New virus strain emerged in Sep, may already be there in India: Experts

India needs to step up its genomic sequencing surveillance to detect coronavirus strains in the country, say experts

A new variant of Sars-Cov-2 has been found in the United Kingdom and is reportedly "out of control", an announcement that set off alarm bells around Europe and elsewhere. Many members of the European Union suspended travel to and from Britain and imposed harsher quarantine rules.

The new variant is likely to cause 60 to 70 per cent more infections than the original strain. With "abundant precaution" India has temporarily suspended flights to and from UK till the end of the year. The Union government is closely following the development and advised people not to panic.

As part of the natural evolving process, RNA-based viruses undergo various changes in their genetic material. Also in these viruses, the mutation is faster as the proof-reading mechanism doesn't exist. That is, when the virus replicates its copies inside the cells, there is no mechanism to find an error copy, that will likely result in a mutated version. For instance, a common-cold virus changes its genetic material so fastly and so frequently, that scientists have to come up with a new vaccine almost every year.

In its defense or to evade the immune responses, the genome of Sars-Cov-2 has also undergone multiple mutations since its origins in China, most of which aren't alarming so far.

Experts say the new strain is a cause for concern, but caution against paranoia.

Speaking to Business Standard, Dr Rakesh Mishra, director of the Centre for Cellular and Molecular Biology (CCMB), says, the new variant has changed the part of its spike protein called receptor-binding domain and it is spreading more efficiently.

"From what we know so far, the mutation is worrying many for two reasons. For one, it appears the virus is finding the cell receptor more quickly, therefore gaining faster access to enter inside. The other thing is the viral load in the new strain, that is the viral particles in the infected individual may be much higher, which leads to more replication inside the cells and people are likely to shed more of it onto others" says Dr Mishra.

A health worker collects swab sample from COVID suspected man at Anand Vihar bus terminal, in New Delhi

Although there may not be much change in the symptoms and the mortality rates remain the same, if the virus spreads more efficiently it may lead to increased hospitalisations, that strain the health systems.

Usually, mutations are random and very difficult to be predict. The milder versions emerge and go away without anyone noticing. The deadlier mutations get noticed, only after different properties of virus genome are seen on a large scale. Then scientists go back and co-relate them by sequencing sample isolates from infected persons.

Some mutations are harmful to the virus itself and they vanish in time. Some of them give selective advantage to the virus. We get to know only those versions, says Dr Shahid Jameel, a noted virologist.

The new virus variant was first emerged in UK in September, it could have been already circulating in our country, but it is difficult to know unless there are large scale infections," adds Dr Jameel. Dr Mishra also notes that the new strain could have entered the country by some means or the other and we have to wait and see if it slowly shows up.

"We have the second highest infection count in the world. How do we know that the new strain is not spreading in the country. Forget about that, how do we find out the other mutations occuring within the country. The strain not only comes from outside. It can independently develop within the country also. That is certainly something we need to be worried about," says Dr Jameel.

It may take a few weeks to determine whether the new strain is present in India. That also depends on the frequent genomic sequencing of the isolates from infected patients. So far we are doing very less of it compared to western nations. For instance, in England, around 10 per cent of the infected virus samples are sequenced to study the nature of the virus. It is entirely possible that the strong surveillance system in UK made it easier to find a new variant in the country.

"By the time we find the new strain in India, it might be too late. If we don't catch mutations quickly, we can't move fast to block the virus. We should be doing more RT-PCR tests and should be sequencing higher percentage of the samples, so that we can understand the evolving nature of the virus," says Dr Mishra.

"The WHO calls for sequencing from 1 out of every 300 confirmed cases. we seem to be doing 10 times less than that. The message should be that we should increase genetic surveillance efforts in the country," says virologist Jameel.

Experts believe the current vaccines will likely work even against the new strain of the virus.

"Vaccines that target multiple parts of the virus may retain their efficacy even after mutations, but mRNA vaccines that target specific part of the protein spike, run the risk of losing their efficacy if there are mutations in that region. For now, although the mutation of the new strain is in the spike protein, all the indications are that the current vaccine will be almost as effecive when compared against most strains that are around. The only concern starts when the virus changes its nature even more and becomes more deadlier," Dr Mishra adds.

Both Pfizer and Moderna's vaccines are based on mRNA technology. Both shots carry a thread of mRNA that induce virus-like protein spikes. The immune system recognises them, launches an attack and, in case of any actual infection, the response would be faster.

Dr Jameel too believes there will be no effect on the vaccines.

"No need to be worried about the vaccines. They will likely counter the mutations. We should be doing more of genetic surveillance. It should be a routine matter. You never know, you may discover variants that may cause severe disease, he says"