Two new descendants of Delta circulating in Canada that appear to have a survival edge — they seem slightly more spreadable — tell us SARS-CoV-2 may still have “plenty more room” to continue adapting to humans, scientists say.
“It’s hard to say what the ceiling is,” said Jesse Shapiro, an associate professor in the department of microbiology and immunology at Montreal’s McGill University.
“It will keep climbing to find a peak of adaptation. But we don’t really know how close to the peak we are.”
The two Delta sub-lineages, dubbed AY.25 and AY.27, were first detected in Canada in the spring. Cases have been detected in every province except Prince Edward Island, with the highest numbers in Western Canada. AY.25 is becoming the predominant circulating strain in Saskatchewan. In Ontario, AY.25 accounted for 31 per cent of 1,670 confirmed cases of COVID-19 sequenced over a recent four-week period.
All told, more than 38,000 genomic sequences of samples from across Canada have been deposited in a global data portal that’s tracking the spread of SARS-CoV-2 variants.
A detailed report from provincial and federal labs, as well as Canada’s own COVID variants rapid response network, is expected to be published next week.
The new variants seem to be increasing in frequency, Shapiro said. What’s not clear is what it means, if anything, for the biology of COVID-19. “If the infections are more severe, if they’re more likely to be causing breakthrough infections, we have no idea.”
The sub-lineages, which evolved from within Delta and were first identified in India, appear to have a slight survival advantage. Modelling suggests they are growing and spreading up to five per cent faster. It’s modest, and nowhere near the transmission advantage that Delta had over Alpha (it was 40 to 60 per cent more transmissible) or what Alpha had over the original strain out of Wuhan, China.
It’s also hard to untangle what’s driving the apparent growth. There could be biases in the cases being sampled, Shapiro said. For example, were outbreaks targeted? Is this the “jackpot” effect, he said, “where cases happened to be growing, particularly in the western provinces, and this was the lucky virus that happened to be at the right place at the right time?”
However, “when you see it in separate jurisdictions, it does become increasing evidence that there is a real transmission advantage.”
None of this is particularly unexpected, Shapiro added. “It’s more or less what we would expect in a growing viral population, as was the case in the reopening, particularly in the western provinces this summer.”
To understand sub-lineages, it helps to think of SARS-CoV-2 as an enormous tree that keeps sprouting new branches as the virus evolves in different parts of the world, said Art Poon, an associate professor in virus evolution at Western University. “The trunk is close to Wuhan 1, because that’s the earliest sequence we have,” Poon said. A “variant of concern” like Delta and Alpha, are like heavy branches, as National Geographic has described them, because they’re significantly different from the original strain, increasing how quickly the virus spreads or causing more severe disease. Sub-lineages are more like twigs.
“We need to have a way of talking about specific parts of that tree,” Poon said, “especially when parts of the tree carry mutations of public health significance.”
From a public health standpoint, a more infectious offspring of Delta is a problem, he said, “because Delta was already problematic.”
It’s not clear what may make the new offshoots marginally more transmissible. AY.27 has changes in the spike protein the virus uses to enter human cells. The same mutation is also present in AY.4.2, the variant dubbed “Delta plus” that has been expanding across the United Kingdom.
There’s no evidence of immune escape yet, said Poon, no evidence they’re better able to evade vaccines. “But it tells us this virus still seems to have plenty of room for adaptation.”
It tells us this virus still seems to have plenty of room for adaptation
The silver lining is that these sub-lineages have been in Canada for a while, he said, at least as early as April, “but through everyone’s contributions, by being vaccinated and wearing your mask indoors and so on, we have still seen (COVID-19) cases go down” in most parts of the country.
That implies that, even if they become the dominant strains nationally, “that there’s not going to be a sudden transition, and everything radically changes,” Poon said.
The capacity of the virus to evolve rests on the number of infections. It doesn’t mean that viral evolution happens exclusively in the fully unvaccinated, Poon said. “But the virus is going to evolve as long as it can infect people. And the best way that we can reduce the number of infections is to have as many Canadians vaccinated as possible.”
The larger the pockets of unvaccinated, the greater the potential “for new mutants, new variants and the replication of those variants across the population,” added Catalina Lopez-Correa, executive director of the Canadian COVID Genomics Network. “There is a clear concern about people who are choosing not to be vaccinated.”
As of this week, 75 per cent of all Canadians are fully vaccinated.