How the next coronavirus variant could emerge
Stopping the next major coronavirus variant involves knowing where it might come from.
With Omicron, those answers are still a mystery: How did a variant that looked so different from all its older cousins appear so suddenly? How to explain its jumble of mutations, many of which had rarely been seen in variants of interest?
"When that virus sequence first started to emerge, it was really hard for me to fathom that that would take off," Emory University virologist Mehul Suthar said.
The alphanumeric soup has also revealed BA.2, a faster-spreading subtype of Omicron that has become dominant in the United States.
Viruses change all the time, often in ways that actually hurt their chances at survival. But once in a while, those mutations can work out in the virus' favour.
The virus you sneeze or cough out may be ever so slightly different from the one you were infected with. That's because viruses mutate -- especially when their genetic code is made of RNA, a close cousin of our DNA.
"As the virus reproduces itself, there are errors in reproducing its code," explained Dr Mike Ryan, executive director of the World Health Organization's health emergencies programme. "Most of those errors result in a virus that's either not competent or just dies away." But rarely, these accidents can give the virus an advantage. Perhaps it becomes more contagious. Or perhaps it becomes better at escaping our immunity.
Sarah Cobey, associate professor of ecology and evolution at the University of Chicago, explained that the coronavirus' transmissibility will hit a ceiling -- eventually. However, it probably won't stop evolving in ways that skirt our immune response.
But not all mutations happen the same way. "Before Omicron, I think most people in the field would say that we would see immune escape through the accumulation of these mutations one by one," Cobey said.
Over time and over the course of hundreds of infections, circulating viruses move further and further away from their ancestors on the evolutionary tree. It's a process known as antigenic drift. However, while this may explain variants that appear closer on the evolutionary tree -- like Omicron and BA.2 -- it doesn't explain how Omicron appeared in the first place.
Marietjie Venter, a professor in the Department of Medical Virology at the University of Pretoria in South Africa, said it's unlikely that a "slow change" led to Omicron. This would mean the virus evolved gradually in a population that wasn't being monitored. And South Africa, where many of Omicron's early samples were identified, has a good surveillance programme, she said.
Thus, it would have been hard for a variant like Omicron to sneak up slowly. Instead, its appearance seemed curiously abrupt. "Delta almost disappeared, and then suddenly we saw Omicron that was completely different,"
Venter said.
In some cases, viruses don't drift; they shift. "Antigenic shift" is a more dramatic change that can happen, for example, when viruses in animals find their way to humans or when two strains infect the same person and exchange genes. Examples of the latter include rare instances of a hybrid virus containing stretches of Delta and Omicron genes.
Researchers at Helix, a company whose Covid-19 tests have helped track a number of variants, identified a handful of combined Delta-Omicron infections in the US among nearly 30,000 coronavirus samples from late November to mid-February, when both variants were circulating. Of those samples, researchers identified 20 cases in which people had gotten infected by both variants at the same time. One of these samples did show some evidence that the variants had exchanged genes, though at low levels. In addition, the researchers found two unrelated cases whose infections originated from hybrid viruses.
"There is currently no evidence that the two DeltaOmicron recombinant viruses identified are more transmissible between hosts compared to the circulating Omicron lineages," the researchers wrote. "We're not calling this Deltacron," Maria Van Kerkhove, WHO's technical lead on Covid-19, said at the March briefing. "That's not terminology that we are using."
At the time, Van Kerkhove said this combination appeared to be circulating "at very low levels" but she offered the caveat that we should be testing more to get a clearer picture of its prevalence and spread -- or lack thereof.
Cobey said that Omicron in particular has lit a fire under scientists to understand its origins and the true breadth of viable mutations. "That's the sort of divergence that is really difficult to study and anticipate in the lab," she said.
Staying ahead of the virus isn't just a question of anticipating its next move, experts say. It's about finding ways to avoid threats and ultimately ensure the durability of our vaccines.