillance samples by week of sampling. Green shaded bars represent BA.2 sublineages, orange bars represent BA.4 sublineags and pink bars BA.5 sublineages. The grey shaded bars comprise recombinant lineages and the white bars comprise other sublineages not assigned to the previous groups. Sublineages ending in .X include all descendants of the sublineage.
Figure 1 in an accessible table format (csv, 28 KB)
Figure 2. Monthly proportions of SARS-CoV-2 sublineages in Uusimaa and other parts of the country, recorded in the national infectious diseases register
Click on the image to enlarge (png, 128 KB). The graph shows the proportions (%) of variants of interest (VOI) and variants under monitoring (VUM) reported from wellbeing services counties to the national infectious diseases register, recorded among sequenced surveillance samples by month of sampling. Green shaded bars represent BA.2 sublineages, orange bars represent BA.4 sublineages and pink bars BA.5 sublineages. The grey bars represent recombinant lineages and the white bar comprise other sublineages not assigned to the previous groups. Sublineages ending in .X include all descendants of the sublineage. Results for the December are based on a relatively small number of samples and are therefore less reliable than data for the previous months.
Figure 2 in an accessible table format (csv, 11 KB)
Figure 3. Weekly distribution of observed SARS-CoV-2 sublineages
Click on the image to enlarge (png, 164 KB). Weekly prevalence of SARS-CoV-2 sublineages among sequenced surveillance samples, by week of sampling. The graph shows the sublineages of which there are 10 or more observations during the observation period. Sublineages with fewer than 10 observations are combined in the group "Other. The gray-toned areas represent XBB sublineages and the green-toned areas represent BA.2 sublineages.
Figure 3 in an accessible table format (csv, 1 KB)
Figure 4. Weekly number of variants of concern recorded in the national infectious diseases register, from December 2020 onwards
Click on the image to enlarge (png, 110 KB). The graph displays the weekly number of variants of concern (VOC) in the national infectious diseases register, from December 2020 onward when the national genomic surveillance for SARS-CoV-2 was initiated.