Patent ID: 7297477

Claim:
A method of determining whether a viral nucleic acid is present in a host cell, comprising the steps of: (a) producing a fragmented DNA sample from the host cell; (b) preparing a first target population of nucleic acids from a first portion of said fragmented DNA sample that is enriched for DNA fragments bound to DNA-binding protein, wherein said preparing comprises immunoprecipitation with an antibody or antigen-binding fragment of an antibody specific for the DNA-binding protein, wherein said immunoprecipitation is with an antibody or antigen-binding fragment of an antibody specific for RNA polymerase II; (c) preparing a second target population of nucleic acids from a second portion of said fragmented DNA sample wherein said second target population of nucleic acids is a non-enriched portion; and (d) contacting the first and second populations of target nucleic acids to an array of probe oligonucleotides, the array comprising probes specific for genomic DNA of the host cell and probes specific for viral nucleic acid; and (e) comparing hybridization of said first and second population of target nucleic acids to said array of probe oligonucleotides, wherein hybridization of the second target population of nucleic acids to probes specific for viral nucleic acid is indicative of a viral infection and hybridization of the first target population of nucleic acids to probes specific for viral nucleic acid is indicative of a productive viral infection and wherein lack of hybridization of the first target population of nucleic acids to probes specific for viral nucleic acid is indicative of a latent viral infection.