Dixon, C. Voong, J. Abhyankar, G. Talbot, A. Bezawada, W . Zhai, M. Zhong, T. Patch and J. Rouhana. We also thank T. Chan for critical review and guidance. Funding was provided by the study sponsor, Gritstone bio. Employees of Gritstone bio received salaries for study conceptualization, design, data analyses, decision to publish and manuscript preparation. No other authors received specific funding for this work from the sponsor. Author contributions C.D.P ., A.R.R., M.D., M.S., G.G., W .B., R.R., R.Y ., A.A., A.F. and K.J. designed the study and wrote the manuscript. C.D.P ., A.R.R., M.D., M.G.H., C.D.S., L.D.K., S.K., A.Y ., L.S., D.S., M.S., K.T., M.M., J.R.J., C.N.N., E.M., R.Z., D.N.G., A.C.G., R.G., K.B., M.D.C. and R.Y . contributed to experimental design, execution and data analysis. A.I.S., S.R., D.C., B.S.H., C.G.D., B.J.S., D.A., A.M., S.B.M., B.J., R.R., C.-Y .L., D.V .T.C. and A.R.F. contributed to clinical oversight, patient recruitment, enrollment and treatment. C.D.S., L.G., S.-J.H., W .B., M.D.C., S.C. and K.J. contributed to vaccine design and production. Competing interests C.D.P ., A.R.R., M.G.H., C.D.S., L.G., S-.J.H., L.D.K., S.K., D.S., M.D., M.M., J.R.J., C.N.N., R.Z., D.N.G., A.C.G., M.D.C., S.C., K.B., R.R., A.A., A.R.F., K.J., A.Y ., L.S., M.S., K.T., E.M., G.G., R.G., W .B. and R.Y . are stockholders and either current or previous employees at Gritstone bio and may be listed as co-inventors on various pending patent applications related to the vaccine platform presented in this study. D.V .T.C. consults/has consulted/has advisory/had advisory roles at Genentech/Roche, Eli Lilly, Merck, Daiichi Sankyo, BMS, Ono, Five Prime, Seattle Genetics, Amgen, Taiho, Astellas, Gritstone bio, Pieris, Zymeworks, Basilea, QED, Foundation Medicine, Pierian, Silverback Therapeutics, Servier, Blueprint Medicines, Arcus Biosciences, Tempus, Guardant Health, Archer and Natera. C.G.D. is currently employed by Janssen R&D. B.S.H. has/had consultant/advisory roles for AstraZeneca, Ideaya, Jazz Pharmaceuticals, and research support from Neximmune. B.J.S. consults/has consulted/had advisory roles for Bristol Myers Squibb, Merck Sharp & Dohme, AstraZeneca, Pfizer, Roche/Genentech, Amgen, Lilly, Sanofi-Regeneron, Glaxo-Smith Kline, Takeda, Novartis and Beigene; has received honoria from Bristol Myers Squibb, Merck Sharp & Dohme, AstraZeneca, Pfizer, Roche/ Genentech, Amgen, Lilly, Sanofi-Regeneron, Glaxo-Smith Kline, Takeda, Novartis and Beigene; has received research funding from Sanofi-Regeneron; and has received royalties from UpToDate. B.J. consulted for/had advisory roles with Taiho Oncology, Insmed Oncology, Gritstone bio, Pfizer and Incyte and received research funding from Gateway for Cancer Research, Bristol Myers Squibb and Syntrix. A.M. is on the Advisory Board for AstraZeneca, QED, and Taiho Oncology. S.R. participated in Advisory Boards for Incyte Corporation (2017), AbbVie (2017), QED Therapeutics (2018, 2019) and Bayer (2020) (healthcare companies <10,000 USD). S.R. received honoraria from IDT (2017) and Illumina (2018) (technology companies). S.R. received consulting fees from QED Therapeutics (2018, 2019) and Merck (2019) (healthcare companies <10,000 USD). S.R. received travel reimbursement from Incyte Corporation (2019) (<999 USD). C.Y .L. received honoraria from Cancer Experts Now and has consulting/advisory board roles with Transthera, BluePrints Medicine, Genentech, QED Therapeutics, Histosonics and Ipsen and is part of the Speaker’s Bureau for Eisai and Incyte. S.B.M. received honoraria from Natera, Bicara, Novartis, Basilea and Daiichi Sankyo and owned stock in Calithera outside the submitted work. The remaining authors declare no competing interests. Additional information Extended data is available for this paper at https://doi.org/10.1038/s41591-022-01937-6. Supplementary information The online version contains supplementary material available at https://doi.org/10.1038/s41591-022-01937-6. Correspondence and requests for materials should be addressed to Karin Jooss.Peer review information Nature Medicine thanks Robert Seder and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Primary Handling editors: Saheli Sadanand and Joao Monteiro, in collaboration with the Nature Medicine team. Reprints and permissions information is available at www.nature.com/reprints. NATuRE MEDICINE | www.nature.com/naturemedicine Articles Nature MediciNe Extended Data Fig. 1 | See next page for caption. NATuRE MEDICINE | www.nature.com/naturemedicine Articles Nature MediciNeExtended Data Fig. 1 | (A) Representative FACS plots (NHP 4 and NHP 10) and pie charts for each population (% of total CD8+ or % of CD8+IFNγ+, mean for each group (n = 6 per group), week 13 post prime (one week post samRNA boost). Analysis of antigen-specific (IFNγ+) memory T cell populations, using CCR7 and CD45RA (Naïve: CCR7+CD45RA+, purple; Central Memory: CCR7+CD45RA-, blue, Effector memory: CCR7-CD45RA-, green; Effector memory RA+: CCR7+CD45RA+, orange). Pie chart represents mean percent of total tetramer population. (B) Analysis of memory T cell populations at 80 weeks post prime (1 year post last boost). Antigen-specific T cells were identified by combinatorial tetramer staining for six different antigens. Memory analysis was performed on total tetramer+ population, using CCR7 and CD45RA (Naïve: CCR7+CD45RA+, purple; Central Memory: CCR7+CD45RA-, blue, Effector memory: CCR7-CD45RA-, green; Effector memory RA+: CCR7+CD45RA+, orange). Pie chart represents mean percent of total tetramer population (n = 6). (C) Antigen-specific T cell response in each individual animal (n=6 animals) 2 years post prime (week 106) and one week post samRNA boost (week 107), for six SIV antigens, as measured by IFNγ ELISpot. SFU/10 6 to each antigen (mean of three technical replicates per antigen with SD; negative control value subtracted) stacked to provide sum total response. Red asterisk represents values that were too numerous to count and were set to maximum measured value (11000 for TL8, plated at 2.5x10 4 cells/well, and 3100 for TL9, plated at 1x105 cells/well). (D) Killing of antigen loaded target cells by CD8 T cells (collected 2 weeks post-boost, week 108), relative viability of SIV-loaded PBMCs (as determined by 7-AAD staining), normalized to negative control peptide-loaded PBMCs for each sample, at specified effector to target ratios. NATuRE MEDICINE | www.nature.com/naturemedicine Articles Nature MediciNe Extended Data Fig. 2 | (A) CONSORT flow diagram of patient enrollment. (B) Schematic outlining personalized vaccine production, planned dosing schedule, and immune monitoring. NATuRE MEDICINE | www.nature.com/naturemedicine Articles Nature MediciNe Extended Data Fig. 3 | See next page for caption. NATuRE MEDICINE | www.nature.com/naturemedicine Articles Nature MediciNeExtended Data Fig. 3 | (A) Data from PBMCs stimulated overnight in ex vivo IFNγ ELISpot with patient-specific peptide pools are shown for all Phase patients with available samples (all except G5). Individual patient IDs legend is shown below graph. Graphs show mean SFU per 106 PBMCs +/- standard deviation (SD) for technical triplicates (ELISpot wells) for all patients and timepoints except for G1 (W20 and W72), G2 (W42), G3 (W0, W5 and W8), G6 (all timepoints), G12 (W12 and W13), G13 (W12), and G14 (all timepoints), where only sufficient cells to test technical duplicates were available. For patient G3 W1 enough cells were available to test a single well. Assay limit of detection (LOD) and upper limit of quantitation (ULOQ) are indicated by dotted lines. ChAd68 boost for patients G1, G3, G8, and G11 are indicated by adenovirus symbol. (B) Longitudinal ELISpot data ≥52 weeks from PBMCs stimulated overnight in ex vivo IFNγ ELISpot with patient-specific CD8 Pools (blue bars) or DMSO (gray bars) are shown for patients G1, G2 and G8. Graphs show mean SFU per 10 6 PBMCs +/- standard deviation (SD) for triplicate ELISpot wells. (C) ELISpot data (fold change of mean of technical triplicates (all except for G6 (pre and post), G12 & G13 (post), where enough cells to test duplicates were available) are shown for all patients relative to pre-samRNA boost timepoint (week 4, available for all patients except G9), and maximum response post samRNA boost (5-36 week timepoints). Graphs show paired data from patients receiving 30µg samRNA (light blue), 100µg samRNA (medium blue), and 300µg samRNA (navy blue). NATuRE MEDICINE | www.nature.com/naturemedicine Articles Nature MediciNe Extended Data Fig. 4 | (A) ELISpot data (mean SFU per 106 PBMCs +/- SD for triplicate wells) are shown for whole PBMCs (black bars), CD4-depleted (CD8enr) PBMCs (navy blue bars), and CD8-depleted (CD4enr) PBMCs (orange bars) stimulated with DMSO, CD8 Pool, or 15mer pool for patients G1, G11, and G14 (pooled posttreatment timepoints). (B) Post-IVS ELISpot data for baseline and posttreatment sample PBMCs stimulated with patient-specific CD8 and minipools are shown for patients G1, G2, G3, G8, G9, G12, G13 and G4. Graphs show mean of technical duplicates (SFU per 106 PBMCs) for all except G2 CD8 Pool, where enough cells to test triplicates were available, with DMSO background subtracted. ULOQ for post-IVS assay is indicated by dotted line. NATuRE MEDICINE | www.nature.com/naturemedicine Articles Nature MediciNe Extended Data Fig. 5 | See next page for caption. NATuRE MEDICINE | www.nature.com/naturemedicine Articles Nature MediciNeExtended Data Fig. 5 | Data from PBMCs stimulated overnight in ex vivo (left graphs) or post-IVS (right graphs) IFNγ ELISpot with individual patient- specific peptides are shown for patient G1, G2, and G8. Graphs show individual duplicate values (SFU per 106 PBMCs) for each stimulation condition. Individual peptides with average responses >LOD (positive response) are shown in color (see mutation-specific coloring in graphs), and responses <LOD (negative response) are shown in clear circles. NATuRE MEDICINE | www.nature.com/naturemedicine Articles Nature MediciNe Extended Data Fig.