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Despite significant progress in vaccine research, the level of protection provided by vaccination can vary significantly across individuals. As a result, understanding immunologic variation across individuals in response to vaccination is important for developing next-generation efficacious vaccines. Accurate outcome prediction and identification of predictive biomarkers would represent a significant step towards this goal. Moreover, in early phase vaccine clinical trials, small datasets are prevalent, raising the need and challenge of building a robust and explainable prediction model that can reveal heterogeneity in small datasets. We propose a new model named Generative Mixture of Logistic Regression (GeM-LR), which combines characteristics of both a generative and a discriminative model. In addition, we propose a set of model selection strategies to enhance the robustness and interpretability of the model. GeM-LR extends a linear classifier to a non-linear classifier without losing interpretability and empowers the notion of predictive clustering for characterizing data heterogeneity in connection with the outcome variable. We demonstrate the strengths and utility of GeM-LR by applying it to data from several studies. GeM-LR achieves better prediction results than other popular methods while providing interpretations at different levels. Author summary: Vaccines have proven to be a powerful tool in preventing infectious diseases, yet their effectiveness can vary significantly from person to person. This variability underscores the need for a better understanding of how individuals' immune systems respond to vaccination, which is essential for achieving successful immunization across a broader population. In our study, we introduce a new model called the Generative Mixture of Logistic Regression (GeM-LR) to predict vaccine effectiveness in different individuals. This model is particularly beneficial when only small datasets are available, a common challenge in vaccine research, whereas many advanced machine learning methods require large training datasets. GeM-LR integrates mixture modeling and logistic regression to provide more accurate predictions while also offering insights into the factors that contribute to varying vaccine responses among individuals. We demonstrate that our model outperforms other standard methods in terms of accuracy and enhances the understanding of data for future research. Our innovative approach holds great promise for improving vaccine development. By revealing hidden patterns within small datasets, GeM-LR aims to make vaccine research more efficient and impactful. [ABSTRACT FROM AUTHOR]

Authorization of the Matrix-M (MM)–adjuvanted R21 vaccine by three countries and its subsequent endorsement by the World Health Organization for malaria prevention in children are a milestone in the fight against malaria. Yet, our understanding of the innate and adaptive immune responses elicited by this vaccine remains limited. Here, we compared three clinically relevant adjuvants [3M-052 + aluminum hydroxide (Alum) (3M), a TLR7/8 agonist formulated in Alum; GLA-LSQ, a TLR4 agonist formulated in liposomes with QS-21; and MM, the now-approved adjuvant for R21] for their capacity to induce durable immune responses to R21 in macaques. R21 adjuvanted with 3M on a 0, 8, and 23–week schedule elicited anti-circumsporozoite antibody responses comparable in magnitude to the R21/MM vaccine administered using a 0-4-8–week regimen and persisted up to 72 weeks with a half-life of 337 days. A booster dose at 72 weeks induced a recall response similar to the R21/MM vaccination. In contrast, R21/GLA-LSQ immunization induced a lower, short-lived response at the dose used. Consistent with the durable serum antibody responses, MM and 3M induced long-lived plasma cells in the bone marrow and other tissues, including the spleen. Furthermore, whereas 3M stimulated potent and persistent antiviral transcriptional and cytokine signatures after primary and booster immunizations, MM induced enhanced expression of interferon- and TH2-related signatures more highly after the booster vaccination. Collectively, these findings provide a resource on the immune responses of three clinically relevant adjuvants with R21 and highlight the promise of 3M as another adjuvant for malarial vaccines. Editor's summary: Most vaccines based on recombinant antigens rely on coadministration with an adjuvant to elicit a robust immune response. Although adjuvants are needed for many vaccines, it is less clear which adjuvant(s) should be paired with each immunogen. In two papers, Bechtold et al. and Arunachalam et al. performed comparative analyses to assess the effect of different adjuvants on the immune response. Bechtold et al. showed that an AS01-adjuvanted hepatitis B virus vaccine, which induces robust CD4+ T cell responses against the vaccine antigen, also elicited trained immunity in human recipients, which was not observed in an alum-adjuvanted vaccine. Arunachalam et al. found that Matrix-M and 3M-052 + aluminum hydroxide (Alum) adjuvantation induced robust immune responses to the R21 malaria vaccine in nonhuman primates, but a third comparator, GLA-LSQ, elicited a lower magnitude of response that was short lived. Although Matrix-M and 3M-052 + Alum induced robust and durable antibody responses, they elicited distinct innate immune responses, demonstrating that multiple innate immune mechanisms can program durable vaccine-induced immunity. These head-to-head comparisons in both humans and nonhuman primates demonstrate that selecting an adjuvant should be done carefully and that different adjuvants have distinct effects on both innate and adaptive immunity. —Courtney Malo [ABSTRACT FROM AUTHOR]

Current seasonal influenza virus vaccines induce responses primarily against immunodominant but highly plastic epitopes in the globular head of the hemagglutinin (HA) glycoprotein. Because of viral antigenic drift at these sites, vaccines need to be updated and readministered annually. To increase the breadth of influenza vaccine–mediated protection, we developed an antigenically complex mixture of recombinant HAs designed to redirect immune responses to more conserved domains of the protein. Vaccine-induced antibodies were disproportionally redistributed to the more conserved stalk of the HA without hindering, and in some cases improving, antibody responses against the head domain. These improved responses led to increased protection against homologous and heterologous viral challenges in both mice and ferrets compared with conventional vaccine approaches. Thus, antigenically complex protein mixtures can at least partially overcome HA head domain antigenic immunodominance and may represent a step toward a more universal influenza vaccine. Editor's summary: A major goal for next-generation influenza vaccines is to elicit antibody responses to more conserved regions, such as the hemagglutinin (HA) stalk. To accomplish this, Luo et al. used a mutagenesis approach to generate a mixture of recombinant HAs that could be used as a vaccine. The mutations were limited to the immunodominant Sb site of the HA head, which the authors hypothesized would push the antibody response to favor immunosubdominant domains. The authors found that vaccination with the HA mixture could boost immune responses against the stalk without negatively affecting head-specific responses. This translated into superior protection against homologous and heterologous influenza challenges in mice and ferrets, supporting further development of this remixed influenza vaccine. —Courtney Malo [ABSTRACT FROM AUTHOR]

The modestly efficacious HIV-1 vaccine regimen (RV144) conferred 31% vaccine efficacy at 3 years following the four-shot immunization series, coupled with rapid waning of putative immune correlates of decreased infection risk. New strategies to increase magnitude and durability of protective immunity are critically needed. The RV305 HIV-1 clinical trial evaluated the immunological impact of a follow-up boost of HIV-1-uninfected RV144 recipients after 6–8 years with RV144 immunogens (ALVAC-HIV alone, AIDSVAX B/E gp120 alone, or ALVAC-HIV + AIDSVAX B/E gp120). Previous reports demonstrated that this regimen elicited higher binding, antibody Fc function, and cellular responses than the primary RV144 regimen. However, the impact of the canarypox viral vector in driving antibody specificity, breadth, durability and function is unknown. We performed a follow-up analysis of humoral responses elicited in RV305 to determine the impact of the different booster immunogens on HIV-1 epitope specificity, antibody subclass, isotype, and Fc effector functions. Importantly, we observed that the ALVAC vaccine component directly contributed to improved breadth, function, and durability of vaccine-elicited antibody responses. Extended boosts in RV305 increased circulating antibody concentration and coverage of heterologous HIV-1 strains by V1V2-specific antibodies above estimated protective levels observed in RV144. Antibody Fc effector functions, specifically antibody-dependent cellular cytotoxicity and phagocytosis, were boosted to higher levels than was achieved in RV144. V1V2 Env IgG3, a correlate of lower HIV-1 risk, was not increased; plasma Env IgA (specifically IgA1), a correlate of increased HIV-1 risk, was elevated. The quality of the circulating polyclonal antibody response changed with each booster immunization. Remarkably, the ALVAC-HIV booster immunogen induced antibody responses post-second boost, indicating that the viral vector immunogen can be utilized to selectively enhance immune correlates of decreased HIV-1 risk. These results reveal a complex dynamic of HIV-1 immunity post-vaccination that may require careful balancing to achieve protective immunity in the vaccinated population. Trial registration: RV305 clinical trial (ClinicalTrials.gov number, NCT01435135). ClinicalTrials.gov Identifier: NCT00223080, ClinicalTrials.gov Identifier: NCT01931358, ClinicalTrials.gov Identifier: NCT01923610, ClinicalTrials.gov Identifier: NCT01461447. Author summary: One strategy for improving vaccine-elicited antibody durability is booster immunization. However, the impact of boosting on the quality of the polyclonal antibody response is not fully understood and may alter vaccine efficacy. We discovered that canarypox vector boost (ALVAC-HIV vectored vaccine component only) drove the recall of HIV-1-specific inverse correlate of risk (V2 IgG) and promoted more durable immunity. We found that delayed boosting increased the concentration of putative protective V1V2-specific IgG circulating in blood, enabling 80% of vaccinees to achieve this level in RV305 compared to 63% in RV144. In contrast to Env IgG1 and IgA1, Env IgG3 was not boosted. However, Env IgG1 correlated with the magnitude of the ADCP response, demonstrating that antibody function can be elevated independent of IgG3 and IgA1. By including a delayed boost as part of a HIV-1 prime-boost vaccine strategy, vaccine-elicited antibodies can reach the putative protective threshold in a larger proportion of the population. However, a second immunogen boost within a 6-month interval shifts the antibody isotype/subclass profile, resulting in decreased antibody functions. A canarypox prime regimen can drive antibody specificity and function. Our study informs selection of immunogen types and immunization intervals for HIV-1 vaccine developers to elicit protective immunity. [ABSTRACT FROM AUTHOR]

Background The malaria vaccine, RTS,S/AS01, demonstrated an enhanced efficacy (86.7%) in a delayed third fractional dose (0.1.7Fx) regimen in controlled human malaria infection trials compared with a standard full-dose (0.1.2) regimen (62.5%). To understand the humoral component of the RTS,S/AS01 vaccine-induced protection against sporozoite infection in these 2 regimens, we investigated the serum antibody dynamics of 0.1.2 and 0.1.7Fx groups vaccinees. Methods The specific binding responses (magnitude) and dissociation rates (avidity) of serum antibodies interaction with a recombinant Plasmodium falciparum circumsporozoite protein (CSP) and peptides corresponding to the central repeat region (NANP6), the C-terminal region (PF16), and the N-terminal junction (N-interface) of CSP, respectively, were measured using a Biolayer Interferometry assay. Results On the day of challenge, higher NANP6-specific antibody responses were associated with protection in the 0.1.2 group. In contrast, slower antibody dissociation rates for CSP and PF16 binding were observed in the protected 0.1.7Fx group. Protected vaccinees of both groups exhibited 2- to 3-fold higher N-interface peptide binding antibody responses. Conclusions Unlike the standard dose, the delayed-fractional third dose of RTS,S/AS01 induced higher avidity CSP and PF16 binding antibodies that were associated with protection against sporozoite infection. [ABSTRACT FROM AUTHOR]

Importance: Preterm infants are recommended to receive most vaccinations at the same postnatal age as term infants. Studies have inconsistently observed an increased risk for postvaccination apnea in preterm infants., Objective: To compare the proportions of hospitalized preterm infants with apnea and other adverse events in the 48 hours after 2-month vaccinations vs after no vaccinations., Design, Setting, and Participants: This randomized, open-label clinical trial took place at 3 US neonatal intensive care units between August 2018 and October 2021. Infants between 6 and 12 weeks' postnatal age who were born at less than 33 weeks' gestational age and were eligible to receive 2-month vaccines were included., Intervention: Infants were randomized 1:1 to vaccinated (received vaccines within 12 hours of randomization) or unvaccinated (no vaccines received during the study period) groups. Cardiorespiratory data were collected during the 48 hours after vaccination or randomization (unvaccinated group)., Main Outcomes and Measures: The primary outcome was apnea, defined as a respiration pause greater than 20 seconds or a respiration pause greater than 15 seconds with associated bradycardia less than 80 beats per minute. Other outcomes included the number and duration of apnea episodes, serious adverse events, respiratory support escalation, and receipt of positive pressure ventilation., Results: Of 223 randomized infants (117 female; median [range] gestational age, 27.6 [23.0-32.9] weeks), 107 (48%) were vaccinated, and 116 (52%) were unvaccinated. For 2 infants in the vaccinated group, the primary outcome was unable to be assessed. The proportion of infants with 1 or more apnea event was 25 of 105 (24%) in the vaccinated group vs 12 of 116 (10%) in the unvaccinated group (adjusted odds ratio, 2.70; 95% CI, 1.27 to 5.73; P = .01). The mean number of apneic episodes did not significantly differ (model point estimate of difference, 0.54; 95% CI, -0.12 to 1.21) between the vaccinated (2.72) and unvaccinated (2.00) groups. The mean duration of apneic episodes did not significantly differ (model point estimate of difference, 4.6; 95% CI, -5.4 to 14.7) between the vaccinated (27.7) and unvaccinated (32.3) groups. No serious adverse events occurred during the 48-hour monitoring period. Other outcomes were not significantly different between groups., Conclusions and Relevance: In hospitalized preterm infants, the odds of apnea within 48 hours were higher after 2-month vaccinations vs after no vaccinations. The similar number and duration of apneic events and lack of serious adverse events suggest that current vaccination recommendations for hospitalized preterm infants are appropriate. Neonatal clinicians should continue providing evidence-based anticipatory guidance about postvaccination apnea risk., Trial Registration: ClinicalTrials.gov Identifier: NCT03530124.

BACKGROUNDThe mechanism(s) responsible for the efficacy of WHO-recommended malaria vaccine RTS,S/AS01 are not completely understood. We previously identified RTS,S vaccine-induced Plasmodium falciparum circumsporozoite protein-specific (PfCSP-specific) antibody measures associated with protection from controlled human malaria infection (CHMI). Here, we tested the protection-predicting capability of these measures in independent CHMI studies.METHODSVaccine-induced total serum antibody (immunoglobulins, Igs) and subclass antibody (IgG1 and IgG3) responses were measured by biolayer interferometry and the binding antibody multiplex assay, respectively. Immune responses were compared between protected and nonprotected vaccinees using univariate and multivariate logistic regression.RESULTSBlinded prediction analysis showed that 5 antibody binding measures, including magnitude-avidity composite of serum Ig specific for PfCSP, major NANP repeats and N-terminal junction, and PfCSP- and NANP-specific IgG1 subclass magnitude, had good prediction accuracy (area under the receiver operating characteristic curves [ROC AUC] > 0.7) in at least 1 trial. Furthermore, univariate analysis showed a significant association between these antibody measures and protection (odds ratios 2.6-3.1). Multivariate modeling of combined data from 3 RTS,S CHMI trials identified the combination of IgG1 NANP binding magnitude plus serum NANP and N-junction Ig binding magnitude-avidity composite as the best predictor of protection (95% confidence interval for ROC AUC 0.693-0.834).CONCLUSIONThese results reinforce our previous findings and provide a tool for predicting protection in future trials.TRIAL REGISTRATIONClinicalTrials.gov NCT03162614, NCT03824236, NCT01366534, and NCT01857869.FUNDINGThis study was supported by Bill & Melinda Gates Foundation's Global Health-Discovery Collaboratory grants (INV-008612 and INV-043419) to GDT.