Chat message

Slack / Private Message Drop, p.760 [SLACK_000974] · slack_pm:msg:07955

Date: 2021-05-07 14:37
Type: chat message · slack
recipient: Kristian G. Andersen, Robert F. Garry, Edward C. Holmes
speaker: Andrew Rambaut
Topics: Natural origin / zoonotic spillover

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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.

Extracted statements

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Statement	Grade	Attribution	Stance
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.	own voice, substantive	speaker_own	asserts

Statement

Grade

Attribution

Stance

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.

own voice, substantive

speaker_own

asserts

In context

A single line often inverts meaning once you see what it answers, so neighbouring messages are always shown.

2021-05-07 14:35 Andrew Rambaut open

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

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?
2021-05-07 14:42 Andrew Rambaut open

We should collaborate on this - we have some githubs and the idea would be to store the definition JSON files wecould all pull off. SLACK_000975

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