Chat message

Slack / Private Message Drop, p.760 [SLACK_000974] · slack_pm:msg:07954

Date: 2021-05-07 14:35
Type: chat message · slack
recipient: Kristian G. Andersen, Robert F. Garry, Edward C. Holmes
speaker: Andrew Rambaut

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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 3nomenclatures (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 indifferent parts of the world.

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2021-05-07 14:35 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 3nomenclatures (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 indifferent parts of the world.
2021-05-07 14:37 Andrew Rambaut open

We are adding a thing into Pangolin that as well as calling a lineage will also call a VOC/VUI based on a set ofdefinition files.
2021-05-07 14:38 Andrew Rambaut open

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 Kristian G. Andersen open

Okay, great - we can probably pull from that then. We just made a quick decision to move over to PHE designationsfor 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 Kristian G. Andersen open

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?

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