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Abstract We present the INSPIRE dataset, a publicly available research dataset in perioperative medicine, which includes approximately 130,000 surgical operations at an academic institution in South Korea over a ten-year period between 2011 and 2020. This comprehensive dataset includes patient characteristics such as age, sex, American Society of Anesthesiologists physical status classification, diagnosis, surgical procedure code, department, and type of anaesthesia. The dataset also includes vital signs in the operating theatre, general wards, and intensive care units (ICUs), laboratory results from six months before admission to six months after discharge, and medication during hospitalisation. Complications include total hospital and ICU length of stay and in-hospital death. We hope this dataset will inspire collaborative research and development in perioperative medicine and serve as a reproducible external validation dataset to improve surgical outcomes.

IntroductionRespiratory syncytial virus (RSV) causes acute respiratory tract infection (ARTI) and reinfects adults throughout life, posing a risk for hospitalization in older adults (>60 years) with frailty and comorbidities.MethodsTo investigate serum and mucosal antibodies for protection against RSV infections, baseline serum samples were compared for RSV-pre- and -post-fusion (F) binding, and RSV-A2 neutralizing IgG antibodies between symptomatic RSV-ARTI (N = 30), non-RSV (RSV negative) ARTI (N = 386), and no ARTI (N = 338). Mucosal RSV-pre-F IgA and IgG levels, as well as serum RSV-G IgG antibodies, were analyzed to determine their association with protection from symptomatic RSV-ARTI in a subset study.ResultsUsing a receiver operating characteristic (ROC) analysis, we established thresholds of 1.4- to 1.6-fold change (FC) for RSV-pre-F and -post-F, and RSV-A2 neutralizing IgG antibodies, respectively, enabling the identification of asymptomatic RSV cases with high sensitivity and specificity (>80% and >90%, respectively). As a result, serum RSV-pre-F, RSV-G IgG, and mucosal pre-F binding IgA antibodies showed correlations with protection against symptomatic RSV infection. RSV-pre-F IgG antibodies were correlated with protection from RSV infections irrespective of the symptoms.DiscussionThis study provides insights into antibody-mediated protection for symptomatic RSV infection in a community-dwelling older-adult population and establishes a threshold to identify asymptomatic RSV infection using a data-driven approach.

Objectives To describe the development, validation and reliability of the Oxford Vaccine Hesitancy Scale (OVHS), a new instrument to assess vaccine hesitancy in the general population.Design Cross-sectional validation study.Setting Internet-based study with participants in the UK and USA.Participants Demographically representative (stratified by age, sex and race) samples from the UK and USA recruited through the Prolific Academic platform.Main outcome measures To demonstrate OVHS development, exploratory factor analysis with categorical variables and a polychoric correlation matrix followed by promax oblique rotation on the UK sample was performed. Confirmatory factor analysis with a Satorra-Bentler scaled test statistic evaluating goodness of fit statistics including the root mean squared error of approximation (RMSEA), standardised root mean squared residual (SRMR) and comparative fit index (CFI) was performed on the US sample. Reliability as internal consistency was assessed using McDonald’s omega. Evidence in support of the predictive, convergent and discriminant validity of the scale was assessed using logistic regression ORs of association (OR) or Pearson correlation coefficients.Results Data for factor analysis were obtained from 1004 respondents, 504 in the UK and 500 in the USA. A scree plot, minimum average partial correlation analysis and parallel analysis suggested a three-factor 13-item scale with domains of vaccine beliefs (seven items), pain (three items) and personal deliberation (three items). Responses were recorded on a Likert scale ranging from disagree completely to agree completely, with higher score reflecting greater hesitancy. Potential total scores ranged from 13 to 65. Goodness of fit was excellent, with RMSEA=0.044, SRMR=0.041 and CFI=0.977. Predictive validity for COVID-19 vaccination status was excellent, with logistic regression ORs of association (95% CI) of 0.07 (0.04, 0.13), p

Despite decades of intense research, our understanding of the correlates of protection against Salmonella Typhi (S. Typhi) infection and disease remains incomplete. T follicular helper cells (TFH), an important link between cellular and humoral immunity, play an important role in the development and production of high affinity antibodies. While traditional TFH cells reside in germinal centers, circulating TFH (cTFH) (a memory subset of TFH) are present in blood. We used specimens from a typhoid controlled human infection model whereby participants were immunized with Ty21a live attenuated S. Typhi vaccine and then challenged with virulent S. Typhi. Some participants developed typhoid disease (TD) and some did not (NoTD), which allowed us to assess the association of cTFH subsets in the development and prevention of typhoid disease. Of note, the frequencies of cTFH were higher in NoTD than in TD participants, particularly 7 days after challenge. Furthermore, the frequencies of cTFH2 and cTFH17, but not cTFH1 subsets were higher in NoTD than TD participants. However, we observed that ex-vivo expression of activation and homing markers were higher in TD than in NoTD participants, particularly after challenge. Moreover, cTFH subsets produced higher levels of S. Typhi-specific responses (cytokines/chemokines) in both the immunization and challenge phases. Interestingly, unsupervised analysis revealed unique clusters with distinct signatures for each cTFH subset that may play a role in either the development or prevention of typhoid disease. Importantly, we observed associations between frequencies of defined cTFH subsets and anti-S. Typhi antibodies. Taken together, our results suggest that circulating TFH2 and TFH17 subsets might play an important role in the development or prevention of typhoid disease. The contribution of these clusters was found to be distinct in the immunization and/or challenge phases. These results have important implications for vaccines aimed at inducing long-lived protective T cell and antibody responses.

Controlled human infection model (CHIM) studies, which involve deliberate exposure of healthy human volunteers to an infectious agent, are recognised as important tools to advance vaccine development. These studies not only facilitate estimates of vaccine efficacy, but also offer an experimental approach to study disease pathogenesis and profile vaccine immunogenicity in a controlled environment, allowing correlation with clinical outcomes. Consequently, the data from CHIMs can be used to identify immunological correlates of protection (CoP), which can help accelerate vaccine development. In the case of invasive Salmonella infections, vaccination offers a potential instrument to prevent disease. Invasive Salmonella disease, caused by the enteric fever pathogens Salmonella enterica serovar Typhi (S. Typhi) and S. Paratyphi A, B and C, and nontyphoidal Salmonella (iNTS), remains a significant cause of mortality and morbidity in low- and middle-income countries, resulting in over 200,000 deaths and the loss of 15 million DALYs annually. CHIM studies have contributed to the understanding of S. Typhi infection and provided invaluable insight into the development of vaccines and CoP following vaccination against S. Typhi. However, CoP are less well understood for S. Paratyphi A and iNTS. This brief review focuses on the contribution of vaccine-CHIM trials to our understanding of the immune mechanisms associated with protection following vaccines against invasive Salmonella pathogens, particularly in relation to CoP.

An oral Controlled Human Infection Model (CHIM) with wild-type S. Typhi was re-established allowing us to explore the development of immunity. In this model, ~55% of volunteers who received the challenge reached typhoid diagnosis criteria (TD), while ~45% did not (NoTD). Intestinal macrophages are one of the first lines of defense against enteric pathogens. Most organs have self-renewing macrophages derived from tissue-resident progenitor cells seeded during the embryonic stage; however, the gut lacks these progenitors, and all intestinal macrophages are derived from circulating monocytes. After infecting gut-associated lymphoid tissues underlying microfold (M) cells, S. Typhi causes a primary bacteremia seeding organs of the reticuloendothelial system. Following days of incubation, a second bacteremia and clinical disease ensue. S. Typhi likely interacts with circulating monocytes or their progenitors in the bone marrow. We assessed changes in circulating monocytes after CHIM. The timepoints studied included 0 hours (pre-challenge) and days 1, 2, 4, 7, 9, 14, 21 and 28 after challenge. TD participants provided extra samples at the time of typhoid diagnosis, and 48-96 hours later (referred as ToD). We report changes in Classical Monocytes -CM-, Intermediate Monocytes -IM- and Non-classical Monocytes -NCM-. Changes in monocyte activation markers were identified only in TD participants and during ToD. CM and IM upregulated molecules related to interaction with bacterial antigens (TLR4, TLR5, CD36 and CD206). Of importance, CM and IM showed enhanced binding of S. Typhi. Upregulation of inflammatory molecules like TNF-α were detected, but mechanisms involved in limiting inflammation were also activated (CD163 and CD354 downregulation). CM upregulated molecules to interact/modulate cells of the adaptive immunity, including T cells (HLA-DR, CD274 and CD86) and B cells (CD257). Both CM and IM showed potential to migrate to the gut as integrin α4β7 was upregulated. Unsupervised analysis revealed 7 dynamic cell clusters. Five of these belonged to CM showing that this is the main population activated during ToD. Overall, we provide new insights into the changes that diverse circulating monocyte subsets undergo after typhoid diagnosis, which might be important to control this disease since these cells will ultimately become intestinal macrophages once they reach the gut.

Abstract We assessed S-268019-b, a recombinant spike protein vaccine with a squalene-based adjuvant, for superiority in its immunogenicity over ChAdOx1 nCoV-19 vaccine among adults in Japan. In this multicenter, randomized, observer-blinded, phase 3 study, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)–naïve participants (aged ≥ 18 years, without prior infection or vaccination against SARS-CoV-2) were randomized (1:1) to receive either S-268019-b or ChAdOx1 nCoV-19 as two intramuscular injections given 28 days apart. Participants who provided consent for a booster administration received S-268019-b at Day 211. The primary endpoint was SARS-CoV-2 neutralizing antibody (NAb) titer on Day 57; the key secondary endpoint was the seroconversion rate for SARS-CoV-2 NAb titer on Day 57. Other endpoints included anti–SARS-CoV-2 S-protein immunoglobulin (Ig)G antibody titer and safety. The demographic and baseline characteristics were generally comparable between S-268019-b (n = 611) and ChAdOx1 nCoV-19 (n = 610) groups. S-268019-b showed superior immunogenicity over ChAdOx1 nCoV-19, based on their geometric mean titers (GMTs) and GMT ratios of SARS-CoV-2 NAb on Day 57 by cytopathic effect assay (GMT [95% confidence interval {CI}] 19.92 [18.68, 21.23] versus 3.63 [3.41, 3.87]; GMT ratio [95% CI] 5.48 [5.01, 6.00], respectively; two-sided p-values

Abstract The immune mechanisms mediating COVID-19 vaccine attenuation of COVID-19 remain undescribed. We conducted comprehensive analyses detailing immune responses to SARS-CoV-2 virus in blood post-vaccination with ChAdOx1 nCoV-19 or a placebo. Samples from randomised placebo-controlled trials (NCT04324606 and NCT04400838) were taken at baseline, onset of COVID-19-like symptoms, and 7 days later, confirming COVID-19 using nucleic amplification test (NAAT test) via real-time PCR (RT-PCR). Serum cytokines were measured with multiplexed immunoassays. The transcriptome was analysed with long, short and small RNA sequencing. We found attenuation of RNA inflammatory signatures in ChAdOx1 nCoV-19 compared with placebo vaccinees and reduced levels of serum proteins associated with COVID-19 severity. KREMEN1, a putative alternative SARS-CoV-2 receptor, was downregulated in placebo compared with ChAdOx1 nCoV-19 vaccinees. Vaccination ameliorates reductions in cell counts across leukocyte populations and platelets noted at COVID-19 onset, without inducing potentially deleterious Th2-skewed immune responses. Multi-omics integration links a global reduction in miRNA expression at COVID-19 onset to increased pro-inflammatory responses at the mRNA level. This study reveals insights into the role of COVID-19 vaccines in mitigating disease severity by abrogating pro-inflammatory responses associated with severe COVID-19, affirming vaccine-mediated benefit in breakthrough infection, and highlighting the importance of clinically relevant endpoints in vaccine evaluation.

Abstract Respiratory syncytial virus (RSV) is the leading cause of hospitalisation for respiratory infection in young children. RSV disease severity is known to be age-dependent and highest in young infants, but other correlates of severity, particularly the presence of additional respiratory pathogens, are less well understood. In this study, nasopharyngeal swabs were collected from two cohorts of RSV-positive infants 100 pathogens, including all common respiratory viruses and bacteria, from samples collected from 433 infants, that burden of additional viruses is common (111/433, 26%) but only modestly correlates with RSV disease severity. In contrast, there is strong evidence in both cohorts and across age groups that presence of Haemophilus bacteria (194/433, 45%) is associated with higher severity, including much higher rates of hospitalisation (odds ratio 4.25, 95% CI 2.03–9.31). There is no evidence for association between higher severity and other detected bacteria, and no difference in severity between RSV genotypes. Our findings reveal the genomic diversity of additional pathogens during RSV infection in infants, and provide an evidence base for future causal investigations of the impact of co-infection on RSV disease severity.

Abstract It is well known that molecules confined very close to a surface arrange into molecular layers. Because solid-liquid interfaces are ubiquitous in the chemical, biological and physical sciences, it is crucial to develop methods to easily access molecular layers and exploit their distinct properties by producing molecular layered crystals. Here we report a method based on crystallization in ultra-thin puddles enabled by gas blowing, which allows to produce molecular layered crystals with thickness down to the monolayer onto a surface, making them directly accessible for characterization and further processing. By selecting four molecules with different types of polymorphs, we observed exclusive crystallization of polymorphs with Van der Waals interlayer interactions, which have not been observed with traditional confinement methods. In conclusion, the gas blowing approach unveils the opportunity to perform materials chemistry under confinement onto a surface, enabling the formation of distinct crystals with selected polymorphism.

The small island nations, territories, and states dotting the Pacific are among the most disproportionately affected populations worldwide in the face of climate change. Sea level rise coupled with increased tropical storms contribute to seawater incursion, flooding, personal injury, trauma, and death. They face an existential threat due to the consequences of global warming, specifically ice melt resulting in sea level rise, repercussions for which they are not historically culpable. Along with these environmental threats, Pacific Island communities are further burdened with high rates of adverse health conditions such as diabetes and obesity yet have limited healthcare resources due to minimal economic development. The Republic of the Marshall Islands (RMI) has one of the highest amputation rates worldwide due to advanced diabetes from lifestyle factors, limited healthcare infrastructure, financial disparities, and a culturally based hesitancy to seek medical attention, all of which lead to an increased incidence of diabetic complications. Challenges posed by non-communicable chronic diseases include diabetes and infectious diseases like tuberculosis, hepatitis, malaria, and Zika. Just as crucial to the narrative of the Marshallese people is a fundamental indigenous knowledge of their surroundings and an inseparable relationship to the environment, aquatic animals, and communities around them, denoting a holistic living system. Though the outlook is precarious, solutions centering on lifestyle interventions that are informed by Indigenous cultural strengths can provide a responsive framework and a ray of hope, offering potential solutions to these two. This short perspective highlights the RMI as a case study of the challenges the Pacific Island nations bear, from a legacy of annexation to the modern threat of climate change, compounded by health disparities.

Background Vaccination of infants with pneumococcal conjugate vaccines is recommended by the World Health Organization. Evidence is mixed regarding the differences in immunogenicity and efficacy of the different pneumococcal vaccines. Objectives The primary objective was to compare the immunogenicity of pneumococcal conjugate vaccine-10 versus pneumococcal conjugate vaccine-13. The main secondary objective was to compare the seroefficacy of pneumococcal conjugate vaccine-10 versus pneumococcal conjugate vaccine-13. Methods We searched the Cochrane Library, EMBASE, Global Health, MEDLINE, ClinicalTrials.gov and trialsearch.who.int up to July 2022. Studies were eligible if they directly compared either pneumococcal conjugate vaccine-7, pneumococcal conjugate vaccine-10 or pneumococcal conjugate vaccine-13 in randomised trials of children under 2 years of age, and provided immunogenicity data for at least one time point. Individual participant data were requested and aggregate data used otherwise. Outcomes included the geometric mean ratio of serotype-specific immunoglobulin G and the relative risk of seroinfection. Seroinfection was defined for each individual as a rise in antibody between the post-primary vaccination series time point and the booster dose, evidence of presumed subclinical infection. Each trial was analysed to obtain the log of the ratio of geometric means and its standard error. The relative risk of seroinfection (‘seroefficacy’) was estimated by comparing the proportion of participants with seroinfection between vaccine groups. The log-geometric mean ratios, log-relative risks and their standard errors constituted the input data for evidence synthesis. For serotypes contained in all three vaccines, evidence could be synthesised using a network meta-analysis. For other serotypes, meta-analysis was used. Results from seroefficacy analyses were incorporated into a mathematical model of pneumococcal transmission dynamics to compare the differential impact of pneumococcal conjugate vaccine-10 and pneumococcal conjugate vaccine-13 introduction on invasive pneumococcal disease cases. The model estimated the impact of vaccine introduction over a 25-year time period and an economic evaluation was conducted. Results In total, 47 studies were eligible from 38 countries. Twenty-eight and 12 studies with data available were included in immunogenicity and seroefficacy analyses, respectively. Geometric mean ratios comparing pneumococcal conjugate vaccine-13 versus pneumococcal conjugate vaccine-10 favoured pneumococcal conjugate vaccine-13 for serotypes 4, 9V and 23F at 1 month after primary vaccination series, with 1.14- to 1.54-fold significantly higher immunoglobulin G responses with pneumococcal conjugate vaccine-13. Risk of seroinfection prior to the time of booster dose was lower for pneumococcal conjugate vaccine-13 for serotype 4, 6B, 9V, 18C and 23F than for pneumococcal conjugate vaccine-10. Significant heterogeneity and inconsistency were present for most serotypes and for both outcomes. Twofold higher antibody after primary vaccination was associated with a 54% decrease in risk of seroinfection (relative risk 0.46, 95% confidence interval 0.23 to 0.96). In modelled scenarios, pneumococcal conjugate vaccine-13 or pneumococcal conjugate vaccine-10 introduction in 2006 resulted in a reduction in cases that was less rapid for pneumococcal conjugate vaccine-10 than for pneumococcal conjugate vaccine-13. The pneumococcal conjugate vaccine-13 programme was predicted to avoid an additional 2808 (95% confidence interval 2690 to 2925) cases of invasive pneumococcal disease compared with pneumococcal conjugate vaccine-10 introduction between 2006 and 2030. Limitations Analyses used data from infant vaccine studies with blood samples taken prior to a booster dose. The impact of extrapolating pre-booster efficacy to post-booster time points is unknown. Network meta-analysis models contained significant heterogeneity which may lead to bias. Conclusions Serotype-specific differences were found in immunogenicity and seroefficacy between pneumococcal conjugate vaccine-13 and pneumococcal conjugate vaccine-10. Higher antibody response after vaccination was associated with a lower risk of subsequent infection. These methods can be used to compare the pneumococcal conjugate vaccines and optimise vaccination strategies. For future work, seroefficacy estimates can be determined for other pneumococcal vaccines, which could contribute to licensing or policy decisions for new pneumococcal vaccines. Study registration This study is registered as PROSPERO CRD42019124580. Funding This award was funded by the National Institute for Health and Care Research (NIHR) Health Technology Assessment programme (NIHR award ref: 17/148/03) and is published in full in Health Technology Assessment; Vol. 28, No. 34. See the NIHR Funding and Awards website for further award information. Plain language summary Pneumococcal disease is a serious illness caused by a bacterial infection that can result in death. Children in the United Kingdom receive a vaccine to prevent this disease that protects against 13 different types of pneumococcal diseases. It is very effective, but other vaccines are also available, such as one that contains 10 types of pneumococcal diseases. Vaccines in the United Kingdom are bought by the government and the choice of which vaccine to provide is based on the cost of the vaccine as well as the benefits to our health. However, there is very little information comparing different vaccines and it is often assumed they are the same. We did a large analysis combining all studies of the two main licensed pneumococcal vaccines to determine which vaccine provides better protection against infection and how this affects costs. We used information from studies published in medical journals, and also data from studies done by the companies that own the vaccines. Our results showed that pneumococcal conjugate vaccine-13 vaccine provided better protection than pneumococcal conjugate vaccine-10 for 5 of the 10 serotypes that are contained in both vaccines. When we used these results to model what might have happened had either of these vaccines been introduced into the United Kingdom vaccination programme in 2006, we found that both vaccines caused a rapid decrease in the amount of disease, but that the decrease in disease was faster with pneumococcal conjugate vaccine-13 than pneumococcal conjugate vaccine-10. This resulted in 2808 cases of diseases prevented over a 25-year time frame with pneumococcal conjugate vaccine-13 compared with pneumococcal conjugate vaccine-10. Our methods can be used to compare other vaccines and we recommend this type of study be done in future when making decisions on vaccine product choice. Scientific summary Streptococcus pneumoniae (pneumococcus) causes severe diseases, including bacterial pneumonia, meningitis and sepsis, leading to substantial morbidity and mortality worldwide, with the highest disease burden being in young children and older adults. Three pneumococcal conjugate vaccines (PCVs) have been widely deployed worldwide in the past two decades: PCV7 (Prevnar; Pfizer, headquartered in New York City, New York, USA), PCV10 (Synflorix; GlaxoSmithKline, headquartered in Brentford, London, UK) and PCV13 (Prevenar 13; Pfizer, headquartered in New York City, New York, USA), resulting in substantial reduction in disease. Between 2009 and 2011, PCV7 was gradually replaced by PCV13 and PCV10 and is no longer available. The World Health Organization (WHO) does not preferentially endorse one PCV over another. Both PCV13 and PCV10 have been shown to provide both direct and indirect protection against pneumococcal pneumonia, invasive pneumococcal disease and nasopharyngeal carriage. Although there are 10 common serotypes in these 2 vaccines, the components of the vaccines differ, with different carrier proteins used in the conjugation process, as well as different amounts of polysaccharide, and these differences may contribute to differences in protection. Large randomised controlled trials directly comparing different PCVs with invasive pneumococcal disease as the primary outcome are not feasible. We previously used ‘seroinfection’ as an outcome for analysis of PCVs, where seroinfection is defined as an increase in antibody levels between the primary vaccination series (typically complete at 5–7 months of age) and the booster dose (typically administered at 9–18 months of age). Seroinfection can be regarded as evidence of exposure to the pathogen and a resultant subclinical infection, given antibody responses wane rapidly during this period otherwise. Seroinfection rates for different vaccines can be compared by calculating the relative risk (RR) of seroinfection, referred to herein as ‘seroefficacy’. We meta-analysed data from studies of PCVs to compare the immunogenicity and seroefficacy of PCV10 with PCV13 for each serotype. We aimed to determine if serotype-specific immune responses were higher for either vaccine and whether this resulted in greater protection again seroinfection. In addition, we explored the overall relationship between the higher immune response and protection against seroinfection in infants. Following this, we show how serotype-specific estimates of seroefficacy can be incorporated in vaccine cost-effectiveness models. Objectives The primary objective of the systematic review was to compare the immunogenicity of PCV10 versus PCV13 for each serotype contained in the vaccines. The secondary objectives were: to compare the seroefficacy of PCV10 versus PCV13 for each serotype contained in the vaccines for PCV10 and PCV13 separately, to estimate immunogenicity and seroefficacy in comparison with the older PCV7 vaccine to determine how the comparisons of immunogenicity and efficacy of PCV10 to PCV13 are affected by the co-administration of different routine vaccines. Methods Systematic review We conducted a systematic review identifying studies that compared the immunogenicity of licensed PCVs in trials which randomised children to one of two different PCVs. The PCVs included in the review were PCV7 (Prevnar; Pfizer), PCV10 (Synflorix; GlaxoSmithKline) and PCV13 (Prevenar 13; Pfizer); PCV7 was included even though no longer available, so that we could compare PCV13 and PCV10 indirectly through them each being compared with PCV7 for the same serotypes. Data sources The databases searched were Cochrane Database of Systematic Reviews and Cochrane Central Register of Controlled Trials, EMBASE, Global Health and MEDLINE. The trial registers searched were ClinicalTrials.gov (https://clinicaltrials.gov/) and WHO International Clinical Trials Registry Platform (https://trialsearch.who.int/). The search comprised title/abstract keywords and subject headings for pneumococcal vaccines and children. A methodological search filter for randomised controlled trials taken from the Cochrane Handbook was used to limit to randomised controlled trials. Pharmaceutical company websites (GlaxoSmithKline and Pfizer) were also hand-searched for relevant studies. No date or language limits were applied. Study selection Randomised controlled trials were included if they provided direct comparisons of either PCV7, PCV10 or PCV13 among infants and children ˂ 2 years of age, and if they provided estimates of antibody responses [serotype-specific anti-pneumococcal immunoglobulin G (IgG) to PCVs for at least one time point of 1] between 4 and 6 weeks after the primary vaccination series and/or 1 month after a booster vaccination. Individual participant-level data were retrieved if available. Aggregate data from publications were extracted if individual participant data were not available. Risk of bias in results of the included studies was assessed independently by two reviewers using the Cochrane Risk of Bias Tool. Data synthesis Each trial with individual participant-level data available was analysed to obtain the log of the ratio of geometric means (log-GMR) and its standard error (SE) for each serotype and time point of interest. The RR of seroinfection was estimated by comparing the proportion of participants with seroinfection between vaccine groups. When no seroinfection occurred in any group (numerator of absolute risk was 0), a small non-zero value (0.5) was added to both sero-infected and sero-non-infected groups to allow estimation of the RR. The log-GMRs, log-RRs and their SEs constituted the input data for evidence synthesis. Only trials supplying individual participant data were included in seroefficacy analyses. For serotypes contained in all three vaccines, evidence could be synthesised using a network meta-analysis (NMA) of all comparisons. For other serotypes, meta-analysis was used for evidence synthesis. To estimate the overall association between antibody geometric mean ratio (GMR) and RR across all serotypes, we fitted a mixed-effect model regressing study-level RRs of seroinfection on GMRs across serotypes, weighted by the sample size of each study. Fixed effects included GMR, serotype and interactions between GMR and serotype (allowing serotype-specific association), while study was included as a random effect. Mathematical modelling and retrospective economic evaluation To illustrate the use of serotype-specific estimates of seroefficacy in modelling vaccine impact and cost-effectiveness, we developed a serotype-specific mathematical model of pneumococcal transmission dynamics to compare the differential impact of PCV10 and PCV13 introduction on invasive pneumococcal disease cases with vaccine serotypes in England and Wales. The model estimated the impact over a 25-year time period from 2006 to 2030. We subsequently assessed the cost-effectiveness of introducing infant vaccination with PCV13 compared with introducing PCV10 from a healthcare payer perspective in England and Wales. More specifically, we retrospectively estimated the additional threshold price per dose below which PCV13 would be more cost-effective than PCV10 had they both been available at the time of introduction of the PCV vaccine programme in England and Wales in 2006. Results Database registry and hand searches identified 4699 publication records of which 47 studies (78 publication reports) satisfied our eligibility criteria. Nineteen studies (24 publication reports) were excluded from the analysis: 6 studies did not provide individual patient or aggregate data and 13 studies (18 publication reports) were studies with the vaccines of interest, but it was not possible to form a loop within the NMA to provide indirect evidence. The remaining 28 studies (54 publication records) from 2009 to 2023 were included in the NMAs. Twenty-two studies provided individual participant data with a further five studies reporting aggregate data. Immunogenicity Geometric mean ratios for comparisons between PCV13 versus PCV10 for any primary series schedule were higher for PCV13 for serotypes 4, 7F, 9V and 23F at 1 month after primary vaccination series, with 1.14- to 1.54-fold higher IgG responses with PCV13. Additional serotypes contained only in the PCV13 vaccine (3, 6A and 19A) also favoured PCV13 as expected. GMRs were similar for the remaining serotypes (1, 5, 6B, 14, 18C and 19F). GMRs favoured PCV7 over either PCV13 or PCV10 for serotypes 4, 6B, 9V, 14 and 23F. There was no difference in GMRs for serotypes 18C and 19F across three vaccines. At the pre-booster time point, data were available from 18 cohorts. IgG responses were lower with PCV13 compared with PCV10 for all PCV7 serotypes except for serotype 14, with the point estimates of GMRs comparing PCV13 versus PCV10 ranging from 0.44 to 0.78. IgG responses were higher for PCV13 for serotypes 1, 5 and 7F. GMRs comparing PCV13 versus PCV7 showed higher IgG with PCV7 for serotypes 4, 6B, 9V, 14 and 23F and higher IgG with PCV13 for serotype 19F. At 28 days post booster, data were available from 26 cohorts. GMRs favoured PCV13 over PCV10 for serotype 6B, 9V, 14 and 23F and favoured PCV10 over PCV13 for serotype 18C. For serotype 1, 5 and 7F, antibody responses were higher in PCV13 compared with PCV10. PCV7 recipients had higher geometric mean concentrations (GMCs) compared with PCV13 for all PCV7 serotypes except 6B for which there was no difference, and 19F, which favoured PCV13. For PCV13-only serotypes (3, 6A and 19A), GMRs favour PCV13 at all three time points. Substantial heterogeneity and network inconsistency were present for most serotypes at all three time points. To explore potential reasons for the observed heterogeneity, we summarised cohort-level GMRs and RRs for each vaccine comparison. These descriptive analyses revealed a lack of consistency in the direction of study-level estimates within each vaccine comparison, resulting in the significant heterogenicity. There was also no observable pattern in any trial-level variable (region, co-administered vaccines, vaccine schedule), from which one might propose a mechanism that would adequately explain this variation in GMRs. Seroefficacy There were 12 studies (15 cohorts) with available individual participant antibody data at both post-primary and prior to the booster dose, allowing serotype-specific estimation of seroefficacy from a total of 5152 participants. Of these 15 cohorts, 6 compared PCV10 versus PCV7, 3 compared PCV13 versus PCV7 and 6 compared PCV13 versus PCV10. Among PCV7 serotypes, the risk of seroinfection was lower with PCV13 than PCV10 for serotypes 4, 6B, 9V, 18C and 23F, while no difference was seen for serotype 14 and 19F. The RRs of seroinfection (PCV13 vs. PCV10) for PCV7 serotypes ranged from 0.32 (95% CI 0.19 to 0.52) for serotype 4 to 1.28 (95% CI 0.95 to 1.74) for serotype 14. For serotypes 1, 5 and 7F, evidence was summarised from six studies directly comparing PCV13 with PCV10. Comparisons between PCV13 and PCV7 favoured neither vaccine over the other, whereas comparisons between PCV7 and PCV10 favoured PCV7 for serotypes 5, 6B, 9V, 18C and 23F. The I2 and p-values indicated some heterogeneity for all PCV7 serotypes except for serotype 4 and 19F. In the mixed-effects model of all serotypes combined, vaccines that produced the same amount of antibody (GMR = 1) had very similar protection (adjusted RR 0.80, 95% CI 0.41 to 1.58). The model estimate indicates that for each twofold increase in antibody response, the risk of seroinfection was halved (GMR of 2.0; RR 0.46, 95% CI 0.23 to 0.96). Mathematical model and economic evaluation Mathematical model results showed that in the absence of any vaccine programme, an increase in invasive pneumococcal disease cases caused by all five serotypes would be seen over the 25-year time frame. With the introduction of either PCV13 or PCV10 vaccine programmes in 2006, case counts would have decreased, achieving near eradication of all serotypes within the time frame modelled. The decrease in cases was most rapid for serotype 6B and least rapid for serotype 4. The decrease in cases was less rapid for PCV10 than for PCV13 due to the lower seroefficacy. The introduction of an infant PCV13 programme was predicted to avoid an additional 2808 (95% CI 2690 to 2925) cases of invasive pneumococcal disease compared with PCV10 introduction between 2006 and 2030. This includes an estimated 326 cases of meningitis, 578 cases of sepsis, 1770 cases of invasive pneumonia and 30,680 cases of non-invasive pneumonia. Under base-case assumptions, this resulted in discounted healthcare savings of £13 million (95% CI £12 to £14 million). Including non-invasive pneumonia increased the savings to £27 million (95% CI £25 to £29 million). Conclusions In our study, we used a novel methodology to define seroinfection from immunogenicity data to compare the relative efficacy of PCVs in preventing infection. Our results using individual-level data from a global meta-analysis provide the first estimates of the comparative protection afforded by different pneumococcal vaccines and show that for many serotypes, carriage events are less common after PCV13 than PCV10, likely due to a higher antibody response. In addition, we quantify the relationship between the immune response to vaccination and protection against infection, measured serologically, and show that higher antibody responses in infants are associated with greater protection from infection. Licensure of new vaccines is based on non-inferiority comparisons with current vaccines and the proportion of antibody responses above the agreed threshold as a minimum requirement. Once a vaccine meets this ‘at-least-as-good-as’ immunogenicity criteria, it has previously not been clear whether exceeding it is of benefit, and the WHO position paper on pneumococcal vaccines states ‘It is unknown whether a lower serotype-specific GMC of antibody indicates less efficacy’. Our results show that lower protection against subclinical infection does indeed follow from lower antibody production and that two vaccines that produce a similar level of antibody will provide similar levels of protection. The implications of these findings are of greatest importance when a new vaccine roll-out is being considered. Lower antibody production or lower seroefficacy for one vaccine product does not necessarily imply limited effectiveness against invasive pneumococcal diseases when considering vaccines such as PCV10 and PCV13 which are highly effective vaccines in many settings. Instead, lower antibody responses lead to less rapidly observed indirect protection after implementation into a national programme as a smaller proportion of transmission events are blocked by the vaccine. This is evident in the mathematical modelling which showed less rapid decreases in the number of cases of invasive disease when introducing PCV10 compared with PCV13. Implications for practice This evidence of differences in serotype-specific protection can be incorporated into cost-effectiveness models used to compare vaccine products. Cost-effectiveness studies have highlighted the lack of evidence of comparative efficacy for different PCVs, resulting in previous cost-effectiveness models that ignore serotype-specific differences and assume equivalent efficacy for all serotypes covered by different PCVs. Our study fills this evidence gap and allows researchers and policy-makers to use more accurate vaccine-specific models in decision-making. Our cost-effectiveness analysis of a hypothetical scenario showed that introducing infant PCV13 was predicted to avert a higher burden of pneumococcal disease compared with PCV10. This would have realised a small saving of £13 million discounted over 24 years. When considering the introduction of new pneumococcal vaccines into the routine immunisation schedule, we recommend that differences in antibody responses for different vaccines be considered in modelling scenarios as higher antibody responses result in reduced transmission and greater impact on invasive diseases. Vaccine-specific threshold prices can then be determined for cost-effective vaccines. Our analysis showed that due to its higher efficacy against some serotypes, a higher threshold price per dose could be paid for PCV13 while remaining cost-effective. Study registration This study is registered as PROSPERO CRD42019124580. Funding This award was funded by the National Institute for Health and Care Research (NIHR) Health Technology Assessment programme (NIHR award ref: 17/148/03) and is published in full in Health Technology Assessment; Vol. 28, No. 34. See the NIHR Funding and Awards website for further award information.

Outbreaks of Ebolaviruses, such as Sudanvirus (SUDV) in Uganda in 2022, demonstrate that species other than the Zaire ebolavirus (EBOV), which is currently the sole virus represented in current licensed vaccines, remain a major threat to global health. There is a pressing need to develop effective pan-species vaccines and novel monoclonal antibody-based therapeutics for Ebolavirus disease. In response to recent outbreaks, the two dose, heterologous Ad26.ZEBOV/MVA-BN-Filo vaccine regimen was developed and was tested in a large phase II clinical trial (EBL2001) as part of the EBOVAC2 consortium. Here, we perform bulk sequencing of the variable heavy chain (VH) of B cell receptors (BCR) in forty participants from the EBL2001 trial in order to characterize the BCR repertoire in response to vaccination with Ad26.ZEBOV/MVA-BN-Filo. We develop a comprehensive database, EBOV-AbDab, of publicly available Ebolavirus-specific antibody sequences. We then use our database to predict the antigen-specific component of the vaccinee repertoires. Our results show striking convergence in VH germline gene usage across participants following the MVA-BN-Filo dose, and provide further evidence of the role of IGHV3–15 and IGHV3–13 antibodies in the B cell response to Ebolavirus glycoprotein. Furthermore, we found that previously described Ebola-specific mAb sequences present in EBOV-AbDab were sufficient to describe at least one of the ten most expanded BCR clonotypes in more than two thirds of our cohort of vaccinees following the boost, providing proof of principle for the utility of computational mining of immune repertoires.

Background There are data suggesting that intravenous immunoglobulin treatment has some benefit for certain forms of encephalitis but robust evidence from large randomised controlled trials in children with all-cause encephalitis is lacking. Objective To evaluate whether intravenous immunoglobulin treatment improves neurological outcomes in childhood encephalitis when given early in the illness. Design Phase 3b, investigator-initiated, randomised, double-blind, placebo-controlled trial of intravenous immunoglobulin for the treatment of encephalitis in children. Setting Twenty-one NHS Hospitals in the UK. Participants Children aged 6 months to 16 years with a diagnosis of acute or sub-acute encephalitis. Intervention Two doses (1 g/kg/dose) of either intravenous immunoglobulin or matching placebo, given 24–36 hours apart, in addition to standard treatment. Main outcome measure Participants were followed up for 12 months (+/– 4 weeks) after randomisation. The primary outcome measure was a ‘good recovery’ defined as a score of ≤ 2 on the Paediatric Glasgow Outcome Score Extended at 12 months after randomisation. Secondary outcomes The secondary outcomes were clinical, neurological, neuroimaging and neuropsychological results, identification of the proportion of children with immune-mediated encephalitis, and intravenous immunoglobulin safety data. Results We planned to recruit 308 children over a 42-month period. After enrolment of 18 participants (8 male; 44%) over 21 months (from December 2015 to September 2017), funding was withdrawn due to slow recruitment and the study was terminated. Ten participants were randomised to the intravenous immunoglobulin group, and eight to the placebo group, and all 18 participants were included in the analysis. At 12 months after randomisation, 9 participants [50%; intravenous immunoglobulin n = 5 (50%), placebo n = 4 (50%)] made good recovery and 5 participants [28%; intravenous immunoglobulin n = 3 (30%), placebo n = 2 (25%)] made a poor recovery. Three participants in the placebo group (43%) experienced a total of 10 serious adverse events compared with none in the intravenous immunoglobulin group but none of the adverse events were judged to be related to the study treatment. No deaths occurred during the study period. Conclusion ImmunoglobuliN in the Treatment of Encephalitis (IgNiTE) was halted prematurely due to slow recruitment. Given the small sample size, the study was underpowered to evaluate the effect of intravenous immunoglobulin when compared with placebo in childhood encephalitis. The study findings, albeit from a small sample size, support existing evidence that encephalitis results in poor neurological outcomes for many children. Lessons learned from the ImmunoglobuliN in the Treatment of Encephalitis trial would be valuable for the success of future trials set up to address the efficacy of early treatment with intravenous immunoglobulin in all-cause encephalitis in children. Study limitations and future work The study was underpowered to evaluate the efficacy of intravenous immunoglobulin in the treatment of childhood encephalitis due to the small sample size achieved. Future trials should seek to address this important question. Trial registration This trial is registered as Clinical Trials.gov (NCT02308982) and ISRCTN15791925. Funding This award was funded by the National Institute for Health and Care Research (NIHR) Efficacy and Mechanism Evaluation (EME) programme (NIHR award ref: 12/212/15) and is published in full in Efficacy and Mechanism Evaluation; Vol. 11, No. 6. See the NIHR Funding and Awards website for further award information. Plain language summary Encephalitis (inflammation of the brain) is a serious but rare condition affecting approximately 5 in 100,000 children in England. Encephalitis can have a big impact on affected children and their families. Approximately 12 out of 100 affected children will die and half of those that survive experience varying difficulties in the long term; these might include problems with memory, physical disabilities, seizures and changes in how they think and behave. There is some evidence that a treatment called intravenous immunoglobulin may benefit people affected by encephalitis. Intravenous immunoglobulin contains antibodies obtained from blood donations by different people, which is used to treat some types of inflammation. However, there have been no research studies investigating the effect of intravenous immunoglobulin when used in large numbers of children with all types of encephalitis. Furthermore, although intravenous immunoglobulin is sometimes used to treat children with encephalitis, it is often given after other treatments have been unsuccessful. Outcomes from encephalitis are determined largely by the amount of brain inflammation; it would therefore seem logical that giving a treatment early in the illness to limit the inflammation would be beneficial. In the ImmunoglobuliN in the Treatment of Encephalitis study, we aimed to find out whether giving intravenous immunoglobulin to children with encephalitis early in the illness can help them get better more quickly and reduce the difficulties they experience later on. Half of the children in the trial received intravenous immunoglobulin and the other half received an inactive medicine, known as placebo, in addition to the normal care they would receive in a hospital. We aimed to compare the recovery and outcomes between children in these two groups. This trial was stopped early due to withdrawal of funding, as fewer children than expected were enrolled into the study. Too few children were enrolled for us to be sure whether intravenous immunoglobulin benefits children with encephalitis. However, the trial findings highlight the impact of encephalitis on affected children, with around half of children demonstrating ongoing difficulties 1 year after the illness. Scientific summary Background There is significant mortality and morbidity from encephalitis in children despite the current standard of care. Thus, strategies to improve outcomes in patients with encephalitis are urgently required. Theoretical and empirical evidence suggest a beneficial role of intravenous immunoglobulin (IVIG) for viral and auto-immune forms of encephalitis. Therefore, we set up a prospective randomised controlled trial (RCT) to ascertain the efficacy of early IVIG treatment for all-cause encephalitis in children. In the study, children with encephalitis were randomised to receive two doses of either IVIG or placebo within five working days from the suspicion of an encephalitis diagnosis, in addition to normal standard of care. They were then followed up for 12 months after randomisation. We hypothesised that IVIG could have therapeutic benefit for children with encephalitis when administered early in the illness. Objectives The primary objective was to evaluate the efficacy of early IVIG treatment in childhood encephalitis. This was assessed by comparing the proportion of children in the 2 treatment groups who made good recovery, assessed using the paediatric version of the Glasgow outcome score extended, at 12 months after randomisation. The secondary objectives were to: (1) compare clinical, neurological, neuroimaging and neuropsychological outcomes between the treatment groups, (2) evaluate the proportion of participants with autoimmune encephalitis and (3) confirm the safety of IVIG. Methods Trial design This was a phase 3b multicentre, double-blind, randomised, placebo-controlled trial to evaluate the early use IVIG in childhood encephalitis. Setting Participants were recruited from 21 NHS Hospitals in the UK. Participants Inclusion criteria Participants were eligible if they were aged between 6 weeks and 16 years they met the case definition for possible encephalitis based on the International Encephalitis Consensus parents/guardians provided written informed consent, or assent if appropriate. Exclusion criteria The exclusion criteria included: (1) a high clinical suspicion of bacterial meningitis, (2) prior receipt of IVIG during the admission or known contraindication to IVIG, (3) traumatic brain injury, (4) history of metabolic encephalopathy, stroke, toxic or hypertensive encephalopathy, (5) pre-existing demyelinating disorder, (6) significant renal impairment, (7) hypercoagulable state, (8) hyperprolinaemia, (9) participation in another research trial involving an immunomodulatory treatment, (10) known to be pregnant, (11) any significant disease or clinical research that would impact on participation, or interfere with compliance with study requirements. Randomisation Participants were randomly assigned 1 : 1 ratio to receive 2 doses (1 g/kg/dose) of either IVIG or matching placebo, in addition to standard care. Randomisation was stratified by age and receipt of steroid treatment. Interventions Two doses of 1 g/kg/dose of either IVIG or a matching volume of placebo were given 24–36 hours apart, with the first dose administered as soon as possible after enrolment and within five working days from the suspicion of an encephalitis diagnosis. The active treatment (IVIG) used in the study was Privigen (100 mg/ml solution), manufactured and provided by CSL Behring. The placebo was a mixture of 0.9% saline + 0.1% human albumin solution, manufactured at the Royal Broadgreen and Liverpool Aseptic Production Unit, Liverpool, UK, under current good manufacturing practice conditions and its Manufacturer’s Importer’s Authorisation licence. The addition of albumin to saline was necessary to make the placebo visually identical to IVIG. Blinding Participants, treating clinicians, parents/guardians and outcome assessors were blinded to the allocated treatment. Primary outcome The primary outcome was good recovery (i.e. score of ≤2) on the paediatric version of the Glasgow Outcome Score-Extended (GOS-E Peds) at 12 months after randomisation. Secondary outcomes Clinical, neurological and neuropsychological outcomes Multiple clinical and neurological measures were collected during the hospital admission, at 4–8 weeks after discharge from acute care, and at 6 and 12 months after randomisation. A blinded neuropsychologist assessment of cognitive function was carried out at 12 months after randomisation. Radiological outcomes Brain magnetic resonance imaging (MRI) findings at 6 months after randomisation were compared with imaging results obtained during the acute illness. Safety data Safety and adverse events (AEs) data were collected until 12 months after randomisation. Identification of immune-mediated encephalitis Presence of specific auto-antibodies in serum was assessed. Statistical methods The analyses were performed on the intention-to-treat population; this included all participants who were randomised, irrespective of study treatment received. In the analysis of the AEs, all participants who received study treatment were included. Since 20% of participants were recruited before the trial was halted, all analyses are descriptive. Results Recruitment took place between 23 December 2015 and 26 September 2017. Recruitment was paused in September 2017 following withdrawal of funding due to slower than anticipated recruitment. Despite strategies implemented to improve recruitment, funding was not reinstated. Attempts at securing alternative funding were unsuccessful; therefore, the trial was closed on 24 October 2017. Participants and demographics At the time of halting the study, 18 participants had been randomised (IVIG n = 10; placebo n = 8). One participant each from the IVIG and placebo groups were withdrawn from the study before receipt of study treatment and one participant in the placebo arm refused a second dose of study treatment. Therefore 16 participants (IVIG n = 9; placebo n = 7) received at least one dose of the study treatment and 15 participants (IVIG n = 9, placebo n = 6) received two full doses of the study treatment. One participant in the placebo group was lost to follow up after the 6 months visit and 1 participant in the IVIG group withdrew consent prior to the visit 12 months after randomisation. The median age at randomisation was 4.09 years [interquartile range (IQR) = 2.0–11.8], 44% were male and 89% were of white ethnicity. Baseline characteristics were well matched across treatment arms. Primary outcome At 12 months after randomisation, 9 participants [50%; IVIG n = 5 (50%); placebo n = 4 (50%)] made a good recovery (score ≤2 on the GOS-E Peds) and 5 participants [28%; IVIG n = 3 (30%), placebo n = 2 (25%)] made a poor recovery (score > 2). Four participants (22%; IVIG n = 2 (20%), placebo n = 2 (25%)] did not undergo a GOS-E Peds assessment at 12 months after randomisation. Secondary outcomes Inpatient data Ten participants [56%; IVIG n = 5 (50%), placebo = 5 (63%)] were admitted to intensive care, and nine of these [90%; IVIG n = 4 (80%), placebo n = 5(100%)] required invasive ventilation, for a median duration of two days (IQR 2.0–3.0). The median length of stay on intensive care was 4.5 days (3.0–6.8) and the overall median length of hospitalisation for acute care was 11 days (7.8–19.5). Epilepsy diagnosis Three participants [17%; IVIG n = 1 (10%), placebo n = 2 (25%)] had a new diagnosis of epilepsy during the study period. Five participants [28%; IVIG n = 2 (20%), placebo n = 3 (38%)] had incomplete data for this outcome. Glasgow Outcome Score-Extended-Peds at 6 months after randomisation Eight participants [44%; IVIG n = 4 (40%), placebo n = 4 (50%)] made a good recovery at 6 months after randomisation, whereas seven participants [39%; IVIG n = 4 (50%), placebo n = 3 (38%)] made a poor recovery. Three participants [17%; IVIG n = 2 (20%), placebo n = 1 (13%)] did not undergo a GOS-E Peds assessment at 6 months after randomisation. Liverpool outcome score At 4–8 weeks after discharge from acute care, 5 participants [28%; IVIG n = 3 (30%), placebo n = 2 (25%)] made a full recovery [defined as a Liverpool Outcome Score (LOS) of >4], whereas 10 participants [56%; IVIG n = 5 (50%), placebo n = 5 (63%)] had minor to severe sequelae. Three participants [17%; IVIG n = 2 (20%); placebo n = 1 (13%)] did not have LOS data collected at this timepoint. At 12 months after randomisation, six participants [33%; IVIG n = 4 (40%), placebo n = 2 (25%)] made full recovery on the LOS assessment, while 8 participants [44%; IVIG n = 4 (40%), placebo n = 4 (50%)] reported minor to severe sequelae. Four participants [22%; IVIG n = 2 (20%); placebo n = 2 (25%)] did not have LOS data collected at this timepoint. Paediatric quality of life assessment Paediatric quality of life scores were available for seven participants [39%; IVIG n = 5 (50%), placebo n = 2 (25%)] at 4–8 weeks after discharge from acute care and for eight participants [44%; IVIG n = 6 (60%), placebo n = 2 (25%)] at 12 months post randomisation. At 4–8 weeks after discharge from acute care, the mean PedsQL score was 77.9 (standard deviation, SD, 11.10) and 56.5 (SD 7.8) for the IVIG and placebo group, respectively. At 12 months, mean PedsQL scores were 79.9 (SD 21.6) and 63.7 (SD 30.1) for the IVIG and placebo groups, respectively. Gross motor function classification system At 4–8 weeks after discharge from acute care, seven participants [39%; IVIG n = 5 (50%); placebo n = 2 (25%)] had mild impairment of gross motor functioning. These data were not available for 11 participants [61%; IVIG n = 5 (50%), placebo n = 6 (75%)] at this timepoint. At 12 months after randomisation, eight participants [44%; IVIG n = 6 (60%); placebo n = 2 (25%)] experienced mild or severe impairment of gross motor function. These data were not available for ten participants [56%; IVIG n = 4 (40%), placebo n = 6 (75%)] at this timepoint. Strengths and difficulties assessment Strengths and Difficulties Questionnaire (SDQ) results were available for seven participants (IVIG n = 5, placebo n = 2) at 4–8 weeks after discharge from acute care and eight participants (IVIG n = 6, placebo n = 2) at 12 months after randomisation. At 4–8 weeks after discharge from acute care, five participants [28%; IVIG n = 4 (40%); placebo n = 1 (13%)] had a close to average SDQ score, one participant [6%, IVIG n = 1 (10%), placebo n = 0] had a slightly raised SDQ score and one participant [6%, IVIG n = 0, placebo n = 1 (13%)] had a very high SDQ score. At 12 months after randomisation, the same number of participants had a close to average score and slightly raised score, but two participants [11%; IVIG n = 1 (10%), placebo n = 1 (13%)] had a very high SDQ score. Adaptive Behaviors Assessment System – second edition At 4–8 weeks after discharge from acute care, five participants [28%; IVIG n = 4 (40%), placebo n = 1 (13%)] had an Adaptive Behaviors Assessment System-second edition (ABAS-II) score that was either similar or higher than the average score of the normative population. At the same time point, three participants [17%; IVIG n = 2 (20%), placebo n = 1 (13%)] had a score that was lower than the average score. Ten participants [56%; IVIG n = 4 (40%), placebo n = 6 (75%)] did not have ABAS-II assessment at this timepoint. At 12 months after randomisation, the same number of participants had a score that was below the average, but four participants [22%; IVIG n = 3 (30%), placebo n = 1 (13%)] had a score that was either similar or higher than the average score, and 11 participants [61%; IVIG n = 5 (50%), placebo n = 6 (75%)] did not have ABAS-II assessment at this timepoint. Neuropsychology assessment Thirteen participants (72%; IVIG n = 8 (80%); placebo n = 5 (63%)] had blinded neuropsychology assessment at 12 months after randomisation; four [30%; IVIG n = 2 (25%), placebo n = 2 (40%)] of these participants were unable to complete the full battery of assessments due to attention or behavioural needs. Five participants [28%; IVIG n = 2 (20%), placebo n = 3 (38%)] did not undergo neuropsychology assessment. Five participants [28%; IVIG n = 4 (40%), placebo n = 1 (13%)] had a score of ≥85 (indicating normal development) for Full-Scale IQ, six [33%; IVIG n = 4 (40%); placebo n = 2 (25%)] for Verbal Comprehension Index (VCI), five [28%; IVIG n = 4 (40%), placebo n = 1 (13%)] for visual spatial; four [22%; IVIG n = 4 (40%), placebo n = 0 (0%)] for working memory index (WMI); and four [22%; IVIG n = 3 (30%); placebo n = 1 (13%)] for Perceptual Reasoning Index (PRI). Two participants (one in each treatment arm) were assessed using the Bayley scale of infant and toddler development, one participant (IVIG arm) had severe neurodevelopmental impairment while the other (placebo arm) had a normal neurodevelopmental outcome. Neuroimaging Nineteen acute neuroimaging scans were available for 13 participants. Five scans (for five unique participants) had abnormal findings; all of these were MRI scans. Four of the abnormal scans showed bilateral lesions. There were nine follow-up scans for eight unique participants of which six scans (for five unique participants) were normal and unchanged from the acute scan. Three follow-up scans (for three unique participants) had abnormal findings; two of these were unchanged from the acute scans and an acute scan was not available for comparison one participant. Autoantibody testing Twelve participants had autoantibody testing. One participant (placebo n = 1) was positive for LGI1 antibodies, and one participant (placebo n = 1) was positive for myelin oligodendrocyte glycoprotein (MOG) antibodies. Two additional participants (IVIG n = 2) were positive for IgG to live neurons, indicating the presence of IgG antibodies binding to neurons, but negative for antibodies to the specific antigens tested for in the study. Safety reporting One participant in the IVIG group reported an AE of special interest; the participant developed a fever during IVIG infusion; however, this was judged to be unrelated to the study treatment. Ten serious AEs occurred in three participants in the placebo group and none in the IVIG group. None of the serious adverse events (SAEs) were judged to be related to the study treatment. No deaths occurred during the study period. Conclusions ImmunoglobuliN in the Treatment of Encephalitis (IgNiTE) was the first RCT to prospectively evaluate the efficacy of IVIG in childhood encephalitis. It was anticipated that data from IgNiTE would provide definitive evidence on which to base the management of children with encephalitis in the UK and worldwide. However, due to slow recruitment, the trial was terminated early. Therefore, the trial did not reach its pre-determined sample size and was underpowered, making it impossible to reach a conclusion on the role of IVIG in treatment of childhood encephalitis. Nonetheless, IgNiTE has highlighted several key learning points. Firstly, IgNiTE has demonstrated the feasibility of setting up a large multi-centre trial efficacy trial in a cohort of children with a rare condition such as encephalitis. Secondly, data from IgNiTE, albeit derived from a small sample size, suggest the safety of IVIG and provide some insight into the burden that encephalitis places on children and the NHS. Over half of the study participants were admitted to the intensive care unit with 90% of those admitted requiring invasive ventilation, with a prolonged overall length of hospitalisation. In addition, a notable proportion of children experienced some degree of disability at follow-up, highlighting the need to prioritise studies aimed at identifying strategies to alleviate the burden from this rare but debilitating disease. For future studies aimed at addressing the efficacy of early IVIG treatment in childhood encephalitis, consideration should be given to practical challenges with setting up RCTs for rare diseases. These include the necessity to recruit from multiple sites to achieve the sample size, the importance of clinical equipoise amongst treating clinicians, and the trade-off between having a stringent but robust set of entry criteria and the impact of this on recruitment. Trial registration This trial is registered as Clinical Trials.gov (NCT02308982) and ISRCTN15791925. Funding This award was funded by the National Institute for Health and Care Research (NIHR) Efficacy and Mechanism Evaluation (EME) programme (NIHR award ref: 12/212/15) and is published in full in Efficacy and Mechanism Evaluation; Vol. 11, No. 6. See the NIHR Funding and Awards website for further award information.

BackgroundDespite the availability of various dietary assessment tools, there is a need for a tool aligned with the needs of lifestyle medicine (LM) physicians. Such a tool would be brief, aimed at use in a clinical setting, and focused on a “food as medicine” approach consistent with recommendations for a diet based predominately on whole plant foods. The objective of this study is to describe the development and initial pilot testing of a brief, dietary screener to assess the proportion of whole, unrefined plant foods and water relative to total food and beverage intake.MethodsA multidisciplinary study team led the screener development, providing input on the design and food/beverage items included, and existing published dietary assessment tools were reviewed for relevance. Feedback was solicited from LM practitioners in the form of a cross-sectional survey that captured information on medical practice, barriers, and needs in assessing patients’ diets, in addition to an opportunity to complete the screener and provide feedback on its utility. The study team assessed feedback and revised the screener accordingly, which included seeking and incorporating feedback on additional food items to be included from subject matter experts in specific cultural and ethnic groups in the United States. The final screener was submitted for professional design, and scoring was developed.ResultsOf 539 total participants, the majority reported assessing diet either informally (62%) or formally (26%) during patient encounters, and 73% reported discussing diet with all or most of their patients. Participants also reported facing barriers (80%) to assessing diet. Eighty-eight percent believed the screener was quick enough to use in a clinical setting, and 68% reported they would use it.ConclusionThe ACLM Diet Screener was developed through iterative review and pilot testing. The screener is a brief, 27-item diet assessment tool that can be successfully used in clinical settings to track patient dietary intakes, guide clinical conversations, and support nutrition prescriptions. Pilot testing of the screener found strong alignment with clinician needs for assessing a patient’s intake of whole plant food and water relative to the overall diet. Future research will involve pilot testing the screener in clinical interventions and conducting a validation study to establish construct validity.

Introduction Physical activity (PA) is protective against type 2 diabetes (T2D). However, data on pragmatic long-term interventions to reduce the risk of developing T2D via increased PA are lacking. This study investigated the cost-effectiveness of a pragmatic PA intervention in a multiethnic population at high risk of T2D.Materials and methods We adapted the School for Public Health Research diabetes prevention model, using the PROPELS trial data and analyses of the NAVIGATOR trial. Lifetime costs, lifetime quality-adjusted life years (QALYs), and incremental cost-effectiveness ratios (ICERs) were calculated for each intervention (Walking Away (WA) and Walking Away Plus (WA+)) versus usual care and compared with National Institute for Health and Care Excellence’s willingness-to-pay of £20 000–£30 000 per QALY gained. We conducted scenario analyses on the outcomes of the PROPELS trial data and a threshold analysis to determine the change in step count that would be needed for the interventions to be cost-effective.Results Estimated lifetime costs for usual care, WA, and WA+ were £22 598, £23 018, and £22 945, respectively. Estimated QALYs were 9.323, 9.312, and 9.330, respectively. WA+ was estimated to be more effective and cheaper than WA. WA+ had an ICER of £49 273 per QALY gained versus usual care. In none of our scenario analyses did either WA or WA+ have an ICER below £20 000 per QALY gained. Our threshold analysis suggested that a PA intervention costing the same as WA+ would have an ICER below £20 000/QALY if it were to achieve an increase in step count of 500 steps per day which was 100% maintained at 4 years.Conclusions We found that neither WA nor WA+ was cost-effective at a limit of £20 000 per QALY gained. Our threshold analysis showed that interventions to increase step count can be cost-effective at this limit if they achieve greater long-term maintenance of effect.Trial Registration number ISRCTN registration: ISRCTN83465245: The PRomotion Of Physical activity through structuredEducation with differing Levels of ongoing Support for those with pre-diabetes (PROPELS)https://doi.org/10.1186/ISRCTN83465245.

Abstract RNAseq data can be used to infer genetic variants, yet its use for estimating genetic population structure remains underexplored. Here, we construct a freely available computational tool (RGStraP) to estimate RNAseq-based genetic principal components (RG-PCs) and assess whether RG-PCs can be used to control for population structure in gene expression analyses. Using whole blood samples from understudied Nepalese populations and the Geuvadis study, we show that RG-PCs had comparable results to paired array-based genotypes, with high genotype concordance and high correlations of genetic principal components, capturing subpopulations within the dataset. In differential gene expression analysis, we found that inclusion of RG-PCs as covariates reduced test statistic inflation. Our paper demonstrates that genetic population structure can be directly inferred and controlled for using RNAseq data, thus facilitating improved retrospective and future analyses of transcriptomic data.

Abstract Tuberculosis (TB) is a prevalent disease causing an estimated 1.6 million deaths and 10.6 million new cases annually. Discriminating TB disease from differential diagnoses can be complex, particularly in the field. Increased levels of complement component C1q in serum have been identified as a specific and accessible biomarker for TB disease but the source of C1q in circulation has not been identified. Here, data and samples previously collected from human cohorts, a clinical trial and a non-human primate study were used to identify cells producing C1q in circulation. Cell subset frequencies were correlated with serum C1q levels and combined with single cell RNA sequencing and flow cytometry analyses. This identified monocytes as C1q producers in circulation, with a pronounced expression of C1q in classical and intermediate monocytes and variable expression in non-classical monocytes.

Abstract Background Universal immunisation is the cornerstone of preventive medicine for children, The World Health Organisation (WHO) recommends diphtheria-tetanus-pertussis (DTP) vaccine administered at 6, 10 and 14 weeks of age as part of routine immunisation. However, globally, more than 17 unique DTP-containing vaccine schedules are in use. New vaccines for other diseases continue to be introduced into the infant immunisation schedule, resulting in an increasingly crowded schedule. The OptImms trial will assess whether antibody titres against pertussis and other antigens in childhood can be maintained whilst adjusting the current Expanded Programme on Immunisation (EPI) schedule to provide space for the introduction of new vaccines. Methods The OptImms studies are two randomised, five-arm, non-inferiority clinical trials in Nepal and Uganda. Infants aged 6 weeks will be randomised to one of five primary vaccination schedules based on age at first DTwP-vaccination (6 versus 8 weeks of age), number of doses in the DTwP priming series (two versus three), and spacing of priming series vaccinations (4 versus 8 weeks). Additionally, participants will be randomised to receive their DTwP booster at 9 or 12 months of age. A further sub-study will compare the co-administration of typhoid vaccine with other routine vaccines at one year of age. The primary outcome is anti-pertussis toxin IgG antibodies measured at the time of the booster dose. Secondary outcomes include antibodies against other vaccine antigens in the primary schedule and their safety. Discussion These data will provide key data to inform policy decisions on streamlining vaccination schedules in childhood. Trial registrations ISRCTN12240140 (Nepa1, 7th January 2021) and ISRCTN6036654 (Uganda, 17th February 2021).

Abstract The pediatric population receives the majority of vaccines globally, yet there is a paucity of studies on the transcriptional response induced by immunization in this special population. In this study, we performed a systems-level analysis of immune responses to the trivalent inactivated influenza vaccine adjuvanted with MF-59 in children (15–24 months old) and in young, healthy adults. We analyzed transcriptional responses elicited by vaccination in peripheral blood, as well as cellular and antibody responses following primary and booster vaccinations. Our analysis revealed that primary vaccination induced a persistent transcriptional signature of innate immunity; booster vaccination induced a transcriptional signature of an enhanced memory-like innate response, which was consistent with enhanced activation of myeloid cells assessed by flow cytometry. Furthermore, we identified a transcriptional signature of type 1 interferon response post-booster vaccination and at baseline that was correlated with the local reactogenicity to vaccination and defined an early signature that correlated with the hemagglutinin antibody titers. These results highlight an adaptive behavior of the innate immune system in evoking a memory-like response to secondary vaccination and define molecular correlates of reactogenicity and immunogenicity in infants.

Introduction Invasive non-typhoidal Salmonella (iNTS) serovars are a major cause of community-acquired bloodstream infections in sub-Saharan Africa (SSA). In this setting, Salmonella enterica serovar Typhimurium accounts for two-thirds of infections and is associated with an estimated case fatality rate of 15%–20%. Several iNTS vaccine candidates are in early-stage assessment which—if found effective—would provide a valuable public health tool to reduce iNTS disease burden. The CHANTS study aims to develop a first-in-human Salmonella Typhimurium controlled human infection model, which can act as a platform for future vaccine evaluation, in addition to providing novel insights into iNTS disease pathogenesis.Methods and analysis This double-blind, safety and dose-escalation study will randomise 40–80 healthy UK participants aged 18–50 to receive oral challenge with one of two strains of S. Typhimurium belonging to the ST19 (strain 4/74) or ST313 (strain D23580) lineages. 4/74 is a global strain often associated with diarrhoeal illness predominantly in high-income settings, while D23580 is an archetypal strain representing invasive disease-causing isolates found in SSA. The primary objective is to determine the minimum infectious dose (colony-forming unit) required for 60%–75% of participants to develop clinical or microbiological features of systemic salmonellosis. Secondary endpoints are to describe and compare the clinical, microbiological and immunological responses following challenge. Dose escalation or de-escalation will be undertaken by continual-reassessment methodology and limited within prespecified safety thresholds. Exploratory objectives are to describe mechanisms of iNTS virulence, identify putative immune correlates of protection and describe host–pathogen interactions in response to infection.Ethics and dissemination Ethical approval has been obtained from the NHS Health Research Authority (London—Fulham Research Ethics Committee 21/PR/0051; IRAS Project ID 301659). The study findings will be disseminated in international peer-reviewed journals and presented at national/international stakeholder meetings. Study outcome summaries will be provided to both funders and participants.Trial registration number NCT05870150

Abstract Whereas most infants infected with respiratory syncytial virus (RSV) show no or only mild symptoms, an estimated 3 million children under five are hospitalized annually due to RSV disease. This study aimed to investigate biological mechanisms and associated biomarkers underlying RSV disease heterogeneity in young infants, enabling the potential to objectively categorize RSV‐infected infants according to their medical needs. Immunophenotypic and functional profiling demonstrated the emergence of immature and progenitor‐like neutrophils, proliferative monocytes (HLA‐DRLow, Ki67+), impaired antigen‐presenting function, downregulation of T cell response and low abundance of HLA‐DRLow B cells in severe RSV disease. HLA‐DRLow monocytes were found as a hallmark of RSV‐infected infants requiring hospitalization. Complementary transcriptomics identified genes associated with disease severity and pointed to the emergency myelopoiesis response. These results shed new light on mechanisms underlying the pathogenesis and development of severe RSV disease and identified potential new candidate biomarkers for patient stratification.

Objectives To develop and validate the Oxford Needle Experience (ONE) scale, an instrument to assess needle fear, attitudes and expectations in the general population.Design Cross-sectional validation study.Setting Internet-based with participants in the UK and USA.Participants UK and US representative samples stratified by age, sex, and ethnicity using the Prolific Academic platform.Main outcome measures Exploratory factor analysis with categorical variables and a polychoric correlation matrix followed by promax oblique rotation on the UK sample for the ONE scale. Confirmatory factor analysis (CFA) with a Satorra-Bentler scaled test statistic evaluating the root mean squared error of approximation (RMSEA), standardised root mean squared residual (SRMR) and comparative fit index (CFI) on the US sample. Reliability as internal consistency using McDonald’s omega. Convergent validity using the Pearson correlation coefficient. Predictive and discriminant validity using logistic regression ORs of association (OR).Results The population included 1000 respondents, 500 in the UK and 500 in the USA. Minimum average partial correlation and a scree plot suggested four factors should be retained: injection hesitancy, blood-related hesitancy, recalled negative experiences and perceived benefits, yielding a 19-question scale. On CFA, the RMSEA was 0.070 (90% CI, 0.064 to 0.077), SRMR 0.053 and CFI 0.925. McDonald’s omega was 0.92 and 0.93 in the UK and US samples, respectively. Convergent validity with the four-item Oxford Coronavirus Explanations, Attitudes and Narratives Survey (OCEANS) needle fear scale demonstrated a strong correlation (r=0.83). Predictive validity with a single-question COVID-19 vaccination status question demonstrated a strong association, OR (95% CI) 0.97 (0.96 to 0.98), p

Introduction Invasive non-typhoidal Salmonellosis (iNTS) is mainly caused by Salmonella enterica serovars Typhimurium and Enteritidis and is estimated to result in 77 500 deaths per year, disproportionately affecting children under 5 years of age in sub-Saharan Africa. Invasive non-typhoidal Salmonellae serovars are increasingly acquiring resistance to first-line antibiotics, thus an effective vaccine would be a valuable tool in reducing morbidity and mortality from infection. While NTS livestock vaccines are in wide use, no licensed vaccines exist for use in humans. Here, a first-in-human study of a novel vaccine (iNTS-GMMA) containing S. Typhimurium and S. Enteritidis Generalised Modules for Membrane Antigens (GMMA) outer membrane vesicles is presented.Method and analysis The Salmonella Vaccine Study in Oxford is a randomised placebo-controlled participant-observer blind phase I study of the iNTS-GMMA vaccine. Healthy adult volunteers will be randomised to receive three intramuscular injections of the iNTS-GMMA vaccine, containing equal quantities of S. Typhimurium and S. Enteritidis GMMA particles adsorbed on Alhydrogel, or an Alhydrogel placebo at 0, 2 and 6 months. Participants will be sequentially enrolled into three groups: group 1, 1:1 randomisation to low dose iNTS-GMMA vaccine or placebo; group 2, 1:1 randomisation to full dose iNTS-GMMA vaccine or placebo; group 3, 2:1 randomisation to full dose or lower dose (dependant on DSMC reviews of groups 1 and 2) iNTS-GMMA vaccine or placebo.The primary objective is safety and tolerability of the vaccine. The secondary objective is immunogenicity as measured by O-antigen based ELISA. Further exploratory objectives will characterise the expanded human immune profile.Ethics and dissemination Ethical approval for this study has been obtained from the South Central—Oxford A Research Ethics Committee (Ethics REF:22/SC/0059). Appropriate documentation and regulatory approvals have been acquired. Results will be disseminated via peer-reviewed articles and conferences.Trial registration number EudraCT Number: 2020-000510-14.

Objective To investigate whether intravenous immunoglobulin (IVIG) improves neurological outcomes in children with encephalitis when administered early in the illness.Design Phase 3b multicentre, double-blind, randomised placebo-controlled trial.Setting Twenty-one hospitals in the UK.Participants Children aged 6 months to 16 years with a diagnosis of acute or subacute encephalitis, with a planned sample size of 308.Intervention Two doses (1 g/kg/dose) of either IVIG or matching placebo given 24–36 hours apart, in addition to standard treatment.Main outcome measure The primary outcome was a ‘good recovery’ at 12 months after randomisation, defined as a score of≤2 on the Paediatric Glasgow Outcome Score Extended.Secondary outcome measures The secondary outcomes were clinical, neurological, neuroimaging and neuropsychological results, identification of the proportion of children with immune-mediated encephalitis, and IVIG safety data.Results 18 participants were recruited from 12 hospitals and randomised to receive either IVIG (n=10) or placebo (n=8) between 23 December 2015 and 26 September 2017. The study was terminated early following withdrawal of funding due to slower than anticipated recruitment, and therefore did not reach the predetermined sample size required to achieve the primary study objective; thus, the results are descriptive. At 12 months after randomisation, 9 of the 18 participants (IVIG n=5/10 (50%), placebo n=4/8 (50%)) made a good recovery and 5 participants (IVIG n=3/10 (30%), placebo n=2/8 (25%)) made a poor recovery. Three participants (IVIG n=1/10 (10%), placebo n=2/8 (25%)) had a new diagnosis of epilepsy during the study period. Two participants were found to have specific autoantibodies associated with autoimmune encephalitis. No serious adverse events were reported in participants receiving IVIG.Conclusions The IgNiTE (ImmunoglobuliN in the Treatment of Encephalitis) study findings support existing evidence of poor neurological outcomes in children with encephalitis. However, the study was halted prematurely and was therefore underpowered to evaluate the effect of early IVIG treatment compared with placebo in childhood encephalitis.Trial registration number Clinical Trials.gov NCT02308982; ICRCTN registry ISRCTN15791925.

Raman spectroscopy is one of the most common methods to characterize graphene-related 2D materials, providing information on a wide range of physical and chemical properties. Because of typical sample inhomogeneity, Raman spectra are acquired from several locations across a sample, and analysis is carried out on the averaged spectrum from all locations. This is then used to characterize the “quality” of the graphene produced, in particular the level of exfoliation for top-down manufactured materials. However, these have generally been developed using samples prepared with careful separation of unexfoliated materials. In this work we assess these metrics when applied to non-ideal samples, where unexfoliated graphite has been deliberately added to the exfoliated material. We demonstrate that previously published metrics, when applied to averaged spectra, do not allow the presence of this unexfoliated material to be reliably detected. Furthermore, when a sufficiently large number of spectra are acquired, it is found that by processing and classifying individual spectra, rather than the averaged spectrum, it is possible to identify the presence of this material in the sample, although quantification of the amount remains approximate. We therefore recommend this approach as a robust methodology for reliable characterization of mass-produced graphene-related 2D materials using confocal Raman spectroscopy.

In this prospective, observational study (ClinicalTrials.gov Identifier: NCT02661464), long-term safety information was collected from participants previously exposed to the Ebola vaccines Ad26.ZEBOV and/or MVA-BN-Filo while enrolled in phase 1, 2, or 3 clinical studies. The study was conducted at 15 sites in seven countries (Burkina Faso, France, Kenya, Tanzania, Uganda, the United Kingdom, and the United States). Adult participants and offspring from vaccinated female participants who became pregnant (estimated conception ≤28 days after vaccination with MVA-BN-Filo or ≤3 months after vaccination with Ad26.ZEBOV) were enrolled. Adults were followed for 60 months after their first vaccination, and children born to female participants were followed for 60 months after birth. In the full analysis set (n = 614 adults; median age [range]: 32.0 [18–65] years), 49 (8.0%) had ≥1 serious adverse event (SAE); the incidence rate of any SAE was 27.4 per 1000 person-years (95% confidence interval: 21.0, 35.2). The unrelated SAEs of malaria were reported in the two infants in the full analysis set, aged 11 and 18 months; both episodes were resolved. No deaths or life-threatening SAEs occurred during the study. Overall, no major safety issues were identified; one related SAE was reported. These findings support the long-term clinical safety of the Ad26.ZEBOV and MVA-BN-Filo vaccines.

IntroductionThe immune mechanisms supporting partial protection from reinfection and disease by the respiratory syncytial virus (RSV) have not been fully characterized. In older adults, symptoms are typically mild but can be serious in patients with comorbidities when the infection extends to the lower respiratory tract.MethodsThis study formed part of the RESCEU older-adults prospective-cohort study in Northern Europe (2017–2019; NCT03621930) in which a thousand participants were followed over an RSV season. Peripheral-blood samples (taken pre-season, post-season, during illness and convalescence) were analyzed from participants who (i) had a symptomatic acute respiratory tract infection by RSV (RSV-ARTI; N=35) or (ii) asymptomatic RSV infection (RSV-Asymptomatic; N=16). These analyses included evaluations of antibody (Fc-mediated–) functional features and cell-mediated immunity, in which univariate and machine-learning (ML) models were used to explore differences between groups.ResultsPre–RSV-season peripheral-blood biomarkers were predictive of symptomatic RSV infection. T-cell data were more predictive than functional antibody data (area under receiver operating characteristic curve [AUROC] for the models were 99% and 76%, respectively). The pre-RSV season T-cell phenotypes which were selected by the ML modelling and which were more frequent in RSV-Asymptomatic group than in the RSV-ARTI group, coincided with prominent phenotypes identified during convalescence from RSV-ARTI (e.g., IFN-γ+, TNF-α+ and CD40L+ for CD4+, and IFN-γ+ and 4-1BB+ for CD8+).ConclusionThe evaluation and statistical modelling of numerous immunological parameters over the RSV season suggests a primary role of cellular immunity in preventing symptomatic RSV infections in older adults.

Background: The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which marks 22 years since the publication of the first Typhi genome, represents the largest Typhi genome sequence collection to date (n=13,000). Methods: This is a meta-analysis of global genotype and antimicrobial resistance (AMR) determinants extracted from previously sequenced genome data and analysed using consistent methods implemented in open analysis platforms GenoTyphi and Pathogenwatch. Results: Compared with previous global snapshots, the data highlight that genotype 4.3.1 (H58) has not spread beyond Asia and Eastern/Southern Africa; in other regions, distinct genotypes dominate and have independently evolved AMR. Data gaps remain in many parts of the world, and we show the potential of travel-associated sequences to provide informal ‘sentinel’ surveillance for such locations. The data indicate that ciprofloxacin non-susceptibility (>1 resistance determinant) is widespread across geographies and genotypes, with high-level ciprofloxacin resistance (≥3 determinants) reaching 20% prevalence in South Asia. Extensively drug-resistant (XDR) typhoid has become dominant in Pakistan (70% in 2020) but has not yet become established elsewhere. Ceftriaxone resistance has emerged in eight non-XDR genotypes, including a ciprofloxacin-resistant lineage (4.3.1.2.1) in India. Azithromycin resistance mutations were detected at low prevalence in South Asia, including in two common ciprofloxacin-resistant genotypes. Conclusions: The consortium’s aim is to encourage continued data sharing and collaboration to monitor the emergence and global spread of AMR Typhi, and to inform decision-making around the introduction of typhoid conjugate vaccines (TCVs) and other prevention and control strategies. Funding: No specific funding was awarded for this meta-analysis. Coordinators were supported by fellowships from the European Union (ZAD received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 845681), the Wellcome Trust (SB, Wellcome Trust Senior Fellowship), and the National Health and Medical Research Council (DJI is supported by an NHMRC Investigator Grant [GNT1195210]).

BACKGROUND Typhoid fever is caused by the Gram-negative bacterium Salmonella enterica serovar Typhi and poses a substantial public health burden worldwide. Vaccines have been developed based on the surface Vi-capsular polysaccharide of S. Typhi; these include a plain-polysaccharide-based vaccine, ViPS, and a glycoconjugate vaccine, ViTT. To understand immune responses to these vaccines and their vaccine-induced immunological protection, molecular signatures were analyzed using bioinformatic approaches.METHODS Bulk RNA-Seq data were generated from blood samples obtained from adult human volunteers enrolled in a vaccine trial, who were then challenged with S. Typhi in a controlled human infection model (CHIM). These data were used to conduct differential gene expression analyses, gene set and modular analyses, B cell repertoire analyses, and time-course analyses at various post-vaccination and post-challenge time points between participants receiving ViTT, ViPS, or a control meningococcal vaccine.RESULTS Transcriptomic responses revealed strong differential molecular signatures between the 2 typhoid vaccines, mostly driven by the upregulation in humoral immune signatures, including selective usage of immunoglobulin heavy chain variable region (IGHV) genes and more polarized clonal expansions. We describe several molecular correlates of protection against S. Typhi infection, including clusters of B cell receptor (BCR) clonotypes associated with protection, with known binders of Vi-polysaccharide among these.CONCLUSION The study reports a series of contemporary analyses that reveal the transcriptomic signatures after vaccination and infectious challenge, while identifying molecular correlates of protection that may inform future vaccine design and assessment.TRIAL REGISTRATION ClinicalTrials.gov NCT02324751.

In this phase 4 study we assessed boosting with fractional doses of heterologous COVID-19 vaccines in Brazilian adults primed with two doses of CoronaVac (Sinovac/Butantan, São Paulo, Brazil) at least 4 months previously. Participants received either full-dose of ChAdOx1-S (Group 1, n = 232), a half dose of ChAdOx1-S (Group 2, n = 236), or a half dose of BNT162b2 (Group 3, n = 234). The primary objective was to show 80% seroresponse rates (SRR) 28 d after vaccination measured as IgG antibodies against a prototype SARS-CoV-2 spike-protein. Safety was assessed as solicited and unsolicited adverse events. At baseline all participants were seropositive, with high IgG titers overall. SRR at Day 28 were 34.3%, 27.1% and 71.2%, respectively, not meeting the primary objective of 80%, despite robust immune responses in all three groups with geometric mean-fold rise (GMFR) in IgG titers of 3.39, 2.99 and 7.42, respectively. IgG immune responses with similar GMFR were also observed against SARS-CoV-2 variants, Alpha, Beta, Delta, Gamma and D614G. In subsets (n = 35) of participants GMFR of neutralizing immune responses against live prototype SARS-CoV-2 virus and Omicron BA.2 were similar to the IgG responses as were pseudo-neutralizing responses against SARS-CoV-2 prototype and Omicron BA.4/5 variants. All vaccinations were well tolerated with no vaccine-related serious adverse events and mainly transient mild-to-moderate local and systemic reactogenicity. Heterologous boosting with full or half doses of ChAdOx1-S or a half dose of BNT162b2 was safe and immunogenic in CoronaVac-primed adults, but seroresponse rates were limited by high baseline immunity.

Summary: Mechanisms of infection and pathogenesis have predominantly been studied based on differential gene or protein expression. Less is known about posttranslational modifications, which are essential for protein functional diversity. We applied an innovative glycoproteomics method to study the systemic proteome-wide glycosylation in response to infection. The protein site-specific glycosylation was characterized in plasma derived from well-defined controls and patients. We found 3862 unique features, of which we identified 463 distinct intact glycopeptides, that could be mapped to more than 30 different proteins. Statistical analyses were used to derive a glycopeptide signature that enabled significant differentiation between patients with a bacterial or viral infection. Furthermore, supported by a machine learning algorithm, we demonstrated the ability to identify the causative pathogens based on the distinctive host blood plasma glycopeptide signatures. These results illustrate that glycoproteomics holds enormous potential as an innovative approach to improve the interpretation of relevant biological changes in response to infection.

Purpose Purpose Regulatory T cells (Tregs) have been implicated in the pathogenesis of several autoimmune disorders and used in adoptive cell transfer therapies. Neither have been explored in patients with autoimmune encephalitis where treated patient outcomes remain suboptimal with frequent relapses. Here, to identify new treatment strategies for autoimmune encephalitis, we sought to evaluate the proportion of circulating Tregs and Treg subpopulations in peripheral blood of patients with N-methyl-ᴅ-aspartate receptor-antibody encephalitis (NMDAR-Ab-E) and compared this with healthy controls. Methods We compared the phenotype of peripheral blood Tregs in four adult NMDAR-Ab-E patients and four age- and sex-matched healthy controls using an 11-color flow cytometry assay panel for characterization of Tregs (CD4+ CD25+ FoxP3+) cells into naïve (chemokine receptor [CCR] 7+ CD45RA+), central memory (CCR7+ CD45RA–), and effector memory (CCR7– CD45RA–) cells. We also examined and compared the expression of the CCR6 by circulating Tregs and the respective Treg subpopulations between the study groups. Results The proportion of circulating Tregs was similar between patients with NMDAR-Ab-E and healthy controls but the proportion of naïve Tregs was lower in NMDAR-Ab-E patients (p = 0.0026). Additionally, the frequency of circulating effector memory Tregs was higher, and the proportion of circulating effector memory Tregs expressing CCR6 was lower, in NMDAR-Ab-E patients compared with healthy controls (p = 0.0026). Conclusion Altered Treg homeostasis may be a feature of patients with NMDAR-Ab-E. Future studies with larger samples are warranted to validate these findings.

Abstract Digital data collection during routine clinical practice is now ubiquitous within hospitals. The data contains valuable information on the care of patients and their response to treatments, offering exciting opportunities for research. Typically, data are stored within archival systems that are not intended to support research. These systems are often inaccessible to researchers and structured for optimal storage, rather than interpretability and analysis. Here we present MIMIC-IV, a publicly available database sourced from the electronic health record of the Beth Israel Deaconess Medical Center. Information available includes patient measurements, orders, diagnoses, procedures, treatments, and deidentified free-text clinical notes. MIMIC-IV is intended to support a wide array of research studies and educational material, helping to reduce barriers to conducting clinical research.

The presence of pollen and charcoal in radiometrically dated speleothems suggest the Naracoorte Cave Complex, South Australia, has been open to the atmosphere for the past 600,000 years, placing an upper limit on the accumulation of fossils inside the caves.

Abstract Since its isolation, graphene has received growing attention from academia and industry due to its unique properties. However, the “what is my material” barrier hinders further commercialization. X‐ray photoelectron spectroscopy (XPS) is considered as a method of choice for the determination of the elemental and chemical composition. In this work the influence of the morphology of graphene particles on the XPS results is studied and investigated as a function of X‐ray energy, using conventional XPS with Al Kα radiation and hard X‐ray photoemission spectroscopy (HAXPES) using Cr Kα radiation. Thereby, the information depth is varied between 10 and 30 nm. For this purpose, two commercial powders containing graphene nanoplatelets with lateral dimensions of either ≈100 nm or in the micrometer range are compared. These larger ones exist as stack of graphene layers which is inspected with scanning electron microscopy. Both kinds of particles are then functionalized with either oxygen or fluorine. The size of the graphene particles is found to influence the degree of functionalization. Only the combination of XPS and HAXPES allows to detect the functionalization at the outermost surface of the particles or even of the stacks and to provide new insights into the functionalization process.

Summary: Background: Vaccination of infants with pneumococcal conjugate vaccines (PCV) is recommended by the World Health Organization. Evidence is mixed regarding the differences in immunogenicity and efficacy of the different pneumococcal vaccines. Methods: In this systematic-review and network meta-analysis, we searched the Cochrane Library, Embase, Global Health, Medline, clinicaltrials.gov and trialsearch.who.int up to February 17, 2023 with no language restrictions. Studies were eligible if they presented data comparing the immunogenicity of either PCV7, PCV10 or PCV13 in head-to-head randomised trials of young children under 2 years of age, and provided immunogenicity data for at least one time point after the primary vaccination series or the booster dose. Publication bias was assessed via Cochrane's Risk Of Bias due to Missing Evidence tool and comparison-adjusted funnel plots with Egger's test. Individual participant level data were requested from publication authors and/or relevant vaccine manufacturers. Outcomes included the geometric mean ratio (GMR) of serotype-specific IgG and the relative risk (RR) of seroinfection. Seroinfection was defined for each individual as a rise in antibody between the post-primary vaccination series time point and the booster dose, evidence of presumed subclinical infection. Seroefficacy was defined as the RR of seroinfection. We also estimated the relationship between the GMR of IgG one month after priming and the RR of seroinfection by the time of the booster dose. The protocol is registered with PROSPERO, ID CRD42019124580. Findings: 47 studies were eligible from 38 countries across six continents. 28 and 12 studies with data available were included in immunogenicity and seroefficacy analyses, respectively. GMRs comparing PCV13 vs PCV10 favoured PCV13 for serotypes 4, 9V, and 23F at 1 month after primary vaccination series, with 1.14- to 1.54- fold significantly higher IgG responses with PCV13. Risk of seroinfection prior to the time of booster dose was lower for PCV13 for serotype 4, 6B, 9V, 18C and 23F than for PCV10. Significant heterogeneity and inconsistency were present for most serotypes and for both outcomes. Two-fold higher antibody after primary vaccination was associated with a 54% decrease in risk of seroinfection (RR 0.46, 95% CI 0.23–0.96). Interpretation: Serotype-specific differences were found in immunogenicity and seroefficacy between PCV13 and PCV10. Higher antibody response after vaccination was associated with a lower risk of subsequent infection. These findings could be used to compare PCVs and optimise vaccination strategies. Funding: The NIHR Health Technology Assessment Programme.

Introduction This is the first efficacy study of an oral live attenuated vaccine against Salmonella Paratyphi A using a human challenge model of paratyphoid infection. S. Paratyphi A is responsible for 3.3 million cases of enteric fever every year, with over 19 000 deaths. Although improvements to sanitation and access to clean water are vital to reduce the burden of this condition, vaccination offers a cost-effective, medium-term solution. Efficacy trials of potential S. Paratyphi vaccine candidates in the field are unlikely to be feasible given the large number of participants required. Human challenge models therefore offer a unique, cost-effective solution to test efficacy of such vaccines.Methods and analysis This is an observer-blind, randomised, placebo-controlled trial phase I/II of the oral live-attenuated vaccine against S. Paratyphi A, CVD 1902. Volunteers will be randomised 1:1 to receive two doses of CVD 1902 or placebo, 14 days apart. One month following second vaccination all volunteers will ingest S. Paratyphi A bacteria with a bicarbonate buffer solution. They will be reviewed daily in the following 14 days and diagnosed with paratyphoid infection if the predefined microbiological or clinical diagnostic criteria are met. All participants will be treated with antibiotics on diagnosis, or at day 14 postchallenge if not diagnosed. The vaccine efficacy will be determined by comparing the relative attack rate, that is, the proportion of those diagnosed with paratyphoid infection, in the vaccine and placebo groups.Ethics and dissemination Ethical approval for this study has been obtained from the Berkshire Medical Research Ethics Committee (REC ref 21/SC/0330). The results will be disseminated via publication in a peer-reviewed journal and presentation at international conferences.Trial registration number ISRCTN15485902.

Summary: Most existing studies characterizing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific T cell responses are peptide based. This does not allow evaluation of whether tested peptides are processed and presented canonically. In this study, we use recombinant vaccinia virus (rVACV)-mediated expression of SARS-CoV-2 spike protein and SARS-CoV-2 infection of angiotensin-converting enzyme (ACE)-2-transduced B cell lines to evaluate overall T cell responses in a small cohort of recovered COVID-19 patients and uninfected donors vaccinated with ChAdOx1 nCoV-19. We show that rVACV expression of SARS-CoV-2 antigen can be used as an alternative to SARS-CoV-2 infection to evaluate T cell responses to naturally processed spike antigens. In addition, the rVACV system can be used to evaluate the cross-reactivity of memory T cells to variants of concern (VOCs) and to identify epitope escape mutants. Finally, our data show that both natural infection and vaccination could induce multi-functional T cell responses with overall T cell responses remaining despite the identification of escape mutations.

Abstract Background Disease caused by the capsular group B meningococcus (MenB) is the leading cause of infectious death in UK infants. A novel adenovirus-based vaccine encoding the MenB factor H binding protein (fHbp) with an N-terminal dual signal sequence induces high titres of protective antibody after a single dose in mice. A panel of N-terminal signal sequence variants were created to assess the contribution of components of this sequence to transgene expression kinetics of the encoded antigen from mammalian cells and the resultant effect on immunogenicity of fHbp. Results The full-length signal sequence (FL SS) resulted in superior early antigen expression compared with the panel of variants, as measured by flow cytometry and confocal imaging, and supported higher bactericidal antibody levels against the expressed antigen in mouse sera

Introduction Inactivated, viral vector and mRNA vaccines have been used in the Nepali COVID-19 vaccination programme but there is little evidence on the effectiveness of these vaccines in this setting. The aim of this study is to describe COVID-19 vaccine effectiveness in Nepal and provide information on infections with SARS-CoV-2 variants.Methods and analysis This is a hospital-based, prospective test-negative case–control study conducted at Patan Hospital, Kathmandu. All patients >18 years of age presenting to Patan Hospital with COVID-19-like symptoms who have received a COVID-19 antigen/PCR test are eligible for inclusion. The primary outcome is vaccine effectiveness of licensed COVID-19 vaccines against laboratory-confirmed COVID-19 disease.After enrolment, information will be collected on vaccine status, date of vaccination, type of vaccine, demographics and other medical comorbidities. The primary outcome of interest is laboratory-confirmed SARS-CoV-2 infection. Cases (positive for SARS-CoV-2) and controls (negative for SARS-CoV-2) will be enrolled in a 1:4 ratio. Vaccine effectiveness against COVID-19 disease will be analysed by comparing vaccination status with SARS-CoV-2 test results.Positive SARS-CoV-2 samples will be sequenced to identify circulating variants and estimate vaccine effectiveness against common variants.Measuring vaccine effectiveness and identifying SARS-CoV-2 variants in Nepal will help to inform public health efforts. Describing disease severity in relation to specific SARS-CoV-2 variants and vaccine status will also inform future prevention and care efforts.Ethics and dissemination Ethical approval was obtained from the University of Oxford Tropical Ethics Committee (OxTREC) (ref: 561-21) and the Patan Academy of Health Sciences Institutional Review Board (ref: drs2111121578). The protocol and supporting study documents were approved for use by the Nepal Health Research Council (NHRC 550-2021). Results will be disseminated in peer-reviewed journals and to the public health authorities in Nepal.

Summary: Background: A cluster-randomised trial of Vi-tetanus toxoid (Vi-TT) conjugate vaccine conducted in urban Bangladeshi children found a high level of direct protection by Vi-TT but no significant vaccine herd protection. We reassessed the trial using a “fried egg” analysis to evaluate whether herd protection might have been obscured by transmission of typhoid into the clusters from the outside. Methods: A participant- and observer-blind, cluster-randomised trial was conducted between February 14, 2018 and August 12, 2019 in three wards of Mirpur, a densely populated urban area of Dhaka, Bangladesh. Children 9 months to under 16 years of age in 150 geographic clusters, which had a total of 311,289 persons present at baseline or entering during follow-up, were randomised by cluster to a single-dose of Vi-TT or Japanese encephalitis (JE) vaccine. Vi-TT protection against typhoid fever, detected at 8 treatment centres serving the study population, was compared in the original clusters for the trial, and for progressively more central subclusters (“yolks” of the “fried egg”) of the cluster residents. If transmission of typhoid into the clusters had diluted observed vaccine herd protection, we hypothesised that analysis of the innermost “yolks” would reveal vaccine herd protection that was not evident in analysis of the entire clusters. The trial is registered at www.isrctn.com as ISRCTN11643110. Findings: At ≤18 months of follow-up, total vaccine effectiveness (protection of Vi-TT recipients relative to JE vaccine recipients) was 85% (95% CI: 76%, 90%); indirect effectiveness (protection of non-Vi-TT recipients in Vi-TT clusters relative to non-JE vaccine recipients in JE vaccine clusters) was 17% (95% CI: −13%, 40%); and overall effectiveness (protection of all residents in the Vi-TT clusters relative to all residents of the JE vaccine clusters) was 57% (95% CI: 44%, 66%). Analyses of subpopulations in inner 75%, 50% and 25% “yolks” of the clusters failed to reveal significant changes in any of these estimates. Interpretation: Our analysis did not reveal Vi-TT herd protection in the trial. Consideration should be given to exploring whether targeting adults as well as children with Vi-TT yields appreciable levels of vaccine herd protection. Funding: Bill & Melinda Gates Foundation (OPP1151153, INV-025388).

Diversity in specificity of polyclonal antibody (pAb) responses is extensively investigated in vaccine efficacy or immunological evaluations, but the heterogeneity in antibody avidity is rarely probed as convenient tools are lacking. Here we have developed a polyclonal antibodies avidity resolution tool (PAART) for use with label-free techniques, such as surface plasmon resonance and biolayer interferometry, that can monitor pAb-antigen interactions in real time to measure dissociation rate constant (kd) for defining avidity. PAART utilizes a sum of exponentials model to fit the dissociation time-courses of pAb-antigens interactions and resolve multiple kd contributing to the overall dissociation. Each kd value of pAb dissociation resolved by PAART corresponds to a group of antibodies with similar avidity. PAART is designed to identify the minimum number of exponentials required to explain the dissociation course and guards against overfitting of data by parsimony selection of best model using Akaike information criterion. Validation of PAART was performed using binary mixtures of monoclonal antibodies of same specificity but differing in kd of the interaction with their epitope. We applied PAART to examine the heterogeneity in avidities of pAb from malaria and typhoid vaccinees, and individuals living with HIV-1 that naturally control the viral load. In many cases, two to three kd were dissected indicating the heterogeneity of pAb avidities. We showcase examples of affinity maturation of vaccine induced pAb responses at component level and enhanced resolution of heterogeneity in avidity when antigen-binding fragments (Fab) are used instead of polyclonal IgG antibodies. The utility of PAART can be manifold in examining circulating pAb characteristics and could inform vaccine strategies aimed to guide the host humoral immune response.

The engagement of immunological memory is a key component to the protective anti-SARS-CoV-2 B and T cell responses. Here the authors assess the B and T cells of a cohort of UK healthcare workers in response to infection and longitudinally track the compartment showing distinct trajectories following early priming.

Abstract The safety of novel therapeutics and vaccines are typically assessed in early phase clinical trials involving “healthy volunteers.” Abnormalities in such individuals can be difficult to interpret and may indicate previously unrecognized medical conditions. The frequency of incidental findings (IFs) in healthy volunteers who attend for clinical trial screening is unclear. To assess this, we retrospectively analyzed data for 1838 “healthy volunteers” screened for enrolment in a UK multicenter, phase I/II severe acute respiratory syndrome‐coronavirus 2 (SARS‐COV‐2) vaccine trial. Participants were predominantly White (89.7%, 1640/1828) with a median age of 34 years (interquartile range [IQR] = 27–44). There were 27.7% of participants (510/1838) who had at least one IF detected. The likelihood of identifying evidence of a potential, new blood‐borne virus infection was low (1 in 238 participants) compared with identification of an elevated alanine transaminase (ALT; 1 in 17 participants). A large proportion of participants described social habits that could impact negatively on their health; 21% consumed alcohol in excess, 10% were current smokers, 11% described recreational drug use, and only 48% had body weight in the ideal range. Our data demonstrate that screening prior to enrollment in early phase clinical trials identifies a range of IFs, which should inform discussion during the consent process. Greater clarity is needed to ensure an appropriate balance is struck between early identification of medical problems and avoidance of exclusion of volunteers due to spurious or physiological abnormalities. Debate should inform the role of the trial physician in highlighting and advising about unhealthy social habits.