Quantitative multiplexed identification of nucleic acid targets

A method for detecting in a sample at least one of a plurality of target nucleic acid molecules, the method comprising the steps of:

• identifying a first amplification region of each of said plurality of target nucleic acid molecules, wherein the first amplification region is conserved among said plurality of target nucleic acid molecules;
• identifying a second amplification region of each of said plurality of target nucleic acid molecules, wherein the second amplification region is not conserved among said plurality of target nucleic acid molecules, and further wherein for each one of the plurality of target nucleic acid molecules, the first amplification region and the second amplification region are in different locations of the nucleic acid molecule;
• generating an amplification reaction mixture, the mixture comprising at least two different target nucleic acid molecules, a first primer pair designed to amplify said first amplification region, a second primer pair designed to amplify said second amplification region, and a first nucleic acid probe designed to hybridize to said first amplification region;
• producing, simultaneously in an amplification reaction comprising the reaction mixture, a first amplification product of the first amplification region of each target nucleic acid molecule present in said sample and a second amplification product of the second amplification region of each target nucleic acid molecule present in said sample, wherein the first and second amplification products are separate products;
• detecting the production of said first amplification product in real time, wherein said first nucleic acid probe hybridizes to said first amplification region;
• and
• detecting said second amplification product to indicate the presence of each target nucleic acid molecule present in said sample.