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In the CYD14 trial of the CYD-TDV dengue vaccine in 2-14 year-olds, neutralizing antibody (nAb) titers to the vaccine-insert dengue strains correlated inversely with symptomatic, virologically-confirmed dengue (VCD). Also, vaccine efficacy against VCD was higher against dengue prM/E amino acid sequences closer to the vaccine inserts. We integrated the nAb and sequence data types by assessing nAb titers as a correlate of sequence-specific VCD separately in the vaccine arm and in the placebo arm. In both vaccine and placebo recipients the correlation of nAb titer with sequence-specific VCD was stronger for dengue nAb contact site sequences closer to the vaccine (p = 0.005 and p = 0.012, respectively). The risk of VCD in vaccine (placebo) recipients was 6.7- (1.80)-fold lower at the 90th vs 10th percentile of nAb for viruses perfectly matched to CYD-TDV, compared to 2.1- (0.78)-fold lower at the 90th vs 10th percentile for viruses with five amino acid mismatches. The evidence for a stronger sequence-distance dependent correlate of risk for the vaccine arm indicates departure from the Prentice criteria for a valid sequence-distance specific surrogate endpoint and suggests that the nAb marker may affect dengue risk differently depending on whether nAbs arise from infection or also by vaccination. However, when restricting to baseline-seropositive 9-14 year-olds, the correlation pattern became more similar between the vaccine and placebo arms, supporting nAb titers as an approximate surrogate endpoint in this population. No sequence-specific nAb titer correlates of VCD were seen in baseline-seronegative participants. Integrated immune response/pathogen sequence data correlates analyses could help increase knowledge of correlates of risk and surrogate endpoints for other vaccines against genetically diverse pathogens. Trial registration: EU Clinical Trials Register 2014-001708-24; registration date 2014-05-26.

The recombinant, live, attenuated, tetravalent dengue vaccine CYD-TDV has shown efficacy against all four dengue serotypes. In this exploratory study (CYD59, NCT02827162), we evaluated potential associations of host human leukocyte antigen (HLA) alleles with dengue antibody responses, CYD-TDV vaccine efficacy, and virologically-confirmed dengue (VCD) cases. Children 4-11 years old, who previously completed a phase 2b efficacy study of CYD-TDV in a single center in Thailand, were included in the study. Genotyping of HLA class I and II loci was performed by next-generation sequencing from DNA obtained from 335 saliva samples. Dengue neutralizing antibody titers (NAb) were assessed as a correlate of risk and protection. Regression analyses were used to assess associations between HLA alleles and NAb responses, vaccine efficacy, and dengue outcomes. Month 13 NAb log geometric mean titers (GMTs) were associated with decreased risk of VCD. In the vaccine group, HLA-DRB1*11 was significantly associated with higher NAb log GMT levels (beta: 0.76; p = 0.002, q = 0.13). Additionally, in the absence of vaccination, HLA associations were observed between the presence of DPB1*03:01 and increased NAb log GMT levels (beta: 1.24; p = 0.005, q = 0.17), and between DPB1*05:01 and reduced NAb log GMT levels (beta: -1.1; p = 0.001, q = 0.07). This study suggests associations of HLA alleles with NAb titers in the context of dengue outcomes. This study was registered with clinicaltrials.gov: NCT02827162.

Human leukocyte antigen (HLA) alleles have been linked to HIV disease progression and attributed to differences in cytotoxic T lymphocyte (CTL) epitope representation. These findings are largely based on treatment-naive individuals of European and African ancestry. We assessed HLA associations with HIV-1 outcomes in 1,318 individuals from Thailand and found HLA-B∗46:01 (B∗46) associated with accelerated disease in three independent cohorts. B∗46 had no detectable effect on HIV-specific T cell responses, but this allele is unusual in containing an HLA-C epitope that binds inhibitory receptors on natural killer (NK) cells. Unbiased transcriptomic screens showed increased NK cell activation in people with HIV, without B∗46, and simultaneous single-cell profiling of surface proteins and transcriptomes revealed a NK cell subset primed for increased responses in the absence of B∗46. These findings support a role for NK cells in HIV pathogenesis, revealed by the unique properties of the B∗46 allele common only in Asia.

Background: SARS-CoV-2 is continuously evolving with the emergence of variants of interest (VOI) or with variants of concern (VOC). While Variants of High Consequence (VOHC) are well defined, no such variants have been formally documented. Here we propose an integrated strategy and application towards discovering VOHC. Methods: We utilized 7,137 viral sequences collected from COVID-19 cases in Washington State from January 19, 2020 to January 31, 2021, to identify genome-wide viral single nucleotide variants (SNVs). Utilizing a non-parametric regression model, we selected a subset of SNVs that had significant and substantial expansions over the collection period. Further, using unsupervised learning, we identified multiple SNVs forming haplotypes. To evaluate their clinical relevance, we assembled a discovery cohort of COVID-19 cases (388 inpatients and 295 outpatients) to identify SNVs and haplotypes associated with hospitalization status, a proxy for disease severity. A logistic regression model was used to assess associations of SNVs with hospitalization status in the discovery cohort. These results were validated on an independent cohort of 964 genome sequences derived from COVID-19 cases in Washington State from June 1, 2020 to March 31, 2021. Finding: The analysis of the 7,137 sequences led to identification of 107 SNVs that were statistically significant (false positive error rate q-value 0.10). Forty-one SNVs were considered urgent, because their SNV proportions persisted or expanded above 10% in January 2021, the last month of the current investigation period. Correlating with clinical data, eight SNVs were found to significantly associate with inpatient status (p-values

BACKGROUND: The emergence and establishment of SARS-CoV-2 variants of interest (VOI) and variants of concern (VOC) highlight the importance of genomic surveillance. We propose a statistical learning strategy (SLS) for identifying and spatiotemporally tracking Spike protein mutations potentially relevant to public health. METHODS: We analyzed 189,284 Spike protein sequences from US COVID-19 cases, deposited at GISAID from January 19, 2020 to March 15, 2021. Alignment against the reference Spike protein sequence led to the identification of viral residue variants (VRVs), i.e., residues harboring a substitution. Next, generalized additive models were applied to model VRV temporal dynamics, to identify VRVs with significant and substantial dynamics (false discovery rate q-value 10% on at least one day). Unsupervised learning was then applied to hierarchically organize VRVs by spatiotemporal patterns and identify VRV-haplotypes. Finally, homology modelling was performed to gain insight into potential impact of VRVs on Spike protein structure. FINDINGS: We identified 88 VRVs, 71 of which have not previously been observed in a VOI/VOC, and 44 of which have emerged recently and appear to be durably present. Compared to identified VOIs/VOCs, our analysis identifies 17 VRVs ~78 days earlier than their first description in a publication. Unsupervised learning revealed several VRV-haplotypes that were of reported lineages in addition to several novel VRV-haplotypes of unknown lineage. Structural modeling supported functional impact of the D1118H and L452R mutations. INTERPRETATION: The SLS approach equally monitors all Spike residues over time without dependence on existing phylogenic classifications, and is thus complementary to existing genomic surveillance methods. FUNDING: National Institute of Allergy and Infectious Diseases DECLARATION OF INTERESTS: No conflicts of interest relevant to this article were reported.

Introduction The paradigm for preventing clinically significant cytomegalovirus (CMV) infection and CMV disease after hematopoietic cell transplantation (HCT) has shifted from preemptive treatment to antiviral prophylaxis with the approval of letermovir. Previously, our group validated the use of quantitative CMV DNA viral load as a surrogate endpoint for tissue-invasive CMV disease (ASBMT 2018) in the pre-emptive treatment setting. Objectives To address whether CMV viral load kinetics could serve as valid surrogate endpoints for CMV disease in the prophylactic setting, we performed CMV viral load testing of frozen serum samples collected during a placebo-controlled randomized trial of ganciclovir (GCV) given at engraftment (Goodrich et al. Ann Intern Med 1993). Because this study pre-dated the approval of ganciclovir, CMV disease occurred in an extremely high proportion of patients, allowing us to link viral load kinetics with CMV disease, which would not be possible in the modern treatment environment. Methods We calculated each patient's CMV viral load kinetics (mean, peak, maximum change, percentage of positive viral loads) from samples collected during the first five weeks after randomization and analyzed their value as surrogates for CMV disease by 24 weeks after randomization. First, we tested each marker for fulfillment of the Prentice criteria for valid surrogate endpoints using multivariable logistic regression, including quantifying the degree to which each marker captured the effect of ganciclovir on CMV disease. Secondly, to determine the ability of the viral load markers to predict CMV disease, we developed a ‘SuperLearner' machine learning model and quantified prediction accuracy by cross-validated area under the receiver-operator characteristic curves (cv-AUCs). Results Mean, peak, change, and percentage of positive viral loads were significantly higher in the placebo group than in the ganciclovir group. See viral loads by group in Fig 1. Percentage of positive viral load satisfied Prentice criteria as a valid surrogate endpoint for CMV disease by week 24 after randomization (Fig 2). All kinetics explained greater than 80% of ganciclovir's reduction in CMV disease (mean: 86%, peak: 83%, maximum change: 95%, percent positive: 94%). We found that a SuperLearner model that included all four viral load kinetics, CMV donor serostatus, acute graft-versus-host disease, and baseline viral load predicted CMV disease with 91% cv-AUC in the placebo group, 78% in the ganciclovir group, and 82% in the combined groups (Fig 3). Conclusion We have shown for the first time in a clinical endpoint-rich, placebo-controlled antiviral prophylaxis trial that CMV viral load kinetics fulfill the Prentice criteria as valid surrogate endpoints and have high predictive value for CMV disease after HCT.

Background: The immunization regimens evaluated to date in the development of HIV vaccines have included purified Env protein vaccines as a part of the boosting components of the vaccination regimen. In the present study, we tested the hypothesis that the co-administration of Env protein with either DNA or NYVAC vector vaccines during the priming results in early generation of antibody responses to the Env V1/V2 region that are important markers for effective protection against infection. This study evaluated a multicomponent HIV vaccine including as immunogens either DNA or NYVAC vectors alone or in combination with Env protein, followed by a co-delivered NYVAC/protein boost. Methods: Ninety-six HIV-1 uninfected subjects were randomized in this double-blind placebo-controlled phase 1b human clinical trial to receive 2x NYVAC followed by 2x NYVAC+AIDSVAX® B/E (n = 20); 4x NYVAC+AIDSVAX® B/E (n = 20); 2x DNA followed by 2x NYVAC+AIDSVAX® B/E (n = 20); 2x DNA+AIDSVAX® B/E followed by 2x NYVAC+AIDSVAX® B/E (n = 20); or placebo (n = 16). Immune response measures included cross-clade and epitopespecific binding antibodies, neutralizing antibodies (nAb), and antibody dependent cell-mediated cytotoxicity (ADCC). Findings: IgG response rates were 74-95% at 2 weeks post 4th vaccination across study groups. Early administration of the gp120 protein was associated with a markedly earlier and higher AUC for gp120 binding, anti-V1V2, neutralizing antibody, and with better antibody response coverage over a period of 18 months than the regimens delaying the gp120 protein until the 6 month vaccination Interpretation: Co-administration of AIDSVAX® B/E gp120 protein components with DNA and/or NYVAC vectors during priming results in early and potent induction of Env V1/V2 IgG binding antibody responses, markers associated with reduced risk of infection in a previous efficacy trial. This immunization approach should be considered for induction of preventative antibodies in future HIV vaccine efficacy trials. Trial Registration: ClinicalTrials.gov: NCT01799954. Funding Statement: UM1 AI068614, UM1 AI068635, UM1 AI068618 and UM1 AI069481. Declaration of Interests: The authors have declared that no conflict of interest exists. Ethics Approval Statement: The study protocol was approved by the institutional ethics committee of the Centre Hospitalier Universitaire Vaudois (CHUV) (Lausanne, Switzerland) and by Swissmedic, the Swiss Agency for Therapeutic Products (Bern, Switzerland). All study participants provided written informed consent prior to participation.

Phase 1 preventive HIV vaccine trials are often designed as randomized, double-blind studies with the inclusion of placebo recipients. Careful consideration is needed to determine when the inclusion of placebo recipients is highly advantageous and when it is optional for achieving the study objectives of assessing vaccine safety, tolerability and immunogenicity. The inclusion of placebo recipients is generally important to form a reference group that ensures fair evaluation and interpretation of subjective study endpoints, or endpoints whose levels may change due to exposures besides vaccination. In some settings, however, placebo recipients are less important because other data sources and tools are available to achieve the study objectives.

To evaluate the role of V3-specific IgG antibodies (Abs) in the RV144 clinical HIV vaccine trial, which reduced HIV-1 infection by 31.2%, the anti-V3 Ab response was assessed. Vaccinees' V3 Abs were highly cross-reactive with cyclic V3 peptides (cV3s) from diverse virus subtypes. Sieve analysis of CRF01_AE breakthrough viruses from 43 vaccine- and 66 placebo-recipients demonstrated an estimated vaccine efficacy of 85% against viruses with amino acids mismatching the vaccine at V3 site 317 (p = 0.004) and 52% against viruses matching the vaccine at V3 site 307 (p = 0.004). This analysis was supported by data showing that vaccinees' plasma Abs were less reactive with I307 when replaced with residues found more often in vaccinees' breakthrough viruses. Simultaneously, viruses with mutations at F317 were less infectious, possibly due to the contribution of F317 to optimal formation of the V3 hydrophobic core. These data suggest that RV144-induced V3-specific Abs imposed immune pressure on infecting viruses and inform efforts to design an HIV vaccine., Highlights • The RV144 vaccine reduced infection by viruses with isoleucine in V3 position 307. • Many vaccine-induced antibodies are cross-reactive and target an epitope including I307. • There was selection for breakthrough viruses carrying F317 in V3 (p = 0.004). • F317 is needed to maintain optimal infectivity. • F317 is a poor or non-contact residue for vaccine induced V3 antibodies.

Summary Background The HVTN 503/Phambili study, which assessed the efficacy of the Merck Ad5 gag/pol/nef subtype B HIV-1 preventive vaccine in South Africa, was stopped when futility criteria in the Step study (assessing the same vaccine in the Americas, Caribbean, and Australia) were met. Here we report long-term follow-up data. Methods HVTN 503/Phambili was a double-blind, placebo-controlled, randomised trial that recruited HIV-1 uninfected, sexually active adults aged 18–35 years from five sites in South Africa. Eligible participants were randomly assigned (1:1) by computer-generated random numbers to either vaccine or placebo, stratified by site and sex. Cox proportional hazards models were used to estimate HIV-1 infection in the modified intention-to-treat cohort, all of whom were unmasked early in follow-up. The trial is registered with ClinicalTrials.gov, number NCT00413725 and the South African National Health Research Database, number DOH-27-0207-1539. Findings Between Jan 24, 2007, and Sept 19, 2007, 801 participants (26·7%) of a planned 3000 were randomly assigned (400 to vaccine, 401 to placebo); 216 (27%) received only one injection, 529 (66%) received only two injections, and 56 (7%) received three injections. At a median follow-up of 42 months (IQR 31–42), 63 vaccine recipients (16%) had HIV-1 infection compared with 37 placebo recipients (9%; adjusted HR 1·70, 95% CI 1·13–2·55; p=0·01). Risk for HIV-1 infection did not differ according to the number of vaccinations received, sex, circumcision, or adenovirus type 5 (Ad5) serostatus. Differences in risk behaviour at baseline or during the study, or annualised dropout rate (7·7% [95% CI 6·2–9·5] for vaccine recipients vs 8·8% [7·1–10·7] for placebo recipients; p=0·40) are unlikely explanations for the increased rate of HIV-1 infections seen in vaccine recipients. Interpretation The increased risk of HIV-1 acquisition in vaccine recipients, irrespective of number of doses received, warrants further investigation to understand the biological mechanism. We caution against further use of the Ad5 vector for HIV vaccines. Funding National Institute of Allergy and Infectious Diseases, Merck, and South African Medical Research Council.

The United States Food and Drug Administration recently issued guidance that CMV DNAemia (quantitative CMV viral load as measured by PCR) could be used in a composite endpoint along with tissue-invasive CMV disease as the primary endpoint in allogeneic HCT CMV prophylaxis trials. However, the specific time points after antiviral treatment initiation at which to measure viral load and the viral load thresholds that most accurately predict clinical CMV disease have not been identified. In order to estimate the treatment effect of an antiviral agent on CMV clinical outcomes, placebo-controlled, randomized trial data with accompanying viral load measurements are needed. Unfortunately, in the modern era of PCR and early preemptive treatment, ethically, placebo-controlled, randomized trials that allow for the development of CMV disease after HCT can no longer be performed. To overcome this limitation, we performed CMV DNA PCR testing on frozen plasma samples collected during the first 100 days post-HCT in the only placebo-controlled, double-blind RCT of ganciclovir for the early treatment of CMV infection after HCT (Goodrich et al. NEJM 1991). We used three analytic methods (Cox proportional hazards models, machine learning, and a novel non-parametric method) to determine which of 14 viral load markers, measured in the first four weeks of treatment, are the most useful surrogates of antiviral treatment for the prevention of CMV disease. All methods identified peak viral load and percentage of positive samples by week 4 as highly associated with or predictive of tissue-invasive CMV disease by week 8 post-randomization. Cox proportional hazards models (Figure 1) yielded significant associations for peak viral load measured by week 4 (HR 1.4, 95% CI 1.1-1.9) and percentage of positive samples by week 4 (HR 1.6, CI 1.1-2.3). The machine-learning ensemble algorithm SuperLearner implemented in R (Figure 2) demonstrated cross-validated area under the receiver-operator curves of at least 75% for peak viral load (75%, CI 62-87%) and percentage of positive plasma samples (77%, CI 63-90%) measured by week 4. Using a novel statistical technique that allows direct estimation of biomarker surrogacy (Parast et al. Stat Med 2017), we estimated that the percentage of ganciclovir treatment effect explained by peak viral load and percentage of positive samples measured by week 4 was greater than 85%—peak viral load 89%, CI 56-100%; percent positive samples 91%, CI 60-100% (Figure 3). Peak viral load and percentage of positive samples by week 4 are highly predictive of CMV disease and the treatment effect of ganciclovir. Our analysis suggests that these may be the best surrogate markers of ganciclovir treatment and introduces novel methods for identifying optimal candidate biomarkers as surrogates for clinical endpoints.

Dozens of human immunodeficiency virus-type 1 (HIV-1) vaccine candidates specifically designed to elicit cytotoxic T-lymphocyte (CTL) responses have entered the pipeline of clinical trials. Evaluating the immunogenicity and potential efficacy of these HIV-1 vaccine candidates is challenging in the face of the extensive viral genetic diversity of circulating strains. Standardized peptide reagents to define the magnitude and potential breadth of the T-cell response, especially to circulating strains of HIV-1, are needed. For this purpose we developed a biometric approach based on T-cell recognition pattern for defining standardized reagents. Circulating strains in the Los Alamos database were evaluated and standardized algorithms to define all potential T-cell epitopes (PTEs) were generated. While many unique PTEs could be identified, a finite number based upon prevalence of circulating strains in the database, which we define as vaccine-important PTEs (VIPs), were used to select a common standardized panel of HIV-1 peptides for CTL-based vaccine evaluation. The usability of PTE peptide set was manifested by detection of Nef-specific CTL responses in HIV-1 subtype B infections.

The HIV pandemic is a pressing threat to global public health; HIV vaccine development is critical. Clinical evaluation of HIV vaccine candidates differs from the standard therapeutics trial framework primarily due to the fact that healthy individuals are studied. We present an early stage evaluation program developed for the HIV Vaccine Trials Network (HVTN) motivated by characteristics unique to the vaccine setting. The program consists of 3 prototypical stages (Phase I, Ib, II) that provide a unified yet flexible approach to the safety and immunogenicity evaluation of diverse vaccine regimens. The goal of these early trials is to narrow the number of candidate vaccines to the most promising candidates worthy of further study in efficacy trials.

Randomization in clinical trials minimizes differences between treatment arms, allowing observed treatment differences to be attributable to an intervention. For prospective clinical trials, we examine the effects on inference when other specified treatment arm differences are also present. These differences are imposed using three measures: time between the unobserved failure event (e.g., HIV infection) and its detection, visit schedule adherence and dropout. Our context of interest is trials with non-recurrent time-to-event outcomes and fixed visit intervals, where treatment efficacy is measured either by a hazard ratio or by a ratio of cumulative incidence functions. Moderate treatment differences in visit adherence, either through missed visits or additional unscheduled visits, were not found to cause substantial bias or to reduce power. However, both differential loss to follow-up (when coincidentally dependent on risk of failure) and differential time between event and detection should be of concern in designing clinical trials. Efforts to re-capture subjects at the end of study for failure assessment are helpful in some contexts, and may be considered in study planning.

Consider an s -sample biased sampling model in which the distribution function for each of the first s −1 samples is related to the unknown distribution function G of the s th sample by a known parametric selection bias weight function. Gilbert et al. (Biometrika 86 (1999) 27) gave a procedure for semiparametric maximum likelihood estimation of the parameters in this model. In many applications, information are scarce for basing the choice of the parametric weight function(s), motivating the need for goodness-of-fit tests of the hypothesis that the weight functions are correctly specified. Cramer–von Mises-type, Anderson–Darling-type, and Kolmogorov–Smirnov-type test statistics are studied which compare discrepancies between the empirical distribution of G and the semiparametric maximum likelihood estimator of G . Finite-sample properties of the tests are evaluated with simulations and with a real example of HIV genetic sequence data.