What you should know about the new COVID-19 variant

Scientists have detected a new Covid-19 variant called B.1.1.529. At least 50 confirmed cases have been identified in South Africa, Hong Kong and Botswana. These spike mutations might make the virus more resistant to vaccines, increase transmissibility and lead to more severe symptoms. Irobiko Chimezie Kingsley of Meziesblog looks into what we know so far. 

South Africa flag Irobiko Chimezie

Where was it found? 

According to The Guardian, early signs from diagnostic laboratories suggest the variant has increased in the South African province of Gauteng and may already be present across the rest of South Africa. 

South Africa has confirmed around 100 cases as B.1.1.529 but the variant has also been found in Botswana and Hong Kong – the Hong Kong case was a traveller from South Africa, The UK Guardian confirms. As many as 90% of new cases in Gauteng could be B.1.1.529, scientists believe. 

The S-gene dropout and the spread 

According to the BBC, this variant gives an S-gene dropout in the standard tests which can be used to track the variant without doing a full genetic analysis. In a press release by Thermo Fisher Scientific called “Why S-Gene Sequencing is Key for SARS-CoV-2 Surveillance”, the S-gene is described as such:  

“The S-gene encodes a surface protein, the spike protein, which is a homotrimeric glycoprotein complex essential for infectivity. The complex is made up of two subdomains; S1 contains a receptor binding domain (RBD) with high affinity for mammalian ACE2 or angiotensin converting enzyme. This cell surface protein modulates the activity of angiotensin II, a vasoactive polypeptide hormone active throughout the body. 

“When the S1 subdomain binds to ACE2, cleavage at the S1-S2 site facilitates SARS-CoV-2 entry to infect the host cell. Since the spike protein is on the virus surface, it plays a role in host immune response and also makes an excellent target for novel therapeutic strategies and vaccine development.” 

South Africa’s S-gene dropout suggests that 90% of cases in Gauteng may already be this variant and it “may already be present in most provinces” in South Africa, the BBC writes. But this does not tell us whether it spreads faster than Delta, is any more severe or to what extent it can evade the immune protection that comes from vaccination, the media outlet explains. 

“It also does not tell us how well the variant will spread in countries with much higher vaccination rates than the 24% of South Africa that is fully vaccinated, although large numbers of people in the country have had Covid”, the BBC said.  

There remains a lot of speculation around the topic, but what we know is that it is a heavily mutated variant. Professor Tulio de Oliveira, the Director of the Centre for Epidemic Response and Innovation in South Africa, said there was an “unusual constellation of mutations” and that it was “very different” to other variants that have circulated. “This variant did surprise us, it has a big jump on evolution [and] many more mutations that we expected,” he said.  

Some of the mutations have been seen before in other variants, which gives some insight into their likely role in this variant. 

Will the vaccine hold up against the new strain? 

The UK Health Security Agency said B.1.1.529 has a spike protein that was dramatically different to the one in the original coronavirus that Covid-19 vaccines are based on. 

“This is the most significant variant we have encountered to date and urgent research is underway to learn more about its transmissibility, severity and vaccine-susceptibility,” UKHSA Chief Executive Jenny Harries said. 

“What we do know is there’s a significant number of mutations, perhaps double the number of mutations that we have seen in the Delta variant,” Health Secretary Sajid Javid told broadcasters. “And that would suggest that it may well be more transmissible and the current vaccines that we have may well be less effective.” 

The BBC describe the concern to be less the nature of mutation and rather that the virus is now radically different to the original that emerged in Wuhan, China. That means vaccines, which were designed using the original strain, may not be as effective. 

How does it compare to other variants? 

Senior scientists on Thursday evening described B.1.1.529 as the worst variant they had seen since the start of the pandemic, The Guardian reported. It has 32 mutations in the spike protein, the part of the virus that most vaccines use to prime the immune system against Covid. “That is about double the number associated with the Delta variant”, the newspaper explained. Mutations in the spike protein can affect the virus’s ability to infect cells and spread, but also make it harder for immune cells to attack the pathogen. 

The Delta variant was first detected in India in late 2020 but has since spread around the world, causing an increase in case rates and deaths. Other coronavirus variants include Alpha (which originated in Kent in the UK), Beta (formerly known as the South African variant) and Gamma (originally found in Brazil). It has been suggested, following a drop in cases in Japan, that variants can “mutate themselves out of existence”, The Guardian said. 

WHO response 

The variant is likely to be given a Greek code-name (like the Alpha and Delta variants) by the World Health Organization in a meeting on November 26, the BBC confirmed. 

The meeting will determine if the B.1.1.529 variant should be designated a variant of “interest” or of “concern”, The Guardian explains.  

International response  

The New York Times reported that The European Commission will propose restricting air travel to the bloc from southern Africa based on concerns over the variant, Ursula von der Leyen, the commission’s president, said in a Twitter post on Friday. 

Within hours of the variant’s identification, Britain, Israel and Singapore had restricted travel from South Africa and some neighboring countries, citing the threat of the new variant.