A CRISPR-endonuclease gene editing composition includes a guide RNA (gRNA) for targeting a specific viral sequence for cleavage by the endonuclease which introduces breaks in the double stranded DNA identified by the gRNA. Placing the gene encoding Cas9 under the control of a minimal promoter of, for example, HIV spanning the 5′-LTR, results in the activation by the HIV-1 transactivator protein, Tat. Co-expression of both a multiplex of, for example, HIV-specific gRNAs and endonuclease, e.g. Cas9, in cells results in the modification and/or excision of the segment of viral DNA, leading to the eradication of the virus in vitro and in vivo.