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Winter Covid outbreak on the cards? Worry over converging virus strains

By, New Delhi
Oct 07, 2022 11:30 PM IST

A new set of Sars-CoV-2 variants, all offshoots of the Omicron classification of the virus, appear to be picking up the same sort of genetic traits after following different evolutionary journeys, prompting concern among experts that it could portend the arrival of a “fitter” version that might lead to a spurt in cases in coming months.

A new set of Sars-CoV-2 variants, all offshoots of the Omicron classification of the virus, appear to be picking up the same sort of genetic traits after following different evolutionary journeys, prompting concern among experts that it could portend the arrival of a “fitter” version that might lead to a spurt in cases in coming months.

Convergent evolution is a situation in which a virus evolves in a manner depending on immunity in the population it infects (REUTERS)
Convergent evolution is a situation in which a virus evolves in a manner depending on immunity in the population it infects (REUTERS)

But how such a new mutated Sars-CoV-2 changes the pandemic will only be answered upon its arrival, multiple scientists who spoke to HT said. The possible outcomes range between an Omicron-like scenario, in which a variant takes hold against the backdrop of large population immunity but with less severe outcomes, and a Delta-like situation, in which the coronavirus regains the ability to cause severe disease.

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The new clues come from two sources. First is a yet to be peer reviewed paper by Chinese scientists who carried out tests on multiple variants and created proxy mutations in the lab to mimic a situation where the Sars-CoV-2 picks up a certain set of mutations (some of which has since occurred in real life), based on the way it has evolved till now.

Second is from data gleaned from global and regional GISAID submissions. Scientists from around the world feed in Sars-CoV-2 mutation information to it, which is then compared with trajectories of case numbers in these regions – the juxtaposition gives a somewhat preliminary picture of which variants could be leading to an increase in infections.

Together, they paint a picture that experts believe needs to be closely tracked, and for efforts to be redoubled during the upcoming northern hemisphere winter season when Covid-19 typically spreads more readily due to festival seasons and more indoor crowding.

In the first, researcher Yunlong Cao and colleagues from the Biomedical Pioneering Innovation Center (BIOPIC) at Beijing’s Peking University find that “despite their rapidly divergent evolutionary courses, mutations [in the newest Omicron family of viruses] on their receptor-binding domain (RBD) converge on several hot spots”.

This is known as convergent evolution, a situation in which a virus evolves in a manner dependant upon immunity in the population it infects, explained noted Indian virologist Shahid Jameel in a conversation over email with HT. “The current population of hosts has varying levels of immunity due to vaccination, infection, and some combination of both. Immunity wanes, but there is a strong selection pressure, whereby mutations that allow the virus to bypass immunity are also very fit.

“What we are therefore seeing are the same mutations coming up in different lineages. That’s convergent evolution. So, instead of completely different VOCs (variants of concern) coming up, we are seeing multiple variants evolving and overlapping in parallel, rather than one replacing the other.” He added that such evolution will continue to happen if “we give up on stopping transmission (that is, steps such as stopping using masks)”.

The Chinese researchers see the convergent evolution, and another phenomenon associated with some Omicron sub-lineages (now the dominant Sars-CoV-2 family) wherein they don’t lead to a broad enough antibody response upon infection, as a dangerous mix.

“The interaction between convergent evolution of escaping variants and less diversified antibody repertoire would ultimately lead to a highly evasive variant, posing a great challenge to current vaccines and antibody drugs,” they said in their paper, released online on September 25.

“Notably, BA.2.75.2, BQ.1, and the constructed convergent mutants have already reached or even proceeded Sars-CoV-1 level antibody evasion capability, indicating extensive antigenicity drift,” they added, referring to a comparison of how little antibodies from vaccinated or Covid-19 convalescent patients neutralised the first Sars virus, a pathogen that spread in 2002-2004 and is considered a close relative of the one that began spreading in 2019.

In addition to BA.2.75.2 and BQ.1, the variants with some convergent evolution are BQ.1.1, BN.1 and XBB.

Moritz Gerstung, a professor at University Heidelberg, cited German genome sequencing and case data to estimate that “one of the fastest moving [variants] is BQ.1.1, which combines five of these mutations”.

“BQ.1.1’s fitness advantage is ~10-15% , around the same value that BA.5 had over BA.2 in spring ’22,” he said in a post on Twitter on Wednesday. While, he added, the recent upswing of Covid cases in Germany seem to be “due to variant agnostic effects — seasonality, waning immunity, behaviour”, the new variants could “add between 0.05-0.15 on top of the growth rate, which is bound to intensify the incoming wave”.

Another expert saw similar clues from global data. “BQ.1.1 to me still looks the best candidate to take over globally & cause an infection wave,” wrote Tom Wenseleers, professor at Netherlands-based KU Leuven university, in a tweet on Thursday, separately adding that the rise in infections in some parts of Europe at present did not appear to be driven by the new variants yet.

While the new variants appear to have the potential to trigger new waves, these alone are unlikely to pose a significant threat, another expert told HT.

“This trend is very reminiscent of the situation at the end of 2020 when the Alpha, Beta and Gamma variants emerged. A big difference though is that the immune evasiveness of these variants does not seem to be linked with increased pathogenicity (ability to cause severe disease) or massively increased transmissibility (as was the case with Beta, Alpha and Gamma),” said Darren P Martin, evolutionary biologist at University of Cape Town, who along with colleagues published a paper on the convergent evolution of the coronavirus last year.

For now, Martin added, “we’ll need to wait and see how things play out during the northern winter where behavioural factors begin fostering easier virus transmission.”

Like Jameel, Martin said the convergent evolution was par for the course. “If something arises that does sweep the world, I think it will be something fundamentally different in the S1 half of spike to both Omicron and previous VOCs (variants of concern),” he said.

The spike protein of the coronavirus splits into two, S1 and S2, during the infection process with the first responsible for latching onto the cell, and the second subunit carrying out the fusion of the pathogen with the target.

“I doubt there will be another VOC because the world in 2022 is very different from that in 2020 in terms of its immunity,” Jameel added. “There may be locals VOCs in areas of low vaccination like Africa, but even there, my sense is that enough infection has already happened to give widespread immunity.”

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  • ABOUT THE AUTHOR
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    Binayak reports on information security, privacy and scientific research in health and environment with explanatory pieces. He also edits the news sections of the newspaper.

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