A quick guide to variants

What are variants: A ‘mutation’ is different from a ‘variant’—which in turn is different from a ‘strain’, and here’s how: 

• This coronavirus—Sars-Cov-2—is a strain of a larger family of coronaviruses, which includes other strains such as Middle East respiratory syndrome (MERS) that caused severe respiratory illnesses in the past.
• Now, viruses spread by replicating themselves at an astonishing speed. 
• So when a virus produces a copy of itself, there are routine changes and sometimes ‘copying errors’—and that may cause changes in a protein molecule's behaviour.  
• These ‘errors’ can make a virus weaker, more harmful—or have no effect at all. The changes are called ‘mutations’.
• When a virus undergoes significant types of mutations that causes it to behave differently from the original virus, then it becomes a variant.

Why we have new variants: The longer the pandemic stretches, the more opportunities the virus has to keep replicating itself. As infections spread, variants typically evolve in immuno-compromised patients who are ill over a long period of time, as The Atlantic explains:

“The variants may have evolved in immunocompromised patients who were infected with the virus for months. Normally… ‘your immune system is going to town on it. It’s really trying to beat it up.’ But immunocompromised patients mount weaker immune responses. ‘It becomes almost like a training course for how to live with the human immune system,’ she says. That may be why these variants have so many new mutations at once, as if a year or two of evolution has been compressed into months. This is probably quite rare, but with tens of millions of infections around the globe, rare things will show up.”

Variants of concern: Not all variants are a cause of worry. Scientists only pay attention when a variant shows that it is more infectious or more likely to cause severe disease. These are called ‘variants of concern’—and there are four right now: Alpha, Beta, Gamma and Delta.

Ok, tell me about this new variant…

The name: It is called B.1.1529, but will likely receive a Greek name like the others soon. The variant likely evolved during a chronic infection of an immuno-compromised person, possibly in an untreated HIV/AIDS patient. 

The location: The variant was first spotted in Botswana, where three cases have now been sequenced. It was also spotted in one case in Hong Kong—in a traveller returning from South Africa. The most cases have been detected in South Africa—but the reporting varies wildly on the exact number. Euro News says there are 22 confirmed cases. Reuters cites “100 specimens,” while BBC News puts the number at 77. But they all agree that the spread is the heaviest in the province of Gauteng—where it accounts for 90% of the cases. And scientists say it “may already be present in most provinces" in the country.

The mutations: The variant has 50 mutations in total—of which 32 are in its spike protein. Any changes in the spike protein are worrying because that’s the part of the virus targeted by vaccines—to block the virus from entering the human cell. And of these 32 changes, 10 are in the exact bit—“receptor binding domain”—that helps the virus attach itself to the cell. In comparison, the highly infectious Delta variant has only two mutations in this location. 

Umm, that sounds worrying…

Yes, scientists are worried for a number of reasons:

One: The sheer number of mutations is unexpected:

“Prof 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.”

Two: If the variant is radically different from the one that originated in Wuhan, then vaccines developed to fight the coronavirus may not be effective. And it may be harder for our body to detect this new version of the virus.

Three: Scientists recognise at least two of the mutations—seen before in other variants. They are known to make the virus more infectious, and make it harder for our antibodies to recognise the virus. According to one South African expert:

“They give us concern this virus might have enhanced transmissibility, enhanced ability to spread from person to person, but might also be able to get around parts of the immune system.”

A big caveat: Simply being able to evade detection by our immune system—vaccinated or not—doesn’t necessarily mean that the virus will spread like wildfire. For example, the Beta variant is very good at ‘immune escape’—but lost out to the Delta which is far more infectious, and is now the dominant variant in the world. For now, we simply don’t know how infectious B.1.1529 is. 

So what happens next?

South Africa has called for an emergency meeting of the WHO to discuss the variant. The Indian government has called on all states to rigorously screen and test all travellers from South Africa, Botswana and Hong Kong. What this means: all states will have to send samples from Covid-positive travellers to designated labs for genome sequencing. The UK has suspended all flights from six African countries. And it is likely other countries will follow suit.

The big picture: A senior UNICEF official recently said:

“We’re seeing huge disparity in the availability of vaccines to high-and low-income countries, which is pretty scandalous. We live in fear of an outbreak or a surge in one of those countries because it would be a disaster for their health system and is the kind of place where … another variant can emerge.”

The bottomline: An infectious new variant poses a huge risk to a world that is only 43% vaccinated—and when many African countries have not even received their first dose. We now have the emergence of B.1.1529 in South Africa where only 24% are fully vaccinated. This while richer countries are pushing for booster shots for their own citizens. The irony is that the new variant will only heighten that sense of urgency in the West—widening the vaccine gap even further, and setting up a vicious cycle.

Reading list

BBC News has the most detailed analysis of the new variant. Be sure to check out virologist Tom Peacock’s Twitter thread—which explains why scientists are worried about it. For the latest findings out of South Africa, watch Prof Tulio de Oliveira’s press conference here and here. Indian Express has details of the government’s latest directive. The Guardian has more on rising Covid numbers in Europe, while ABC News has more on the surge in the US. Politico looks at the failure of the global vaccination campaign and the rising vaccine gap.