In 2020, the World Health Organization (WHO) came up with a system for naming coronavirus variants based on the Greek alphabet, but in recent weeks, subvariants such as BA.1, BA.2, and XD have gained notoriety. Writing for The Atlantic, Sarah Zhang explains the naming system for Covid-19 variants.

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How the naming system started

In March 2020, scientists studying viral evolution had trouble figuring out what to name new lineages of the coronavirus after a genome was sequenced. "People in the U.S. were calling it one thing; people in Europe were calling it another," said Áine O'Toole, a postdoctoral researcher at the University of Edinburgh.

So Andrew Rambaut, O'Toole's advisor, alongside a group of researchers, developed a naming system called Pango. At first, there were only two main lineages of the coronavirus, which were called A and B, Zhang writes. Then, as each lineage mutated, Pango was used to name each sublineage.

Perhaps one of the most well-known variants is B.1.1.7, which was later called the alpha variant. B.1.1.7 was the seventh variant of the B.1.1 subvariant, which was the first subvariant of B.1, Zhang writes.

However, according to O'Toole, the Pango system was designed for researchers who were tracking the mutations of the coronavirus, not the general public. "We hadn't considered how difficult it would be to tell apart B.1.17, B.1.351, and B.1.128," O'Toole said.

That's where WHO's naming system came in, which was designed to separate "variants that are epidemiologically important" from "variants that simply exist," Zhang writes.

Why some variants don't have Greek letter names

WHO's naming system worked well until omicron, Zhang writes. In the Pango system, omicron is known as B.1.1.529, and the first subvariant of omicron was named BA.1, followed by BA.2 and BA.3. In the Pango system, when a subvariant's name gets too long, the first part of the name is replaced with a letter, starting with A, Zhang writes. So rather than naming a subvariant B.1.1.529.2, it's called BA.2.

In February, WHO determined that, despite BA.2 causing large Covid-19 waves in parts of Europe, the subvariant should still be called omicron, as should BA.4 and BA.5. According to O'Toole, there's a balance between giving a subvariant a name as quickly as possible and naming it once scientists know it's of epidemiological importance.

Recombinants of subvariants have also appeared in recent months, Zhang writes. Early in the pandemic, the different lineages of the coronavirus were similar enough that a recombination didn't mean much. However, in recent months, parts of the world have seen coronavirus waves caused by delta and omicron, which offer more potential for recombination, Zhang writes.

In the Pango system, a recombinant starts with the letter X and then continues its usual naming system. WHO is currently monitoring recombinant XD, and if a recombinant starts driving a surge in Covid-19 cases, it could receive a Greek letter, Zhang writes.

According to Zhang, viral evolution is "like watching a tree branch and grow … you don't know which branches will become stunted and which will go on to grow long and dense with twigs. Nor can you know which distant branches might fuse with one another into a recombinant branch that itself grows long and dense."

WHO's Greek letter naming system "is meant to highlight the most important branches in this tree of viral evolution," Zhang writes. "But it doesn't cover anything—not even close." (Zhang, The Atlantic, 4/14)