Scientists first identified the Omicron variant of SARS-CoV-2, the virus that causes COVID-19, in South Africa in late November 2021.
Mutations in Omicron’s genome have allowed the variant to evade some of the immunity that vaccination or a previous SARS-CoV-2 infection has offered.
Omicron is also more transmissible than previous variants, including Delta, which has allowed it to become the most widespread variant worldwide.
So the news that a more contagious subvariant of Omicron, called BA.2, is spreading rapidly in several countries, including the U.S., the U.K., and Denmark, has raised concerns.
Omicron comprises three distinct evolutionary lineages, called BA.1, BA.2, and BA.3, that split from a common ancestor.
An initial survey of contact tracing data by the UK Health Security Agency, published on January 24, 2022, found that BA.2 appears to be spreading more rapidly in England than BA.1.
This preliminary analysis suggested that vaccines are more effective against BA.2 than against BA.1.
Research in Denmark has now confirmed that BA.2 is more transmissible than BA.1 and that vaccination still protects against infection and onward transmission of the virus.
However, this study found that the degree of protection that vaccines conferred was lower against BA.2 than BA.1.
The research did not provide any evidence about the severity of illness that BA.2 causes.
The study, which has not yet been peer-reviewed, has been published as a preprint on the medRxiv server.
By a happy accident, standard polymerase chain reaction (PCR) tests can identify whether someone has an infection with the BA.1 version of Omicron.
The tests work by detecting three of the virus’s genes, including the gene that makes its spike protein.
But the BA.1 version of Omicron has a mutation in its spike gene, so PCR tests only detect two out of their three gene targets. This makes it easy to tell whether someone has an infection with this variant.
BA.2 lacks this particular mutation, meaning PCR tests cannot distinguish it from other common variants.
This has led to health experts dubbing BA.2 the “stealth” Omicron variant because scientists must sequence its genome in order to identify it.
Sequencing samples from people with the infection reveals that BA.2 has been spreading rapidly in Denmark, despite the country’s high vaccination rates.
In the final week of 2021, BA.2 appeared to account for around 20% of all cases of SARS-CoV-2 infections in the country. But by the second week of 2022, around 45% of cases were due to BA.2. This indicates that this subvariant carries an advantage over BA.1 within the vaccinated population of Denmark.