Viral diversity is an obligate consideration in CRISPR/Cas9 designs for HIV cure
Authors: Roychoudhury Pavitra , De Silva Feelixge Harshana , Reeves Daniel , Mayer Bryan T. , Stone Daniel , Schiffer Joshua T. , Jerome Keith R. 
Published: January 2018

RNA-guided CRISPR/Cas9 systems can be designed to mutate or excise the integrated HIV genome from latently infected cells and have therefore been proposed as a curative approach for HIV. However, most studies to date have focused on molecular clones with ideal target site recognition and do not account for target site variability observed within and between patients. For clinical success and broad applicability, guide RNA (gRNA) selection must account for circulating strain diversity and incorporate the within-host diversity of HIV. To address this, we identified a set of gRNAs targeting HIV LTR, gag and pol using publicly available sequences for these genes. We ranked gRNAs according to global conservation across HIV-1 group M and within subtypes A-C. By considering paired and triplet combinations of gRNAs, we found triplet sets of target sites such that at least one of the gRNAs in the set was present in over 98% of all globally-available sequences. We then selected 59 gRNAs from our list of highly-conserved LTR target sites and evaluated in vitro activity using a loss-of-function LTR-GFP fusion reporter. We achieved efficient GFP knockdown with multiple gRNAs and found clustering of highly active gRNA target sites near the middle of the LTR. Using published deep-sequence data from HIV-infected patients, we found that globally conserved sites also had greater within-host target conservation. Lastly, we developed a mathematical model based on varying distributions of within-host HIV sequence diversity and enzyme efficacy. We used the model to estimate the number of doses required to deplete the latent reservoir and achieve functional cure thresholds. Our modeling results highlight the importance of within-host target site conservation. While increased doses may overcome low target cleavage efficiency, inadequate targeting of rare strains is predicted to lead to rebound upon ART cessation even with many doses.

Author summary

The field of genome engineering has exploded over the last decade with the discovery of targeted endonucleases such as CRISPR/Cas9. Endonucleases are now being used to develop a wide range of therapeutics and their use has expanded into antiviral therapy against latent viral infections like HIV. The idea is to induce mutations in latent viral genomes that will render them replication-incompetent, thereby producing a functional cure. Although a great deal of progress has been made, most studies to date have relied on molecular clones that represent “ideal” targets. For clinical success and broad applicability, these therapies need to account for viral genetic diversity within and between individuals. Our paper examines the impact of HIV diversity on CRISPR-based cure strategies to determine the predictors of future clinical success. We performed an exhaustive and detailed computational analysis to identify optimal CRISPR target sites, taking into consideration both within-host and global viral diversity. We coupled this with laboratory testing of highly-conserved guides and compared measured activity to predicted results. Finally, we developed a mathematical model to predict the impact of enzyme activity and viral diversity on the number of doses of a CRISPR-based therapy needed to achieve a functional cure of HIV.