Remains of the virus Why Omicron might stick around

NEW YORK: Where is pi? Last year, the World Health Organization began assigning Greek letters to worrying new variants of the coronavirus. The organisation started with alpha and swiftly worked its way through the Greek alphabet in the months that followed. When omicron arrived in November, it was the 13th named variant in less than a year. But 10 months have passed since omicron’s debut, and the next letter in line, pi, has yet to arrive.

That does not mean SARS-CoV-2, the coronavirus that causes COVID-19, has stopped evolving. But it may have entered a new stage. Last year, more than a dozen ordinary viruses independently transformed into major new public health threats. But now, all of the virus’s most significant variations are descending from a single lineage: omicron.

“Based on what’s being detected at the moment, it’s looking like future SARS-CoV-2 will evolve from omicron,” said David Robertson, a virus expert at the University of Glasgow. It’s also looking like omicron has a remarkable capacity for more evolution. One of the newest subvariants, called BA.2.75.2, can evade immune responses better than all earlier forms of omicron.

For now, BA.2.75.2 is extremely rare, making up just .05% of the coronaviruses that have been sequenced worldwide in the past three months. But that was once true of other omicron subvariants that later came to dominate the world. If BA.2.75.2 becomes widespread this winter, it may blunt the effectiveness of the newly authorised boosters from Moderna and Pfizer. Every time SARS-CoV-2 replicates inside of a cell, it might mutate. On rare occasions, a mutation might help SARS-CoV-2 replicate faster. Or it might help the virus evade antibodies from previous bouts of COVID-19. Such a beneficial mutation might become more common in a single country before fading away. Or it might take over the world. At first, SARS-CoV-2 followed the slow and steady course that scientists had expected based on other coronaviruses.

Its evolutionary tree gradually split into branches, each gaining a few mutations. Evolutionary biologists kept track of them with codes that were useful but obscure. No one else paid much attention to the codes, because they made little difference to how sick the viruses made people. But then one lineage, initially known as B.1.1.7, defied expectations. When British scientists discovered it, in December 2020, they were surprised to find it bore a unique sequence of 23 mutations. Those mutations allowed it to spread much faster than other versions of the virus. Within a few months, several other worrying variants came to light around the world — each with its own combination of mutations, each with the potential to spread quickly and cause a surge of deaths. To make it easier to communicate about them, the WHO came up with its Greek system. B.1.1.7 became alpha Different variants experienced varying levels of success. Alpha came to dominate the world, whereas beta took over only in South Africa and a few other countries before petering out.

What made the variants even more puzzling was that they arose independently. Beta did not descend from alpha. Instead, it arose with its own set of new mutations from a different branch of the SARS-CoV-2 tree. The same held true for all the Greek-named variants, up to omicron. It’s likely that most of these variants got their mutations by going into hiding. Instead of jumping from one host to another, they created chronic infections in people with weakened immune systems.

Omicron did particularly well in this genetic lottery, gaining more than 50 new mutations that helped it find new routes into cells and to infect people who had been vaccinated or previously infected. As it spread around the world and caused an unprecedented spike in cases, it drove most other variants to extinction.