How to classify SARSr-CoVs in iNaturalist taxonomy

Recent additions curators made to iNaturalist taxonomy include SARSr-CoV (species), and SARS-CoV-1, SARS-CoV-2, and Bat SL-CoV-WIV1 (currently, subspecies). The linked taxa pages give common names and scientific names (the first are used here, but correspond to the sci. names).

Defining SARSr-CoV as a species follows the CSG 2020 standard, although it didn’t specifically term SC1/SC2 subspecies. Various articles classify SC2 as a strain, subspecies, or unspecified rank, and SC2 variants as variants, subspecies, or unspecified. NCBI lists SC2 as no rank, although implies it’s a subtaxon of (species) SARSr-CoV (they also consider MERS-CoV a species).

  • Is SC2 best to define as a subspecies or strain? - I’m undecided but currently favor strain, partly since iNat ssp. names include “ssp.” followed by a word or number, which doesn’t fit well.

  • Are SC2 variants best to assign to the same taxonomic rank as SC2, or to the rank below it?

  • Would it be better for iNaturalist to add “no taxon” ranks vs. using subspecies or strain?

Related, see this new feature request to add strain and variant to iNat. taxonomy.

*Topic updated

It’s interesting to see a question about virus taxonomy. My response below is a little bureaucratic, but I hope it’s helpful.

For any matters related to virus taxonomy it is essential we refer to the universal authority; The International Committee on Taxonomy of Viruses (ICTV). According to the ICTV, the following taxonomy is accepted:

Genus: Betacoronavirus
Subgenus: Sarbecovirus
Species: Severe acute respiratory syndrome-related coronavirus

Abbreviations, such as “SARS-CoV” are not accepted species names, but rather, they allude to accepted species names such as the one above. And according to the ICTV’s International Code of Virus Classification and Nomenclature (ICVCN), section 3.4:

“The ICTV is not responsible for classification and nomenclature of virus taxa below the rank of species. The classification and naming of serotypes, genotypes, strains, variants and isolates of virus species is the responsibility of acknowledged international specialist groups.”

As such, you will find a diversity of opinion on the naming and classification of the so-called subspecies, strains, and/or variants. So your questions about what “should” be done cannot be answered satisfactorily because the ICTV is not concerned with it, and there is no consensus among other specialist groups such as institutions and authors.

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it is essential we refer to the universal authority

The CSG link is The Coronaviridae Study Group of the International Committee on Taxonomy of Viruses.

Abbreviations, such as “SARS-CoV-2” are not accepted species names, but rather, they allude to accepted species names.

Those are common names, which correspond to scientific names (see links). There is a question about if they should stay abbreviated or be written out fuller in common names.

your questions about what “should” be done cannot be answered satisfactorily because the ICTV is not concerned with it, and there is no consensus among other specialist groups

I know but I mean what is the most common view, and/or what fits best for iNat. taxonomy (since it’s the taxa are required to be assigned taxonomic ranks one way or another.

NCBI gives SARSr-CoV species-rank, but give SC2 no rank. They give MERS species rank. Update: you later reminded me there is consensus about MERS being a species.

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Do we have taxon entries for Measles viruses? Or anything in the Chickenpox/Herpes family?
There is no way we can document this with a photo/date/time.
Which curators are adding these taxon and why?

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I only noticed the CoV examples recently, so haven’t checked yet. The evidence being given is mostly positive test results (including photos of medical results or messages). This may sound unusual but can verified as well as many kinds of records here can be. Bear in mind that for example for wildlife, there are many ways to document in addition to direct field photos (e.g. photos of track or nests, specimens, spectrogram results, audio of calls, genetic analysis results).

How can we not document avian pox with a photo? Its symptoms are clear, there’s an observation field for it if you wanna check, as rarely it’s posted separately from the bird, but there’re enough sick birds with it.

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I don’t think that this a place where we can possibly track virus transmission/any pandemic and nor should we.

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This is not a biosecurity site?

I did (the CSG link is The Coronaviridae Study Group of the International Committee on Taxonomy of Viruses).

Yes, that’s good to see. I wrote out my reasoning in full for the benefit of anyone reading who is less familiar with virus taxonomy than you clearly are.

These are the common names, which correspond to the valid scientific names (I said both are listed on the linked taxa pages). I only wrote out common names here (but referred to both throughout). I’m unsure if any represent abbreviations (of what the common names were supposed to be). If they do, I’d favor updating them to be longer. It also was other users who originally added these names to iNat.

I suppose you could treat them as common names, but it’s worth noting that better known viral species typically have a more typical common name. For example the species Tobacco mosaic virus is known by the acronym “TMV” and also by the common name “tobacco mosaic virus”.

I alluded to subspecies seeming a poor choice for SARS-CoV-2 (vs. if other choices are/could be made available). Because it seems rarely used in virology nomenclature (as you said). I didn’t state this with certainty because I want to learn how many sources/articles believe it should be a subspecies, vs. a different subtaxon.

I agree. Virology doesn’t use the term “subspecies”, but as you note, no better alternatives are currently available on iNaturalist.

Should SARS-CoV-2 variants be at the same taxonomic rank as it, or a lower one? (regardless of what ranks, relative position in taxonomic hierarchy).

The so-called variants presumably descended from one original zoonotic lineage. So phylogenetically it must be the case that the variants and inferior to the original lineage. But whether the distinction is considered important enough to be reflected in the taxonomy is another question that I can’t answer.

Should iNat. add taxon ranks (if not already present) mostly used in virology, including some under the species rank? For example, if it were thought that SARS-2 should be a strain/other subtaxon (vs. subspecies), it could be switched. It currently displays with “ssp.” in the scientific name, which doesn’t fit unless subspecies were preferred.

Virus taxonomy already doesn’t quite fit with the ranks established with only cellular organisms in mind. Currently on iNaturalist, viruses are placed as a kingdom. However, viruses are actually classified into multiple kingdoms, which are then classified into several realms. The rank of realm doesn’t exist on iNaturalist, but I suspect making a feature request for it won’t result in any change given the high work to low benefit ratio. There’s relatively few virus observations.

I also checked ncbi. They give SARSr-CoV species-rank, but give SARS-2 no rank. They give MERS-CoV species rank though (although not closely related, it’s rank itself should be analogous to that of SARS-2).

MERS-CoV isn’t equivalent to SARS-CoV-2. The former is an accepted species (Middle East respiratory syndrome–related coronavirus) whereas the latter is subspecies / strain / variant within an accepted species.

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The viruses were already added to iNat taxonomy by curators (see links to taxa pages). I don’t mean this would become a “tracking” source exactly. I just mean it could provide additional info., of value when people consult it in combination with other sources. Just by normal site usage. It does depend on if many people observe/identify it though, which is hard to predict.

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So? What should it mean, we can’t add viruses as observations because we’re not authorities studying them? iNat is designed to document personal interactions with objects of life, even those without cells as long as they have scientific name.

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To answer your second question first: I’m adding many of these taxa.

To answer your first question: There are currently no observations of measles virus, but there are of chickenpox and others in the herpesvirus family (Herpesviridae). See here: https://www.inaturalist.org/taxa/953471-Herpesviridae

There is no way we can document this with a photo/date/time.

Why not? I’m certain I can! Many viral diseases are ambiguous in appearance and can’t be identified without laboratory diagnostic tests, hence the high rate of ‘Needs ID’ virus observations. But some are absolutely obvious, in which case I don’t see why the time and location can’t be documented. And some people actually have used diagnostic techniques for their observations. The same applies for other pathogenic microorganisms. Do you think pathogenic fungi and bacteria should be disallowed on iNaturalist? If so, I’d like to understand your reasoning why. They’re integral parts of nature.

I don’t think that this a place where we can possibly track virus transmission/any pandemic and nor should we.

I’m not keen on using iNaturalist to track the pandemic either. We have no chance of doing that successfully. But I also don’t think coronavirus observations should be banned. Do you think they should be? If anything, this pandemic has demonstrated the importance of virology, and I’d like to see the iNaturalist virology community grow, not be discouraged.

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Hi folks, if you have a question or comment about a specific taxon or group of taxa on iNat, please flag it for curation by going to the taxon page and clicking Curation, then Flag for curation on the right side of the page under the graph. https://www.inaturalist.org/taxa/1044608-Severe-acute-respiratory-syndrome-related-coronavirus

Here’s the description of this forum category:

thanks!

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I suppose you could treat them as common names.

I used common names most often used in literature and iNat. But I support making them longer if applicable based on sources. “Abbreviation” has benefits though, in this case.

Virus taxonomy already doesn’t quite fit with the ranks established with only cellular organisms in mind. Currently on iNaturalist, viruses are placed as a kingdom.

I agree they don’t fit well. Realms are interesting but it seems the species-rank and lower taxon ranks are where the questions come up here.

MERS-CoV isn’t equivalent to SARS-CoV-2. The former is an accepted species whereas the latter is subspecies / strain / variant within an accepted species.

I agreed MERS isn’t equivalent. I’d temporarily forgotten it’s species status, recently misreading it called “a representative of a new, yet-to-be-established species in lineage C of the genus Betacoronavirus” (Groot et al. 2013). On the other hand, I assume there may be some parallels to SC1/SC2 in considering if many different MERS isolates or strains (from animals, humans, etc.) are to be considered species or subtaxa.

I agree SC2 is within a species. Which taxonomic ranks do you think are best to assign SC2 and variants to? (subspecies or strain)

Thank you @jameskdouch I’ve learnt a lot through this exchange.

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Thanks for commenting. Although I think this Topic was slightly broader and warranted more discussion than an ordinary taxon curation flag would (curation requests are also being considered or made).

Thank you @jameskdouch I’ve learnt a lot through this exchange.

Excellent! I think that’s the mark of a wise mind.

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This is a bit off topic, but is there a taxonomy for Prions? Is the Prion responsible for scrapie in sheep the same as the one that causes BSE or the other wasting diseases in other mammals? If not, has there been a system developed to classify them? Just curiosity.

I agree they don’t fit well. Realms are interesting but it seems the species-rank and lower taxon ranks are where the questions come up here.

Yes, for the most part it’s the lower taxonomy that makes a difference to identifications.

It also raises the question, are animal versions of MERS (isolates), or different human variants of MERS, all to be considered (a) species?

Apparently the answer here is, simply, “yes”.

I agree SARS-2 is within a species. I’d phrase the question: Given SARS-2 and variants (supposing any were added) need to be assigned to taxonomic rank, which do you think are most accurate or commonly used for each, e.g. subspecies, strain, variant, etc.?

Ok, I understand now. Drawing from experience with other viruses, I think distinct, below-species viral categories (SARS-CoV and SARS-CoV-2) are usually called “strains”, and very slight genetic varieties are called “variants” or “genotypes”.

Prions aren’t amenable to typical taxonomy, because, unlike cellular organisms and viruses, they (are thought to) spontaneously appear into existence. Therefore, different prions don’t descent from a common ancestor, so they can’t be placed into a hierarchical evolutionary tree.

However, you can still group the different prions based on various subjective criteria. There was a paper that did this but unfortunately I can’t find it at the moment.

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