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A key objective in vaccine studies is to evaluate vaccine-induced immunogenicity and determine whether participants have mounted a response to the vaccine. Cellular immune responses are essential for assessing vaccine-induced immunogenicity, and single-cell assays, such as intracellular cytokine staining (ICS) and B-cell phenotyping (BCP), are commonly employed to profile individual immune cell phenotypes and the cytokines they produce after stimulation. In this article, we introduce a novel statistical framework for identifying vaccine responders using ICS data collected before and after vaccination. This framework incorporates paired control data to account for potential unintended variations between assay runs, such as batch effects, that could lead to misclassification of participants as vaccine responders or non-responders. To formally integrate paired control data for accounting for assay variation across different time points (ie before and after vaccination), our proposed framework calculates and reports two values, both adjusting for paired control data but in distinct ways: (i) the maximally adjusted value, which applies the most conservative adjustment to the unadjusted value, ensuring validity over all plausible batch effects consistent with the paired control samples’ data, and (ii) the minimally adjusted value, which imposes only the minimal adjustment to the unadjusted value, such that the adjusted value cannot be falsified by the paired control samples’ data. Minimally and maximally adjusted values offer a balanced approach to managing Type I error rates and statistical power in the presence of batch effects. We apply this framework to analyze ICS data collected at baseline and 4 wks post-vaccination from the COVID-19 Prevention Network (CoVPN) 3008 study. Our analysis helps address two clinical questions: (i) which participants exhibited evidence of an incident Omicron infection between baseline and 4 wks after receiving the final dose of the primary vaccination series, and (ii) which participants showed vaccine-induced T cell responses against the Omicron BA.4/5 Spike protein.

In this cohort study of 1.26 million patients who underwent isolated CABG, intraoperative TEE was associated with survival benefits at low and medium surgical volume hospitals, particularly among patients with greater than 50% left-main coronary stenosis, 3 or more diseased vessels, or preoperative inotrope use. No survival benefit was observed at high surgical volume hospitals.These findings support a more individualized approach to TEE use during isolated CABG surgery and provide a rationale for future randomized evaluation.

In febrile comatose patients living in malaria-endemic areas, overlapping symptoms and limited laboratory capacity make it difficult to distinguish parasitic, bacterial, and viral central nervous system infections. We evaluated electroencephalography (EEG) as a biomarker to differentiate the microbiologic etiology of pediatric febrile coma at a major referral center in Malawi.This was a retrospective case-control study comparing EEG recordings of Malawian children with cerebral malaria to those with febrile coma of nonmalarial cause (bacterial meningitis, viral encephalitis, or unknown cause). Participants were admitted to Queen Elizabeth Central Hospital (Blantyre, Malawi) between 2013 and 2021. Inclusion criteria were fever, coma (Blantyre Coma Score ≤2), and coma etiology (malarial or nonmalarial) defined by laboratory testing. Four supervised machine learning algorithms were used to train a balanced ensemble classifier, SuperLearner, generating test characteristics of the diagnostic ability of EEG features.Two hundred three children with cerebral malaria and 87 children with nonmalarial coma were included. Univariate analysis of qualitative (visual) EEG interpretations revealed higher voltage, slower background frequency, more sleep elements, less variability, more abnormal organization, and less continuity in cerebral malaria. Quantitative waveform analysis showed greater power in cerebral malaria. Both quantitative and qualitative EEG interpretation distinguished coma etiology (area under the receiver operating characteristic curve [AUROC] = 0.85 and 0.86, respectively). Combining qualitative and quantitative interpretation methods, the test characteristic improved (AUROC = 0.90).EEG features distinguish malarial from nonmalarial coma in febrile Malawian children. This technology may aid in distinguishing the microbiologic etiology of febrile coma in malaria-endemic areas.

People with HIV (PWH) are understudied in COVID-19 vaccine trials, leaving knowledge gaps on whether the identified immune correlates of protection also hold in PWH. CoVPN 3008 (NCT05168813) enrolled predominantly PWH and reported lower COVID-19 incidence for a Hybrid vs. Vaccine Group (baseline SARS-CoV-2-positive and one mRNA-1273 dose vs. negative and two doses). Using case-cohort sampling, antibody markers at enrolment (M0) and four weeks post-final vaccination (Peak) are assessed as immune correlates of COVID-19. For the Hybrid Group [n = 287 (195 PWH)], all M0 markers inversely correlate with COVID-19 through 230 days post-Peak, with 50% inhibitory dilution BA.4/5 neutralizing antibody titer (nAb-ID50 BA.4/5) the strongest and only independent correlate (HR per 10-fold increase=0.46, 95% CI 0.28, 0.75; P = 0.002). For the Vaccine Group [n = 115 (86 PWH)], Peak nAb-ID50 BA.4/5 correlates with reduced COVID-19 risk (1.9%, 1.1%, and 0.3% at titers 10, 100, and 1000 AU/ml) through 92, but not 165, days post-Peak. Using multivariable Cox analysis of binding and nAb, nAb titers predict COVID-19 in PWH. Two doses of a 100-µg Ancestral strain mRNA vaccine in baseline-SARS-CoV-2-negative individuals elicit sufficient cross-reacting Omicron antibodies to reduce COVID-19 incidence for 90 days post-Peak, but viral evolution and waning antibodies abrogate this protection thereafter.

Covid-19 vaccines are updated to match circulating strains based on reasoning that better strain-matched immunogenicity should provide better protection. Randomized evidence with disease endpoints to support strain matching is lacking. We evaluated COVID-19 incidence among adults randomized to a second booster of Prototype or Omicron-based vaccines. COVAIL was a four-stage Phase 2 clinical trial; results from Stages 1 (mRNA-1273 [Moderna]) and 2 (BNT162b2 [Pfizer/BioNTech]) are described here. Adults who had received a primary series and one booster of an authorized COVID-19 vaccine were eligible. Participants received one dose of either Prototype vaccine or a monovalent or bivalent Omicron BA.1 vaccine. SARS-CoV-2 neutralization titers (ID50) were measured pre- and post-vaccination. Covariate-adjusted cumulative COVID-19 incidence and Cox regression analyses were conducted separately for each stage. 706 participants with pre- and day 15 post-vaccination ID50 titers (n = 503 in Stage 1, n = 203 in Stage 2) were included. Within stages, participant characteristics and baseline ID50 titers were similar between Prototype and Omicron-based arms. There was no difference in cumulative COVID-19 incidence for Prototype vs. Omicron-based vaccine in Stage 1 (RR 1.04, 95 % CI 0.73–1.48), while incidence was higher among Prototype recipients in Stage 2 (RR 2.56, 1.44–4.52). Cox regression analysis showed no difference in Stage 1 (HR 1.04, 0.68–1.58), but higher incidence for Prototype recipients in Stage 2 (HR 2.95, 1.52–5.72). Omicron-based vaccines as second boosters were more protective against COVID-19 relative to Prototype among those receiving BNT162b2 but not mRNA-1273. Differences between stages such as force of infection, antigen matching, and vaccine differences may explain this finding.

We investigated the expression and distribution of 5 cytoadhesion receptors for the Plasmodium falciparum erythrocyte membrane protein 1 in 12 regions of post-mortem brains of 50 Malawian children, that is, 27 with the clinical and pathological diagnosis of cerebral malaria (CM) and 23 with a non-malarial cause of death. We quantified the expression of each receptor by microvascular endothelium and the colocalization of receptor-expressing microvessels with sequestered infected red blood cells (iRBC) and calculated a receptor-independent sequestration ratio. There were differences in the level of expression and regional distribution of the five receptors: ICAM-1 was the most widely expressed receptor, followed by CD36, VCAM-1, E-selectin, and thrombospondin. Receptor-expressing microvessels were most numerous in the frontal lobe and least numerous in the brainstem and cerebellum. Colocalization of receptor-expressing endothelial cells with iRBC was present in all brain regions; it was highest for ICAM-1 and CD36 and greatest in the frontal lobe. The sequestration ratios were close to 100% for all receptors across all brain regions and were similar in cerebral and extracerebral microvessels. Receptor expression and colocalization ratios were greater in the brain than in the lung, heart, liver, spleen, and subcutaneous tissue. These differences in cerebral endothelial expression of cytoadhesion receptors and their preferential regional distribution may underpin differences in iRBC sequestration and lesion development in CM. Moreover, greater expression of these receptors in the brain vs peripheral organs may explain a comparatively greater degree of iRBC sequestration in the brain.

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.

HIV vaccine trial participants include sexually active cisgender females who agree to avoid pregnancy during the active vaccination period. Nevertheless, some pregnancies occur in almost all studies. We examined contraceptive use, pregnancy incidence, and the relationship between pregnancy and HIV seroconversion in one HIV vaccine trial. We performed an exploratory analysis of data collected for HVTN 705/HPX2008, a phase IIb HIV vaccine trial enrolling cisgender women across 23 sites in five southern African countries. Baseline characteristics and contraceptive use were assessed among participants who became pregnant and those who did not during the active vaccination phase (months 0–15). Pregnancy incidence rates were calculated for this phase and the duration of follow up (36 months). Cox regression analysis was used to assess factors associated with incident pregnancy. There were 2,636 participants who received at least one vaccine or placebo dose (mean age: 23 years, standard deviation: 3 years). At enrolment, when contraception was required, 62.9% reported using injectable contraceptives. Overall pregnancy rate was 2.95 per 100 person-years (95% CI: 2.40, 3.58), with 101 pregnancies reported by month 15. Cumulative incidence of pregnancy at month 15 was similar between trial arms (log-rank p = 0.688). Each additional year of age was associated with an 8% decrease in pregnancy incidence (p = 0.014). Women aged 31–35 years had the lowest pregnancy incidence [1.75 (0.48, 4.48) per 100 person-years]. In a Cox regression analysis covering months 0–15, all contraceptive methods significantly reduced the incidence of pregnancy compared to no contraceptive use. Oral contraception was associated with the least reduction in pregnancy risk; implants were associated with the most reduction in pregnancy risk (p < 0.001).In HVTN 705/HPX2008, higher incidence of pregnancy was associated with younger age and oral contraception (compared to other methods). These data may inform future designs of HIV prevention or vaccine trials.

Adjustment for prognostic baseline variables can reduce bias due to covariate imbalance and increase efficiency in randomized trials. While the use of covariate adjustment in late-phase trials is justified by favorable large-sample properties, it is seldom used in small, early-phase studies, due to uncertainty in which variables are prognostic and the potential for precision loss, type I error rate inflation, and undercoverage of confidence intervals. To address this problem, we consider adjustment for a valid negative control outcome (NCO), or an auxiliary post-randomization outcome believed to be completely unaffected by treatment but more highly correlated with the primary outcome than baseline covariates. We articulate the assumptions that permit adjustment for NCOs without producing post-randomization selection bias, and describe plausible data-generating models where NCO adjustment can improve upon adjustment for baseline covariates alone. In numerical experiments, we illustrate performance and provide practical recommendations regarding model selection and finite-sample variance corrections. We apply our methods to the reanalysis of two early-phase vaccine trials in HIV exposed uninfected (HEU) infants, where we demonstrate that adjustment for auxiliary post-baseline immunological parameters can enhance the precision of vaccine effect estimates relative to standard approaches that avoid adjustment or adjust for baseline covariates alone.