‘Double Mutant’/‘Triple Mutant’/‘Bengal Strain’: Why Experts Are Asking Everyone To Calm Down About SARS-CoV-2 Variants

India is being hit by a terrible second wave of Covid-19, the pandemic caused by the novel coronavirus SARS-CoV-2. The number of daily infections are rising rapidly and have been reported to be over three lakh for the past three days and are expected to increase further.

Last month, this day, India had reported just 44,000 odd cases. The sudden surge has taken everyone by surprise and overwhelmed healthcare infrastructure across major hotspots in the country.

The avalanche of daily cases has led many to speculate if there is something ‘scientifically’ different about this wave.

Some are hinting that the new variant identified as B.1.617 and popularised by the media as ‘double mutant’ or the ‘Indian variant’ is to be blamed. However, there is not enough data to prove that this is the reason nationally.

As per Sujeet Singh, director of the National Centre for Disease Control (NCDC), surge in Delhi is more likely associated with the UK variant (B.1.1.7). ‘The UK variant was found in 28% of samples in the second week of March. In the last week of the month, 50% of samples had this variant,’ he says.

In Maharashtra, it’s the so-called Indian variant that has been detected in majority of the samples in many cities.

Out of 1,770 samples sequenced for variants in the state, 427 cases were found to be of the Indian ‘double mutant’ variant, 64 cases of the UK strain, six cases of the South African strain and only one of the Brazilian strain.

So, different variants may be responsible for the current surge in different states.

This is what Kristina Andersen, an infectious disease scientist at Scripps Research Institute, also says. "We also know the B.1.1.7 [the variant first detected in the U.K.] is circulating in India, and we know that P.1. [the variant first detected in Brazil] is also circulating there, too. So they could also play a role in this surge. We simply don't have the data yet,” he says.

The genome sequencing and analysis is being done by Indian SARS-CoV-2 Consortium on Genomics (INSACOG), a grouping of 10 national laboratories established by Ministry of Health in December. So far, a total of 15,133 samples have been sequenced by INSACOG and these variants were detected in around 11.5 per cent of the cases.

What’s up with so many ‘variants’?

The evolution of genomic variants of viruses is a natural phenomenon. The genetic material of the novel coronavirus (ribonucleic acid - RNA) directs the production of proteins as it’s needed for its survival.

With every unit of new production, the genetic material is being manufactured as well as a copy. In each term of copying, small changes in the genetic material take place.

Millions of copies of the virus are being multiplied even within a single patient so it’s hardly surprising that the virus is mutating (changing) when it has been around for such a long time and run through such a large and diverse population across the world.

RNA sequence (represented by a string of letters) of the virus is crucial in fighting it from developing RT-PCR tests for diagnosis to even making RNA-based vaccines.

Mutations (at certain places in the RNA sequence) can alter the behaviour of the virus. Some variants can be more/less infectious and lethal depending on where the mutations are taking place in the RNA code.

As per the Centre for Disease Control, ’variants of concern’ are those for which ‘there is evidence of an increase in transmissibility, more severe disease (e.g., increased hospitalizations or deaths), significant reduction in neutralization by antibodies generated during previous infection or vaccination, reduced effectiveness of treatments or vaccines, or diagnostic detection failures.’

While ‘variant of interest’ (VOI) has ‘specific genetic markers that have been associated with changes to receptor binding, reduced neutralization by antibodies generated against previous infection or vaccination, reduced efficacy of treatments, potential diagnostic impact, or predicted increase in transmissibility or disease severity.’

VOI can be become VOC if there is solid evidence about their problematic nature.

Significant changes in the RNA can alter the nature of the pandemic because the disease caused may differ from variant to variant and can have an impact on existing therapies, vaccines and tests. So, it’s important for scientists to constantly look out for variants and their evolving nature via genome sequencing.

What about B.1.617, the so-called double mutant?

Thankfully, the ’double mutant’ or the ‘Indian variant’ is still a VOI and not VOC. Though the B.1.617 lineage is characterised by more than 15 mutations (six of them in spike protein), it has earned its notoriety for two particular mutations in the spike protein - L452R and E484Q.

Spike proteins of the virus are basically the keys which the virus uses to open the locks to receptor proteins in humans, attach itself and enter into the body.

Changes to these spike proteins aka the keys can make them better or worse at opening the ’locks’ to our bodies.

The L452R and E484Q mutations make the B.1.617 lineage a ‘variant of interest’ because they are known to have immunity escape power (people with antibodies can get reinfected) and are associated with increased infectivity (meaning that this mutation makes it a better key).

While some would use this as a confirmation for their theory that this variant is driving the sudden surge in India, Jeffrey Barrett, a Statistical geneticist at Wellcome Sanger Institute in the UK, says that ‘this lineage has existed for months at low levels in India, and has been seen occasionally elsewhere. There's lots of caveats around different local conditions, but the fact that it hasn't grown sooner makes it likely to not be as transmissible as B.1.1.7 in my view.’

B.1.1.7 is the so-called UK variant which spread like wildfire in that country and caused huge devastation and has been established to be over 40 per cent more infectious than the original Wuhan virus.

Will vaccines work on this variant?

On L452R and E484Q, Barrett says that both have ‘shown evidence of reduced neutralisation by some monoclonal antibodies. But vaccine induced immunity is polyclonal and involves T-cell response. So I think it's not that likely that it truly "escapes"’.

‘Also, 484Q has not turned up in experiments selecting better ACE2 binding (and hence infectivity) compared to 484K. Plus B.1.617 is missing N501Y, which is a key factor increased binding for other VOCs’, he adds. Both 484K and N501Y mutations were present in the UK, Brazil and South Africa variants which made them a matter of huge concern.

Chise, a Molecular Biologist whose lab’s research focuses on uncovering mechanisms of viral pathogenesis, host immunity and develop more effective vaccines, agrees.

On L452R mutation, Chise says that the California variant B.1.429 exhibited ‘neutralization that was similar to that of wild-type and the parental D614G variant amongst those who received two doses of vaccine’.

‘Vaccines make polyclonal antibody responses and involve T-cell responses. This means that the antibodies you make after vaccination will be able to bind the coronavirus spike in multiple places, not just one. With this in mind, it is unlikely variants will truly “escape” them,’ Chise tweeted citing a study which ‘found CD4+ and CD8+ T-cell mediated responses were MINIMALLY affected by mutations found in SARS-CoV-2 VOCs B.1.1.7, B.1.351, P.1 AND B.1.429 (the one that shares the same mutation as B.1.617)’.

These views have been further confirmed by the studies. Indian Council of Medical Research which has developed India’s first indigenous vaccine in collaboration with Bharat Biotech claims that its candidate Covaxin neutralises against multiple variants of SARS-CoV-2 including the ‘double mutant’ strain apart from the UK variant and the Brazil variant.

Covidshield vaccine produced by Serum Institute of India also offers similar protection. The Centre for Cellular and Molecular Biology (CCMB) Director Rakesh K Mishra says that Covidshield works against ‘double mutant’ strain.

"Early results using in vitro neutralisation assay show that both convalescent (prior infection) sera and Covidshield vaccinated sera offer protection against the B.1.617 variant, aka double mutant," he declared on Twitter.

While experts are questioning claims of higher infectivity and immune escape capability of the two mutations (L452R and E484Q), the data on the ‘double mutant’ being a more virulent strain is even shakier.

The number of deaths are higher than last year for certain but so are the cases. Additionally, it is more likely that overwhelming of the healthcare infrastructure and lack of life saving medical supplies such as oxygen or medicines are bigger factors behind lot of deaths that we are witnessing.

But what about ‘Triple Mutant’ variant aka ‘Bengal variant’?

This refers to the B.1.618 lineage which was first identified in West Bengal in October last year.

Again, while its lineage is growing in the state significantly over the past few months with almost as many cases as that of B.1.617, the fact that it’s been around for over six months raises doubts over its supposedly bad characteristics.

Nonetheless, what is concerning is that it has the E484K mutation which was in the UK, Brazil and South Africa variants and that is known for its immune escape capabilities.

Divya Tej Sowpati, a biologist with CCMB, took to Twitter to clarify that Bengal variant (B.1.618), India variant (B.1.617) and the ‘triple variant’ aren’t the same. ‘Triple variant’ is simply a part of the B.1.617 lineage and is termed as such because it has a third mutation in its spike protein apart from the two discussed above.

‘The extra mutation, V382L, is just a mutation of "interest" at this point because it's in the RBD of Spike, and was listed as a low frequency in the US. So far, its frequency seems to remain low and constant,’ Sowpati tweeted adding that ‘given its behavior elsewhere so far, it probably less likely to be "destructive"’ instead of being lethal and more infectious as is being claimed in media reports to create panic.

Further, he said that Bengal variant has ‘nothing to do with B.1.617, except for a couple of shared variants that all SARS-CoV-2 strains have at this point such as D614G.’

To sump up, there is no need to worry too much about these variants based on media reports and without listening to experts.

As Chise says, ‘anyone using triple, double, or quadruple at this point to describe a variant isn’t worth listening to honestly. That’s just language for shock value and isn’t even scientifically valid. I’m sorry they’re even subjecting people to this.’

So, keep calm and get vaccinated.