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A nurse holds up a vial of vaccine at a hospital in Srinagar. India has administered more than 55 million shots of Covid-19 vaccine so far. (Photo: Yawar Nazir/Getty Images)
A nurse holds up a vial of vaccine at a hospital in Srinagar. India has administered more than 55 million shots of Covid-19 vaccine so far. (Photo: Yawar Nazir/Getty Images)

ScienceMarch 29, 2021

As India confronts a ‘double mutation’, what is the state of Covid variants, and what do they mean for vaccines?

A nurse holds up a vial of vaccine at a hospital in Srinagar. India has administered more than 55 million shots of Covid-19 vaccine so far. (Photo: Yawar Nazir/Getty Images)
A nurse holds up a vial of vaccine at a hospital in Srinagar. India has administered more than 55 million shots of Covid-19 vaccine so far. (Photo: Yawar Nazir/Getty Images)

India has reported a new, double mutation coronavirus variant. Mirjam Guesgen explains what that means and what we know so far about the global variants.

What are variants?

You can think of variants a bit like breeds of dog. The variants may look different but they’re all still part of the same species so to speak (SARS-CoV-2).

Variants are when a group of mutations, changes to the genetic code, get passed down the virus family tree. When a group of coronaviruses share the same inherited set of mutations, that’s a new variant. 

How are we getting new variants?

Siouxsie Wiles and Toby Morris produced an explainer about how those mutations happen. The gist of it is when the virus makes new copies of itself inside a host cell, its genetic material gets reshuffled or changed. Those modifications in the genetic material lead to changes in proteins that make up the new virus. 

You’ll often hear scientists talking about spike proteins, those that jut out from the surface of the Covid-19 virus surface. Changes to those proteins are worth noting because those proteins help lock onto our cells and infect them, and are also the target of our body’s immune response.

Why are we getting new variants?

The mixing of genetic material is natural part of the virus copying itself but there are a number of things that can help the virus along according to University of Otago virologist Jemma Geoghegan.

For example, the more cases you have the more chance the virus has at getting better at infecting and spreading between people. 

That might be part of why we’re seeing a new variant spring up in India this past week. The Indian government is saying it’s not so much that the spike in the country’s case numbers is due to the new variant as it is the other way around, said Geoghegan. More cases made it more likely a new variant would arise.

“When you let a virus spread out of control, it’s going to evolve and it’s going to get better at infecting that host because that’s what it does,” she explained. 

How many variants are there?

There are thousands of variants popping up in different countries, but the vast majority don’t change how the virus infects us, transmits between us or causes disease, and many of them stop circulating around.

There are a handful of variants, however, where there’s evidence that they might be passed on more easily, lead to more severe disease or be harder to detect or treat. Those are the so-called variants of concern. 

Right now, the Centers for Disease Control and Prevention (CDC) in the US has identified four variants of concern: 

  1. UK variant B.1.1.7
  2. South Africa variant B.1.351 
  3. Brazil/Japan variant P.1
  4. California variant CAL.20C. 

The California one is currently limited to the US state but the others have been found worldwide. 

According to a New Zealand Ministry of Health spokesperson, “multiple variants have been documented in New Zealand, including three variants which are currently considered to be of concern.” Those being the UK, South Africa and Brazil/Japan variants.

What makes these variants spread more easily or lead to more severe disease?

Different variants have different combinations of mutations, which work in different ways to help the virus spread. 

Like variants of concern, there are also mutations of concern – ones that give the virus some kind of advantage. Those mutations are often found in several variants, which is also evidence that they’re helpful to the virus in some way. 

The UK variant for example has the N501Y mutation that helps the spike proteins cling on more tightly to the receptors on the surface of human cells. 

The South Africa variant has N501Y but also the K417N and E484K mutations. K417N interferes with the forces that push the virus away from a cell, and E484K makes the virus better at avoiding the body’s defences called neutralising antibodies, which bind to the virus to stop it entering and infecting our cells.

The Brazil/Japan variant has the tight-binding N501Y mutation and antibody-resisting E484K mutation but also the K417T mutation, which researchers think is pretty similar to the binding K417N mutation.

What is the new Indian variant?

It’s being reported as a double mutation variant. 

What does ‘double mutation variant’ mean?

It’s when a variant has two mutations of concern. It might have a bunch of other mutations too, but it has at least two that could give the virus some advantage over our defences. “The vast majority of these variants of concern are from a cluster or constellation of mutations,” says Geoghegan. 

The Indian one is a combination of mutation L452R (also in the Californian variant) and the E484Q mutation found in India. 

So what do the mutations in the new Indian variant do?

The L452R mutation is found on a spot on the virus’s genetic material that codes for binding, so researchers think it might help the virus cling more tightly to cells. It may also help the virus get around neutralising antibodies, which our body makes to try and fend off the virus from latching onto and entering our cells. They think the E484Q might also help the virus get around those neutralising antibodies. 

Are there other double mutation variants?

Technically the Brazil/Japan and South Africa variants are triple mutation variants, since they have three mutations of concern each.

Why do we care about double or triple mutation variants?

The more mutations of concern, potentially the more of an advantage the virus has over our defences. 

“The individual effects might accumulate,” said Geoghegan. “And the combination may give the virus variant an advantage over all other variants.”  

What does this mean for the vaccines?

So far there’s evidence that the Moderna and Pfizer vaccines are still effective against the UK and South Africa strains. The AstraZenica vaccine seems to work well against the UK variant but less so against the South Africa one.

There’s no research about how effective the currently-available vaccines are against the Indian variant. 

Researchers have said before that they’re confident the vaccines will work to get the body geared up to deal with the new variants. Nonetheless vaccine manufacturers may need to take extra steps like putting more than one variant (or the information for its proteins) in a jab or giving an extra booster shot.

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