When a virus replicates, it can change very slightly every time. These changes (or mutations) are usually so small that they have almost no effect on the properties of the virus, such as how ill you become and how the virus spreads. Sometimes changes do cause a virus to behave differently, for example allowing it to spread more easily. RIVM monitors changes in the coronavirus SARS-CoV-2 in the Netherlands and the consequences of those changes.

There are many different variants of the coronavirus SARS-CoV-2 by now. RIVM is conducting laboratory research to see which variants are present in the Netherlands and whether the percentage of infections from each variant is increasing. To make that possible, samples from positive SARS-CoV-2 tests from all across the Netherlands are investigated to check which variant was involved.

This pathogen surveillance research is important to know whether new variants with changed characteristics may also be increasing in the Netherlands. Some changes (mutations) can cause a variant to spread more quickly or make people more severely ill. Other mutations change the external appearance of the virus, making it harder for the immune system to detect it after a previous infection or vaccination.

Research on the incidence of variants and sub-variants of the virus is also taking place in the context of the National Sewage Surveillance programme at RIVM.

Current situation: BA.2.86 sub-variant JN.1 is most prevalent in the Netherlands

Since early 2022, most of the variants of SARS-CoV-2 circulating in the Netherlands have been in the Omicron lineage: sub-variants BA.1 through BA.5. Mutations are still emerging within these sub-variants. There are also recombinant strains that combine characteristics of other variants, such as the XBB variants, (including XBB.1.5, XBB.1.9, XBB.1.16 and EG.5). The same pattern is occurring in other countries as well.

Multiple sub-variants of BA.2 and BA.5 are currently circulating in the Netherlands. From BA.2, for example, we are seeing sub-variant BA.2.75 (including CH.1.1). Sub-variants of BA.5 include BF.7 and BQ.1 (including BQ.1.1). There are also recombinant strains that combine characteristics of other variants, such as the XBB variants (including XBB.1.5, XBB.1.9, XBB.1.16 and EG.5).

From week 7 to week 45 of 2023, EG.5 was responsible for the highest number of infections in the Netherlands. EG.5 is an XBB.1.9 sub-variant that was recently designated by the World Health Organisation (WHO) as a ‘Variant of Interest’ (VOI), due to possible changes in characteristics compared to previous variants.

Since week 46, the most common variant seen in pathogen surveillance is BA.2.86, a BA.2 sub-variant which has also been designated as a VOI by the WHO. Since week 48, BA.2.86 sub-variants have been dominant in the Netherlands. The most prevalent in the Netherlands at this time is JN.1, which has been designated as a VOI by the WHO. BA.2.86 variants show many genetic differences compared to the other variants currently circulating internationally, and is therefore being closely monitored worldwide. At this time, there are no indications that these sub-variants would be more likely to cause severe illness compared to previous Omicron sub-variants. 

The trends seen in sewage generally correspond to the trends observed in pathogen surveillance. At this time, sewage research shows the presence of BA.2.86 and mainly the sub-variant JN.1. 

Percentage of variants found most frequently per week since December 2020

Skip chart Percentage of variants found most frequently per week since December 2020 and go to datatable

The underlying data is public. The relevant sequences are shared in an international database by GISAID.

Due to an update to the classification tools, a number of recombinants that were previously shown under XBB subtypes are now shown in the ‘other’ category.

Many Omicron sub-variants appear to have the same minor changes (mutations) that developed separately. Most of these changes seem to occur in the ‘spike protein’, the lines bristling out from the coronavirus. The minor changes give the virus a slightly better chance to evade immunity resulting from previous infection or vaccination. Sometimes they also make it easier for a variant to attach to host cell receptors. At this time, there are no indications that these variants would be more likely to cause severe illness compared to previous Omicron sub-variants.

Alpha variant, B.1.1.7

The Alpha variant of the coronavirus, first found in the UK, was also detected in the Netherlands in December 2020. The Alpha variant then became the dominant strain in the Netherlands, supplanting the former variant of the virus. In summer 2021, the Alpha variant was ‘pushed out’ by the more contagious Delta variant.

Beta variant, B.1.351

The Beta variant of the coronavirus, first found in South Africa, was detected in the Netherlands in early January 2021. This variant of the virus, like the Alpha variant, also appears to be more contagious than the variant that had been dominant in the Netherlands until that point. The Beta variant is no longer detected in pathogen surveillance.

Gamma variant, P.1

The P.1 Gamma variant of the coronavirus was found mainly in outbreaks in and around Manaus, the capital of the Brazilian state of Amazonas. It is not yet clear whether the course of illness is different for this variant. Among other mutations, the variant has three changes in the spike protein, the lines bristling out from the coronavirus, that are considered cause for concern. These three changes are almost identical to the changes in the Beta variant. The immune response due to vaccination or due to previous infection with the virus may possibly be less effective against this variant.  The P.1 Gamma variant is currently no longer detected in pathogen surveillance.

Delta variant, B.1.617.2

The B.1.617.2 variant of the coronavirus was first found in October 2020 in India. In summer 2021, the Delta variant (B.1.617.2) replaced the Alpha variant as the dominant strain in the Netherlands. The Delta variant is much more contagious than the Alpha variant. The COVID-19 vaccines are effective in preventing hospital and ICU admissions, even against the Delta variant. At the end of 2021, the Delta variant was in turn replaced by the Omicron variant B.1.1.529. The same trend is occurring all over the world.

Emergence of Omicron variant B.1.1.529

The first cases involving the Omicron variant (B.1.1.529) of the coronavirus SARS-CoV-2 were reported in South Africa at the end of November 2021. The percentage of cases involving the Omicron variant rose rapidly around the world. Similar to other variants, the small changes (mutations) in this new variant were seen mainly in the lines bristling out from the coronavirus: the spike protein. A striking feature of this variant was that it proved to have an unusually large number of mutations in the spike protein. Never before had a new variant of the coronavirus spread as quickly as the Omicron variant. It became apparent that vaccine effectiveness against Omicron infection without booster vaccination was considerably lower compared to the Delta variant.
 

Frequently asked questions

How can you tell which variant of the coronavirus someone has?

If you test positive for COVID-19, the test results do not tell you which coronavirus variant you have. When analysing a COVID-19 test, a laboratory technician cannot see which variant of the coronavirus SARS-CoV-2 caused the infection. This requires further research, known as sequencing. This means further investigation of the virus sample that was taken with a cotton swab in the nose (and/or throat). Sequencing looks at the building blocks of the virus. By looking at how the virus is constructed, it is possible to recognise characteristic ‘building blocks’ of a variant. Sequencing is performed on random samples in the context of pathogen surveillance

Do the self-tests also detect the Omicron variant?

Yes, antigen tests are also effective in detecting the Omicron variant. This also applies to the self-tests. Various laboratories have investigated this and confirmed that they are effective. RIVM has done this for 6 self-tests; see also technical evaluation of SARS-CoV-2 self-test with Omicron variant and previous technical evaluation of the same self-tests with the wild-type virus.  A self-test is an antigen test which is suitable for home use. Antigen tests, like PCR tests, only check if you are carrying the virus at that moment. The test does not check which coronavirus variant you have. This requires further research. For that purpose, a new PCR test sample must be taken, which is then used for sequencing. This means further investigation of the virus sample that was taken with a cotton swab in the nose (and/or throat). Sequencing looks at the building blocks of the virus. By looking at how the virus is constructed, it is possible to recognise characteristic ‘building blocks’ of a variant. 

Are the virus variants also being found in coronavirus monitoring in sewage?

Yes. Sewage samples are also analysed to check for the presence of different variants of the coronavirus SARS-CoV-2.