Hello,

Its old question, I hope you solved it, or other, let me advice you that, not every BLAST result is counted as a result, some criteria of selection should be considered. Query coverage, e-value, and similarity. The good thing about geneious is it can give you an additional indicator rather than the usual ones (NCBI-BLAST). Its called grade, and maybe a little bit to the right from the frame you captured.

If I were you, I would consult some reviews on pairwise similarity % between viruses from the same species, or closely related within one genus, and accordingly, then use the Pairwise % as your first filtering criteria, all below X % should be removed. Then based on the grade of those show query coverage 85% or above and similarity above your X level, mark your lowest grade value, and apply to filter again the selected results. In which the retained sequences should be tested by a simple PCR for your sample by means of quantification or simple PCR detection to validate your findings.

Hope you find that useful for your research,

Regards