When coronavirus variants appeared in full force in late 2020, the news suddenly turned into alphanumeric soup. Remember? UK variant, B.1.351, GR / 501Y.V3. After this initial period of turmoil, the World Health Organization came up with a conservation system that named these variants alpha, beta and gamma, respectively. And we went under the Greek alphabet, until we reached Omicron. The system worked.
Lately though, the post-Omicron News landscape is turning into alphanumeric soup again. Is called an omicron subvariant BA.2 Now influential worldwide. BA.4 And BA.5 Has just been discovered. And the new recombinants have a cornocopier name that seems to follow some vague argument: XD (Recombinant of Delta and BA.1), CAR (A reconnection of BA.1 and BA.2), XF (A Different Delta and recombinant of BA.1, and so on, all the way down XS (Recombinant of Delta and BA.1.1).
Would it help if I told you that the names actually follow a coherent internal logic, which is quite enjoyable once you read and digest the 1,800 word rules? No? Okay, okay, I’ll try to explain instead where the rules came from and why they are still in use, despite the WHO having a much simpler Greek-alphabet system.
In March 2020, scientists studying viral evolution began tracking how the novel coronavirus is changing. They had a very basic communication problem: what could a new family be called after genome sequencing? “People in the United States called it a thing; Europeans were calling each other by different names, “said Ain O’Toole, a postdoctoral researcher at the University of Edinburgh. So O’Toole’s adviser, Andrew Rambout, and a group of collaborators came up with a naming system. They call it pango. And O’Toole, now chairman of Pango’s genealogy committee, worked on a piece of software called Pangolin, which allows scientists to determine the possible Pango name in any viral genome.
(Yes, Pango A tongue-in-cheek reference to pangolins, which were briefly suspected of having a role in the origin of the coronavirus – several of the group’s computational tools are named after animals – and yes, when it becomes confusing. Pangolin clan Can be used to refer to the viral lineage found in pangolins or the lineage determined by the pangolin tool. Again, scientists have not fully figured out how their semantics can be interpreted by others.
At the moment, no one still knows the dramatic role that forms will play in the epidemic. Scientists were mostly interested in tracking the lineage to see how the virus spread from country to country. And at first there were only two major genera of the coronavirus: A and B. Since the virus accumulated various mutations in different parts of the world, scientists used the Pango system to give subline names by adding numbers. B.1.1.7, for example, the seventh sub-line discovered by B.1.1, resulting in the first sub-line discovered by B.1. You probably know B.1.1.7 as “alpha”. O’Toole remembers listening to the BBC talk about “B.1.1.7” at Christmas 2020. “It was very surreal for me,” he told me. “I remember saying to my sister, ‘Oh, you know that name there?’ And he likes, ‘Yeah, that’s awful.’ “These names were designed for scientists looking for lots and lots of different forms. For the general public, he said, “we did not consider how difficult it would be to distinguish B.1.1.7, B.1.351, and B.1.128.”
Until the end of 2020, however, the general public did not need to speak of separate clans. Alpha was the first form to truly change the course of the epidemic. The world now needs a system that distinguishes between “forms that are epidemiologically important” and “forms that only exist.” The WHO Greek-letter system is meant to be the former, the Pango system the latter.
This division of responsibilities has worked fairly well, although Omicron has made things a little more complicated. The variant originally nominated by the WHO as Omicron is called B.1.1.529 under Pango. Scientists then quickly found more variants of Omicron, which you know as BA.1, BA.2 and BA.3. This is because under the Pango naming system, when the names become too long, the first part of the name is replaced with a new letter – or a pair of letters if all the single letters are taken. When the Omicron subvarients were described, the next available pair of characters was B. A.. So instead of B.1.1.529.2, we have BA.2. Coincidentally, we ended up with some relatively easy-to-remember Omicron subvariant names.
BA.1 and BA.2 have created large, continuous waves in some parts of Europe. The two subvariates are actually quite distinct from each other, almost as evolutionarily Alpha was from Delta. But the WHO again decided in February that BA.2 would still be considered Omicron and more recently, it decided that BA.4 and BA.5 should also be. Can an Omicron subvariate look and behave so differently that it should actually get a new Greek character? In retrospect, BA.2 falls into somewhat controversial areas: the BA.2 wave has grown in some European countries, if not larger than the actual BA.1 wave, but it still does not seem so dramatic. The US has a balance, O’Toole says. , Giving a name to a clan as soon as possible and giving a name when you know the importance of its epidemic. The earlier we try to choose a variant with the Greek-letter name, the less we know about what they can possibly do. The WHO also nominated several forms of interest — Epsilon, Eta, Iota, and Lambda, to name a few — which ultimately failed to have an epidemic effect.
In recent months, more recombinants have appeared and this is not a coincidence. This coronavirus, like other coronaviruses, is always capable of recombination. But in the beginning, the different clans were so similar to each other that reunion meant switching to very similar sequences — in other words, it didn’t mean much. Recently, however, a delta wave has been observed in some parts of the world followed by a BA.1 wave and a BA.2 wave. The high co-occurrence of several distinct clans means more possibility of reconnection. The Pango system saves the letter, expecting recombinant from the start X. For recombinant lineage. Then you just scroll down the alphabet and continue adding letters or numbers as usual. The WHO is monitoring a recombinant, XD, and if any recombinant cases start to drive upwards, they too can get a Greek-letter name. The new generation of misleading pangos continues to make headlines before we realize their importance, reflecting the truly unusual levels of media and public interest in the rigors of viral evolution.
A nomenclature that follows the Greek alphabet could signify a linear progression of the new form. But viral evolution is much like watching tree branches grow. And you don’t know which branches will hang and which will grow long and thick with stalks. Or you may not know which distant branches can meet in a recombinant branch which is itself long and dense. The Greek-letter method is meant to highlight the most important branches of this tree of viral evolution. But it does not cover everything – not even close. The Pango system now contains more than 2,000 genera, most of which are transmitted for obscurity. And in all likelihood, the names of most of the alphabetical-soup in today’s news will soon return to obscurity. If they don’t, OK, then maybe we all have a new Greek alphabet to learn.