After genome sequencing of more than 10,000 Covid-19 cases in India, researchers have discovered a new variant with two new mutations that can better help evade the immune system.
In 15-20% of the samples from the Indian state of Maharashtra (the state that makes up 62% of the cases in the country) a new, double mutation was detected in key areas of the virus. These are now known as the E484Q and L452R mutations.
What makes the variant different?
Both of these mutations are of concern because they are located in an important part of the virus – the peak protein – that it uses to penetrate human cells. Vein proteins attach via a “receptor binding domain”, which means that the virus can attach to receptors in our cells.
These new mutations include changes in the vein protein that make it a ‘better fit’ for human cells. This means that the virus can access more easily and multiply faster. Given what we have seen with other similar mutations, it can also make our immune system more difficult to recognize the virus due to the slightly different form. This means that our immune system may not recognize the virus as something against which antibodies must be produced.
The emergence of these new variants was only possible due to the continued viral replication in areas with high circulation.
Although the Indian government has said that the data on the variants distributed in India (including this new Indian variant and others including the British tribe) is not sufficient to link it to the rapid increase in the number of cases in the country, we think this is the most likely explanation. The country managed to lower the rate in February, but a sudden increase in the number of reported cases is now reported.
Implications
The implications of these developments are very worrying – not only for India but also for the rest of the world. Mutations can lead to 20% more deaths in hospital, as we saw during the second wave in South Africa. This is because some mutant variants have the ability to spread faster, leading to sudden bumps and thus an overloaded health system.
But there is hope. Places around the world with higher vaccination coverage such as the UK and Israel are seeing a gradual decline in cases.
It has been found that most of the currently approved vaccines around the world elicit an immune response to some extent against several variants. But no trials have yet been conducted on the efficacy of vaccines against these new Indian mutations.
To make it difficult for the mutant strains to develop vaccine resistance, we need to ensure wider and faster coverage for vaccines around the world.
What should happen now?
Apart from the efforts of vaccine manufacturers to update the composition of vaccines to better handle new strains, it is important to include transmission worldwide. Countries can use the World Health Organization’s SARS-CoV-2 Framework for Risk Monitoring and Evaluation to assist in the rapid identification, monitoring and evaluation of variants.
To establish a direct link between a variant and a strong increase in cases within a short period of time, it is important to use genomic sequencing to link clusters together. But unless contact detection is done carefully, it is not easy to do so.
It is also important to understand the mechanisms involved in the infectivity and virulence of the newer variants. This requires laboratory models to effectively mimic distribution and virulence mechanisms.
To combat the effects of mutations in India, its pandemic response should include several measures. Genomic surveillance should be proactive and coincide with the epidemiological investigation of the group of cases for early identification and prompt action.
Since some variants can escape naturally induced immunity, vaccine manufacturers in India will need to develop better vaccines to cover these new variants. Continuous surveillance and control measures need to be strengthened to prevent the emergence of new variants by minimizing viral replication.
And lastly, rapid and rapid coverage of vaccines is not only necessary but essential to ensure modest levels of success in tackling this pandemic.
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