An I-CreI variant, wherein at least one of the two 1-Cre1 monomers has at least two substitutions, one in each of the two functional subdomains of the LAGLIDADG core domain situated from positions 26 to 40 and 44 to 77 of I-CreI, said variant being able to cleave a DNA target sequence from the genome of a non-integrating virus, in particular herpes simplex virus (HSV) or Hepatitis B virus (HBV) for use in genome engineering and for in vivo and ex vivo (gene cell therapy) genome therapy as well as the treatment of a virus infection.