Thursday, January 20, 2022

Denmark SSI: Omicron Subvariant BA.2 Now Accounts For Nearly Half Of All Danish Cases


Credit NIAID


In mid-December, in The Omicron Uncertainty Principle, we looked at the discovery of a significant sibling variant to Omicron  - dubbed BA.2 - which lacked Omicron's signature SGTF (S-gene target failure), making it more difficult to detect without full sequencing. 

According to the latest WHO Weekly COVID epidemiological report (Jan 18th):

The Omicron variant includes Pango lineages B.1.1.529, BA.1, BA.2 and BA.3.  BA.1 accounts for >99% of sequences submitted to GISAID as of 18 January 2022. All these variants are being monitored by WHO under the umbrella of ‘Omicron’ 

While siblings, these `4 flavors' of Omicron may not all act the same.  BA.1 appears to be the most transmissible right now, but without SGTF, the BA.2 sublineage may be spreading `under the radar' in some countries.  BA.2 has been detected in over 30 countries, while BA.3 remains very rare. 

Other potential differences (if any) - in terms of transmission, or severity - have yet to be determined. It also seems likely that other sublineages of Omicron will emerge over time.

With the BA.1 subvariant believed to be the overwhelmingly dominant (> 99%) version of Omicron, the following report from Denmark's Statens Serum Institut (SSI) - finding nearly half of all Danish infections due to BA.2 - will likely raise a few eyebrows. 

A subvariant of omicron, BA.2, now accounts for almost half of all Danish omicron cases

So far, 3 subvariants of omicron have been described: BA.1, BA.2 and BA.3. Worldwide, BA.1 accounts for the vast majority of cases. In Denmark, however, BA.2 wins at the expense of BA.1.

Last edited 19 January 2022

The subvariant BA.2 accounted for 20% of all cases of infection in Denmark in week 52, while in week 2 it accounts for approx. 45%. At the same time, the share of BA.1 has fallen.

There is also an increase in BA.2 cases in other countries, i.a. Great Britain, Norway and Sweden, but apparently not quite at the same level as in Denmark.

Different mutations

BA.1 and BA.2 have many differences in mutations in the important areas. In fact, the difference between BA.1 and BA.2 is greater than the difference between the original variant and the alpha variant.

Such differences can lead to different characteristics which, for example, may relate to infectivity, vaccine effect or severity. There is as yet no final clarification of whether BA.1 and BA.2 have different properties, but SSI is continuously working to investigate this.

So far no difference in admissions

Preliminary analyzes from SSI show that there is no difference in the risk of admission with BA.2 compared to BA.1. Analyzes regarding infectivity and vaccine effectiveness etc. has been initiated, just as attempts are also being made to grow BA.2 so that antibody neutralization studies can be performed. The expectation is that vaccines also have an effect against serious illness when it comes to BA.2.

Many people are convinced that Omicron (specifically BA.1) signals the last gasp of the COVID pandemic and the virus will soon become an endemic, likely seasonal, respiratory virus.  

While this would be the best possible outcome at this point, it is far from guaranteed. 

The rise of BA.2 in Denmark may be a fluke, or ultimately of little consequence to the course of the pandemic - but it is a reminder that SARS-CoV-2 continues to evolve and adapt - which is why reports of COVID's imminent demise may be premature.