Compositions and methods to treat latent viral infections

1. A method for treating an infection by a virus, the method comprising:

introducing into a cell a vector comprising an origin of replication of the virus, said origin of replication is not transcribed to generate a sequence-specific targeting moiety, a sequence encoding a nuclease, and a sequence encoding a sequence-specific targeting moiety that targets the nuclease to a genome of the virus;

targeting the nuclease to a viral nucleic acid within the genome of the virus by means of the sequence-specific targeting moiety; and

cleaving the viral nucleic acid with the nuclease without interfering with the host genome.

2. The method of claim 1 , wherein the nuclease is selected from the group consisting of a zinc-finger nuclease, a transcription activator-like effector nuclease, and a meganuclease.

3. The method of claim 1 , wherein the nuclease is a Cas9 nuclease and the sequence-specific targeting moiety comprises a guide RNA.

4. The method of claim 1 , wherein the viral nucleic acid is latent in a host cell.

5. The method of claim 1 , wherein said cleaving step comprises creating a double-strand break in said viral nucleic acid.

6. The method of claim 1 , further comprising the step of inserting a polynucleotide into the viral nucleic acid.

7. The method of claim 1 , wherein the viral nucleic acid is from a virus selected from the group consisting of adenovirus, herpes simplex virus, varicella-zoster virus, Epstein-Barr virus, human cytomegalovirus, human herpesvirus type 8, human papillomavirus, BK virus JC virus, and smallpox.

8. The method of claim 1 , wherein the vector is a viral vector selected from the group consisting of retrovirus, lentivirus, adenovirus, herpesvirus, poxvirus, alphavirus, vaccinia virus, and adeno-associated viruses.

9. The method of claim 1 , wherein the vector is introduced into the cell via a non-viral vector.

10. The method of claim 9 , wherein said non-viral vector is selected from the group consisting of a nanoparticle, a cationic lipid, a cationic polymer, a metallic nanoparticle, a nanorod, a liposome, microbubbles, a cell-penetrating peptide, and a liposphere.

11. The method of claim 9 , wherein the non-viral vector comprises polyethyleneglycol.

12. The method of claim 1 , wherein the vector is a plasmid.

13. The method of claim 12 , wherein the nuclease is a Cas9 nuclease and the sequence-specific targeting moiety comprises a guide RNA.

14. The method of claim 13 , wherein the viral nucleic acid is latent in a host cell.

15. The method of claim 14 , wherein the viral nucleic acid is from Epstein-Barr virus.

16. The method of claim 15 , wherein the cleaving step comprises creating a double-strand break in the viral nucleic acid.

17. A method for treating an infection by a virus, the method-comprising:

introducing into a cell a plasmid that comprises an origin of replication of the virus, said origin of replication is not transcribed to generate a guide RNA, a sequence encoding a Cas9 nuclease, and a sequence encoding a guide RNA that targets a portion of a genome of the virus;

targeting the Cas9 nuclease to the portion of the genome of the virus by means of the guide RNA; and

cleaving the genome of the virus with the Cas9 nuclease without interfering with the host genome.

18. The method of claim 17 , further comprising increasing copy number of the plasmid preferentially in cells infected by the virus by means of the viral origin of replication of the virus.

19. The method of claim 18 , wherein the portion of the genome of the virus comprises a 20 nucleotide segment 5′ to a protospacer adjacent motif within the genome of the virus, and wherein a portion of the guide RNA is at least 60% complementary to the portion of the genome of the virus, and wherein the portion of the guide RNA has no match in a human genome.

20. The method of claim 18 , wherein the guide RNA binds to the genome of the virus within a latency-related target.