Omicron’s sister variant spreads faster. So why did the one we call Omicron hit first?

Two years into a pandemic that turned us all into amateur virologists, we’ve learned that the best-spreading coronavirus variant will outcompete any slowpokes.

But something curious happened with Omicron: The more transmissible version didn’t take off first.

The virus that the world came to know as Omicron — and that ignited outbreaks in countries around the world — is just one lineage that made up the broader Omicron grouping. It’s known officially as BA.1. For some time, its sister viruses, including one named BA.2, didn’t seem to be doing much.

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Now, however, evidence is accruing that BA.2 is in fact more transmissible than BA.1. Already, it has become the dominant variant in India, Denmark, and a handful of other countries. Which begs the question: Why was BA.1 the variant that first raced around the globe?

The best guess as of now reflects all the randomness and chance that can influence global transmission patterns, on top of the virus’ biology.

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If BA.1 and BA.2 emerged around the same time, perhaps BA.1 just got lucky: A few superspreading events might have given it a head start, and made it more likely that it was going to be transported to other countries. Say it got seeded among university students, who have lots of contact with lots of other people, or circulated at a conference. It could have started snowballing before BA.2 had a chance to snag a toehold.

“It’s not just how transmissible it is,” but a result of lots of random occurrences as well, said Tulio de Oliveira of the Centre for Epidemic Response and Innovation in South Africa, whose team identified the Omicron lineages in November.

Now BA.2 is catching up. It has been gathering steam in countries around the world, from South Africa to the Philippines to Sweden; the United Kingdom last week predicted it would become the dominant strain there in the next month. Estimates of its U.S. prevalence have just been a few percent so far, but it’s growing. (One reason it became dominant in a place like Denmark first while it’s still at relatively low levels in other European countries could again be the result of those chance encounters: Perhaps it got introduced into Denmark earlier and more frequently than elsewhere.)

More research is confirming BA.2’s advantage. Data out of Denmark and the U.K. have shown that people with BA.2 are more likely to infect others in their households than those with BA.1, though vaccines and boosters reduce the transmission risk.

Scientists have been tracking BA.2 since it was identified, and “for a long time it did not seem to grow,” Emma Hodcroft, a molecular epidemiologist at the University of Bern, wrote in an email. She said there was not a clear explanation for that — perhaps it was chance — but that as researchers study it more, “we might get more insight into what is behind the ‘delay’ of BA.2.”

Scientists are still estimating exactly what edge BA.2 has over BA.1, but it doesn’t seem to be anything as dramatic as the Omicron family had over the previously dominant Delta variant. Maria Van Kerkhove, the World Health Organization’s technical lead for Covid-19, said Tuesday that the data indicate BA.2 has “a slight increase in growth rate above BA.1.”

Variants can be better spreaders in different ways. They can have an inherent transmission advantage, and they can cause reinfections or breakthrough infections at higher rates than other circulating strains. Omicron’s edge over Delta seemed to come from a combination of both. And considering early data suggest that vaccines work as well against BA.2 as against BA.1 — meaning both viruses can get around immune responses to roughly the same extent — BA.2 could have an intrinsic boost in spreading over BA.1.

The most pressing question, of course, is what the ascendance of BA.2 means for the pandemic. It doesn’t seem to have a change in the average disease severity it causes. So the real difference is one of transmission.

How that advantage plays out could differ from country to country, in part based on where each is in its decline from the original Omicron wave. In a place like the United States, which still has a ways to go to reach its pre-Omicron case counts, the burgeoning BA.2 variant could perhaps prolong that descent. Other countries that were closer to pre-Omicron baselines could see an uptick, or a stubborn plateau.

BA.2 “appears to be a fitter virus that is having more success at transmitting,” said Jacob Lemieux, an infectious diseases physician at Massachusetts General Hospital who is tracking variants. “What’s not clear is whether BA.2 is going to cause a significant number of cases or a significant burden on health care systems” like BA.1.

In South Africa, the increase in prevalence of BA.2 has come as total case counts so far have continued to decline, de Oliveira noted. That’s an important trend to keep in mind given that global attention on emerging variants has typically foreshadowed major new spikes.

“Increasing prevalence of a variant with decreasing number of infections, hospitalizations, and deaths is very different than increasing prevalence of a variant with increasing number of infections, hospitalizations, and deaths,” de Oliveira told STAT.

The Omicron family hasn’t really been around long enough to see if people who recover from BA.1 are immune to infection from BA.2, or after how long they might become susceptible again. Scientists are trying to study that in lab experiments as well.

Still, the general expectation is that with vaccination or each additional exposure to the virus, regardless of its form, subsequent infections are more and more likely to be mild or even insignificant (unless the virus evolves to become more virulent). All that population immunity broadly explains why hospitalization and death rates have been lower during the Omicron wave than earlier in the pandemic. Experts anticipate that those metrics — infections vs. subsequent hospitalizations and deaths — will become even more “decoupled.” 

Source: STAT