Preliminary report on genomic epidemiology of the 2024 H5N1 influenza A virus outbreak in U.S. cattle (Part 2 of 2)

Thank you for your very thorough analyses of the available consensus sequences. I do not know how much you may have looked at the details of the actual deposited reads, acknowledgement to USDA-APHIS for sharing sequence read data on SRA-BioProject PRJNA1102327, but close inspection of a few of the deposited SRAs, indicate a low, and potentially interesting presence of reads with short insertions in HA. Looking briefly at a few of the SRAs, I detected short insertions in HA in 5 of 9 samples each having 1-4 short inserts in 1-6 reads. These insertions, in a very few reads, are 2-15 nt in size and all represent insertion of a repeated sequence, consistent with virus polymerase stuttering. Of a total of 11 different short insertions, 9 are in the HA2 part after the cleavage site and only 2 are in HA1. This finding may or may not be of biological significance, but I wanted to hear if anyone else has spotted something similar?