Long primed germinal centers with enduring affinity maturation and clonal migration

Germinal centers (GCs) are the engines of antibody evolution. Using HIV Env protein immunogen priming in rhesus monkeys (RM) followed by a long period without further immunization, we demonstrate GC B cells (BGC) lasted at least 6 months. A 186-fold BGC cell increase was present by week 10 compared to a conventional immunization. Single cell transcriptional profiling revealed both light and dark zone GC states were sustained. Antibody somatic hypermutation (SHM) of BGC cells continued to accumulate throughout the 29-week priming period, with evidence of selective pressure. Env-binding BGC cells were still 49-fold above baseline at 29 weeks, suggesting they could be active for even longer periods of time. High HIV neutralizing antibody titers were generated after a single booster immunization. Fully glycosylated HIV trimer protein is a complex antigen, posing significant immunodominance challenges for B cells. Memory B cells (BMem) generated under these long priming conditions had higher levels of SHM, and both BMem cells and antibodies were more likely to recognize non-immunodominant epitopes. Numerous BGC cell lineage phylogenies spanning the >6-month GC period were identified, demonstrating continuous GC activity and selection for at least 191 days with no additional antigen exposure. A long prime, slow delivery (12-day) immunization approach holds promise for difficult vaccine targets, and suggests that patience can have great value for tuning GCs to maximize antibody responses. Lymph node fine needle aspirations were used to collect samples from the left and right inguinal lymph nodes of Indian rhesus macaques (RMs). HIV Env+ and Env- BGC cells were then isolated via Fluorescence-activated cell sorting (FACS) and sequenced using the Chromium Next GEM Single Cell V(D)J Reagent Kit v1.1. PBMCs were collected from the same RMs and HIV Env+ BMem cells were isolated via FACS and sequenced using the Chromium Next GEM Single Cell 5’ Reagent Kit v2 (Dual Index)