Thread by @jbloom_lab

@Nucleocapsoid @HNimanFC @mrmickme2 @0bFuSc8 @PeacockFlu @CVRHutchinson Good observations. See also this thread posted by @SCOTTeHENSLEY:

I have added a few notes to the bottom of that thread.

To recap here:bsky.app/profile/scotte…

@Nucleocapsoid @HNimanFC @mrmickme2 @0bFuSc8 @PeacockFlu @CVRHutchinson @SCOTTeHENSLEY To add to thread linked above, human British Columbia H5 case has a HA sequence (GISAID EPI_ISL_19548836) that is ambiguous at *both* site Q226 and site E190 (H3 numbering)

Both these sites play an important role in sialic acid binding specificity

@Nucleocapsoid @HNimanFC @mrmickme2 @0bFuSc8 @PeacockFlu @CVRHutchinson @SCOTTeHENSLEY If you are searching literature, these sites are E190 and Q226 in H3 numbering, E186 and Q222 in mature H5 numbering, and E202 and Q238 in sequential H5 numbering (see: )dms-vep.org/Flu_H5_America…

@Nucleocapsoid @HNimanFC @mrmickme2 @0bFuSc8 @PeacockFlu @CVRHutchinson @SCOTTeHENSLEY Ambiguous codons are "ga[gt]" and "ca[at]"

The possible amino under these codes are E or D at 190, and G or H at 226

It would be great to examine deep sequencing data at these sites

Thanks to British Columbia CDC & Canada Public Health for sharing consensus sequences already

@Nucleocapsoid @HNimanFC @mrmickme2 @0bFuSc8 @PeacockFlu @CVRHutchinson @SCOTTeHENSLEY So sorry, that should read *Q* or H at 226 (for "ca[at]")

@Nucleocapsoid @HNimanFC @mrmickme2 @0bFuSc8 @PeacockFlu @CVRHutchinson @SCOTTeHENSLEY Below are HA mutations relative to two major candidate vaccine viruses

Several are in antigenic regions. However, our deep mutational scanning (dms-vep.org/Flu_H5_America…) suggest none of these mutations have a dramatic antigenic effect re neutralization by mouse or ferret sera