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Related:

When does one decide to refer to a virus as a new variant?

I've been thinking about all the news related to "variants" of the SARS-CoV-2 virus, including the infamous "Delta Variant". One thing that strikes me as odd is that there seems to be no discussion on the possibility of a variant of this virus evolving so much that it becomes a distinct virus species - something other than SARS-CoV-2 but clearly descended from it.

I know that biologists typically define a species as a set of organisms whose members can produce fertile offspring (that is, if two populations either cannot produce offspring or can only produce sterile offspring, they are considered two different species), but this definition would not seem to work here as viruses do not reproduce sexually.

So, is there a general definition or consensus on when a virus lineage has experienced sufficient genetic drift from its sister lineages that it is a brand new virus rather than a variant? Is it based on percentages of base pairs changed? Is it based on changes in the clinical effects of infection (e.g. if a human Influenza virus underwent a mutation that made it unable to infect humans but highly infectious to the spleens of small marsupials, then it would be a new virus, even if the mutation consisted of only a single base pair change)?

Somehow, I'm imagining that a future 31st century biology textbook is going to say something like this:

While SARS-CoV-2 is no longer with us, its descendants live on as a family of viruses that cause Exploding Camel Brain Syndrome as well as a distinct cluster of closely related species that cause muscle inflammation in dogs.

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    $\begingroup$ Take two coronaviruses and the closest relatives of both, if they have the same host species, same geographical distribution and are genetically close enough then they will experiment a lot of recombination and the phylogentic tree will become messy enough to make clear that they are not distinct species. Conversely if they don't have the same hosts or geographical distribution then they tend to be quite divergent genetically. $\endgroup$
    – reuns
    Jul 25 at 18:02
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The general issue of what exactly a "species" is has been addressed numerous times here, in different forms. Some good answers can be found at:

Defining "species" (Are species an emergent property or an ensemble of quantitative differences?)

How could humans have interbred with Neanderthals if we're a different species?

When has an organism evolved enough to be called a new species?

and a so far unanswered question:

References for historical momentum in asexual species definitions

I think Remi.b's answer that says:

The concepts of lineage and clade / monophyletic group are much more helpful. IMO, the only usefulness of this poorly defined concept that is the "species" is to have a common vocabulary for naming lineages.

is the place to start. A virus "species" is just a label to a lineage at one point in time. When we discover separate lineages of a virus, historically they have gotten a new label. It's then possible follow the lineages from there into strains/substrains, etc.

SARS-CoV-2 was first identified as the cause of a novel illness with a placeholder name 2019-nCoV. Its relation to the earlier SARS-CoV lineage was quickly identified and it's now been grouped alongside SARS-CoV-1 as a strain of the SARS-CoV species. So, given that SARS-CoV-1 and SARS-CoV-2 are considered strains of the same species, it seems highly unlikely that any variants of SARS-CoV-2 will be known as their own species any time soon.

One could consider other virus lineages as well. Influenza A is a species whose subtypes are described by two antigens, H and N, giving the perhaps somewhat familiar naming convention like "H1N1" or "H3N2". Each of these has contained different lineages often named by those causing illness in humans or animals, but at no time have these been considered separate species, they are all still considered the same species Influenza A.

The naming conventions for influenza A are pretty solid from long-term study and following precedent. The International Committee on Taxonomy of Viruses sets some conventions for naming, but their principles are:

Stability

To avoid or reject the use of names which might cause error or confusion

To avoid the unnecessary creation of names

None of these attempt to put any standardized distance between what are considered "different" versus the "same" species across different lineages. The ICTV code says this in vague terms, bold mine:

The criteria by which different species within a genus are distinguished shall be established by the appropriate Study Group. These criteria may include, but are not limited to, natural and experimental host range, cell and tissue tropism, pathogenicity, vector specificity, antigenicity, and the degree of relatedness of their genomes or genes. The criteria used should be published in the relevant section of the ICTV Report and reviewed periodically by the appropriate Study Group.

So, different study groups choose which criteria to use, and these need not be the same criteria each time. Introducing any would likely result in this situation. Instead, we have a fairly ad-hoc system given there is no particular biological meaning to "species" except as a lineage label, and this system is governed as much by scientific history as by any set level of genetic similarity. In the interest of maintaining stability, it seems unlikely that new virus species will be recognized under existing known virus species without novel discovery.

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    $\begingroup$ ICTV says monophyly is the major characteristic: A species is a monophyletic group of viruses whose properties can be distinguished from those of other species by multiple criteria. from 3.20 ICTV code. Criteria include but not limited to Natural and experimental host range, cell and tissue tropism, pathogenicity, vector specificity, antigenicity, and the degree of relatedness of their genomes or genes $\endgroup$
    – bob1
    Jul 21 at 21:34
  • $\begingroup$ @bob1 Yes, but monophyly doesn't tell you where to draw the species line (as compared to some other level of classification). The other characteristics are vague and not consistently applied in different lineages. $\endgroup$
    – Bryan Krause
    Jul 21 at 21:49
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    $\begingroup$ I totally agree, you can randomly pull a branch out of the IAV H1 tree and call it monophyletic. Classifications in virus below about the family level are pretty wishy-washy in general. There are some where we can easily call it a species, but for many families it is very difficult. $\endgroup$
    – bob1
    Jul 22 at 0:00

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