ICMR confirms coronavirus strain present in Silchar is the same "Variant of Concern" - B.1.617.2

Adwoy Purkayastha and Anirban Roy Choudhury

India is in the midst of a devastating covid second wave which started in mid-March. Deaths and the daily rise in infections have broken worldwide records. The peak of the wave however is thought to be over now as nationwide recoveries are outnumbering daily infections every day. Sero surveys conducted last year in metro cities pointed out more than half of the population was immunised after recovering from SARS-CoV-2 infection during the first wave. But the recent massive rise in cases as well official death figures is almost 4X of what it was before suggesting that the meteoric surge can be attributed to new virulent variants which can also escape prior immunity to some extent.

Silchar Medical College and Hospital (SMCH) had sent five samples for genome sequencing to ICMR-Regional Medical Research Center lab located in Lahowal, Dibrugarh on the initiative of Microbiology Department Head Dr. Debadatta Dhar Chanda. This was done to understand the virus better. The samples were taken from patients admitted at the hospital all of whom had a CT score below 22 correlating to a very high viral load. After genome sequencing, all five samples were found to be of the B.1.617.2 Delta variant. Though only five samples were sequenced all of them belonging to a single sub-lineage could very well mean that the second wave in Barak Valley was triggered by the new Delta Variant following the national pattern and might as well explain the sudden rise in infections and deaths in the Valley since April.

Every time a virus spreads to a new host it mutates a bit. SARS-CoV-2 is no different but it also has a proofreading mechanism that checks out for errors while copying and corrects them. This was a major reason why virologists were hoping that the virus wouldn’t change much at a rapid pace like the flu and vaccinations would keep it at bay. However, it is also true that even with a virus that changes slowly but has been able to spread worldwide, a few changes to its own advantage would have massive repercussions from a macro point of view. Evolutionary pressure induced by largescale immunity might have forced the virus to undergo certain deletions in its spike protein for survival in hosts making them susceptible.

By the beginning of this year, reports already started emerging from countries like the UK, South Africa, and Brazil of a new second wave that alarmed scientists. The variants found in Brazil and South Africa were able to escape immunity gained from previous infection or vaccination though the variant found in UK’s Kent area showed only better transmissibility but not increased virulence as it could be contained by vaccines.

Gradually it became necessary for countries to checkout for variants through genome surveillance and note any unusual mutation which could have an effect on potential disease severity.

Indian Government constituted the Indian SARS-CoV-2 Genomics Consortium (INSACOG) last year comprising of 10 National Laboratories established by the Ministry of Health and Family Welfare. It was tasked with the objective of genomic sequencing and analysis of circulating SARS-CoV-2 variants as well as correlating the epidemiological trends with genomic variants. While initially variants from the UK and South Africa were detected from air travellers returning to India, slowly the trend started tilting towards a lesser-known variant B.1.617 first detected in Maharashtra on October 5.

There were two important mutations E484Q and L452R in the spike protein of the virus which also led to its misleading moniker “Double Mutant” used in media. However, the name was a misnomer as the variant had many mutations and not two. The Vidarbha region in Maharashtra had already seen a surge in infections before the second wave started nationwide. Notably, some of the same mutations were also found in Brazil and South Africa which meant that the coronavirus is undergoing convergent evolution from different places of the world independently. As the second wave of the pandemic ravaged through the nation of 1.38 billion, samples collected from different states showed the B.1.617 strain getting dominant in the country very quickly overtaking the foreign strains which clearly pointed out an evolutionary advantage. Three lineages – B.1.617.1, B.1.617.2, and B.1.617.3 of the variant have been detected till now of which B.1.617.2 also known as the Delta Variant is the dominant one in most of the states. The B.1.617.1 strain has been termed as the Kappa Variant by WHO on Monday as they discouraged naming variants after their place of origin and resorted to the Greek Alphabet system instead.

WHO classified the B.1.617 variant first detected in India as a Variant of Concern (VOC) on 11th May, 2021. The characteristic of the variant is that it is more transmissible and it can cause more severe illness which shows an increased virulence. A person may fail to respond to treatment owing to the variant. Though RT-PCR is the standard for covid testing still because of this variant sometimes an infection may go undetected.

The head of the microbiology department, who herself got infected by the virus said, “We’re dealing with the same strain in Barak Valley like the rest of the country and it is something we expected. There are very little chances of us finding a variant unique to this region. While we had send five samples voluntarily, now have to mandatorily send samples for sequencing as per government instruction. It would help in swiftly identifying any new changes.”

When asked about the efficacy of vaccines on this strain, Dr. Chanda said, despite vaccination, a person might have a symptomatic infection because of its immune escape mechanism, but the disease severity will be low in most cases. She urged the general public to take both doses as that is important to complete the vaccination process.