When a virus replicates, it can change very slightly every time. This change (or mutation) is usually so small that it has almost no effect on how ill you become and how the virus spreads. Sometimes a change does cause a virus to behave differently, for example allowing it to spread more easily. RIVM closely monitors changes in the coronavirus SARS-CoV-2 in the Netherlands and the consequences of those changes. Omicron is currently the most prevalent variant of the coronavirus in the Netherlands.

It is known that viruses change frequently. There are already thousands of variants of the coronavirus SARS-CoV-2. Working with other research labs, RIVM is conducting laboratory research to see which variants are present in the Netherlands and what that means for the spread of the virus in the Netherlands. This is known as pathogen surveillance. It is mainly important to know whether the variants that are circulating also have new characteristics that pose additional risks. For example if they are more easily transmitted, if they make people more ill, or if the virus variants do not respond as well to vaccination.

Omicron variant is dominant in the Netherlands

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 is rising rapidly around the world. In the Netherlands, it is the dominant variant. This means that most people who test positive for COVID-19 have the Omicron variant of the coronavirus. 

Similar to other variants, the small changes (mutations) in this new variant are seen mainly in the lines bristling out from the coronavirus: the spike protein. A striking feature of this variant is that it has an unusually large number of mutations in the spike protein.  Never before has a new variant of the coronavirus spread as quickly as the Omicron variant.

Vaccine effectiveness against infection without booster vaccination is considerably lower compared to the Delta variant. People can get the Omicron variant of the virus, even if they have had the coronavirus before or have already been vaccinated. Protection against infection with the Omicron variant increases significantly after a booster jab. However, protection against infection with the Omicron variant decreases faster after a booster jab compared to protection against the Delta variant. The Omicron variant is detected by the PCR tests and antigen tests used in the Netherlands for COVID-19 testing. 

The Omicron variant has been designated as a Variant of Concern by WHO and ECDC.

What are the BA subvariants of the Omicron variant?

So far, the Omicron variant has five subvariants that are currently being monitored closely. These have been designated BA.1, BA.2, BA.3, BA.4 and BA.5. The five subvariants differ in terms of the number and type of changes (mutations), including in the spike protein. In December 2021 and January 2022, BA.1 was initially the dominant Omicron variant in the Netherlands. Since week 7 of 2022, the dominant Omicron variant has been BA.2. At this time, >95% of SARS-CoV-2 infections in the Netherlands are caused by BA.2. 

BA.3 is found occasionally worldwide. This variant is only found sporadically in pathogen surveillance in the Netherlands. The percentage of cases involving this variant is not showing systematic increase at this time. 

More recently, the subvariants BA.4 and BA.5 have also been found in various countries. So far, BA.5 has been found once in the Netherlands in the context of in-depth surveillance research based on variant PCR testing in partnership with Saltro (the relevant specimen was taken on 11 April 2022). Since week 14, BA.4 has been detected in the random sampling in the context of pathogen surveillance in the Netherlands.

All variants are monitored and mapped on an ongoing basis. This allows us to identify any high-risk characteristics as quickly as possible and see how the variants are spreading.

Reproduction number R: how fast is the virus spreading?

When assessing the risks of a virus variant, it is important to know how contagious the variant is and how easily it spreads. Once there are more cases involving a specific virus variant, RIVM can calculate the reproduction number for that variant. The R number represents the number of people infected by someone who has the virus. It shows how quickly a specific variant can spread.

Monitoring variants in the Netherlands

The World Health Organization (WHO) and the European Centre for Disease prevention and Control (ECDC) publish weekly overviews of Variants of Concern and Variants of Interest. These variants are tracked due to their (potential) high-risk characteristics and degree of spread. RIVM is following the recommendations of the WHO and the ECDC in this respect, and advising these bodies based on its own findings. 

During pathogen surveillance, randomly selected samples are examined every week. These samples come from people who tested positive for the virus in a GGD test lane or a hospital in the Netherlands. In 2020, it started with dozens of samples every week. More and more laboratories joined the efforts, and RIVM now analyses about 1800 samples a week, about 1500 of those from the samples randomly selected in the context of pathogen surveillance.

Results pathogen surveillance

The table below shows the pathogen surveillance results for the Variants of Concern and Variants of Interest identified by WHO and ECDC.  The total number of samples analysed in the context of pathogen surveillance includes not only the variants in this table, but all other variants as well. These results show the samples that were successfully analysed. The samples that were not successfully analysed are not shown in this table. The underlying data is public. The full data set also contains the data on the current Variants under Monitoring.

Weeknumber Total  2022/18 2022/17 2022/16 2022/15 2022/14 2022/13 2022/12 2022/11 2020/49 t/m 2022/10
Designation 107886 703 1076 1219 1429 1546 1595 1789 1680 96849
Beta (B.1.351)  443 0 0 0 0 0 0 0 0 443
Gamma (P.1)  382 0 0 0 0 0 0 0 0 382
Delta (B.1.617.2) 44451 0 0 0 1 0 0 0 0 44450
Omicron (B.1.1.529) 30624 680 1060 1178 1383 1497 1554 1746 1654 19872
BA.1* 15202 4 8 18 22 38 80 134 188 14710
BA.2* 15391 661 1044 1156 1360 1458 1474 1612 1466 5160
BA.3* 3 0 0 1 0 0 0 0 0 2
BA.4* 20 10 6 2 1 1 0 0 0 0
BA.5* 8 5 2 1 0 0 0 0 0 0

Download the table of virus variants (PDF, 122 kb)

Pathogen surveillance data is updated weekly. New reports may be added up to and including week 17 of 2022 from the submissions provided by the (current and new) laboratories participating in pathogen surveillance. In any case, the figures for week 18 of 2022 are not yet complete. In addition, numbers per week may differ from previous publications due to updates of sample collection dates or reclassification of the sample in the registration system (source and contact tracing instead of random sampling). These weekly figures are updated retroactively. 

As of 26 November 2021, ECDC escalated B.1.1.529 variant of interest (VOI) and is therefore included in the table from now on. AY.4.2, B.1.616, B.1.620, B.1.427/429 (Epsilon), P.3 (Theta), B.1.525 (Eta), B.1.526 (Iota), B.1.617.1 (Kappa) and P.2 (Zeta) are de-escalated  and removed by the WHO and ECDC. As of 20 March 2022 B1.1.7 (Alpha), B.1.621 (Lambda) and C.37 (Mu) are de-escalated and removed by the WHO and ECDC.

* The numbers for BA.1, BA.2, BA.3, BA.4 and BA.5 are also included in the total number for Omicron variant (B1.1.529).

	Inschatting van aandeel coronavarianten Alfa, Beta, Gamma, Omikron BA.1 en Omikron BA.2

The graph shows the delta variant and the omicron variant of SARS-CoV-2.

Difference in proteins

So far, the main difference in the virus variants and the B.1.525 variant seems to be the changes in the ‘spike protein’, the lines bristling out from the coronavirus. The proteins of these virus variants may be able to attach themselves to human cells more effectively.

Before the Omicron variant became the most common variant in the Netherlands, other variants were dominant over time. Examples include the Delta variant and the Alpha variant. In addition, variants are sometimes found in pathogen surveillance that disappear again after a while.

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. All the infections that have been typed in the context of pathogen surveillance in the Netherlands currently involve the Delta variant. The same trend is occurring all over the world. 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.

Prevent infection with variants

What can you do to prevent the virus from spreading? The recommendations are the same for all variants of the coronavirus: if you have symptoms, stay home and use a self-test or get tested by the GGD, keep distancing, and wash your hands regularly.

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 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

Can the PCR tests accurately identify the Omicron variant?

Yes. Various laboratories, including the WHO Reference Laboratories at RIVM and Erasmus MC, have investigated this and confirmed that they do.

The PCR tests detect the presence of small fragments of genetic material from the coronavirus SARS-CoV-2 in nasal and throat mucus. PCR tests are used to determine if you have the virus right now. If you test positive for COVID-19, the test results do not tell you which coronavirus variant you have. 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 throat. By looking at how the virus is constructed, it is possible to recognise characteristic ‘building blocks’ of a variant.

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 confirmed 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 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?

Sewage samples are also analysed to check for the presence of different variants of the coronavirus SARS-CoV-2. Since week 48 of 2021 (29 November to 5 December), the Omicron variant has also been found in sewage in the Netherlands. In the weeks before that, only the Delta variant had been found in the sewage samples.