IntroductionGuidelines for the management of rheumatoid arthritis (RA) recommend using influenza and pneumococcal vaccinations to mitigate infection risk. The level of adherence to these guidelines is not well known in the UK. The aims of this study were to describe the uptake of influenza and pneumococcal vaccinations in patients with RA in the UK, to compare the characteristics of those vaccinated to those not vaccinated and to compare vaccination rates across regions of the UK.MethodsA retrospective cohort study of adults diagnosed with incident RA and treated with non-biologic immunosuppressive therapy, using data from a large primary care database. For the influenza vaccination, patients were considered unvaccinated on 1st September each year and upon vaccination their status changed to vaccinated. For pneumococcal vaccination, patients were considered vaccinated after their first vaccination until the end of follow-up. Patients were stratified by age 65 at the start of follow-up, given differences in vaccination guidelines for the general population.ResultsOverall (N = 15,724), 80% patients received at least one influenza vaccination, and 50% patients received a pneumococcal vaccination, during follow-up (mean 5.3 years). Of those aged below 65 years (N = 9,969), 73% patients had received at least one influenza vaccination, and 43% patients received at least one pneumococcal vaccination. Of those aged over 65 years (N = 5,755), 91% patients received at least one influenza vaccination, and 61% patients had received at least one pneumococcal vaccination. Those vaccinated were older, had more comorbidity and visited the GP more often. Regional differences in vaccination rates were seen with the highest rates in Northern Ireland, and the lowest rates in London.ConclusionsOne in five patients received no influenza vaccinations and one in two patients received no pneumonia vaccine over five years of follow-up. There remains significant scope to improve uptake of vaccinations in patients with RA.

This dataset is no longer updated, find vaccination data here From 24 March 2022, Public Health Scotland (PHS) began reporting the number of people who have received a fourth dose of Covid-19 vaccination. Vaccine uptake statistics among care home residents and those who are severely immunosuppressed will be reported initially. PHS will include further updates as the Spring/Summer vaccination programme rolls out. In addition, as part of our continuous review of reporting, PHS made some changes to vaccine uptake statistics. From 24 March 2022, the deceased and those who no longer live in Scotland are no longer be included in vaccine uptake statistics. Historic trend data have been updated to take into account this new methodology for all apart from the Daily Trends by JCVI Priority Group table (more details about the data in this table are below). Scotland level data for all vaccinations administered (i.e. including those who have since died or moved from Scotland) are still available in the Daily Trend of All Vaccinations Delivered in Scotland table. Also from 24 March 2022, Dose 3/Booster doses are termed "Dose 3". To allow new data to be fully processed and available at 14:00, the Daily COVID-19 in Scotland and COVID-19 Vaccination in Scotland datasets will be temporarily unavailable from 12:45 to 14:00. During this window, the datasets will not be visible and any queries made to these datasets will return a 404 - Not found error. At all other times the datasets will be available in full as usual. PHS reviewed the JCVI priority group uptake figures from 18 November 2021, specifically how we derive the numerator and the denominator. The rational for the change is to ensure we report on most up to date living population for each group. For this, the list of individuals in each cohort has been refreshed to be more current. We have also removed individuals who have since died to reflect the current living population. From the 24 March 2022 those who are no longer living in Scotland have also been removed from the numerator and denominator for JCVI priority group uptake figures. This means all the JCVI cohorts and populations have changed for both numerator and denominators on these two dates and care should be taken when interpreting trends. On 08 December 2020, a Coronavirus (COVID-19) vaccine developed by Pfizer BioNTech (Comirnaty) was first used in the UK as part of national immunisation programmes. The AstraZeneca (Spikevax) vaccine was also approved for use in the national programme, and rollout of this vaccine began on 04 January 2021. Moderna (Vaxzevria) vaccine was approved for use on 8 January 2021 and rollout of this vaccine began on 07 April 2021. These vaccines have met strict standards of safety, quality and effectiveness set out by the independent Medicines and Healthcare Products Regulatory Agency (MHRA). Those giving the vaccine to others were the first to receive the vaccination. In the first phase of the programme, NHS Scotland followed the independent advice received from the Joint Committee on Vaccination and Immunisation (JCVI) and prioritised delivery of the vaccine to those with the greatest clinical need, in line with the recommended order of prioritisation. For booster vaccinations a similar approach has been adopted. Definitions used in the vaccine uptake by JCVI priority group resource can be found in the JCVI Priority Group Definitions table. Individuals can appear in more than one JCVI priority group. This dataset provides information on daily number of COVID vaccinations in Scotland. Data on the total number of vaccinations in Scotland is presented by day administered and vaccine type, by age group, by sex, by non-age cohorts and by geographies (NHS Board and Local Authority). As the population in the cohorts can change with time, these will be refined when updated data are available. Additional data sources relating to this topic area are provided in the Links section of the Metadata below. Data visualisation and additional notes are available on the Public Health Scotland - Covid 19 Scotland dashboard.

Local authority level vaccine coverage estimates for the school-based meningococcal ACWY adolescent vaccination programme for 14 to 15 year olds.

Rationale The MenACWY vaccination was introduced into the national immunisation programme in autumn 2015 to respond to a rapid and accelerating increase in cases of invasive meningococcal group W (MenW) disease, which was declared a national incident. The MenACWY conjugate vaccine provides direct protection to the vaccinated cohort and, by reducing MenW carriage, will also provide indirect protection to unvaccinated children and adults. This follows advice from the Joint Committee on Vaccination and Immunisation (JCVI). It is routinely offered through schools in academic school Years 9 and 10 (rising 14 and rising 15 year olds). The indicator measures local authority level MenACWY vaccine coverage for students at the end of school Yr 10. Vaccination coverage is the best indicator of the level of protection a population will have against vaccine preventable communicable diseases. Coverage is closely correlated with levels of disease. Monitoring coverage identifies possible drops in immunity before levels of disease rise. Previous evidence shows that highlighting vaccination programmes encourages improvements in uptake levels. May also have relevance for NICE guidance PH21: Reducing differences in the uptake of immunisations (The guidance aims to increase immunisation uptake among those aged under 19 years from groups where uptake is low).

Definition of numerator Total number of adolescents in LA responsible population whose 15th birthday falls within the time period who have ever received MenACWY vaccine.

Definition of denominator Total number of adolescents attending school in LA plus adolescents resident in the LA not linked to any school whose 15th birthday falls within the time period.

Caveats On 23 March 2020, all educational settings in England were advised to close by the UK Government as part of COVID-19 pandemic measures. Although the importance of maintaining good vaccine uptake was impressed, operational delivery of all school-aged immunisation programmes was paused for a short period of time as a consequence of school closures limiting access to venues for providers and children who were eligible for vaccination and to ensure that lockdown regulations were not breached.

The NHSEI central public health commissioning and operations team rapidly established an Immunisation Task and Finish Group, with regional NHSEI and UKHSA representation. The group was established to:

assess the impact of COVID-19 on all immunisation programmes, including school-aged programmes develop technical guidance and a plan for restoration and recovery of school-aged programmes, once education settings were reopened

From 1 June 2020, some schools partially reopened for some year groups for a mini summer term. NHSEI published clinical guidance for healthcare professionals on maintaining immunisation programmes during COVID-19, and the Department of Education published further guidance which led to schools allowing vaccination sessions to resume on site.

NHSEI commissioned, school-aged immunisation providers were able to implement their restoration and recovery plans to commence catch-up during the summer of 2020. This included delivery of programmes in school and community settings following a robust risk assessment and in line with UK Government Public Health COVID-19 guidance.

In September 2020, schools across the UK reopened for general in-person attendance. During the 2020 to 2021 academic year, students were required to stay at home and learn remotely if they tested positive for COVID-19 or if they were a contact of a confirmed COVID-19 case, and so school attendance rates in England were lower than normal, especially in areas with very high COVID-19 incidence rates. In England, as part of a wider national lockdown in January 2021, schools were closed to all except children of keyworkers and vulnerable children. From early March 2021, primary schools reopened, with a phased reopening of secondary schools.

Although this led to some disruption of school-based elements of programme delivery in the 2020 to 2021 academic year, NHSEI Regional Public Health Commissioning teams worked with NHSEI commissioned school-aged immunisation providers to maintain the delivery of the routine programme and catch-up. As the routine programme is commissioned for a school-aged cohort rather than a school-based cohort, providers were able to build on existing arrangements such as community-based clinics in place for children not in mainstream education. A wide variety of local arrangements were established to ensure programme delivery continued effectively and safely in the school and community premises, during the term time and school breaks.

Mean (SD) or percentage reported.

Additional file 12. The numbers and rates of people developing dementia in zoster vaccinated and unvaccinated cohorts. The file depicted numbers and rates per 1000 year of people developing dementia in zoster vaccinated and unvaccinated cohorts.

This dataset contains COVID-19 Vaccination events in Scotland since December 2020. This includes information such as eligibility cohort, date of vaccination and vaccination product.

Additional file 9. International Classification of Diseases codes for Charlson Comorbidity Index in Aurum database. The file listed ICD-10 codes for Charlson Comorbidity Index used in Aurum database.

Abstract copyright UK Data Service and data collection copyright owner.

Background:
The Millennium Cohort Study (MCS) is a large-scale, multi-purpose longitudinal dataset providing information about babies born at the beginning of the 21st century, their progress through life, and the families who are bringing them up, for the four countries of the United Kingdom. The original objectives of the first MCS survey, as laid down in the proposal to the Economic and Social Research Council (ESRC) in March 2000, were:

• to chart the initial conditions of social, economic and health advantages and disadvantages facing children born at the start of the 21st century, capturing information that the research community of the future will require
• to provide a basis for comparing patterns of development with the preceding cohorts (the National Child Development Study, held at the UK Data Archive under GN 33004, and the 1970 Birth Cohort Study, held under GN 33229)
• to collect information on previously neglected topics, such as fathers' involvement in children's care and development
• to focus on parents as the most immediate elements of the children's 'background', charting their experience as mothers and fathers of newborn babies in the year 2000, recording how they (and any other children in the family) adapted to the newcomer, and what their aspirations for her/his future may be
• to emphasise intergenerational links including those back to the parents' own childhood
• to investigate the wider social ecology of the family, including social networks, civic engagement and community facilities and services, splicing in geo-coded data when available

Additional objectives subsequently included for MCS were:

• to provide control cases for the national evaluation of Sure Start (a government programme intended to alleviate child poverty and social exclusion)
• to provide samples of adequate size to analyse and compare the smaller countries of the United Kingdom, and include disadvantaged areas of England

Further information about the MCS can be found on the Centre for Longitudinal Studies web pages.

The content of MCS studies, including questions, topics and variables can be explored via the CLOSER Discovery website.

The first sweep (MCS1) interviewed both mothers and (where resident) fathers (or father-figures) of infants included in the sample when the babies were nine months old, and the second sweep (MCS2) was carried out with the same respondents when the children were three years of age. The third sweep (MCS3) was conducted in 2006, when the children were aged five years old, the fourth sweep (MCS4) in 2008, when they were seven years old, the fifth sweep (MCS5) in 2012-2013, when they were eleven years old, the sixth sweep (MCS6) in 2015, when they were fourteen years old, and the seventh sweep (MCS7) in 2018, when they were seventeen years old.
End User Licence versions of MCS studies:
The End User Licence (EUL) versions of MCS1, MCS2, MCS3, MCS4, MCS5, MCS6 and MCS7 are held under UK Data Archive SNs 4683, 5350, 5795, 6411, 7464, 8156 and 8682 respectively. The longitudinal family file is held under SN 8172.

Sub-sample studies:
Some studies based on sub-samples of MCS have also been conducted, including a study of MCS respondent mothers who had received assisted fertility treatment, conducted in 2003 (see EUL SN 5559). Also, birth registration and maternity hospital episodes for the MCS respondents are held as a separate dataset (see EUL SN 5614).

Release of Sweeps 1 to 4 to Long Format (Summer 2020)To support longitudinal research and make it easier to compare data from different time points, all data from across all sweeps is now in a consistent format. The update affects the data from sweeps 1 to 4 (from 9 months to 7 years), which are updated from the old/wide to a new/long format to match the format of data of sweeps 5 and 6 (age 11 and 14 sweeps). The old/wide formatted datasets contained one row per family with multiple variables for different respondents. The new/long formatted datasets contain one row per respondent (per parent or per cohort member) for each MCS family. Additional updates have been made to all sweeps to harmonise variable labels and enhance anonymisation.

How to access genetic and/or bio-medical sample data from a range of longitudinal surveys:
For information on how to access biomedical data from MCS that are not held at the UKDS, see the CLS Genetic data and biological samples webpage.

Secure Access datasets:
Secure Access versions of the MCS have more restrictive access conditions than versions available under the standard End User Licence or Special Licence (see 'Access data' tab above).

Secure Access versions of the MCS...

Protein-Protein, Genetic, and Chemical Interactions for Angyal A (2022):T-cell and antibody responses to first BNT162b2 vaccine dose in previously infected and SARS-CoV-2-naive UK health-care workers: a multicentre prospective cohort study. curated by BioGRID (https://thebiogrid.org); ABSTRACT: Previous infection with SARS-CoV-2 affects the immune response to the first dose of the SARS-CoV-2 vaccine. We aimed to compare SARS-CoV-2-specific T-cell and antibody responses in health-care workers with and without previous SARS-CoV-2 infection following a single dose of the BNT162b2 (tozinameran; Pfizer-BioNTech) mRNA vaccine.We sampled health-care workers enrolled in the PITCH study across four hospital sites in the UK (Oxford, Liverpool, Newcastle, and Sheffield). All health-care workers aged 18 years or older consenting to participate in this prospective cohort study were included, with no exclusion criteria applied. Blood samples were collected where possible before vaccination and 28 (±7) days following one or two doses (given 3-4 weeks apart) of the BNT162b2 vaccine. Previous infection was determined by a documented SARS-CoV-2-positive RT-PCR result or the presence of positive anti-SARS-CoV-2 nucleocapsid antibodies. We measured spike-specific IgG antibodies and quantified T-cell responses by interferon-? enzyme-linked immunospot assay in all participants where samples were available at the time of analysis, comparing SARS-CoV-2-naive individuals to those with previous infection.Between Dec 9, 2020, and Feb 9, 2021, 119 SARS-CoV-2-naive and 145 previously infected health-care workers received one dose, and 25 SARS-CoV-2-naive health-care workers received two doses, of the BNT162b2 vaccine. In previously infected health-care workers, the median time from previous infection to vaccination was 268 days (IQR 232-285). At 28 days (IQR 27-33) after a single dose, the spike-specific T-cell response measured in fresh peripheral blood mononuclear cells (PBMCs) was higher in previously infected (n=76) than in infection-naive (n=45) health-care workers (median 284 [IQR 150-461] vs 55 [IQR 24-132] spot-forming units [SFUs] per 106 PBMCs; p

Supplementary Material. (DOC)

Conjugate vaccine against typhoid fever has been shown to be safe and effective in field trials. The mechanism through which the vaccine protects remains elusive. Recent data have implicated antibody glycosylation, and specifically afucosylated antibodies, as an important factor in vaccine-induced effector function for a range of viral infections. Here, we studied IgG glycosylation after conjugate vaccine in a UK cohort, who were then challenged with virulent S.typhi, and among Nepalese children living in a typhoid endemic region. We compared vaccine-induced responses to another licensed typhoid polysaccharide vaccine and correlated these measures with antibody-dependent function to understand if a vaccine against a bacterial infection elicited similar glycosylation/function associations as has been seen for viral infections. Robust antigen-specific IgG Fc galactosylation and sialylation modifications were induced by both polysaccharide and tetanus toxoid-conjugated Salmonella Typhi vaccines in UK adults. These modifications were not able to differentiate controlled human infection model (CHIM) participants who became ill after ingestion of virulent S.typhi from those who remained well after infection. However, among those who did become ill, disease severity was associated with a distinct glycosylation profile. Interestingly, both vaccines induced vaccine-specific IgG1 antibodies that were more fucosylated than total circulating IgG1 and these were not associated with a particular functional profile. While bulk IgG glycosylation was different between Nepalese children and UK adults, vaccination with the Vi-tetanus toxoid-conjugate vaccine resulted in similar Vi-specific IgG glycosylation profiles 28 days after vaccination in both cohorts.

In the last two years, the coronavirus disease 19 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a scientific and social challenge worldwide. Vaccines have been the most effective intervention for reducing virus transmission and disease severity. However, virus genetic variants are still circulating among vaccinated individuals with different symptomatology disease cases. Understanding the protective or disease associated mechanisms in vaccinated individuals is relevant to advance in vaccine development and implementation. To address this objective, serum protein profiles were characterized by quantitative proteomics and data analysis algorithms in four cohorts of vaccinated individuals uninfected and SARS-CoV-2 infected with asymptomatic, nonsevere and severe disease symptomatology. The results showed that immunoglobulins were the most overrepresented proteins in infected cohorts when compared to PCR-negative individuals. The immunoglobulin profile varied between different infected cohorts and correlated with protective or disease associated capacity. Overrepresented immunoglobulins in PCR-positive individuals correlated with protective response against SARS-CoV-2, other viruses, and thrombosis in asymptomatic cases. In nonsevere cases, correlates of protection against SARS-CoV-2 and HBV together with risk of myasthenia gravis and allergy and autoantibodies were observed. Patients with severe symptoms presented risk for allergy, chronic idiopathic thrombocytopenic purpura, and autoantibodies. The analysis of underrepresented immunoglobulins in PCR-positive compared to PCR-negative individuals identified vaccine-induced protective epitopes in various coronavirus proteins including the Spike receptor-binding domain RBD. Non-immunoglobulin proteins were associated with COVID-19 symptoms and biological processes. These results evidence host-associated differences in response to vaccination and the possibility of improving vaccine efficacy against SARS-CoV-2.

Conjugate vaccine against typhoid fever has been shown to be safe and effective in field trials. The mechanism through which the vaccine protects remains elusive. Recent data have implicated antibody glycosylation, and specifically afucosylated antibodies, as an important factor in vaccine-induced effector function for a range of viral infections. Here, we studied IgG glycosylation after conjugate vaccine in a UK cohort, who were then challenged with virulent S.typhi, and among Nepalese children living in a typhoid endemic region. We compared vaccine-induced responses to another licensed typhoid polysaccharide vaccine and correlated these measures with antibody-dependent function to understand if a vaccine against a bacterial infection elicited similar glycosylation/function associations as has been seen for viral infections. Robust antigen-specific IgG Fc galactosylation and sialylation modifications were induced by both polysaccharide and tetanus toxoid-conjugated Salmonella Typhi vaccines in UK adults. These modifications were not able to differentiate controlled human infection model (CHIM) participants who became ill after ingestion of virulent S.typhi from those who remained well after infection. However, among those who did become ill, disease severity was associated with a distinct glycosylation profile. Interestingly, both vaccines induced vaccine-specific IgG1 antibodies that were more fucosylated than total circulating IgG1 and these were not associated with a particular functional profile. While bulk IgG glycosylation was different between Nepalese children and UK adults, vaccination with the Vi-tetanus toxoid-conjugate vaccine resulted in similar Vi-specific IgG glycosylation profiles 28 days after vaccination in both cohorts.

Characteristics of RA cohort, by vaccination status (N = 15724).

This primary care dataset covers all participants from the BiB longitudinal birth cohort study UK, which means it can be linked to all BiB surveys and data. This includes basic patient demographics, information about consultation events, medical history including diagnoses and investigations, laboratory results, medications and vaccinations for ~29,000 BiB participants.

SystmOne data is easily searchable by using Read CTV3 or BNF drug codes.

pone.0279285.t001 - Parents’ intention to vaccinate their child for COVID-19: A mixed-methods study (CoVAccS–wave 3)

Clear cell renal cell carcinoma (ccRCC) is the dominant subtype of renal cancer. With currently available therapies, cure of advanced and metastatic ccRCC is achieved only in rare cases. Here, we developed a workflow integrating different -omics technologies to identify ccRCC-specific HLA-presented peptides as potential drug targets for ccRCC immunotherapy. We analyzed frequent ccRCC-specific peptides by MS-based HLA ligandomics of 55 ccRCC tumors (cohort 1), paired non-tumor renal tissues and 158 benign tissues from other organs. Pathways enriched in ccRCC compared to its cell type of origin were identified by transcriptome and gene set enrichment analyses in 51 tumor tissues of the same cohort. To retrieve a list of candidate target genes with involvement in ccRCC pathogenesis, ccRCC-specific pathway genes were intersected with the source genes of tumor-exclusive peptides. The candidates were validated in an independent cohort from the Cancer Genome Atlas (TCGA KIRC, n=452), yielding 113 candidate genes. DNA methylation (TCGA KIRC, n=273), and somatic mutations (TCGA KIRC, n=392), as well as correlations with tumor metabolites (cohort 1, n=30) and immune-oncological markers (cohort 1, n=37) were analyzed to refine regulatory and functional involvements of candidates. Immunogenicity analysis identified candidate epitopes able to activate native CD8+ T cells. Functional analysis of EGLN3, a candidate with frequent ccRCC-specific immunogenic peptides, revealed possible tumor-promoting functions. Integration of HLA ligandomics, transcriptomics, genetic and epigenetic data leads to the identification of novel functionally relevant therapeutic targets for ccRCC immunotherapy. Validation of the identified targets is now mandatory to expand the treatment landscape of ccRCC.

The expected versus received influenza and pneumonia vaccinations of the RA cohort, by age group.

Additional file 7. International Classification of Diseases 10th Revision (ICD-10) codes for dementia. The file listed ICD-10 codes for dementia outcome.

IntroductionThe key to understanding the COVID-19 correlates of protection is assessing vaccine-induced immunity in different demographic groups. Young people are at a lower risk of COVID-19 mortality, females are at a lower risk than males, and females often generate stronger immune responses to vaccination.MethodsWe studied immune responses to two doses of BNT162b2 Pfizer COVID-19 vaccine in an adolescent cohort (n = 34, ages 12–16), an age group previously shown to elicit significantly greater immune responses to the same vaccine than young adults. Adolescents were studied with the aim of comparing their response to BNT162b2 to that of adults; and to assess the impacts of other factors such as sex, ongoing SARS–CoV–2 infection in schools, and prior exposure to endemic coronaviruses that circulate at high levels in young people. At the same time, we were able to evaluate immune responses to the co-administered live attenuated influenza vaccine. Blood samples from 34 adolescents taken before and after vaccination with COVID-19 and influenza vaccines were assayed for SARS–CoV–2-specific IgG and neutralising antibodies and cellular immunity specific for SARS–CoV–2 and endemic betacoronaviruses. The IgG targeting influenza lineages contained in the influenza vaccine were also assessed.ResultsRobust neutralising responses were identified in previously infected adolescents after one dose, and two doses were required in infection-naïve adolescents. As previously demonstrated, total IgG responses to SARS–CoV-2 Spike were significantly higher among vaccinated adolescents than among adults (aged 32–52) who received the BNT162b2 vaccine (comparing infection-naïve, 49,696 vs. 33,339; p = 0.03; comparing SARS-CoV–2 previously infected, 743,691 vs. 269,985; p