Indian samples in the B1.1.7 clade

[hodcroftlab]

Indian samples in the B1.1.7 clade

[rooklift]

I wrote initially that N501Y is not present; I see that it is, so I have corrected the comment.

[emmahodcroft]

Thanks @fohristiwhirl ! This is a good question. The sequences do have N501Y, as you corrected. They do not seem to have the deletion in the sequence, but we should probably be cautious in interpreting this. Gaps/deletions can cause problems both with sequencing and with mapping, and my guess would be that there's been an error in one of these. The rest of the genome does seem to put the sequences within this cluster quite solidly, so I think these likely are members of the 501Y.V2 variant, but have had some issues with the gaps.