Chimera detection algorithms

Algorithms/Softwares meant for finding chimeras in 16S sequences work by comparing
the ends of the 16S sequences to reference database. Query sequences, whose ends match
two different 16S reference sequences are flagged as potential chimeras.

My question is as follows. In case, the query sequence (whether chimeric or not chimeric)
originates from an entirely new species/phylum (as in metagenomics), its ends will obviously not show
any sort of alignment with existing reference 16s sequences.

In that case, how do existing chimera programs identify whether the query sequence is a chimera ?
Are existing programs validated for this scenario.

You are correct - if a query is very novel it will be difficult for it to be detected as chimeric. I’d say this would be pretty unlikely unless you have id’d a new phyla. If that is the case and you’d suspect it was chimeric, you could always cut the sequence in half and put it into a reference tree and see if the two halve associate with different parts of the tree.