Understanding the New Covid strain that is wreaking havoc

A mutant strain of the novel coronavirus- first identified in the UK in September and which is rapidly replacing other variations of the virus- may in fact be already present in several countries. Initial data suggests it is up to 70 per cent more transmissible.

Mutations are a natural part of virus evolution. In the case of SARS-CoV-2, these mutations may arise due to random errors during virus replication, be induced by antiviral proteins within infected people, or via genetic shuffling – known as recombination. Though signs of recombination are not currently detected in SARS-CoV-2.

The variant carries 14 defining mutations including seven in the spike protein, the protein that mediates entry of the virus into human cells. This is a relatively large number of changes compared to the many variants we have in circulation globally.

The variant has been named as VUI–202012/01 or lineage B.1.1.7 and it was seen to be witnessed first in the county of Kent on September 20. The new variant is responsible for 62% of the new COVID-19 cases in the UK since September.

The reason this strain stands out is because eight of the mutations are linked to the gene responsible for the spike protein. In particular, two are of concern: the N501Y mutation, which can make the virus more effective in invading cells, and the H69/V70 deletion mutation, which can hamper the immune response in some immunocompromised patients. Data suggests that this strain might be spreading faster and causing more severe illness.

The particular deletions identified in the spike protein of B.1.1.7 have appeared in multiple other lineages of the virus at increasing frequency and are also observed in chronic infections where they may alter antigenicity – recognition by immune antibodies. These deletions may also be associated with other mutations in the binding region of the coronavirus spike protein, including those observed in infections among farmed mink and a mutation shown to play a role in the virus's ability to evade the immune system in humans. B.1.1.7 also harbours a truncated ORF8 gene, with deletions in this region previously associated with decreased disease severity.

The functional effect of these mutations and deletions, particularly when in the combination reported in B.1.1.7, are still to be determined.

Researchers have recorded thousands of tiny modifications in in the genetic material of the coronavirus as it has hopscotched across the world. Some variants become more common in a population simply by luck, not because the changes somehow supercharge the virus. But it becomes more difficult for the pathogen to survive mainly because of the developing scope of vaccinations and, also due the growing immunity in human populations.

"The new variant could increase transmission of COVID-19 by as much as 70 percent and increase the R or reproduction number by 0.4 percent", explains Boris Johnson, the UK prime minister, and his chief scientific advisors.

Dr. Rajesh Malhotra, Head of AIIMS Corona Center, said that since the corona virus has come, it has mutated 4 thousand times.

Scientists also expect the virus to gain useful mutations enabling it to spread more easily or to escape detection by the body`s immune system. In a routine press briefing, Niti Aayog's Dr VK Paul said there was no cause for concern for now over the new strain of coronavirus found in the UK. "The new strain of Covid-19 in the United Kingdom has increased transmissibility. This mutation is not affecting the severity of the disease. Case fatality is not affected by this mutation," he said.

However, this spread has not been seen in India so far, says the Government. The Health Ministry also issued Standard Operating Procedure (SOP) for passengers who have travelled from or transited through the UK in the past four weeks. Compulsory RT-PCR tests on arrival, separate isolation of those testing positive for the new variant of coronavirus and institutional quarantine for co-passengers of those testing positive are some of the requirements mentioned by the Centre to the states.

The high number of mutations and the recent increase in prevalence of this particular variant, together with the biological relevance of some of the mutation candidates, emphasizes the need for in-depth study.