Patent ID: 8214153

Claim:
A method for determining the genetic affinity of organisms or viruses in a test sample containing a target nucleic acid, comprising in combination the steps of: A. Obtaining or creating a nucleic acid sequence database of a plurality of sequences, each nucleic acid sequence being from the same corresponding nucleic acid from all organisms or viruses that will be incorporated into the determination; B. Obtaining or developing a bifurcating phylogenetic tree having multiple nodes that establishes the genetic affinity between substantially all the organisms or viruses included in the nucleic acid sequence database; C. Computationally fragmenting each target nucleic acid sequence such fragmentation being performed in a programmed computer so as to create a signature subsequence database of all nucleic acid subsequences of length N where N is at least seven; D. Tabulating in a programmed computer the extent to which the presence of each particular nucleic acid subsequence of length N is characteristic of each node in the bifurcating phylogenetic tree of genetic relationship by examining the occurrence frequency of each subsequence in the target nucleic acid of the organisms and viruses encompassed by or not encompassed by each node in the tree to create a database of characteristic signature sequences herein that extent is identified by: calculating the occurrence frequency and distribution of each subsequence of length N in the sequence database and calculating a signature quality index which measures the extent to which each subsequence of length N is characteristic of each node in the bifurcating node phylogenetic tree of genetic relationships; E. Deriving a plurality of signature probes from the signature database of characteristic signature sequences that will be complementary to a portion of the target nucleic acid sequence of the organism or virus if the signature sequence is present; F. Hybridizing a plurality of the signature probes representing multiple nodes in the bifurcating tree to the target nucleic acid obtained from the test sample under conditions where a detectable signal will be produced by signature probes that hybridize to the target nucleic acid of the organism or virus and detecting such signals; G. Identifying the nodes in the bifurcating phylogenetic tree of genetic relationship that are represented by the signature probes that produced detectable signal, in order to determine the genetic affinity of organisms or viruses in the test sample.