Depth drop in some regions when analyzing B.1.1.529 variant (omicron)

[SergioBuenestadoSerrano]

Hi everyone,

We are sequencing B.1.1.529 samples, both by Illumina and MinION, and we are having depth drops in certain regions.

As happened with the B.1.617.2 variant and the V3 primers, I don't know if the V4 primers are getting outdated this time and it must be readapted to this new variant, maybe due to the large agglomeration of mutations in the spike, it would not be possible.

I attach below the regions in which we have that depth drop.

22784-22974 (~ 190bp)
26339-26586 (~ 250bp)
26957-27177 (~ 220bp)

Could you please provide any advice?

Best,

p)