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1. 2021-01-31 15:38 Andrew Rambaut open
   An interesting repeat here CTTTA CTTG CTTTA - don't know if it means anything
2. 2021-01-31 15:38 Kristian G. Andersen open
   NEVER
3. 2021-01-31 15:39 Andrew Rambaut open
   Just looks nice
4. 2021-01-31 15:39 Kristian G. Andersen open
   Recombination. I'm telling you
5. 2021-01-31 15:39 Kristian G. Andersen
   We should volley it over to Billy - I'm sure he'd figure this one out for us.
6. 2021-01-31 15:40 Robert F. Garry open
   Put Yuri on it - I'm sure that some blasterbating will solve the riddle.
7. 2021-01-31 15:40 Andrew Rambaut open
   We should have a convention - when ambiguous, always call the most 5' position or something.
8. 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
9. 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.

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