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Although the choice of vector is critical, quantitative comparison of AAVs, especially in large animals, remains challenging.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"abs2\">\n                    <jats:title>Methods:<\/jats:title>\n                    <jats:p>Here, we developed an efficient single-cell AAV engineering pipeline (scAAVengr) to simultaneously quantify and rank efficiency of competing AAV vectors across all cell types in the same animal.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"abs3\">\n                    <jats:title>Results:<\/jats:title>\n                    <jats:p>To demonstrate proof-of-concept for the scAAVengr workflow, we quantified \u2013 with cell-type resolution \u2013 the abilities of naturally occurring and newly engineered AAVs to mediate gene expression in primate retina following intravitreal injection. A top performing variant identified using this pipeline, K912, was used to deliver SaCas9 and edit the rhodopsin gene in macaque retina, resulting in editing efficiency similar to infection rates detected by the scAAVengr workflow. scAAVengr was then used to identify top-performing AAV variants in mouse brain, heart, and liver following systemic injection.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"abs4\">\n                    <jats:title>Conclusions:<\/jats:title>\n                    <jats:p>These results validate scAAVengr as a powerful method for development of AAV vectors.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"abs5\">\n                    <jats:title>Funding:<\/jats:title>\n                    <jats:p>This work was supported by funding from the Ford Foundation, NEI\/NIH, Research to Prevent Blindness, Foundation Fighting Blindness, UPMC Immune Transplant and Therapy Center, and the Van Sloun fund for canine genetic research.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.7554\/elife.64175","type":"journal-article","created":{"date-parts":[[2021,10,18]],"date-time":"2021-10-18T22:25:34Z","timestamp":1634595934000},"update-policy":"https:\/\/doi.org\/10.7554\/elife.64175","source":"Crossref","is-referenced-by-count":63,"title":["scAAVengr, a transcriptome-based pipeline for quantitative ranking of engineered AAVs with single-cell resolution"],"prefix":"10.7554","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5117-077X","authenticated-orcid":true,"given":"Bilge E","family":"\u00d6zt\u00fcrk","sequence":"first","affiliation":[{"name":"Department of Ophthalmology, University of Pittsburgh","place":["Pittsburgh, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9575-3192","authenticated-orcid":true,"given":"Molly E","family":"Johnson","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology, 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