Immunogenicity of standard and extended dosing intervals of BNT162b2 mRNA vaccine.

Extension of the interval between vaccine doses for the BNT162b2 mRNA vaccine was introduced in the United Kingdom to accelerate population coverage with a single dose. At this time, trial data were lacking, and we addressed this in a study of United Kingdom healthcare workers. The first vaccine dose induced protection from infection from the circulating alpha (B.1.1.7) variant over several weeks. In a substudy of 589 individuals, we show that this single dose induces severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) neutralizing antibody (NAb) responses and a sustained B and T cell response to the spike protein. NAb levels were higher after the extended dosing interval (6-14 weeks) compared with the conventional 3- to 4-week regimen, accompanied by enrichment of CD4+ T cells expressing interleukin-2 (IL-2). Prior SARS-CoV-2 infection amplified and accelerated the response. These data on dynamic cellular and humoral responses indicate that extension of the dosing interval is an effective immunogenic protocol.

Single-cell reconstruction of the early maternal-fetal interface in humans.

During early human pregnancy the uterine mucosa transforms into the decidua, into which the fetal placenta implants and where placental trophoblast cells intermingle and communicate with maternal cells. Trophoblast-decidual interactions underlie common diseases of pregnancy, including pre-eclampsia and stillbirth. Here we profile the transcriptomes of about 70,000 single cells from first-trimester placentas with matched maternal blood and decidual cells. The cellular composition of human decidua reveals subsets of perivascular and stromal cells that are located in distinct decidual layers. There are three major subsets of decidual natural killer cells that have distinctive immunomodulatory and chemokine profiles. We develop a repository of ligand-receptor complexes and a statistical tool to predict the cell-type specificity of cell-cell communication via these molecular interactions. Our data identify many regulatory interactions that prevent harmful innate or adaptive immune responses in this environment. Our single-cell atlas of the maternal-fetal interface reveals the cellular organization of the decidua and placenta, and the interactions that are critical for placentation and reproductive success.

Oxidized micrometeorites suggest either high pCO2 or low pN2 during the Neoarchean.

Tomkins et al. [A. G. Tomkins et al., Nature 533, 235-238 (2016)] suggested that iron oxides contained in 2.7-Ga iron micrometeorites can be used to determine the concentration of O2 in the Archean upper atmosphere. Specifically, they argued that the presence of magnetite in these objects implies that O2 must have been near present-day levels (∼21%) within the altitude range where the micrometeorites were melted during entry. Here, we reevaluate their data using a 1D photochemical model. We find that atomic oxygen, O, is the most abundant strong oxidant in the upper atmosphere, rather than O2 But data from shock tube experiments suggest that CO2 itself may also serve as the oxidant, in which case micrometeorite oxidation really constrains the CO2/N2 ratio, not the total oxidant abundance. For an atmosphere containing 0.8 bar of N2, like today, the lower limit on the CO2 mixing ratio is ∼0.23. This would produce a mean surface temperature of ∼300 K at 2.7 Ga, which may be too high, given evidence for glaciation at roughly this time. If pN2 was half the present value, and warming by other greenhouse gases like methane was not a major factor, the mean surface temperature would drop to ∼291 K, consistent with glaciation. This suggests that surface pressure in the Neoarchean may need to have been lower-closer to 0.6 bar-for CO2 to have oxidized the micrometeorites. Ultimately, iron micrometeorites may be an indicator for ancient atmospheric CO2 and surface pressure; and could help resolve discrepancies between climate models and existing CO2 proxies such as paleosols.

Racial-ethnic disparities in adolescent sexual behaviours: the cross-sectional Youth Risk Behavior Survey, 2009–19.

BACKGROUND: There are notable disparities by race/ethnicity in the sexual health of US adolescents and young adults. Our objective was to examine change over time in racial-ethnic disparities in sexual behaviours among US high school students. METHODS: Data were analysed from six biennial cycles of the national Youth Risk Behavior Survey (2009-19), conducted among cross-sectional, nationally representative samples of 9th-12th grade students. Data were collected via self-administered questionnaires. Multivariable logistic regression models tested for linear trends by race/ethnicity (White, Black, Hispanic) and differences in these trends in: ever had sex, current sexual activity, having four or more lifetime sexual partners, and condomless sex. Prevalence ratios and risk differences by race/ethnicity for each cycle were used to calculate average percent change in the estimates to determine if health disparities changed over time. RESULTS: During 2009-19, prevalence estimates for ever had sex, current sexual activity, and having four or more lifetime sexual partners decreased overall and across all racial-ethnic groups. For condomless sex, prevalence estimates increased over time overall (38.9-45.7%) and for Black (37.6-51.8%) and White (36.7-44.2%) students, but not Hispanic (45.1-43.8%) students. Significant differences in trends by race/ethnicity were observed for all variables. Data suggest that racial-ethnic health disparities for sexual behaviours decreased over time, except for condomless sex. CONCLUSIONS: Although racial-ethnic gaps in sexual behaviours may be shrinking for many behaviours, work is still needed to achieve health equity in risks associated with HIV/AIDS, sexually transmitted infections, and pregnancy.

Impact of HLA-driven HIV adaptation on virulence in populations of high HIV seroprevalence.

It is widely believed that epidemics in new hosts diminish in virulence over time, with natural selection favoring pathogens that cause minimal disease. However, a tradeoff frequently exists between high virulence shortening host survival on the one hand but allowing faster transmission on the other. This is the case in HIV infection, where high viral loads increase transmission risk per coital act but reduce host longevity. We here investigate the impact on HIV virulence of HIV adaptation to HLA molecules that protect against disease progression, such as HLA-B*57 and HLA-B*58:01. We analyzed cohorts in Botswana and South Africa, two countries severely affected by the HIV epidemic. In Botswana, where the epidemic started earlier and adult seroprevalence has been higher, HIV adaptation to HLA including HLA-B*57/58:01 is greater compared with South Africa (P = 7 × 10(-82)), the protective effect of HLA-B*57/58:01 is absent (P = 0.0002), and population viral replicative capacity is lower (P = 0.03). These data suggest that viral evolution is occurring relatively rapidly, and that adaptation of HIV to the most protective HLA alleles may contribute to a lowering of viral replication capacity at the population level, and a consequent reduction in HIV virulence over time. The potential role in this process played by increasing antiretroviral therapy (ART) access is also explored. Models developed here suggest distinct benefits of ART, in addition to reducing HIV disease and transmission, in driving declines in HIV virulence over the course of the epidemic, thereby accelerating the effects of HLA-mediated viral adaptation.

Kernel machine testing for risk prediction with stratified case cohort studies.

Large assembled cohorts with banked biospecimens offer valuable opportunities to identify novel markers for risk prediction. When the outcome of interest is rare, an effective strategy to conserve limited biological resources while maintaining reasonable statistical power is the case cohort (CCH) sampling design, in which expensive markers are measured on a subset of cases and controls. However, the CCH design introduces significant analytical complexity due to outcome-dependent, finite-population sampling. Current methods for analyzing CCH studies focus primarily on the estimation of simple survival models with linear effects; testing and estimation procedures that can efficiently capture complex non-linear marker effects for CCH data remain elusive. In this article, we propose inverse probability weighted (IPW) variance component type tests for identifying important marker sets through a Cox proportional hazards kernel machine (CoxKM) regression framework previously considered for full cohort studies (Cai et al., 2011). The optimal choice of kernel, while vitally important to attain high power, is typically unknown for a given dataset. Thus, we also develop robust testing procedures that adaptively combine information from multiple kernels. The proposed IPW test statistics have complex null distributions that cannot easily be approximated explicitly. Furthermore, due to the correlation induced by CCH sampling, standard resampling methods such as the bootstrap fail to approximate the distribution correctly. We, therefore, propose a novel perturbation resampling scheme that can effectively recover the induced correlation structure. Results from extensive simulation studies suggest that the proposed IPW CoxKM testing procedures work well in finite samples. The proposed methods are further illustrated by application to a Danish CCH study of Apolipoprotein C-III markers on the risk of coronary heart disease.

Robust risk prediction with biomarkers under two-phase stratified cohort design.

Identification of novel biomarkers for risk prediction is important for disease prevention and optimal treatment selection. However, studies aiming to discover which biomarkers are useful for risk prediction often require the use of stored biological samples from large assembled cohorts, and thus the depletion of a finite and precious resource. To make efficient use of such stored samples, two-phase sampling designs are often adopted as resource-efficient sampling strategies, especially when the outcome of interest is rare. Existing methods for analyzing data from two-phase studies focus primarily on single marker analysis or fitting the Cox regression model to combine information from multiple markers. However, the Cox model may not fit the data well. Under model misspecification, the composite score derived from the Cox model may not perform well in predicting the outcome. Under a general two-phase stratified cohort sampling design, we present a novel approach to combining multiple markers to optimize prediction by fitting a flexible nonparametric transformation model. Using inverse probability weighting to account for the outcome-dependent sampling, we propose to estimate the model parameters by maximizing an objective function which can be interpreted as a weighted C-statistic for survival outcomes. Regardless of model adequacy, the proposed procedure yields a sensible composite risk score for prediction. A major obstacle for making inference under two phase studies is due to the correlation induced by the finite population sampling, which prevents standard inference procedures such as the bootstrap from being used for variance estimation. We propose a resampling procedure to derive valid confidence intervals for the model parameters and the C-statistic accuracy measure. We illustrate the new methods with simulation studies and an analysis of a two-phase study of high-density lipoprotein cholesterol (HDL-C) subtypes for predicting the risk of coronary heart disease.

Absenteeism and Employer Costs Associated With Chronic Diseases and Health Risk Factors in the US Workforce.

INTRODUCTION: Employers may incur costs related to absenteeism among employees who have chronic diseases or unhealthy behaviors. We examined the association between employee absenteeism and 5 conditions: 3 risk factors (smoking, physical inactivity, and obesity) and 2 chronic diseases (hypertension and diabetes). METHODS: We identified 5 chronic diseases or risk factors from 2 data sources: MarketScan Health Risk Assessment and the Medical Expenditure Panel Survey (MEPS). Absenteeism was measured as the number of workdays missed because of sickness or injury. We used zero-inflated Poisson regression to estimate excess absenteeism as the difference in the number of days missed from work by those who reported having a risk factor or chronic disease and those who did not. Covariates included demographics (eg, age, education, sex) and employment variables (eg, industry, union membership). We quantified absenteeism costs in 2011 and adjusted them to reflect growth in employment costs to 2015 dollars. Finally, we estimated absenteeism costs for a hypothetical small employer (100 employees) and a hypothetical large employer (1,000 employees). RESULTS: Absenteeism estimates ranged from 1 to 2 days per individual per year depending on the risk factor or chronic disease. Except for the physical inactivity and obesity estimates, disease- and risk-factor-specific estimates were similar in MEPS and MarketScan. Absenteeism increased with the number of risk factors or diseases reported. Nationally, each risk factor or disease was associated with annual absenteeism costs greater than $2 billion. Absenteeism costs ranged from $16 to $81 (small employer) and $17 to $286 (large employer) per employee per year. CONCLUSION: Absenteeism costs associated with chronic diseases and health risk factors can be substantial. Employers may incur these costs through lower productivity, and employees could incur costs through lower wages.

Impact of HLA selection pressure on HIV fitness at a population level in Mexico and Barbados.

UNLABELLED: Previous studies have demonstrated that effective cytotoxic T lymphocyte (CTL) responses drive the selection of escape mutations that reduce viral replication capacity (VRC). Escape mutations, including those with reduced VRC, can be transmitted and accumulate in a population. Here we compared two antiretroviral therapy (ART)-naive HIV clade B-infected cohorts, in Mexico and Barbados, in which the most protective HLA alleles (HLA-B*27/57/58:01/81:01) are differentially expressed, at 8% and 34%, respectively. Viral loads were significantly higher in Mexico than in Barbados (median, 40,774 versus 14,200; P < 0.0001), and absolute CD4(+) T-cell counts were somewhat lower (median, 380/mm(3) versus 403/mm(3); P = 0.007). We tested the hypothesis that the disparate frequencies of these protective HLA alleles would be associated with a higher VRC at the population level in Mexico. Analysis of VRC in subjects in each cohort, matched for CD4(+) T-cell count, revealed that the VRC was indeed higher in the Mexican cohort (mean, 1.13 versus 1.03; P = 0.0025). Although CD4 counts were matched, viral loads remained significantly higher in the Mexican subjects (P = 0.04). This VRC difference was reflected by a significantly higher frequency in the Barbados cohort of HLA-B*27/57/58:01/81:01-associated Gag escape mutations previously shown to incur a fitness cost on the virus (P = 0.004), a difference between the two cohorts that remained statistically significant even in subjects not expressing these protective alleles (P = 0.01). These data suggest that viral set points and disease progression rates at the population level may be significantly influenced by the prevalence of protective HLA alleles such as HLA-B*27/57/58:01/81:01 and that CD4 count-based guidelines to initiate antiretroviral therapy may need to be modified accordingly, to optimize the effectiveness of treatment-for-prevention strategies and reduce HIV transmission rates to the absolute minimum. IMPORTANCE: Immune control of HIV at an individual level is strongly influenced by the HLA class I genotype. HLA class I molecules mediating effective immune control, such as HLA-B*27 and HLA-B*57, are associated with the selection of escape mutants that reduce viral replicative capacity. The escape mutants selected in infected patients can be transmitted and affect the viral load and CD4 count in the recipient. These findings prompt the hypothesis that the frequency of protective alleles in a population may affect viral set points and rates of disease progression in that population. These studies in Mexico and Barbados, where the prevalence rates of protective HLA alleles are 8% and 34%, respectively, support this hypothesis. These data suggest that antiretroviral therapy (ART) treatment-for-prevention strategies will be less successful in populations such as those in Mexico, where viral loads are higher for a given CD4 count. Consideration may therefore usefully be given to ART initiation at higher absolute CD4 counts in such populations to optimize the impact of ART for prevention.

Adaptation of HIV-1 to human leukocyte antigen class I.

The rapid and extensive spread of the human immunodeficiency virus (HIV) epidemic provides a rare opportunity to witness host-pathogen co-evolution involving humans. A focal point is the interaction between genes encoding human leukocyte antigen (HLA) and those encoding HIV proteins. HLA molecules present fragments (epitopes) of HIV proteins on the surface of infected cells to enable immune recognition and killing by CD8(+) T cells; particular HLA molecules, such as HLA-B*57, HLA-B*27 and HLA-B*51, are more likely to mediate successful control of HIV infection. Mutation within these epitopes can allow viral escape from CD8(+) T-cell recognition. Here we analysed viral sequences and HLA alleles from >2,800 subjects, drawn from 9 distinct study cohorts spanning 5 continents. Initial analysis of the HLA-B*51-restricted epitope, TAFTIPSI (reverse transcriptase residues 128-135), showed a strong correlation between the frequency of the escape mutation I135X and HLA-B*51 prevalence in the 9 study cohorts (P = 0.0001). Extending these analyses to incorporate other well-defined CD8(+) T-cell epitopes, including those restricted by HLA-B*57 and HLA-B*27, showed that the frequency of these epitope variants (n = 14) was consistently correlated with the prevalence of the restricting HLA allele in the different cohorts (together, P < 0.0001), demonstrating strong evidence of HIV adaptation to HLA at a population level. This process of viral adaptation may dismantle the well-established HLA associations with control of HIV infection that are linked to the availability of key epitopes, and highlights the challenge for a vaccine to keep pace with the changing immunological landscape presented by HIV.

Early antigen presentation of protective HIV-1 KF11Gag and KK10Gag epitopes from incoming viral particles facilitates rapid recognition of infected cells by specific CD8+ T cells.

CD8(+) T cells are major players in antiviral immunity against human immunodeficiency virus type 1 (HIV-1) through recognition of viral epitopes presented on the surface of infected cells. However, the early events involving HIV-1 epitope presentation to CD8(+) T cells remain poorly understood but are nonetheless crucial for the rapid clearance of virus-infected cells. Here, we comprehensively studied the kinetics of antigen presentation of two protective epitopes, KF11Gag and KK10Gag, restricted by HLA alleles B*57:01 and B*27:05, respectively, and compared these to KY9Pol and VL9Vpr epitopes in a single cycle of HIV-1 replication. We consistently demonstrate differences in epitope presentation kinetics, with very early presentation, within 3 h postinfection, for the protective KF11Gag, KK10Gag epitopes, and KY9Pol but only late presentation for VL9Vpr. We show that this early presentation relies on the antigen being presented from incoming viral particles and is correlated with rapid CD8(+) T cell activation and clearance of virus-infected cells. Additionally, our data indicate a dose-response dependency between the levels of CD8(+) T cell activation and the amount of virus inoculum. These data reflect a proof of principle emphasizing the importance of identifying early-presented viral epitopes for rapid elimination of HIV-1-infected cells.

HLA-specific intracellular epitope processing shapes an immunodominance pattern for HLA-B*57 that is distinct from HLA-B*58:01.

HLA-B*57 is strongly associated with immune control of HIV and delayed AIDS progression. The closely related, but less protective, HLA-B*58:01 presents similar epitopes, but HLA-B*58:01(+) individuals do not generate CD8(+) T cells targeting the KF11-Gag epitope, which has been linked to low viremia. Here we show that HLA-B*58:01 binds and presents KF11 peptide, but HIV-infected HLA-B*58:01(+) cells fail to process KF11. This unexpected finding demonstrates that immunodominance patterns can be influenced by intracellular events independent of HLA binding motifs.

CD8+ T-cell responses to different HIV proteins have discordant associations with viral load.

Selection of T-cell vaccine antigens for chronic persistent viral infections has been largely empirical. To define the relationship, at the population level, between the specificity of the cellular immune response and viral control for a relevant human pathogen, we performed a comprehensive analysis of the 160 dominant CD8(+) T-cell responses in 578 untreated HIV-infected individuals from KwaZulu-Natal, South Africa. Of the HIV proteins targeted, only Gag-specific responses were associated with lowering viremia. Env-specific and Accessory/Regulatory protein-specific responses were associated with higher viremia. Increasing breadth of Gag-specific responses was associated with decreasing viremia and increasing Env breadth with increasing viremia. Association of the specific CD8(+) T-cell response with low viremia was independent of HLA type and unrelated to epitope sequence conservation. These population-based data, suggesting the existence of both effective immune responses and responses lacking demonstrable biological impact in chronic HIV infection, are of relevance to HIV vaccine design and evaluation.

Risks to patient safety in remote consulting.

BACKGROUND: Remote consulting was rolled out across general practice in 2020 in response to the COVID-19 pandemic. Although most consultations are carried out safely, in some cases remote care has contributed to adverse outcomes. AIM: To understand where the risks lie in delivering primary care remotely. METHOD: Mixed method study in UK primary care settings including general practice, out of hours and 111 services. Data was collated from NHS England complaints quarterly reviews, NHS Resolution cases, 111 Wales, the HSIB report into 111 COVID services and longitudinal case ethnographic cases studies of 11 general practices. 2 reviewers coded the data and identified themes. RESULTS: There are staff, patient, and setting factors that contribute to risk in remote consulting. Staff factors include communication skills, over-reliance on a previous diagnosis made remotely, failure to recognise clinical findings or the urgency of a case, over/under prescribing/investigating and referring and safety netting. Patient factors include impaired communication, repeated telephone consultations, unstable chronic disease, and certain medical conditions such as chest and abdominal pain. Risk was encountered when settings had limited telephone lines, call handlers or clinicians, or where access to appointments was either restricted, hard to navigate, or where inappropriate layers of triage were applied. Processes had not always adapted for remote working, leading to risk in delayed access to acute prescriptions and delayed referrals. CONCLUSION: Attention to staff, patient, and setting factors can allow risk to be identified and addressed when providing care remotely. .

Media depictions of primary care tele-consultation safety: analysis of UK newspapers.

Background The COVID-19 pandemic necessitated the widespread rollout of teleconsultations across primary care services in the UK. The media's depiction of remote consultations, especially regarding their safety, is not well-established. These insights are important: newspapers' coverage of healthcare-related news can influence public perception, national policy and clinicians' job satisfaction. Aim To explore how the national newspapers in the UK depicted both the direct and indirect consequences of the remote-first approach on patient safety. Design and setting We performed thematic analysis of newspaper articles which discussed patient safety in primary care teleconsultations, published between 21st January 2021-22nd April 2022. Methods We identified relevant articles using the LexisNexis Academic UK database. We categorised data from these articles into codes before developing these into emergent themes through an iterative process. Results Across the 57 articles identified, the main safety concern identified was missed and/or delayed diagnoses over tele-appointment(s), while isolated cases of inappropriate prescribing were also reported. The media reported that the transition to a remote-first approach reduced the accessibility to primary care appointments for some groups (especially patients with lower digital literacy/access), and heightened the burden on other healthcare services: in particular, there were reports of patient care being compromised across NHS emergency departments (ED). Conclusions The media predominantly reported negative impacts of remote consultations on patient safety, particularly involving missed and/or delayed diagnoses. Our work highlights the importance of further exploration into the safety of remote consultations, and the impact of erroneous media reporting on policies and policymakers.

In vitro permeation of nicotine and tobacco specific nitrosamines from smokeless tobacco product extracts in a 3D buccal tissue model.

Tobacco product use is a risk factor in the development of oral cancer, although epidemiology studies show this risk is far less with smokeless tobacco product use than cigarette smoking. While smokeless tobacco contains harmful and potentially harmful constituents (HPHCs), the oral permeation of HPHCs in oral tobacco products is not completely understood. To improve the understanding, three different extract concentrations of the CORESTA reference products (CRP) for snus (CRP1.1) and moist snuff (CRP2.1) were applied to cellular tissue derived from two donors of EpiOral™ model, a 3D human buccal model, and permeation of nicotine and tobacco-specific nitrosamines (TSNAs) were measured over two hours. Permeation of 0.15% caffeine in complete artificial saliva and cell viability were also measured. Results showed that a consistent and concentration dependent cumulative permeation of nicotine and TSNAs was observed with high percent recovery in all conditions. A high degree of sensitivity was seen for all analytes, with minimal cytotoxicity for both CRPs. The data presented here show the EpiOral™ model is fit-for-purpose to evaluate the permeation of nicotine and TSNAs in nicotine-containing snus and moist snuff oral tobacco.

Training needs for staff providing remote services in general practice: a mixed-methods study.

BACKGROUND: Contemporary general practice includes many kinds of remote encounter. The rise in telephone, video and online modalities for triage and clinical care requires clinicians and support staff to be trained, both individually and as teams, but evidence-based competencies have not previously been produced for general practice. AIM: To identify training needs, core competencies, and learning methods for staff providing remote encounters. DESIGN AND SETTING: Mixed-methods study in UK general practice. METHOD: Data were collated from longitudinal ethnographic case studies of 12 general practices; a multi-stakeholder workshop; interviews with policymakers, training providers, and trainees; published research; and grey literature (such as training materials and surveys). Data were coded thematically and analysed using theories of individual and team learning. RESULTS: Learning to provide remote services occurred in the context of high workload, understaffing, and complex workflows. Low confidence and perceived unmet training needs were common. Training priorities for novice clinicians included basic technological skills, triage, ethics (for privacy and consent), and communication and clinical skills. Established clinicians' training priorities include advanced communication skills (for example, maintaining rapport and attentiveness), working within the limits of technologies, making complex judgements, coordinating multi-professional care in a distributed environment, and training others. Much existing training is didactic and technology focused. While basic knowledge was often gained using such methods, the ability and confidence to make complex judgements were usually acquired through experience, informal discussions, and on-the-job methods such as shadowing. Whole-team training was valued but rarely available. A draft set of competencies is offered based on the findings. CONCLUSION: The knowledge needed to deliver high-quality remote encounters to diverse patient groups is complex, collective, and organisationally embedded. The vital role of non-didactic training, for example, joint clinical sessions, case-based discussions, and in-person, whole-team, on-the-job training, needs to be recognised.