Covid-19: Mutations may not be driving spike, say experts

The E484K mutation, which occurs on the spike protein used by the virus to enter human cells, is thought to cause loss of sensitivity to immune response generated by current vaccines or previous infections.

Researchers from India’s consortium mapping the genetic changes in Sar-Cov-2 virus have found the E484K mutation, found in the variants linked to Brazil and South Africa, in less than 10% of samples from Maharashtra, leading them to believe that the resurgence in the state may not be due to this factor.

Scientists are also keeping a track of a variant with the N440K mutation that might be transmitting at a slightly faster pace than other variants in India.(Pratham Gokhale/HT file photo)

The E484K mutation, which occurs on the spike protein used by the virus to enter human cells, is thought to cause loss of sensitivity to immune response generated by current vaccines or previous infections. This, in effect, means the current vaccines approved world over may not work well against the mutation and there is a chance of re-infection.

The mutation is present in both the South African B.1.351 variant and Brazilian P.1 variant that are of international concern. Experts in the UK last month said that the variant there, labelled B.1.1.7, has also picked up the E484K mutation.

“The mutation was seen in a few samples from Maharashtra. However, it is not a variant of concern at the moment as it does not seem to be driving the current surge in the number of cases in the state. A variant is said to be of concern if it is spreading faster, if it leads to disease in a higher proportion of the people, or if it escapes the vaccine – which is currently not the case with this variant,” said Dr Rakesh Mishra, director, Centre for Cellular and Molecular Biology – one of the ten labs that constitute the Indian Sars-CoV-2 Genomics Consortium (INSACOG).

“To prevent the spread of this variant or any other for that matter, we need to follow containment and quarantine strategy along with Covid appropriate behaviour,” he said.

The mutation was found in less than 10% of the samples from the state, according to Dr Anurag Agarwal, director, Institute of Genomics and Integrative Biology (IGIB), which is another lab in INSACOG.

“The variant does not seem to be driving the current surge in infections. But, we need more data. These samples are from across Maharashtra, we need to sequence more samples from areas of outbreak such as Amravati. The current surge could just be because of susceptible people getting the infection,” said Dr Agarwal.

Scientists are also keeping a track of a variant with the N440K mutation that might be transmitting at a slightly faster pace than other variants in India.

“The N440K mutation has been circulating in south India for some months now but it doesn’t seem to cause any significant clinical changes in the disease,” said Dr Mishra.

Dr Agarwal added, “This variant is present across southern India and has now reached Maharashtra too.

Although our analysis shows that it might be spreading a little faster, but nearly 30% of samples from Andhra Pradesh had the variant in September but their trajectory was not very different from other states.”

The researchers have, however, said that they did not find any UK variant or other variants with similar mutations in India.

“Surprisingly, we have not seen any UK variant in India. This could be either because conditions in India are not conducive to its spread or perhaps the quarantine was done extremely well,” said Dr Mishra.

In updated technical guidance issued on Thursday, the World Health Organization said a Sars-Cov-2 variant can be classified as a variant of interest (VOI) if it has significant phenotype changes compared to the reference variant -- the virus that has been predominant in the world -- and has either spread significantly or is otherwise under the investigation by the WHO working group on virus evolution.

A VOI can then be classified as a variant of concern (VOC) under any of the three criteria: if it shows an increase in transmissibility or detrimental change in Covid-19 epidemiology; has increase in virulence or change in clinical disease presentation; or leads to a decrease in effectiveness of public health and social measures or available diagnostics, vaccines and therapeutics.