Directed evolution of Brec1: A broad-range recombinase that inactivates HIV-1 in patient-specific humanized mice

Current combination antiretroviral therapies (cART) efficiently suppress HIV-1 reproduction in infected humans. However, cART does not eradicate HIV-1 from the body, necessitating lifelong medication. Therefore, intervention at additional critical steps of the virus life cycle might be indispensible to ultimately achieve an HIV cure. The most direct approach to eradicating HIV-1 is the physical removal of the integrated provirus from infected cells. Here, we evolved a broad-range recombinase (Brec1) that site-specifically recognizes a 34 bp sequence present in long terminal repeats (LTRs) of the majority of HIV-1 strains and subtypes. Brec1 efficiently, precisely and safely removes the integrated provirus from infected cells. Moreover, Brec1 acts efficaciously on clinical HIV-1 isolates in vitro and in vivo, particularly in humanized mice “personalized” with patient-derived cells. Furthermore, we performed whole genome sequencing totaling over 1.3 billion reads on primary CD4+ T cells isolated from an HIV-1 infected patient that had been transduced with LV-Brec1 or LV-Ctr, respectively, and found no signs of inadvertent Brec1-mediated genetic alterations. Thus, Brec1 represents a novel and potent antiviral reagent with a broad clinical application in the context of future curative HIV-1 therapy strategies.