Using DADA2 for finding viral sequence variants

Question

[Saran]

Hello,

I decided to use the Dada2 basic pipeline for 16S in order to detect variants in my viral amplicon sequences. I have PCR amplified sequences from a 302 base-pair region of the viral genome. I used the DADA2 pipeline to detect the variants because I like chart with counts for each ASV that it outputs at the end. We have variants for 6 different time-points to track if there is a tropism switch between which virus predominates over time. I of course just skip the phylogeny step. Is there any bias towards microbiome sequencing in the pipeline that I used?

At a late time-point, a clear tropism switch is evident but the asv that is most dominate matches the reference exactly and if this had evolved from a tropism switch to this virus type then it wouldn't likely match exactly. Perhaps it is contamination. I am wondering if there is any aspect of the dada() function that would not be appropriate for finding the variants of my viral sequences?

Thanks, SARA

Answer 1

[antonioggsousa]

Hi,

I don't see any obvious reason why DADA2 wouldn't work with viral amplicon sequences, though, I should clear state that I never worked with viral amplicon sequences.

A quick search on google scholar pop up the following benchmarking of amplicon sequence bioinformatic tools for norovirus: https://journals.asm.org/doi/full/10.1128/aem.01522-22

The benchmark includes DADA2 supporting what I said above.

Although, they provided their code on github, they've used QIIME2 as interface for DADA2, but you can at least check the parameters.

I hope this helps.

Best regards,

António