Hi all, I have sequenced several samples of influenza that contain the same virus using NGS and performed minor variant analysis to identify genomic positions where there are sub-populations within the sample. I was wondering can alpha and beta diversity analyses be used to compare the richness and diversity of these sub-populations between samples? I know alpha and beta diversity are primarily used in microbiome analyses where the different OTUs are used to assess the diversity and richness within and between samples, but I wasn't sure if the OTUs could be substituted with nucleotide positions where I have observed variation.

Any help you can provide will be very much appreciated.