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hodcroftlab / covariants

Real-time updates and information about key SARS-CoV-2 variants, plus the scripts that generate this information.
https://covariants.org/
GNU Affero General Public License v3.0
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Add Delta-Plus #196

Closed anjali-gopinathan closed 3 years ago

anjali-gopinathan commented 3 years ago

With all the concern in the media about the Delta-Plus variant (AY.1 or B.1.617.2.1), it would be helpful to see its spread in different countries displayed on the per-country charts.

emmahodcroft commented 3 years ago

Thanks for the suggestion @anjali-gopinathan ! At the moment, though any 'Delta Plus' isn't tracked in the graphs, there is a dedicated focal build showing sequences that are Delta but also have the 417N mutation here. Because of downtime on our cluster, this is a little old now, but I'm starting new builds today.

As you can see in that build, 'Delta Plus' isn't a very meaningful name - there are actually 2 clusters that are Delta + 417N (AY.1 and AY.2), but also a number of individual sequences. Because these are separate phylogenetically, I would need add a separate variant for AY.1 and AY.2.

At the moment, the total number of sequences that are Delta + 417N is about 500 - assuming that's split evenly between AY.1 and AY.2, that's about 250 each. That's a pretty small number compared to most of the other variants I track, so that's why it hasn't been added yet. However, I'm keeping an eye on these clusters, and if they continue to grow, I will consider adding them as tracked variants!