BACKGROUND:A heterologous Ad26.Mos4.HIV and clade C gp140 vaccine regimen did not show overall significant efficacy against HIV-1 acquisition [point estimate 14.1%; 95% confidence interval (CI), -22.0 to 39.5] in the HVTN 705/HPX2008 trial in southern African women. We examined whether and how vaccine efficacy (VE) against HIV-1 diagnosis over 7-24 months post-first dose varied by HIV-1 Envelope (Env) amino acid sequence features. METHODS:HIV-1 viral sequences were generated by PacBio SMRT-UMI sequencing from the first RNA-positive sample of participants who acquired HIV-1. Env amino acid sequence features were prespecified for analyses based on 1) being hypothesised to impact VE; and 2) having sufficient variability. Sieve analyses assessed VE by a single representative sequence and by viral population composition. FINDINGS:The majority of Env features showed no evidence of differential VE, with only two signals having familywise error rate (FWER) P-values <0.10. In single-sequence analyses, VE declined with increasing physicochemical-weighted Hamming distance from the C97ZA vaccine insert in clade C broadly neutralising antibody resistance-associated signature positions (FWER P = 0.08). Sequence-predicted Env structural features showed no significant vaccine vs. placebo differences in structural divergence from the C97ZA vaccine-insert Env sequence. In multi-sequence analyses (median 121 sequences/individual), VE was higher against viral populations with ≥99% vs. <99% L832 prevalence (VE = 91.7%; 95% CI, 67.4-97.9 vs. VE = -7.0%; 95% CI, -55.5 to 26.4) (unadjusted P = 0.0002 for differential VE, FWER P = 0.023). INTERPRETATION:Despite extensive prespecified and exploratory analyses including Env features supported by prior studies to potentially impact VE, there was only limited, weak evidence that Env sequence features modified VE in HVTN 705. Although previous work suggested a protective role of IgG3 binding to V1V2 in a small subgroup of vaccine recipients, a V1V2 sieve signal was absent. FUNDING:National Institutes of Health and Johnson & Johnson.

Understanding the selective forces acting upon HIV early in infection is crucial to design prevention strategies. By leveraging deep sequencing and the short diagnostic intervals of the FRESH and RV217 cohorts (median 4 days) between the last-negative and first-positive RNA tests, we captured a precise and early snapshot of acute HIV infection. The frequency of multiple transmitted viruses of 38% in these as well as placebo recipients from the AMP trials was higher than previously published, with the true frequency likely to be higher. The relative abundance of lineages fluctuated substantially over time in two-thirds of the multilineage infections, generating uncertainty in identifying the specific viruses that were transmitted and founding the infection. Viral populations exhibited diversity and selection on the Gag and Env proteins at the earliest times examined, with sites inferred to be undergoing negative selection most evident. These data may help explain vaccination failures and provide new targets for prevention.

Abstract In the antibody mediated prevention (AMP) trials, the broadly neutralizing antibody (bNAb) VRC01 demonstrated protective efficacy against susceptible HIV strains. To understand how VRC01 shaped breakthrough infections, deep sequencing was performed on 172 participants (>100,000 gag-Δpol and rev-env-Δnef sequences), at diagnosis and over time, in the placebo and treatment arms of the African (HVTN703/HPTN081; NCT02568215) and Americas/Europe (HVTN704/HPTN085; NCT02716675) cohorts. A high frequency of multilineage infections was detected (38%), including co-infection with both VRC01 sensitive and resistant viruses. This high frequency is largely accounted for by low-abundance lineages. Although VRC01 does not significantly affect the genetic transmission bottleneck compared to placebo, higher VRC01 doses trend towards greater VRC01 neutralization differences among co-infecting lineages. Two-thirds of multilineage infections showed evidence of recombination at the diagnostic timepoint. In the treatment group there is evidence of recombinant viruses preferentially inheriting resistance-associated mutations. This study provides critical insights into viral genetic and antigenic diversity that needs to be targeted to achieve protection, and highlights the role of recombination in facilitating escape.

Few studies have characterized immune correlates of SARS-CoV-2 infection risk in children, particularly those with hybrid immunity from vaccination and prior infection. We conduct a prospective community-based cohort study of 1509 U.S. children (2022-2024), performing weekly SARS-CoV-2 PCR testing and measuring baseline binding and neutralizing antibody titers against multiple variants. Higher antibody levels, notably nucleocapsid-binding and Omicron-specific neutralizing antibodies, are significantly associated with reduced risk of SARS-CoV-2 infection after adjusting for age, recent infection, exposure settings, and temporal trends (adjusted hazard ratios ranging from 0.60 to 0.87 per positive unit difference in log10-fold antibody level (AU/mL)). Secondary analyses suggest these findings are robust to multiple stratifications of SARS-CoV-2 immune status, are relevant across different pediatric age groups, and appear to apply to both overall and symptomatic infection risk. Together, the results suggest that specific antibodies can predict relative infection risk in pediatric populations with diverse immune histories. Understanding these immune correlates may inform tailored vaccination strategies and risk assessments as SARS-CoV-2 continues to evolve.

The first workshop dedicated to Lassa virus–specific correlates of protection (CoP) was held in 2024 and was convened by the Coalition for Epidemic Preparedness Innovations (CEPI). Experts from multiple disciplines reviewed existing knowledge and identified gaps in understanding Lassa virus- and vaccine-induced immune responses. Discussions covered key areas including epidemiology, immunogenicity, preclinical and clinical research, data science, and regulatory considerations, with the goal of pinpointing opportunities to discover CoP.

BACKGROUND:We previously showed that ancestral-specific anti-Spike binding IgG concentration and 50% inhibitory dilution neutralizing antibody titer (nAb-ID50) measured at 2 weeks postdose 2 (∼peak) were inverse correlates of risk (CoRs) of COVID-19 over 2 months post ∼peak in the PREVENT-19 trial of the NVX-CoV2373 vaccine; there were not sufficient data to assess CoRs of severe COVID-19. METHODS:Here, we assessed, in the same vaccinated cohort, Delta- and ancestral-specific Spike IgG and nAb-ID50 at ∼peak and over time as CoRs of severe COVID-19 and of Delta COVID-19 over 3.5-10 months post ∼peak (287 breakthrough Delta cases, including 8 severe; 446 noncases). RESULTS:Peak antibody levels were much higher for noncases versus severe cases (all inferred Delta), with nAb-ID50 Delta geometric mean 209.5 arbitrary units (AU)/mL (95% CI: 176.1, 249.1) versus 9.6 AU/mL (95% CI: 2.4, 38.6), respectively. Frequency of detectable nAb-ID50 titer was 98.3% (97.2, 99.0) for noncases versus 62.5% (22.3, 93.9) for severe cases. All markers were inverse CoRs of severe COVID-19, with a ∼peak hazard ratio (HR) of 0.13 (95% CI: .03, .57) per 10-fold nAb-ID50 Delta increase. Severe COVID-19 risk through 305 days postday 35 was 0.0338 (0.0043, 0.206) at the nAb-ID50 Delta 2.5th percentile (8.4 AU/mL), and 0.002 (0.0000, 0.0108) and 0.0002 (0.0000, 0.0035) at the 50th and 95th percentiles (210, 2522 AU/mL). CONCLUSIONS:Postvaccination NVX-CoV2373 antibody levels are stronger predictors of severe COVID-19 than any-severity Delta COVID-19. Low antibody responses indicate vulnerability to severe COVID-19.

The test-negative design (TND) is a resource-efficient observational study design that can assess vaccine effectiveness and exposure-proximal immune correlates of disease. The TND enrolls symptomatic individuals seeking diagnostic testing and compares case status by an exposure variable, such as vaccination status or immune marker level, that is measured at testing. While the TND reduces confounding by healthcare-seeking behavior, other sources of confounding may remain. TND studies may also have missing data in the exposure variable due to incomplete records or two-phase sampling designs. We present a targeted maximum likelihood estimation approach involving a semiparametric logistic regression model that targets a causal conditional risk ratio of symptomatic disease in the healthcare-seeking population. Under causal and missing at random assumptions, our method produces an efficient, asymptotically linear estimator that provides flexible, data-driven confounding control and valid causal inference when analyzing TND studies with missing exposure variable data. We evaluate our method's finite sample properties using plasmode simulations of a two-phase TND immune correlates study. We also apply our method to assess COVID-19 vaccine effectiveness and antibody marker correlates of COVID-19 from TND study cohorts derived from the Moderna Coronavirus Efficacy phase 3 trial.

The association between vaccine efficacy (VE) and force of infection (FoI) remains incompletely understood. Previous analyses have been primarily based on trial-level summary data—not accounting for the effect of time and constrained by the number of trials. Here, we leverage individual-level data from three phase 3 randomized, placebo-controlled COVID-19 vaccine trials—the COVE trial (Moderna, CoVPN3001), the AZD1222 trial (AstraZeneca, CoVPN3002), and the ENSEMBLE trial (Janssen/Johnson & Johnson, CoVPN3003)—and contemporaneous geographic-location-specific SARS-CoV-2 surveillance data from the start of the pandemic through November 14, 2021 (including the blinded follow-up periods of the trials) to conduct five cohort- and vaccine-specific analyses: COVE (U.S.), AZD1222 overall (U.S. + non-U.S.), AZD1222 U.S., ENSEMBLE overall (U.S. + non-U.S.), and ENSEMBLE U.S. In AZD1222 U.S., higher VE was associated with higher FoI (p = 0.01). In ENSEMBLE overall, lower VE was marginally associated with higher FoI (p = 0.21), further supported by a region-specific analysis. In COVE, AZD1222 overall, and ENSEMBLE U.S., no VE-FoI association was found. These findings highlighted a new perspective: the VE–FoI association appears complex, potentially influenced by FoI levels, with patterns suggesting an inverted U-shaped relationship, showing a positive association at low FoI levels and a negative association at high levels.

Causal mediation analysis provides techniques for defining and estimating effects that may be endowed with mechanistic interpretations. With many scientific investigations seeking to address mechanistic questions, causal direct and indirect effects have garnered much attention. The natural direct and indirect effects, the most widely used among such causal mediation estimands, are limited in their practical utility due to stringent identification requirements. Accordingly, considerable effort has been invested in developing alternative direct and indirect effect decompositions with relaxed identification requirements. Such efforts often yield effect definitions with nuanced and challenging interpretations. By contrast, relatively limited attention has been paid to relaxing the identification assumptions of the natural direct and indirect effects. Motivated by a secondary aim of a recent non-randomized vaccine prospective cohort study (NCT05168813), we present a set of relaxed conditions under which the natural direct effect is identifiable in spite of unobserved baseline confounding of the exposure-mediator pathway; we use this result to investigate the effect mediated by putative immune correlates of protection. Relaxing the commonly used but restrictive cross-world counterfactual independence assumption, we discuss strategies for evaluating the natural direct effect in non-randomized settings that arise in the analysis of vaccine studies. We revisit prior studies of semi-parametric efficiency theory to demonstrate the construction of flexible, multiply robust estimators of the natural direct effect and discuss efficient estimation strategies that do not place restrictive modeling assumptions on nuisance functions.

In the Coronavirus Variant Immunologic Landscape Trial (COVAIL) conducted in the United States in 2022-2023, 985 participants received a second COVID-19 booster with one of twelve monovalent or bivalent mRNA inserts. Pseudovirus serum inhibitory dilution 50% neutralizing antibody titer (nAb titer) measured two-weeks post booster significantly associated with lower COVID-19 incidence over six months follow-up in this trial. COVAIL investigators sequenced SARS-CoV-2 Spike amino acid sequences for all COVID-19 cases, with a sequence successfully obtained from 129 of 195 cases. For COVID-19 endpoint cases we calculated five distances of the case-causing sequence to a reference sequence, the first two physico-chemical weighted Hamming distances of Spike or receptor binding domain (RBD) to a participant's nearest Spike or RBD vaccine-insert sequence, and the other three estimated degrees of neutralizing antibody escape from the XBB.1.5 RBD strain calculated with deep mutational scanning. Hypothesizing that the nAb titer correlate of risk may have a stronger association with COVID-19 when focusing on COVID-19 infections more closely matched to the vaccine insert in Spike or RBD amino acid sequence or with lower RBD antibody escape score, we tested this hypothesis for the combined group receiving a monovalent Prototype (ancestral strain) booster (n = 143) and for the combined group receiving an Omicron-containing booster (n = 744). For both combined groups, the nAb titer correlate of risk did not significantly vary across any of the assessed sequence distances from the vaccine insert (all p-values >0.10), although RBD Hamming distance had point estimates consistent with a weakening correlate with distance, motivating further exploration in settings with greater antigenic heterogeneity. Indeed, statistical power was bounded by the limited antigenic variability of viruses infecting trial participants over the follow-up period (April 21, 2022 to May 25, 2023), which spanned only a 3.02-fold nAb titer range of differential sensitivity to sera from XBB.1.5-infected individuals. ClinicalTrials.gov Identifier: NCT05289037.

Background The COVID-19 Prevention Network (CoVPN) co-conducted six COVID-19 phase 3 vaccine efficacy (VE) trials that featured harmonized immunogenicity analyses using validated antibody assays. These trials enabled a uniquely comprehensive characterization of immunogenicity produced by different vaccine platforms and regimens in individuals with and without prior SARS-CoV-2 acquisition. Methods Comparisons of serum binding antibody concentration and serum neutralization antibody ID50 titers were performed across three strata: vaccine immunity (vaccination in SARS-CoV-2-naïve individuals), natural immunity (placebo with prior SARS-CoV-2 acquisition), and hybrid immunity (vaccination after prior SARS-CoV-2 acquisition). We compared immunogenicity across immunity strata for each trial and each dose, adjusting for age, sex assigned at birth, and body mass index. Antibody levels were also examined in relation to VE. Results Antibody levels in response to a single vaccine dose varied across trials and generally increased most substantially after a second dose in naïve participants. Fold rise in antibody levels after a single dose were more pronounced in participants with hybrid immunity: a single dose of any of the tested vaccine yielded responses comparable to or exceeding the post-dose-two (peak) response of any two-dose vaccine in naïve participants. Population-level antibody levels demonstrated high concordance with VE across trials and immunity strata. Conclusions In SARS-CoV-2-naïve individuals, a two-dose vaccine regimen is needed to provide antibody levels correlated with protection against disease caused by the cognate virus strain. In contrast, in individuals with prior SARS-CoV-2 acquisition, a single dose of any of the tested vaccines/platforms (mRNA/protein/vector) provides comparably high antibody levels.

Refined vaccine regimens containing variant-matched inserts are often authorized based on historical phase 3 efficacy trials together with immunobridging studies. Phase 3 trials are essential for establishing immune biomarkers that reliably predict disease risk or vaccine efficacy against clinical endpoints. Once such immune correlates are identified, updated vaccine regimens can be approved through immunobridging designs that compare the immunogenicity of the updated regimen to that of an already-approved vaccine. We develop methods of inference for the counterfactual cumulative incidence curve using participant-level data from both a historical vaccine efficacy trial and an immunobridging study. We further extend these methods to pathogens with multiple serotypes – such as dengue virus and influenza – by estimating cause-specific cumulative incidence curves. We describe the identification assumptions, propose efficient and multiply robust estimators, and assess their finite-sample performance through simulation studies. We then apply the proposed methods to (1) estimating the hypothetical cumulative incidence curve for a bivalent mRNA booster and (2) testing a key assumption of no controlled direct effects, using data from the COVID-19 Variant Immunologic Landscape (COVAIL) Trial, a multistage randomized clinical study evaluating the safety and immunogenicity of a second COVID-19 booster dose.

In the phase 3 AZD1222 COVID-19 vaccine trial, anti-Spike (vaccine-matched and Delta) binding IgG antibody concentration and neutralizing antibody (nAb) titer (vaccine-matched+D614G and Delta), measured four weeks post-dose two (D57), were assessed as correlates of risk of severe COVID-19 and Delta COVID-19 over ~4 to ~13 months (severe) or ~11 months (Delta) post-D57. Using a case-control design, antibodies were measured in baseline SARS-CoV-2-negative per-protocol ChAdOx1 nCoV-19 recipients (19 severe COVID-19 cases, 57 Delta COVID-19 cases, 111 controls). The hazard ratio (HR) of severe COVID-19 per 10-fold vaccine-matched D57 marker increase was 0.16 (95% CI: 0.05, 0.54; p = 0.004) for Spike IgG and 0.13 (0.03, 0.59; p = 0.009) for nAb titer. D57 Delta antibodies were weak correlates of Delta COVID-19: HR per 10-fold increase 0.70 (0.14, 3.47; p = 0.66) for Delta Spike IgG; 0.46 (0.14, 1.47; p = 0.19) for Delta nAb titer. Binding and nAb levels strongly predicted severe COVID-19, even with antibody waning.

Negative control outcomes (NCOs) are useful tools for hidden bias detection, but empirical evidence validating NCOs for COVID-19 is lacking. To address this gap, we examined the blinded phase of the randomized, placebo-controlled Coronavirus Vaccine Efficacy (COVE; NCT04470427) trial of the mRNA-1273 COVID-19 vaccine. We confirmed that acute respiratory illness with a positive test for a non-SARS-CoV-2 respiratory pathogen on a multiplex PCR panel was a valid NCO for COVID-19, considering that it was unaffected by vaccination (vaccine efficacy, VE = 3.3% (95% CI, -22.3 to 23.6)) yet strongly associated with COVID-19 (odds ratio = 2.95 (95% CI, 2.00, 4.24)). Subsequently, we leveraged non-SARS-CoV-2 infections to detect bias in time-varying VE estimates from COVE's blinded and booster phases. Balanced incidence of non-SARS-CoV-2 infection between vaccinated and unvaccinated COVID-19-free risk sets suggested low selection bias in VE estimates of two-dose mRNA-1273 against COVID-19 during the blinded phase (VE = 92.5% (95% CI, 88.8, 94.9) 14 days post-dose-two, stable for 5 months). In COVE's booster phase, higher non-SARS-CoV-2 incidence was observed after the single booster (intensity ratio, IR = 2.38 (95% CI, 1.75, 3.25) 14 days post-boost), suggesting that booster VE estimates may underestimate the true VE against COVID-19. Our findings demonstrate the potential of off-target infections for unraveling complex biases in COVID-19 vaccine studies. Trial registration: NCT04470427, https://clinicaltrials.gov/study/NCT04470427.

Traditional vaccine clinical trials sample blood from all participants. In contrast, the test-negative immune correlates (TNIC) design only samples blood from participants who develop symptoms. We compared traditional to test-negative immune correlates methods in the mRNA-1273 severe acute respiratory syndrome coronavirus 2 vaccine efficacy clinical trial. Using a neutralizing antibody assay, hazard ratios were 0.48 (95% confidence interval [CI], .29–.73) and 0.55 (95% CI, .28–1.06) for traditional and test-negative methods, respectively. Analogous ratios for binding antibody assay were 0.69 (95% CI, .52–.94) and 0.78 (95% CI, .50–1.20). The results support use of the logistically simpler TNIC design.

BACKGROUND:HIV-1 T cell responses are associated with viral control and may be protective in a prophylactic vaccination setting. Traditional methods for analysing these responses might be biased towards specific functionalities or epitopes. This study presents an unsupervised and unbiased clustering analysis workflow, using the Leiden algorithm followed by selection of antigen-specific clusters using MIMOSA positivity calls, for high-dimensional flow cytometry data to identify distinct T cell populations associated with protection in the HVTN 705/HPX2008/Imbokodo HIV-1 vaccine efficacy trial. METHODS:Participants were vaccinated with Ad26.Mos4.HIV (M0, M3) and Ad26.Mos4.HIV + Clade C gp140 (M6, M12), and a validated 28-colour intracellular cytokine staining assay was performed on PBMC isolated at M7, M13 and M24 in a pilot immunogenicity (n = 60) and case-control cohort (n = 283). 28-colour phenotyping assays were also performed on PBMC from the case-control cohort (n = 334). FINDINGS:Our clustering analysis workflow allowed identification of vaccine-induced subpopulations of both CD4+ and CD8+ T cells expressing combinations of the 28 markers. Durable HIV-1 antigen-specific CD4+ and CD8+ T cell responses were observed for up to 2 years, comprising mainly clusters of polyfunctional T cells expressing anti-viral cytokines and activation markers. Eight CD4+ and six CD8+ HIV-1 antigen-specific T cell clusters were induced by vaccination; only one CD4+ T cell cluster specific for Gag was mildly elevated in cases (acquiring HIV) compared to controls. INTERPRETATION:Our study introduces an innovative analysis approach to identify vaccine-induced T cell subpopulations in vaccine trials. Comparison of T cell clusters between cases and controls holds promise for improving the efficacy of future HIV-1 vaccination strategies. FUNDING:This work was funded by the National Institute of Allergy and Infectious Diseases (NIAID) and the Division of AIDS (DAIDS), both of the US National Institutes of Health (NIH) [NIAID grants to the HIV Vaccine Trials Network (HVTN) (Fred Hutchinson Cancer Center): UM1AI068618 (HVTN LC to M.J.M.) and UM1AI068635 (HVTN SDMC to P.B.G.)] and by Janssen Vaccines & Prevention B.V. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health or Janssen.

Administration of HIV-1 neutralizing antibodies can suppress viremia and prevent infection in vivo. However, clinical use is challenged by broad envelope sequence diversity and rapid emergence of viral escape1-9. Here, we performed single B cell profiling of 32 top HIV-1 elite neutralizers to identify broadly neutralizing antibodies (bNAbs) with highest potency and breadth for clinical application. From 831 expressed monoclonal antibodies, we identified 04_A06, a new VH1-2-encoded CD4 binding site bNAb with remarkable breadth and potency against extended multiclade pseudovirus panels (GeoMean IC50 = 0.059 μg/ml, breadth = 98.5%, 332 virus strains). Moreover, 04_A06 was not susceptible to classic viral CD4bs escape variants and maintained full viral suppression in HIV-1-infected humanized mice. Structural analyses revealed that antiviral activity is mediated by an unusually long 11-amino acid heavy chain insertion. This insertion facilitates inter-protomer contacts and interactions with highly conserved residues on the adjacent gp120 protomer. Finally, 04_A06 demonstrated high activity against contemporaneously circulating viruses from the Antibody Mediated Prevention (AMP) trials (GeoMean IC50 = 0.082 μg/ml, breadth = 98.4%, 191 virus strains) and in silico modeling for 04_A06LS predicted HIV-1 prevention efficacy of >93%. Thus, 04_A06 will provide unique opportunities for effective treatment and prevention strategies of HIV-1 infection.

It is often of interest to study the association between covariates and the cumulative incidence of a right-censored time-to-event outcome. When time-varying covariates are measured on a fixed discrete time scale, it is desirable to account for these more up-to-date covariates when addressing censoring. For example, in vaccine trials, it is of interest to study the association between immune response levels after administering the vaccine and the cumulative incidence of the endpoint, while accounting for loss to follow-up explained by immune response levels measured at multiple post-vaccination visits. Existing methods rely on stringent parametric assumptions, do not account for informative censoring due to time-varying covariates when time is continuous, only estimate a marginal survival probability, or do not fully use the discrete-time structure of post-treatment covariates. We propose a nonparametric estimator of the continuous-time survival probability conditional on covariates, accounting for censoring due to time-varying covariates measured on a fixed discrete time scale. We show that the estimator is sequentially doubly robust: it is consistent if, within each time window between adjacent visits, the censoring distribution is consistently estimated, or both the time-to-event distribution and a conditional mean probability are consistently estimated. We also show that, in the special case of estimating the marginal survival probability, our estimator is asymptotically efficient. We demonstrate the superior performance of our estimator in a simulation experiment, and apply the method to a COVID-19 vaccine efficacy trial.

The Antibody Mediated Prevention (AMP) trials showed that passively infused VRC01, a broadly neutralizing antibody (bNAb) targeting the CD4 binding site (CD4bs) on the HIV-1 envelope protein (Env), protected against neutralization-sensitive viruses. We identified six individuals from the VRC01 treatment arm with multi-lineage breakthrough HIV-1 infections from HVTN703, where one variant was sensitive to VRC01 (IC50 < 25 ug/mL) but another was resistant. By comparing Env sequences of resistant and sensitive clones from each participant, we identified sites predicted to affect VRC01 neutralization and assessed the effect of their reversion in the VRC01-resistant clone on neutralization sensitivity. In four pairs, a single mutation restored partial or full sensitivity to VRC01, whereas in the fifth participant, transfer of the entire [Formula: see text]23-V5 loop was required. No VRC01 resistance mutations could be identified in the sixth participant, with the discordant clones differing by >100 amino acids. Mutations responsible for the differential neutralization phenotypes occurred at distinct sites across Env, including residues in loop D, the CD4-binding loop, and between the [Formula: see text]23 and V5 loops. Analysis of deep sequencing env data showed that VRC01 resistance was likely the property of the acquired virus, rather than occurring through post-acquisition evolution. Although VRC01-resistant parental clones generally retained sensitivity to other CD4-binding site bNAbs, they were less potently neutralized than the VRC01-sensitive clones. In conclusion, VRC01 resistance mutations occurred through multiple mutational pathways, but sensitivity to second-generation CD4bs bNAbs was retained even in VRC01-resistant transmitted viruses, confirming the potential of these bNAbs for HIV-1 prevention studies.IMPORTANCEThe Antibody Mediated Prevention (AMP) trials provided proof of principle that VRC01, a CD4-binding site (CD4bs) HIV-1 broadly neutralizing antibody (bNAb), prevented the acquisition of antibody-sensitive viruses. However, understanding common mutations that confer resistance to different bNAbs provides important insights into the genetic barrier to resistance. Here we studied six AMP trial participants with breakthrough infections mediated by multiple viral lineages with discordant VRC01 sensitivity. We identified different mutations across the CD4-binding site that conferred resistance to VRC01 and showed that these mutations were a property of the acquired virus, rather than a result of post-acquisition evolution. We found that although VRC01 resistance was associated with reduced neutralization potency of second-generation CD4-binding site bNAbs, overall neutralization sensitivity was generally retained, which is promising for future use of such bNAbs in clinical trials.

Abstract Background Vaccines are widely recognized as one of the most effective health interventions in the world. The development of novel vaccines against the world’s deadliest diseases is a global health priority. Large, randomized clinical trials are the main mechanism used to determine the efficacy of a vaccine prior to licensure. These trials are expensive and resource intensive. Given the public health importance of these trials, understanding how often they succeed vs. fail and which pathogens they are targeting is paramount to global vaccine programs. Vaccine efficacy estimates for large vaccine clinical trials against novel pathogens Vaccine efficacy Definitions: highly efficacious (lower bound vaccine efficacy 95% confidence interval ≥65%), moderately efficacious (lower bound vaccine efficacy 95% confidence interval 10-65%), possibly efficacious: lower bound of any of the 95% confidence intervals were 0-10%, and not efficacious: lower bound of any of the 95% confidence intervals were <0. Abbreviations: Enterovirus 71 (EV71), Human Papilloma Virus (HPV), Respiratory Syncytial Virus (RSV), Cytomegalovirus (CMV), Human Immunodeficiency Virus (HIV), and Herpes Simplex Virus (HSV). Methods We searched Pubmed and the International Clinical Trials Registry Platform and identified large (≥ 1000 participants), randomized, vaccine efficacy trials completed between 1995-2019 against infectious disease pathogens for which no efficacious vaccine previously existed. Summary of characteristics of large vaccine efficacy trials: Distribution by journal of publication, funding source, and pathogen Results Using the search criteria above, 3483 unique trials were identified in the International Clinical Trials Registry Platform (ICTRP) and 1867 unique citations were identified through Pubmed for a total of 5350 unique entries. During the study period, 43 trials were identified which evaluated vaccines against 18 novel pathogens. Highly efficacious vaccines were developed against EV71, Hepatitis E, and HPV (Figure 1). Moderately efficacious vaccines were developed against Dengue, H. pylori, Malaria, and RSV. A possibly efficacious vaccine was developed against Tuberculosis. Vaccine candidates against ten other novel pathogens failed: C. difficile, CMV, E. coli, HIV, HSV, Leishmania, Norovirus, Shigella, Staph aureus, and Zika. We summarized trial characteristics by journal of publication, funding type, and pathogen (Figure 2). We also performed an exploratory analysis to investigate which studies might have been underpowered and found that the trials for vaccine candidates against Norovirus and Zikavirus were possibly underpowered (Figure 3). Exploratory sub-analysis conducted to identify trials that were possibly underpowered Panel A: Trials in the upper left quadrant represent trials with high efficacy but a significantly lower than expected incidence (compared to the pre-trial estimated incidence that was used to determine the sample size needed to have sufficient power to prove efficacy). Panel B: Vaccine trials are sorted by efficacy estimate, demonstrating that there were some trials that had a high efficacy estimate but wide confidence intervals which might indicate underpowering. Conclusion The past quarter century has seen both major successes in new vaccine development and failures. The HPV vaccine has been deployed around the world and is expected to save millions of lives. The malaria vaccine became the first effective vaccine licensed against a parasite. However, many promising candidates failed. Continued efforts to predict efficacy prior to large efficacy trials are needed. Disclosures Lawrence Corey, MD, NA: HSV Antigens|The Vaccine Company: Ownership Interest|Vir Biotechnology: Ownership Interest Peter B. Gilbert, PhD, Sanofi: Advisor/Consultant|Sanofi: Dengue Vaccine research contracts