Hello,

I am using Dada2 to find variants of my HIV viral sequences because I like the clean output in csv format with counts of each variant. I have samples at different time points and some are dually-infected with R5-tropic and X4-tropic HIV virus, while others are X4-infected only. We expect a tropism switch from R5 to X4 virus dominating as time continues. While I do see that X4 becomes more dominant. The majority of the ASVs either match the X4 or R5 reference exactly for any sample at any time point. I see X4 slowly become more dominant in later samples but it is the exact reference sequence that is increasing and not a variant as would be expected? Is there anything within the Dada2 pipeline that would correct these sequences to match this majority or anything I am missing? Otherwise, I guess it could be contamination prior to sequencing.

Thanks, Sara