The idea that the novel coronavirus has different strains – some more lethal than the others – took wings in the Indian imagination quite early on in the pandemic. First, it was a Bharatiya Janata Party politician who quoted his “scientist friend” quoting another unnamed “US researcher” that the virus “strain in India is a less virulent mutation”. Then, a mainstream daily said India may have got a “lucky break” from the virus after a gastroenterologist they interviewed said that the “coronavirus in India is different from that found in other countries” and less dangerous.
But as it turned out that India was not quite having a lucky break as predicted, and people were getting infected and dying, more so in some states than others, a new strain theory emerged. This one was more specific. This time, it came from the Gujarat government who claimed that the high mortality rate in the state was a result of it being affected by the “virulent L-strain” of the virus. States like Kerala, which had managed to keep deaths low and the spread somewhat limited (at that point), were affected by a milder “S-strain” of the virus, Gujarat’s top health official said on video.
The implication was this: it was for reasons beyond the state’s control that Gujarat was seeing more deaths than others.
While most news reports took the state’s contention at face value, some pointed out Gujarat’s theory ran contrary to available scientific evidence.
Yet, the multiple-strain explanation has continued to endure among Indian administrators. In an interview in July, Gujarat’s chief minister Vijay Rupani again attributed the state’s high mortality in the pandemic to a more “fatal” strain of the coronavirus.
An enduring legend
Earlier this month, the Odisha government’s technical adviser on Covid-19, a practising physician, invoked the “virulent” strain theory in an interview to this reporter. The case load was disproportionately high in the state’s Ganjam district because migrant workers from Surat had imported the “L-strain” with them, he said. Scientists from the state, he said, had established this in a study where they were able to isolate four “strains”. The other three strains, which were found among people who had brought the virus in from other Indian states, were found to be much less virulent, he said.
Yet again, the implication was the same: that the state’s failure to contain the outbreak in Ganjam lay beyond administrative reasons.
But most virologists stick to what they said earlier: that there is no virus strain in India that is any less or more virulent than the others. In fact, there is, in all likelihood, just one strain of the novel coronavirus in India, and indeed, the earth.
What then of the several news stories from appear from time to time in publications across the world announcing the discovery of new strains of the virus? That is because there is no clear consensus on when a new mutation qualifies to be called a strain even among virologists. “While mutation is defined and accepted by science, strain is not so defined,” explained T Jacob John, one of India’s leading virologists and emeritus professor at Vellore’s Christian Medical College.
Of viral strains and clades
That, however, does not mean there is only one kind of coronavirus. Far from it, in fact. “There are [as of August 10] over 80,000 SARS-CoV-2 genomic sequences in the GISAID database,” said virologist Shahid Jameel who is chief executive officer at Wellcome Trust/DBT India Alliance.
SARS-CoV-2 is the novel coronavirus that causes Covid-19 and the GISAID database is a free-to-access collaborative initiative of the German government and Friends of GISAID, a non-profit.
To understand what that means, one needs to take a step back and understand how viruses (all kinds, not just the novel coronavirus) operate. As a virus infects a host (a human being in this case), it replicates itself or makes multiple copies of itself. Often, this copying process is not perfect and this leads to “mutations”, a seemingly major event in science fiction, but rather commonplace in real life, scientists say.
The greater the length of a pandemic, more the number of mutations, and consequently, more diverse the virus’s family. Not all of the new lineages are stable, though.
“Some of the variants survive or transmit better than others, and thus become more visible,” said Jameel.
But not even all the stable ones qualify to be called strains. For a new strain to emerge, the mutation has to be dramatic and result in significantly different physical attributes, most virologists believe.
To qualify as a separate strain, “transmissibility (monitored as R and Ro), virulence (qualified as disease-causing potential) or antigenicity (one reagent works for all; one vaccine will protect against any and all)” have to be different, said John.
So far, John said that has not happened. Not in India, not anywhere else in the world. “By my definition, there are not multiple strains. Only one,” he said.
Thus, what we have so far are only different “clades” (scientific parlance for groups) of the novel coronavirus. Jamil explained further, “[Different] clades have varying genetic sequences but the same physical attributes. So, if there were clades (or groups) of viruses that caused mild vs severe infection, they would be called strains. There is however no evidence for this so far.”
Some clades more infectious than others?
So now that the more-lethal-virus thesis is out of the way, what about transmissibility? Are some clades more infectious than others? Yes, they are.
But first, how many clades are there of the virus really? “In December 2019, the virus started out as Clade 19 first, diversifying into Clades 19A and 19B sometime around late January/early February 2020,” said Jameel.
At that point, a somewhat significant mutation – though not major enough for a new strain to emerge – took place. “A major mutation in the spike protein of the virus, called D614G, was seen,” said Jameel.
A spike protein is a major surface protein of the virus that it uses to bind to a receptor. It could be visualised as something that provides the virus a passage to a human cell. “The aspartic acid (abbreviated as D) at position 614 in the spike protein of Clade 19 viruses was changed to glycine (abbreviated as G),” Jamil elaborated.
Thus, emerged Clade 20, a more efficient off-shoot of Clade 19. Efficient because glycine is a less bulky amino acid that aspartic acid which means a “more flexible hinge region and thus more efficient cutting”, said Jameel. In simpler terms: a better doorway to the human cell.
Consequently, most novel coronaviruses are now of the Clade 20 variety and its subgroups. “In March 2020, about one-third of the viruses belonged to Clade 19 and the rest to Clade 20,” said Jameel. “By July 2020, very few viruses belong to Clade 19; most belong to Clade 20.”
Fortunately, though, the mutation will have no effect on the efficacy of vaccines that are being developed. “This mutation falls outside the region that is responsible for raising neutralising antibodies,” said Jamil.
India and Gujarat
Now, is it likely the virulent “strain” of Gujarat is actually Clade 20? Yes, all the viruses sequenced from Gujarat belong to Clade 20, said Jameel. But not only are they no more virulent, the pattern is no different from the rest of the country – or the rest of the world, for that matter. “What we see is that over time, all over the world, the virus is shifting from the D614 to the G614 variant because it offers the virus a selective advantage in infection and transmission,” said Jameel.
Genome sequencing data also reveals that Clade 20A is the most dominant clade in Gujarat. Not surprisingly perhaps, India, as a whole, echoes the same pattern.
The fatal L-strain of Gujarat, thus, as Jameel put it, is a “figment of imagination”.
“Politicians are free to use any excuses for any success or failure,” said John.
This reporting was supported by a grant from the Thakur Family Foundation. Thakur Family Foundation has not exercised any editorial control over the contents of this article.