I have sequenced a vp1 partial gene of FMD virus and I have detected serotype O with sequence similarity of 95% to the closest on on blast search. I am struggling on how to determine the topotype of my sequence as well as lineage by phylogic tree, after I constructed the tree by nighbour joining it showed that my sequence is to far by distance from the closest one.
the phylogenic tree is attached.
I'm not much of a virologist. However, based on your phylogenetic tree, it seems to be a problem of sampling. I suggest you sample slightly outside the current OTUs. Your query OTU is behaving like an outgroup taxon which will not be helpful to the question you are hoping to answer.
I honestly would not know if there was an error with your sequences. You could replicate the entire experiment. My take will be to chat with someone familiar with the taxonomy of the group to advise as to how to expand your sampling. Basically you want to sample in such a way that your query taxon nests within a known clade. At the moment, you've sampled in such a way that your query is outside your sample limits, which goes back to my earlier point.
All the best.
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