Prediction of Human Immunodeficiency Virus Type 1 Subtype-Specific Off-Target Effects Arising from CRISPR-Cas9 Gene Editing Therapy.

Chronic human immunodeficiency virus type 1 (HIV-1) disease is characterized by the retention of provirus within latently infected cells. Anti-HIV-1 CRISPR-Cas9 gene editing is an attractive strategy to excise or inactivate the HIV-1 genome. Recent strategies have focused on designing gRNAs that target the long terminal repeat (LTR) because 5' and 3' LTR symmetry can facilitate proviral excision. However, the promiscuity of CRISPR-Cas9 gene editing system necessitates the investigation of potential off-target effects. Here, potential gRNAs designed from HIV-1 phylogenetic subtypes using the CRISPRseek tool were investigated. Across the LTR, it was found that certain regions show higher human homology than others. When using recommended cutoffs, 96.40% of gRNAs were predicted to have no high probability off-target effects. Given this observation, while high-probability off-target effects are a potential danger, they can be avoided with proper gRNA design.