A new COVID-19 variant detected in South Africa and Botswana has experts pretty worried. While the number of cases identified is currently small – just 82 at the time of writing, according to local experts – it has a high number of concerning mutations that could allow the virus to evade vaccines and spark further waves of disease.
“I would definitely expect it to be poorly recognized by neutralizing antibodies relative to Alpha or Delta,” UCL Genetics Institute director Francois Balloux told The Guardian. “It is difficult to predict how transmissible it may be at this stage.”
It can be tempting to think of medical discoveries and developments as a kind of to-do list. You know – first, we eradicate smallpox, then we find a vaccine for polio, then we cure cancer, and then we’re done. In reality, it’s often more of a never-ending tug of war between humanity and diseases. Along comes a new virus, and so scientists develop a treatment to thwart it – only for the virus to evolve a way to beat that treatment, and the whole thing starts all over again. We’ve already seen that happen with SARS-CoV-2, the virus responsible for the COVID-19 pandemic – in fact, at this point 99 percent of COVID-19 infections aren’t from even the original virus at all, they’re from the Delta variant.
But so far, our vaccines have more or less held strong. That’s because the mutations in the spike protein – the bit of the virus that binds to a human cell, leading to an infection – have not been dramatic enough to outsmart antibodies trained on current vaccines.
This new variant is different. The spike mutation profile is “really awful,” said virologist Tom Peacock of Imperial College London’s Department of Infectious Disease in a series of tweets on the discovery, adding that he “would take a guess that this would be worse antigenically than nearly anything else about.”
“This variant contains not one, but two furin cleavage site mutations,” Peacock explained. Furin is a protein in our cells that gets duped by SARS-CoV-2 into snipping (or “cleaving”) a line of amino acids in the virus spike protein. The furin cleavage site is one of the main properties of COVID-19 that makes it so incredibly contagious. The variant combines two mutations on that site: “P681H (seen in Alpha, Mu, some Gamma, B.1.1.318) combined with N679K (seen in C.1.2 amongst others),” per Peacock.
“This is the first time I've seen two of these mutations in a single variant,” he said.
At the moment, scientists suspect the huge number of mutations occurred together – in one “single burst,” Balloux told the Guardian – suggesting it may have evolved inside someone with a weakened immune system. There’s also “some evidence the virus has grabbed a (very short) piece of human RNA and copied it into its genome,” noted Peacock – “this isn’t that uncommon for viruses,” he added, “but it is interesting.”
For now, the new lineage has been designated B.1.1.529 – it “will become a variant with a Greek name probably tomorrow,” explained bioinformatician Tulio de Oliveira, director of the University of Stellenbosch’s Centre for Epidemic Response & Innovation, who first identified the beta variant of COVID-19 in December last year.
While it was first detected in South Africa, with nearly all cases found so far occurring within the country, a handful of cases have also been recorded in neighboring Botswana. One case has also been detected in Hong Kong in a traveler from South Africa.
While the new variant “does certainly look a significant concern based on the mutations present,” said clinical microbiologist Ravi Gupta in The Guardian, he cautioned that “a key property of the virus that is unknown is its infectiousness, as that is what appears to have primarily driven the Delta variant.”
Two of the mutations present in B.1.1.529 have been found by Gupta’s lab to increase infectivity and reduce antibody recognition, and de Oliveira described the variant’s “very high number of mutations” as giving cause for “concern for predicted immune evasion and transmissibility.” Nevertheless, Gupta noted that “immune escape is only part of the picture of what may happen.”
“[It’s] worth emphasizing this is at super low numbers right now in a region of Africa that is fairly well sampled,” tweeted Peacock. “However it very very much should be monitored due to that horrific spike profile.”
“One [piece of] good news, if there is any,” pointed out de Oliveira, is that the new variant is very simple to detect – it takes just one PCR assay and does not require whole-genome sequencing. This means “we can detect it very quick,” de Oliveira explained, “and this will help us to track and understand the spread.”
While scientists and policymakers across the world get to work monitoring the new variant, researchers in South Africa have spent the last 36 hours in a frenzy of meetings and analysis to get ahead of the spread. De Oliveira’s group will be meeting with an emergency WHO Technical Working Group tomorrow to discuss B.1.1.529, and preliminary results are already coming in regarding the distribution and makeup of the variant.
“What we can see is very early signs from diagnostic laboratories that this lineage has rapidly increased in Gauteng [the South African province where the variant was first detected] and may already be present in most provinces,” de Oliveira said.
“We can make some predictions about the impact of the mutations,” he added. “[They come] from our knowledge and other scientific knowledge during this pandemic. But the full significance remains uncertain, and the vaccines remain the critical tool to protect us from severe disease.”