Scientific Publications

HIV broadly neutralizing antibodies (bnAbs) are promising reagents for prevention and therapy of disease; however, their elicitation is constrained by genetic limitations of the human B cell antigen-receptor (BCR) repertoire. Precision genome-editing offers a potential solution by enabling bnAb genes to be programmed into the BCR repertoire as IgH-modified B cells. Such cells can be vaccinated to elicit durable bnAb memory responses in mice; however, extending this success to non-human primates (NHPs) would be a major advance towards clinical translation. Here, we show that ex vivo reprogrammed NHP B cells can survive autologous infusion and respond to immunization, differentiating into antibody-secreting cells (ASCs) that can produce up to 1 µg/ml of a bnAb in serum following vaccination prime. Although durable transgenic memory responses were not generated, vaccination of engineered cells in secondary lymphoid organoid (SLO) cultures recapitulated transient ASC responses in vitro. These findings suggest that NHP-derived SLOs could provide a platform to optimize engineering and vaccination conditions that drive germinal center maturation of IgH-reprogrammed B cells in a clinically relevant NHP model, supporting the development of engineered B-cell vaccines that generate durable bnAb responses as a potential functional cure for HIV.

Malaria is a leading cause of disease in developing countries. The licensed malaria vaccine RTS,S/AS01 confers partial protection in part due to the elicitation of circumsporozoite protein (CSP) antibodies, of which those to the CSP repeat and junctional regions offer the most potent protection. Anti-repeat region antibodies, including the protective antibody L9, frequently develop mutations that promote inter-Fab contacts when bound to CSP in "spiral" quaternary structures. As a first step toward the design of immunogens that elicit L9-like antibodies, we utilized generative deep learning models to design epitope scaffolds that incorporated up to three junctional repeat epitopes with structural conformations and relative spatial orientations matching those of the multivalent complex of CSP bound to three copies of L9. Affinity and structural studies demonstrated accurate scaffolding of two epitopes with the intended relative orientation, and displacement of the third epitope, while maintaining inter-Fab contacts between L9 antibodies. In a mouse model of malaria liver invasion, immunization with nanoparticles displaying these scaffold immunogens inhibited liver invasion as potently as matched nanoparticles displaying a short junctional peptide but less potently than the same nanoparticles displaying longer junctional peptides. This study demonstrates a substantial advance for design of multiepitope scaffolds with predetermined relative epitope spatial positioning. The study also represents an initial step toward development of multiepitope immunogens to elicit antibodies that utilize homotypic interactions to bind pathogens in multivalent clusters.

Germline targeting (GT) is a promising strategy to activate rare broadly neutralizing antibody (bnAb)-producing B cells against HIV, but induction of such responses in outbred animals has not been achieved. Using antibody-guided structure-based design, we engineered a GT HIV trimer immunogen, Q23-APEX-GT2, which primes diverse V2-apex bnAb precursors. Q23-APEX-GT2 efficiently activated rare V2-apex-specific B cells in humanized knockin mice and consistently elicited immunofocused antibody responses in outbred rhesus macaques, priming multiple long heavy-chain complementarity-determining region 3 (CDRH3)-loop bnAb-B cell lineages. Monoclonal antibodies isolated from immunized macaques showed broad heterologous HIV trimer recognition and modest cross-neutralization of diverse tier-2 viruses. Cryoelectron microscopy (cryo-EM) structural studies confirmed precise epitope targeting and revealed CDRH3-mediated binding modes that mirrored those of human V2-apex bnAbs. Together, these findings establish proof of principle for priming and early maturation of authentic V2-apex bnAb precursors in outbred macaques and highlight the promise of V2-apex-targeted HIV vaccines.

HIV vaccine strategies include aims to elicit broadly neutralizing antibodies (bnAbs) targeting the CD4-binding site, that are derived from immunoglobulin heavy-chain variable genes 1-2 (VH1-2) and 1-46 (VH1-46). Here, we present an integrated analysis of VH1-46 bnAbs, including in vitro functional studies, cryo-electron microscopy structures of two VH1-46 bnAbs (1-23 and 9-71) complexed with envelope trimers, and comprehensive structural and immunogenetic analyses, to help guide vaccine design. We show that VH1-46-derived bnAbs use diverse light-chain variable (VK/VL) genes and LCDR3 lengths commonly found in human antibody repertoires, which generate unique LCDR3 signatures that influence both the antibody paratope and approach angle. We identify three VH1-46 bnAb classes, 1B2530 (VL1-47), CH235 (VK3-15), and 561 (VK3-20), with the 561 class further subdivided into types I and II. Our findings indicate that VH1-46 priming immunogens should be tailored to each bnAb class, with 561-class bnAbs presenting optimal targets for germline-targeting vaccine design.

Introduction Screening for acute and early HIV infections (AEHI) among men who have sex with men (MSM) remains uncommon in sub-Saharan Africa (SSA). Yet, undiagnosed AEHI among MSM and subsequent failure to link to care are important drivers of the HIV epidemic. We conducted a systematic review and meta-analysis of AEHI yield among MSM mobilized for AEHI testing; and assessed which risk factors and/or symptoms could increase AEHI yield in MSM. Methods We systematically searched four databases from their inception through May 2020 for studies reporting strategies of mobilizing MSM for testing and their AEHI yield, or risk and/or symptom scores targeting AEHI screening. AEHI yield was defined as the proportion of AEHI cases among the total number of visits. Study estimates for AEHI yield were pooled using random effects models. Predictive ability of risk and/or symptom scores was expressed as the area under the receiver operator curve (AUC). Results Twenty-two studies were identified and included a variety of mobilization strategies (eight studies) and risk and/or symptom scores (fourteen studies). The overall pooled AEHI yield was 6.3% (95% CI, 2.1 to 12.4; I2 = 94.9%; five studies); yield varied between studies using targeted strategies (11.1%; 95% CI, 5.9 to 17.6; I2 = 83.8%; three studies) versus universal testing (1.6%; 95% CI, 0.8 to 2.4; two studies). The AUC of risk and/or symptom scores ranged from 0.69 to 0.89 in development study samples, and from 0.51 to 0.88 in validation study samples. AUC was the highest for scores including symptoms, such as diarrhoea, fever and fatigue. Key risk score variables were age, number of sexual partners, condomless receptive anal intercourse, sexual intercourse with a person living with HIV, a sexually transmitted infection, and illicit drug use. No studies were identified that assessed AEHI yield among MSM in SSA and risk and/or symptom scores developed among MSM in SSA lacked validation. Conclusions Strategies mobilizing MSM for targeted AEHI testing resulted in substantially higher AEHI yields than universal AEHI testing. Targeted AEHI testing may be optimized using risk and/or symptom scores, especially if scores include symptoms. Studies assessing AEHI yield and validation of risk and/or symptom scores among MSM in SSA are urgently needed.

Combination vaccine formulations contain distinct components targeting multiple strains of a single pathogen or multiple pathogens. By minimizing the number of separate vaccine administrations required, combination vaccines have been critical in allowing the broad expansion of the number and range of diseases that can now be prevented by immunization. Recent advances in vaccine development and our understanding of the immune system now make it possible to envision how new combination vaccines could play a major role in helping immunization programs address a much wider range of emerging or still problematic pathogens. However, few combinations are currently in the pipeline, in part due to their inherently increased complexity and cost of development compared to standalone formulations. This complexity, in turn, is partly driven by the regulatory requirements surrounding the clinical study program for the combination vaccine, especially the primary clinical endpoints and the required degree of precision around those endpoints, as these ultimately determine the sample size, cost, and duration of the study. As part of a larger effort to facilitate combination vaccine development, vaccine experts at the World Health Organization and PATH coordinated a one-day meeting in March 2025 gathering current and former national regulatory agency staff from a dozen countries, together with vaccine developers, representatives from funding and procurement agencies, and public health and policy officials. The convened participants held spirited discussions on how multiple immune markers and controlled human infection models (CHIM) might contribute to the demonstration of vaccine efficacy. In addition, participants considered the possibility of relying on clinical endpoints when the vaccine components are directed against pathogens causing the same disease syndrome but etiological determination of each component's contribution is not feasible. Regulators welcomed scientifically sound, creative proposals for demonstration of efficacy, and agreed that the benefit-risk of the combination vaccine as a whole should be the primary focus.

Circulating antibodies from previous immune encounters impact subsequent humoral responses. Here, we investigated how local epitope-specific competition shapes ongoing germinal center (GC) responses by delivering an mRNA-LNP-encoded membrane-bound immunogen displaying three conserved HIV-1 envelope (Env) epitopes to mouse models bearing B cell receptors (BCRs) of defined affinities. High-affinity B cells exhibited shorter GC residency than lower-affinity counterparts. B cells engaged GC reactions at equivalent rates in the presence or absence of clonal lineages binding the same epitope with similar affinities; however, higher-affinity clones suppressed lower-affinity counterparts targeting the same epitope. Spatial transcriptomics revealed plasma-like cells within and adjacent to the GC, and early immunoglobulin G (IgG) was detectable in draining lymph nodes. Our findings suggest that a self-modulating local antibody feedback loop limits epitope-specific recognition-dampening selection for higher-affinity B cells and facilitating epitope spreading by redirecting the response toward alternative epitopes.

Current immunization strategies to elicit broadly neutralizing antibodies (bnAbs) against HIV-1 generally propose complex, multiboost regimens. In rhesus macaques, simian-human immunodeficiency virus (SHIV) infection rapidly drives the development of some bnAb classes sharing structural similarities with those in humans. Here, we generated a knockin (KI) mouse model with B cells bearing the unmutated common ancestor of a V2 apex-targeted bnAb lineage, V033-a. A single immunization with a germline-targeting native-like trimer, Q23-APEX-GT1, recapitulated the ontogeny of the mature rhesus bnAb in KI mice, including rare, disfavored somatic mutations. Resulting antibodies exhibited potent neutralization against a broad panel of heterologous HIV-1 strains. Boosting with Env escape mutant trimers further improved breadth and potency, and cryo-electron microscopy analysis revealed the structural basis for heterologous neutralization breadth. Nonhuman primate and mouse models combined with structure can serve as a platform for identifying and validating immunogens that streamline HIV vaccination regimens.

Transmembrane glycoproteins of enveloped viruses are targets of neutralizing antibodies and essential vaccine antigens. mRNA-LNP technology allows in vivo expression of transmembrane glycoproteins, but in vitro biophysical characterization of transmembrane antigens and analysis of post-immunization antibody responses typically rely on soluble proteins. Here, we present a platform for assembling transmembrane glycoprotein vaccine candidates into lipid nanodiscs. We demonstrate the utility of nanodiscs in HIV membrane proximal external region (MPER)-targeting vaccine development by binding assays using surface plasmon resonance (SPR), ex vivo B cell sorting with fluorescence-activated cell sorting (FACS), and by determining the structure of a prototypical HIV MPER-targeting immunogen nanodisc in complex with three broadly neutralizing antibodies (bnAbs), including MPER bnAb 10E8, to 3.5 Å by cryogenic electron microscopy (cryo-EM), providing a template for structure-based immunogen design. To demonstrate general applicability we characterize Ebola virus glycoprotein nanodiscs. Overall, the platform offers a tool for accelerating development of next-generation vaccines.

Background/Objectives: The rapid development of safe and efficacious vaccines is often hindered by extensive, mandated non-clinical safety evaluations in animals. With the aim to provide scientific evidence supporting a "vaccine platform approach", here we present the complete non-clinical studies for two investigational vaccines, GRAd-COV2 and GRAdHIVNE1, based on GRAd, a gorilla-derived group C adenoviral vector. Methods: The biodistribution of GRAd genomes following the intramuscular administration of the vaccines was assessed in rats by a sensitive qPCR method. Local tolerance and systemic toxic effects were evaluated in single- and repeated-dose toxicity studies in rabbits. Results: GRAd-COV2 and GRAdHIVNE1 were well-tolerated. Distribution was highly confined to the injection site and draining lymph nodes, and toxicity profile consisted of transient, non-adverse inflammatory responses, while the expected immune responses to the encoded antigens were successfully induced. Notably, both vaccines demonstrated a consistent safety profile despite transgene and backbone differences, comparable to other replication-defective adenoviral vectors. Conclusions: The established non-clinical safety profile of the GRAd platform provides a robust foundation for a more efficient and streamlined regulatory pathway. By leveraging this prior knowledge, future GRAd-based vaccines can achieve accelerated clinical development while fully adhering to the ethical principles of replacement, reduction, and refinement of animal use in research.

Priming rare subdominant precursor B cells in germinal centers (GCs) is a central goal of vaccination to generate broadly neutralizing antibodies (bnAbs) against HIV. Multivalent immunogen display on protein nanoparticle scaffolds can promote such responses, but it also generates scaffold-specific B cells that could theoretically limit bnAb precursor expansion in GCs. We rationally designed DNA origami-based virus-like particles (DNA-VLPs) displaying a germline-targeting HIV envelope protein immunogen, which elicited no scaffold-specific antibody responses. Compared with a state-of-the-art clinical protein nanoparticle, these DNA-VLPs increased the expansion of epitope-specific GC B cells relative to off-target B cells and enhanced expansion of bnAb-lineage B cells in a humanized mouse model of CD4 binding site priming. Thus, minimizing off-target responses enhances bnAb priming and indicates that DNA-VLPs are a promising vaccine platform.

Introduction: HIV testing is at the cornerstone for interventions aimed at controlling the number of new HIV infections in Sub-Saharan Africa. The current HIV RDTs in use are not able to identify acute HIV infection. Methods: We collaborated with 10 health centers in Uganda, offering HIV voluntary counselling and testing services to obtain 'left-over' EDTA blood samples after HIV RDT. We investigated for HIV RNA using the GeneXpert HIV-1 Viral Load assay among individuals who had non-reactive Determine (HIV negative) or an inconclusive test result (Indeterminate). We used a formula from Brookmeyer and Quinn to estimate HIV incidence. The study started on the 17th February 2021 and ended on the 24th December 2021. Study activities were suspended between June and September 2021, due to travel restrictions instituted by government of Uganda aimed at reducing levels of connectivity between and within communities, to curb the rising number of COVID-19 infections. Results: Fourteen of 4,941 'left-over' plasma samples retested were reactive with a mean pVL of 1.5X106 copies per ml. The overall HIV incidence per 100 person years was 7.4 (95% CI: 4.3-12.5): higher for females at 9.4 (95% CI: 5.2-16.9) compared to 4.2 (95% CI: 1.3-12.9) for males. The HIV Incidence per 100 person years was 7.8 (95% CI: 3.7-16.4) before travel restrictions were instituted and 7.0 (95% CI: 3.3-14.7) after they were lifted. Conclusion: We demonstrated that incident HIV infection can be determined without assembling a longitudinal cohort. GeneXpert HIV-1 Viral Load assay can detect acute infection. There is no evidence that COVID-19 travel restrictions was associated with increased HIV Incidence rates in our communities.

Applying cryoelectron microscopy (cryo-EM) to small protein complexes is usually challenging due to their lack of features for particle alignment. Here, we characterized antibody responses to 21 kDa human immunodeficiency virus (HIV) membrane-proximal external region germline-targeting (MPER-GT) immunogens through cryo-EM by complexing them with 10E8 or Fabs derived from MPER-GT-immunized animals. Distinct antibody-antigen interactions were analyzed using atomic models generated from cryo-EM maps. Mutagenesis screening revealed that off-target monoclonal antibodies (mAbs), which do not compete with 10E8, bind non-MPER epitopes, and the binding of two most dominant epitopes were verified by cryo-EM. The structures of 10E8-class on-target Fabs showed binding patterns that resemble the YxFW motif in the 10E8 heavy chain complementarity-determining region 3 (HCDR3) loop. Additionally, we demonstrate that high-resolution maps can be generated from heterogeneous samples with pooled competing Fabs. Overall, our findings will facilitate the optimization of MPER-GT antigens and push the size limit for cryo-EM-based epitope mapping with smaller antigens and heterogeneous antibody mixes.