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I read that the newly discovered variant of Covid-19 has a higher number of mutations than the other variants. Isn't it more likely that it is the variant of a variant? It would be absolutely normal, after all, viruses of this family mutate so frequently that they are continuously evolving.

There would be a missing point though, is the intermediate variant a known one or is it a variant that passed under the radar?

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    $\begingroup$ It's pretty straightforward (in theory) to determine whether a new variant is a sub-category of an existing variant, or a new variant on the same level as e.g. Delta, by building a phylogenetic tree and looking at where the new samples fall. $\endgroup$
    – user438383
    Commented Nov 29, 2021 at 16:31
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    $\begingroup$ Useful resource: cov-lineages.org/lineage.html?lineage=B.1.1.529 $\endgroup$
    – Dan Bryant
    Commented Nov 29, 2021 at 20:51
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    $\begingroup$ From what I've read (which isn't much beyond a few synopsis articles), despite containing some genetic features of some previously identified variants of concern, Omicron genomes are not directly descended from any of these other variants. Apparently the closest ancestor is from a mid-2020 lineage that hasn't been of much concern. There's a twitter thread from Trevor Bedford (Fred Hutch faculty member) here breaking it down into a pretty digestible chunks and citing some cool interactive resources. $\endgroup$
    – MikeyC
    Commented Nov 29, 2021 at 21:24

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At the point of its discovery, Omikron wasn't a "variant of a variant", but goes down directly to the Pango lineage B.1.1.

Now we know something more, with the discovery of the outgroup now named BA.2 and the original Omikron being BA.1: There was a common ancestor to the two sister lineages, now named B.1.1.529.

Note that this still does not make it a "variant of a variant" because for being named a variant, a lineage must fulfill some additional criteria, such as becoming dominant or at least a notable fraction of all cases in some region, or being in other terms different and interesting enough to be worth additional attention.

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