What we know about the new omicron subvariants from South Africa, UK

Two sublineages are responsible for a surge in cases in South Africa and a study shows that they may evade natural immunity from original omicron.
woman wearing mask walking past mural
A woman wearing a mask walks past a mural of former South Africa’s president Nelson Mandela, in Katlehong, east of Johannesburg, South Africa, Friday, April 29, 2022. South Africa’s health minister says it is likely the country has entered a new wave of COVID-19 earlier than expected as new infections and hospitalizations have risen rapidly over the past two weeks. (AP Photo/Themba Hadebe)

Story at a glance

  • Two subvariants of omicron are rapidly taking over in South Africa and leading to a rise in cases. 

  • A study suggests that these subvariants may be able to escape immunity acquired from original omicron.

  • Another variant is a combination of two omicron variants and has been spreading in the U.K.  

Health officials and scientists around the world continue to keep track of any new variations and variants of the SARS-CoV-2 coronavirus. Now new omicron subvariants have emerged in South Africa and the U.K., which have been detected in the U.S. at low levels. A new study suggests that some of the new subvariants may be able to evade immunity acquired from previous infections. Experts are keeping an eye on the data, but they are concerned that unvaccinated people may be poorly protected even if they had omicron in the first wave. 

BA.4 and BA.5 

New subvariants of omicron named BA.4 and BA.5 are sublineages of earlier omicron variants, but “what’s concerning about them is their arrival in South Africa coincides with a spike in cases,” said Seema Yasmin, journalist and professor in medicine at Stanford University, in an email to Changing America.  

These new strains are estimated to have emerged in mid-December 2021 and have reached 50 percent of sequences in South Africa as of the first week of April. Cases are rising rapidly again in South Africa.

“But the increase in infections is likely due to a confluence of factors including possible new mutations in the spike proteins of BA.4 and BA.5 but also a relaxation in measures to prevent the spread of the coronavirus and waning immunity in the population following earlier waves of infection,” Yasmin said. “We’re still waiting on data to see if these newer variants are linked to more severe infections and hospitalizations.” 

These subvariants have also been detected in the U.S. and elsewhere at low levels. The subvariants do not currently seem to cause more severe disease than BA.2 and other omicron variants, according to the World Health Organization. However, officials think that the data suggest they may be more transmissible than BA.2. 

A study posted on a pre-print server over the weekend suggests that these two variants may be able to evade immunity acquired from an original omicron infection. The study hasn’t gone through the peer review process yet and has not yet been published in an academic journal. 

The researchers collected blood samples from people who were infected with BA.1 early in the omicron wave in Nov. and Dec. 2021. Of the participants, 24 were unvaccinated and 15 were vaccinated. The team compared the neutralization effects of antibodies from the samples on BA.1, BA.4 and BA.5. Neutralization is when antibodies can attach efficiently to a pathogen. They found that overall antibodies from BA.1 infection were less capable of neutralizing the BA.4 and BA.5 viruses. This suggests that there is some level of immune escape with these two new subvariants. In addition, neutralization of BA.1 was lower in unvaccinated individuals compared to vaccinated individuals.  

This research indicates that “unvaccinated people who were infected with BA.1 seem to have poor protection against BA.4 and BA.5 whereas vaccinated people who were infected with BA.1 had a higher degree of protection against infection with newer variants,”said Yasmin. 

A combo variant 

Omicron XE is a subvariant that is a combination of two previous variants: BA.1 and BA.2.

“The arrival of the XE variant was predictable given how widely BA.1 and BA.2 variants have spread,” said Yasmin. 

It came into existence through the process called recombination, where multiple viruses interchange genetic material when occupying and replicating in the same cell.

“But also present in XE are genetic mutations not seen in BA.1 or BA.2,” Yasmin said. 

This variant was first detected in the U.K. on Jan. 19, 2022. It has been tied to more than a thousand cases as of last month, according to a report from the British government. A report from the World Health Organization on April 5 states that their scientists estimate that it may be 10 percent more transmissible than BA.2. It may be too soon to know how it compares in severity, but a U.K. virologist wrote in The Conversation that it is likely very similar to BA.2. 

Virologists expect recombination to happen occasionally. We’ve also seen recombinants from delta and omicron variants, although they don’t seem to be spreading as much. XE has also been detected in Thailand, Israel, India, Japan and the U.S