Slack / Private Message Drop — page 760

And of course, we can look at actual data to completely take down that argument. No, the 2020 election wasn't stolen. [2021-05-07 10:36:32] [Kristian Andersen] @Andrew Rambaut / @Eddie Holmes have you guys thought about VOC/VOI type of stuff in extension to your pango lineages? Separate, of course, but kinda in the same spirit. We need to come up with something better for outbreak.info and we're struggling a little - and certainly don't want to duplicate efforts. We have thought about setting up a voting system and have a large 'board of advisors', but would be better to hook into other systems already in place. IMO, the way PHE does it is the way to go and I think we'll just defer to PHE for VOC classifications. However, we have politics to deal with and the CDC has a different set of VOCs - which I don't agree with. We can of course also have a way in which people can use whatever list they prefer, but it gets messy - would be much better to have a single system (which is why pango is so important - because we're moving towards exactly that across the entire "variant" space). [2021-05-07 14:35:01] [Andrew Rambaut] We should talk - I think we should have labels for VOC/VOIs that are separate from lineages. We have been discussing this at the WHO for a while but as you can imagine it is a mess. The WHO is obsessed with there being 3 nomenclatures (Pango, Nextstrain and GISAID) whereas in fact no one uses the other 2. They imagine that their names will become standard but it is not clear they understand what they are trying to label. The important thing is to realise you are labelling a constellation not a lineage or clade (i.e., it is not synonymous with Pango). This is what PHE has got right - B.1.1.7+E484K is a VOC even though it will never be a lineage because it has occurred > 10 times independently. Potentially the same VOC could arise multiple times in different parts of the world. [2021-05-07 14:37:13] [Andrew Rambaut] We are adding a thing into Pangolin that as well as calling a lineage will also call a VOC/VUI based on a set of definition files. [2021-05-07 14:38:58] [Andrew Rambaut] The other thing I think we need with VOC/VUI definitions is to have a 'type' genome. The example (preferably early) genome to act as a reference. [2021-05-07 14:39:35] [Kristian Andersen] Okay, great - we can probably pull from that then. We just made a quick decision to move over to PHE designations for VOCs - we'll peg ours to the most current list from them. Problem is, it'll piss off the CDC - but they're behind the curve and we need to do the right thing. Everybody is already moving over to Pango lineages and it's time that GISAID/NextStrain designations go the way of the dodo. Hopefully VOC/VUI can be standardized around a similar 'community' driven effort as Pango. [2021-05-07 14:40:17] [Kristian Andersen] And YES to type genome - I have been bugging our team for introducing exactly that feature for weeks. Are you planning on having this reflected somewhere? [2021-05-07 14:42:58] [Andrew Rambaut] We should collaborate on this - we have some githubs and the idea would be to store the definition JSON files we could all pull off.