Early this February, it looked like India was celebrating its happiest month since March 2020. Daily new cases had troughed to 12,000 from a September peak of 92,000. In Haridwar, the Kumbh Mela was on in full swing. The Health Minister claimed the pandemic was in its “endgame” and Prime Minister Narendra Modi declared India had “shown the world” how to tackle a pandemic. There were two local vaccines and healthcare workers had begun to get their shots. Everything was looking up.
But in mid-February, Maharashtra saw a sudden spike in COVID-19 cases, with Amravati emerging as a new hotspot. In just one day, the district reported nearly 900 cases, about 12% of Maharashtra’s case load. Average daily new cases spiked from 2,500 in the last week of January to 3,500 in February 10-15. A doctor at Pune’s B.J. Medical College, who declined to be identified, remarks: “It did look like something had changed.” Four of 12 novel coronavirus samples from Amravati tested for changes in genome sequence revealed a mutation that was initially labelled E484K.
Unlike any other virus in history, SARS-CoV-2 is the first one responsible for a pandemic in an era when it is possible to quickly, cheaply and universally ascertain the unique genomic structure of a pathogen. Like cartographers, who with satellites can trace a river’s journey from its source, watch it fibrillate into distributaries, and see some branches fuse again, bend, curve back in and yawn out into a mesh of rivulets before draining into the sea, virologists and genome-scientists tracked changes in the genetic structure of the evolving virus from sourced samples; they grouped them into phylogenetic trees where those that share similar mutations are often grouped together.
A woman receives a dose of the COVID-19 shot inside a bus turned into a mobile vaccination unit in Ahmedabad.
E484K or ‘Eek’, as genome-scientists nicknamed it, was one such that was first associated with a highly virulent and contagious variant from South Africa (B.1.135); later, it was also found in the highly contagious Brazilian (B1.1.28) variant. Eek is an ‘escape mutation’ because it allows the virus to evade the body’s immune system. Often, the number of antibodies generated following a vaccination weren’t enough to stop Eek and thus it was linked to reducing the neutralising efficiency of vaccines. However, the mutation in Amravati and in neighbouring Yavatmal and Akola, it turned out, was a slip of the alphabet. E484K is an abbreviation for glutamate (E) to lysine (K) substitution at position 484 (E484K) in the receptor binding domain (RBD) of the spike protein. The spike protein is a jumble of around 1,200 amino acids.
Rapid mutations
The specific sequence of these acids determines its structure and stability, and a missing amino acid can mean the death of the virus itself. But sometimes lucky twists — a lysine here instead of a glutamate there — improves the spike protein’s chances. What in Maharashtra was ‘K’ being substituted with ‘Q’ didn’t matter much, as other studies had shown that E484Q could escape four kinds of monoclonal (lab-made) antibodies.
“There were four other mutations,” says the doctor: “L452R, E154K, P681R and Q107H. L452R especially was linked to a rapid rise in cases in California. We had just got our genome sequencing machine but nobody was trained to use it. We flew down three doctors to Bengaluru, who within days learned to use this machine, returned, analysed and found this.” But the Maharashtra health authorities were sceptical. The Centre in December formed an India SARS-CoV-2 Genetics Consortium (INSACOG), a collaboration of 10 labs across the country that would sample a percentage of novel coronavirus genomes to check for mutations.
A health worker on vaccine duty in Vellore, Tamil Nadu.
The overwhelming focus of the group, which was overseen by the Department of Biotechnology and by the Health Ministry, was to examine if travellers from abroad, who tested positive, harboured mutant forms of the virus. WHO had highlighted three prominent variants — the ‘U.K. variant’, ‘South Africa variant’ and ‘Brazil variant’ — that countries with genome sequencing facilities were advised to watch out for. None of the Maharashtra strains showed all the defining mutations and, therefore, it couldn’t be one of these. “That was true, but why assume that a highly contagious variant would only come in from abroad? At that time nobody seemed willing to accept that a dangerous home-grown variant could emerge too,” the doctor adds.
By late February, the ascent in coronavirus numbers was palpable. The oasis of relief became a mirage. Talk of a ‘double mutant’ (E484Q and L452R) had transgressed beyond researcher circles in Maharashtra, where one in five tested samples seemed to manifest it, and there were reports of it in Delhi, Punjab and Gujarat. It wouldn’t be until March 24, when daily cases were edging near 50,000, that the INSACOG and the Health Ministry appeared open to accepting the possibility of a new variant. There was still no word on its potency and if it would blunt India’s infant vaccination drive.
Exploding cases and deaths
On April 8, when daily cases had touched an all-time high of close to a lakh, the variant was formally classified as B.1.617. The INSACOG revealed that the variant was actually first known in India in December 2020 and was, by April, present in at least eight countries with close to 70% of genome sequences manifesting characteristic mutations. Its spike protein had at least 15 lineage-defining mutations and a third significant mutation, P614R. All of these mutations on the spike protein were focussed on the RBD, which bound to the body’s cells and appeared to give the virus better leverage to infiltrate.
In April, as cases and deaths exploded and the sick gasped for oxygen, the B.1.617 spawned three other lineages: B.1.617.1, B.1.617.2 and B.1.617.3. The Indian government took umbrage to these being called ‘India variants’ even though they were confirmed to have been first found in India. Then, by the end of May, when the WHO finalised a system to name coronavirus variants in a way that didn’t stigmatise places and was less unwieldy, another transformative shift was underway. ‘Kappa’, for the Greek letter ‘K’, was the name given to B.1.617.1. It had all the defining mutations associated with its parent, but later analysis revealed that most of the cases linked with India’s devastating second wave weren’t Kappa, but a sibling lineage, B.1.617.2, christened by WHO as ‘Delta’.
A health technician collects COVID-19 samples at a testing centre in Vijayawada.
How Delta managed to so overwhelmingly out-compete Kappa and even B.1.617.3, despite being so extremely similar, and is now the dominant variant globally, is still to be clearly answered, but it is a question that is occupying the minds of researchers everywhere from the U.K, to the U.S. and India. “In fact, Delta has been around since October 2020 in Maharashtra but because the whole genome sequencing exercise was so limited it wasn’t picked up,” says a senior scientist affiliated to INSACOG.
Elaborate experiments
Among the scientists most intensely probing the mystery of Delta is Ravinder Gupta of the University of Cambridge, U.K., where the variant is driving a surge despite over 60% of the population being fully vaccinated. That Delta wasn’t something to be trifled with comes through in a series of elaborate experiments in his laboratory, where the variant was grown in a lab and tested on how it replicated in human tissues, lab-grown lungs, and respiratory cells.
When blood serum from those vaccinated with Pfizer and AstraZeneca vaccines was confronted with Delta, it showed that more of the virus managed to escape the antibodies. Even though being doubly vaccinated significantly protects against severe disease and death, there’s the worry that Delta may be a precursor to vexing changes in the virus.
“... it seems as though it is adapted for vaccinated people because it is much more transmissible, it makes a lot more virus in each infected human cell, and makes more copies of itself,” says Gupta in an interview to Roger Highfield, Science Director, U.K. Science Museum Group. Lipi Thukral, a scientist at the CSIR-Institute of Genomics and Integrative Biology, combs through the structure of coronaviruses to explain how they evolve. She and her group make computer models of the virus and, based on past trends in mutations, attempt to forecast what portions are likely to change in ways that will advantage the virus. The Delta variant presented a puzzle. A key mutation E484Q that was part of the parent B.1.617 lineage that improved the novel coronavirus’ ability to evade detection was missing, and the other key mutation, L452R, wasn’t known to be associated with severe outbreaks. Yet, the overwhelming evidence from India’s devastating second wave was that it was Delta, rather than Kappa, that wreaked havoc.
Artist Indrajit Paul’s take on the virus’s deadly avatar takes shape for the upcoming Durga Puja in Kolkata.
In Thukral’s view, a combination of mutations at three regions of Delta made it formidable, involving amino acids beyond RBD. So far, mutations in RBD are the best known because that’s the point of closest interaction with the cell. And several mutations that help this binding are the most studied, particularly for designing vaccines. However, there’s another key region of the spike protein called the N-terminal domain (NTD) that envelopes the RBD. Says Thukral: Delta has important mutations here that help the coronavirus to better bind and increase its stability. “Some mutations help the virus get a little bit closer to the cell.”
Evading detection
The many mutations that have so far been identified in RBD help the novel coronavirus avoid detection, but there’s also a trade-off in that too many changes affect the efficiency with which the RBD can bind onto the human cell. This is where the N-terminal domain comes in. Hisashi Arase and colleagues, at the University of Osaka, posited in a study last month that several mutations in the N-terminal domain were compensating for the reduced efficiency from too many RBD mutations that Delta seemed to be particularly rich in. In fact, there were regions in the NTD, which, if targeted by certain antibodies, ended up enhancing infection.
It is possible, says Arase, that in time the Delta variant could completely evade detection because of these NTD mutations. Arase proffers evidence from his lab’s studies, in which antibodies from vaccinated individuals appear to be significantly unable to suppress Delta.
Satyajit Rath, immunology professor at the Indian Institute of Science Education and Research, Pune, says that Arase’s theory, while grave, appears to be “an over-statement.” For one, there was still a large pool of unvaccinated and uninfected people and because distancing and vaccination make it harder for variants to suitably evolve, it would be a while before variants completely overwhelm the protection from antibodies. Moreover, says Rath, cellular immunity — the other kind of immunity that the body’s cells generate independently of antibodies — too has a significant role in affording protection. This was why, although Delta proliferated globally, and was significantly able to continue infecting even those doubly vaccinated, there were fewer instances of disease and death among the inoculated.
Rakesh Mishra, former head of the Centre for Cellular and Molecular Biology, Hyderabad, says that while Delta had structural advantages, it was social conditions — crowds, proximity to the infected, undetected infections — that largely fuelled the evolution of new variants. “That a variant like Delta was first found in India is in large part due to our population, which affords opportunities for mixing and a host of combinations to emerge. We can never predict how evolution will go, but wearing masks and being vaccinated can ensure that most can be spared the disease.”
Presently, Delta itself comes in a dazzling variety of combinations — nearly 35 — that are collectively referred to as ‘Delta-plus’ variants, though none so far have been found to be individually more threatening. India’s trajectory is again on a decline, but nowhere near the lows of February. Two-thirds of India’s cases are being reported out of Kerala, along with Maharashtra, with the strongest genome surveillance programme. Nearly all of those cases are Delta-linked.
