How to classify SARSr-CoVs in iNaturalist taxonomy

What are prions?

Thank you. It’s just that this discussion prompted me to wonder if self-replicating proteins did have a taxonomy. If you do find the paper - and there is no rush - I would be interested in reading it. I find them fascinating, but don’t know too much about them.

Prions are self-replicating, infectious proteins that cause neurodegeneration in mammals, leading to cognitive disorders and eventual death. Mad cow disease is the most famous example. Prions are also a group of sea-birds.

2 Likes

I found it.

Harbi and Harrison (2014) Classifying prion and prion-like phenomena. Prion 8: 161–165 [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4189883].

2 Likes

Yeah, there are a lot of plant viruses that are decently easy to identify, and that are well documented and tracked by farmers. I haven’t checked to see how many of those are posted on iNat, but it would be surprising if they weren’t.

3 Likes

Nothing can spontaneously appear. A gas bottle can blow up but not much else!!!

And as many cultivated plants’ patterns are a product of viral activity we could potentionally get thousands of their observations.

1 Like

Yes, “spontaneously appear” would, strictly speaking, imply the violation of a law of thermodynamics! To be more careful in my wording, they can form in the brain from protein as the result of error, as opposed to descending from pre-existing infectious material.

2 Likes

Oh, thank you so much! It’s been a long time since I thought about them, but they are fascinating. I scanned it and will peruse it more fully later.

Although - “Group I comprises prion proteins that have been demonstrated to be infectious.”! The techniques used are questionable. From the paper!

I don’t think iNat. has a strain option, only subspecies. I prefer additional viral categories be added to help virus taxonomy fit better broadly. For SC2 variants, if any could be observed, I’d be okay if they were added at the same taxon rank as SC2 (but as separate names/items), or at the level below the taxon of SC2.

1 Like

There is some use of subspecies with viruses. See https://www.sciencedirect.com/science/article/pii/B9780128202678000030

But, as in eukaryotes, there’s inconsistent usage of ranks below species. In a recent paper on virus taxonomy, they state “…no consensus on the definition of ‘subspecies’ could be reached.”
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7186216/

2 Likes

I agree some sources use subspecies. Also see this on Zika, Dengue, etc. (https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0007231). They use a computational method to determine “species and subspecies (i.e. serotypes and/or genotypes).” Some SARS-2 sources define it as a subspecies. So, possibly it’s good enough to leave it assigned to ssp. on iNat. for now. There currently aren’t options to use strains, variants, etc. My main question is just which rank is best for SC2, and for SC2 variants (this could also apply to unrelated virus taxa).

I didn’t realise that. Thanks.

So, possibly it’s good enough to leave it assigned to ssp. on iNat. for now.

I think, if there’s no expert consensus on the nomenclature of virus ranks below species, it makes sense for iNaturalist to take the simplest approach and just use the ranks already available. Especially if some virologists already use “subspecies”.

I’m not aware that there are options to use strains, variants, etc. as ranks (can anyone confirm this?).

Below species, iNaturalist has the following ranks available, from highest to lowest:

  • Hybrid
  • Subspecies
  • Variety
  • Form
  • Infrahybrid

If SARS-CoV-2 is placed as a subspecies, specific variants (e.g. the “delta variant”) could potentially be placed as varieties.

1 Like

I may agree with this. The possible classification schemes I can see are:

SC2 = subspecies, SC2 variants = varieties (your suggestion)
SC2 and SC2 variants all = either subspecies, or all = varieties

I may email additional virus researchers to see their take. I’d be glad to help more directly with this or other virus curation. My curator application is pending, so I’m currently limited to flagging taxa for curation (slower process). For example, we could add the subgenera of genus Betacoronavirus, or various other animal CoVs (murine, etc).

SC2 and SC2 variants all = either subspecies, or all = varieties

Yes, I can imagine that working as well.

For example, we could add the subgenera of genus Betacoronavirus , or various other animal CoVs (murine, etc).

We could, but there’s no pressing need to do so now. Most virus species aren’t curated on iNaturalist yet. My way of operating is to curate taxa on the basis of what needs to be identified. I remember reading on an iNaturalist page that curators are not to think of iNaturalist as a taxonomic database, and all taxa need not be curated; only those that people actually want to use as identifications. If someone uploads an observation of a murine coronavirus, I’ll gladly do the necessary curation.

While your application is still processing you can try tagging me.

1 Like

I think it may help to populate some of the well-known taxa in Betacoronavirus, like the subgenera, and MERS. I agree it’s not a rush, and could be added slowly over time. I also just made a feature request to add strain and variant to iNat. taxonomic rank options here.

I just added all Betacoronavirus subgenera and MERS-CoV for you.

Great.