Improved detection of genomic sequences and probe molecules therefor

A method of detecting if a first microorganism having a first genome or a second microorganism of the same genus having a second genome is present in a test sample or an initial sample from which the test sample was prepared, comprising:

• (a) probing the test sample with a virtual probe comprising a plurality of probe molecules, wherein:
• (i) the virtual probe comprises at least two probe molecules each capable of specifically hybridizing to one or more target nucleic acids corresponding to the first genome and/or one or more homologous target nucleic acids corresponding to the second genome,
• (ii) at least one of the probe molecules is a meter probe capable of hybridizing to a target nucleic acid corresponding to the first genome and a homologous target nucleic acid corresponding to the second genome, such that the hybridizing of the meter probe to such target nucleic acids can provide a measure of the relative amount of target nucleic acids in the test sample,
• (iii) the probe molecules of the virtual probe cannot individually distinguish the target nucleic acids corresponding to the first and second genomes, and
• (iv) the probe molecules hybridize non-identically to the target nucleic acids corresponding to the first and second genomes, such that the hybridizing of the probe molecules to the target nucleic acids corresponding to the first and second genomes can distinguish between the target nucleic acids corresponding to the first and second genomes;
• (b) detecting and/or quantifying signals from hybridization of the probe molecules in the virtual probe to nucleic acids, if any, in the test sample;
• and
• (c) if hybridization of the probe molecules to nucleic acids in the test sample is detected, then:
• (i) analyzing the signals detected and/or quantified in step (b) according to a first formula if the signal from hybridization of the meter probe to nucleic acids in the sample is greater than or equal to a threshold value, and
• (ii) analyzing the signals detected and/or quantified in step (b) according to a second formula if the signal from hybridization of the meter probe to nucleic acids in the sample is less than the threshold value.