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1. 2021-01-31 15:40 Andrew Rambaut open
   We should have a convention - when ambiguous, always call the most 5' position or something.
2. 2021-01-31 15:56 Andrew Rambaut open
   Virus taxonomists really don't seem to understand virus evolution: ```I have a very stupid question before delving into the madness of a WHO-supported global and uniform SARS-CoV-2 nomenclature this week: As a taxonomist the name SARS-CoV-2 has always bothered me. In all organismal taxonomies, any taxon has only a single member, i.e., there is only one animal per species (except if there are subspecies, but then there is only animal per subspecies). The logic behind this is obvious: either something is a representative of "same" (for instanceyou and me are genetically so much alike that we are both [isolates of] "human") or something is distinct from something else and hence needs to be classified differently (I hope I have more in common genetically with you than with a chimpanzee).Gorbalenya et al. did this wonderful mental split in their original article in which they kind of acknowledged that the new Chinese virus really is SARS-CoV but not at the same time, by basically assigning two allegedly distinct animalsto the same species (both SARS-CoV and SARS-CoV-2 are assigned to the same species Severe acute respiratory syndrome-related coronavirus). So, my question: does this hold up - for example, if you throw all SARS-CoV genomes into your global phylogenetic tree of all SARS-CoV-2 genomes, does the SARS-CoV clade remain as atrue sister clade to the entire SARS-CoV-2 branch? Thanks, Jens```I
3. 2021-01-31 15:58 Andrew Rambaut open
   I just sent Jens a link to Boni et al which presumably will blow his mind trying to fit all that recombination into nestedtaxonomic boxes.
4. 2021-01-31 16:08 Edward C. Holmes open
   The problem lies in 'In all organismal taxonomies...'. What are these people on?
5. 2021-01-31 16:11 Andrew Rambaut
   My reply: ```The problem is that taxonomy doesn't really work for virus as far as I am concerned as there is essentially astructured continuum of diversity - i.e. completely artifactual notions of species. And with recombination that just makes thing completely arbitrary. I don't mind labelling bits of the phylogenetic tree for convenient discussion but Ithink we get too focused on trying to replicate a metazoan taxonomy on viruses. That said - to answer you final question - yes, SARS1 and SARS2 are completely distinct (not even sibling clades)with the diversity within each minuscule compared to the divergence between them. This paper gives an overview oftheir relative positions (and some of the complex recombinant history in the sarbecovirus clade):https://www.nature.com/articles/s41564-020-0771-4```
6. 2021-01-31 16:12 Andrew Rambaut open
   Glad I can't make the WHO nomenclature meeting this week - will be carnage.
7. 2021-01-31 16:26 Kristian G. Andersen open
   Lol. Jens was right about one thing though - that was indeed a dumb question. "What do you mean, we can't fit these little things into neat little boxes?! Nein!!"
8. 2021-01-31 16:37 Edward C. Holmes open
   The WHO nomenclature thing will be horrendous. Tulio and Jens is an interesting combination.
9. 2021-01-31 16:43 Robert F. Garry open
   Germans and their neat little boxes - yes I believe it's a thing...

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