A new variant of the coronavirus that originated in the United Kingdom sometime in September is likely to have already reached India, experts said on Tuesday, calling for increased whole genome-sequencing based surveillance to detect the new mutation and prevent further spread.
The new variant, VUI–202012/01, which accounted for nearly 60% of all cases in London by mid-December, is thought to be 70% more transmissible than earlier versions of the coronavirus. Scientists are still researching on the effects, virulence and severity of the new strain.
To prevent the new mutation from taking hold in the country, the government has banned flights from UK from Tuesday night, and administered tests to passengers who have arrived from Britain. On Tuesday, 22 people — including six from Delhi — tested positive for the virus, and their samples were sent for genome sequencing.
“The possibility that it hasn’t arrived in India is low,” said Dr Anurag Agarwal, director of the Institute of Genomics and Integrative Biology (IGIB), one of the labs sequencing Sars-CoV-2 genomes. He explained that the virus was found to be more transmissible. but added that the transmission could occur only if people were not wearing masks.
If precautions are not followed, the new variant may lead to superspreading events, other experts warned.
“It is likely that the new variant may have already come to India, you will find it only if you are looking for it. This is the reason why we need to scale up the number of genomic sequencing that we are doing. India has the second highest number of Covid-19 cases in the world and it is likely that some variant like it might have generated within the country too,” said Dr Shahid Jameel, virologist and director of Trivedi School of Biosciences at Ashoka University.
He estimated that the country sequences one genome of the virus for every 3,000 positive cases, whereas the World Health Organization said that one genome in 300 positive cases should ideally be sequenced. “And, it is not like we do not have the capability. There needs to be more focus on it,” he said.
At a government briefing on Tuesday, NITI Aayog member Dr VK Paul said that India will use its network of laboratories under the Indian Council of Medical Research, Department of Biotechnology, and Council of Scientific and Industrial Research to sequence more samples, especially from the travellers from UK who test positive.
“Our labs have been asked to prioritise the recent virus samples and send them for genetic sequencing. The ICMR, CSIR, and DBT labs have been doing it so far but it will be scaled up. The positive specimen from passengers from UK in the last few days will also be sequenced,” he said.
Dr Agarwal said some Reverse Transcription-Polymerase Chain Reaction (RT-PCR) kits that use the particular gene where the mutation has happened for detecting virus may give out false negatives. “We need to recalibrate our tests. The RT-PCR usually uses two genes to detect the presence of the virus, we might not insist on a double gene positive to give a positive report,” said Agarwal.
The United Kingdom has already issued guidelines for its labs to adapt the processes to ensure that the RT-PCR tests can detect this variant.
A cause of concern was that the mutation was at the receptor-binding domain of the spike protein, which the virus uses to enter the human body. This protein is also one of the targets of vaccines currently being developed.
But experts said that vaccines would remain effective despite the mutation.
“Think of the protein used by a vaccine as a surface; the immune response generated is against the complete surface, so even if there is a change in a particular point the vaccine still remains effective,” said Dr Jameel.
Dr Agarwal added, “The vaccine produces many antibodies and even if some do not bind, the vaccine remains effective. Other than that, there is T-cell immunity that is generic and a mutation in the binding site does not change that,” referring to cells that kill infected cells and prevent the virus from spreading.
Increased surveillance through genomic sequencing might also help the country find the “ideal variant” for a natural vaccine for Covid-19.