Reducing barriers to accessing administrative data on SARS-CoV-2 vaccination for research.
Ontology highlight
ABSTRACT:
SUBMITTER: McRae AD
PROVIDER: S-EPMC9299746 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Use of administrative data for research and for planning services has increased over recent decades due to the value of the large, rich information available. However, concerns about the release of sensitive or personal data and the associated disclosure risk can lead to lengthy approval processes and restricted data access. This can delay or prevent the production of timely evidence. A promising solution to facilitate more efficient data access is to create synthetic versions of the original datasets which are less likely to hold confidential information and can minimise disclosure risk. Such data may be used as an interim solution, allowing researchers to develop their analysis plans on non-disclosive data, whilst waiting for access to the real data. We aim to provide an overview of the background and uses of synthetic data and describe common methods used to generate synthetic data in the context of UK administrative research. We propose a simplified terminology for categories of synthetic data (univariate, multivariate, and complex modality synthetic data) as well as a more comprehensive description of the terminology used in the existing literature and illustrate challenges and future directions for research.
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Project description:Introduction: Observational studies of SARS-CoV-2 vaccine effectiveness depend on accurate ascertainment of vaccination receipt, date, and product type. Self-reported vaccine data may be more readily available to and less expensive for researchers than assessing medical records. Methods: We surveyed adult participants in the COVID-19 Community Research Partnership who had an authenticated Electronic Health Record (EHR) (N = 41,484) concerning receipt of SARS-CoV-2 vaccination using a daily survey beginning in December 2020 and a supplemental survey in September-October 2021. We compared self-reported information to that available in the EHR for the following data points: vaccine brand, date of first dose, and number of doses using rates of agreement and Bland-Altman plots for visual assessment. Self-reported data was available immediately following vaccination (in the daily survey) and at a delayed interval (in a secondary supplemental survey). Results: For the date of first vaccine dose, self-reported "immediate" recall was within ±7 days of the date reported in the "delayed" survey for 87.9% of participants. Among the 19.6% of participants with evidence of vaccination in their EHR, 95% self-reported vaccination in one of the two surveys. Self-reported dates were within ±7 days of documented EHR vaccination for 97.6% of the "immediate" surveys and 92.0% of the "delayed" surveys. Self-reported vaccine product details matched those in the EHR for over 98% of participants for both "immediate" and "delayed" surveys. Conclusions: Self-reported dates and product details for COVID-19 vaccination can be a good surrogate when medical records are unavailable in large observational studies. A secondary confirmation of dates for a subset of participants with EHR data will provide internal validity.
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Project description:We studied the impact of a vaccine prime dose on CD8 T cell gene expression We first immunized mice with an Ad5-SARS CoV-2 spike vaccine and then evaluated gene expression on SARS CoV-2 specific CD8 T cells at week 4.
2021-08-11 | GSE173567 | GEO
Project description:Coronavirus disease 2019 (COVID-19) is a disease that causes fatal disorders including severe pneumonia. To develop a therapeutic drug for COVID-19, a model that can reproduce the viral life cycle and can evaluate the drug efficacy of anti-viral drugs is essential. In this study, we established a method to generate human bronchial organoids (hBO) from commercially available cryopreserved primary human bronchial epithelial cells (hBEpC) and examined whether they could be used as a model for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) research. The hBO were found to contain basal, club, ciliated, and goblet cells. Also, angiotensin-converting enzyme 2 (ACE2), which is a receptor for SARS-CoV-2, and transmembrane serine proteinase 2 (TMPRSS2), which is an essential serine protease for priming spike protein of SARS-CoV-2, were highly expressed. After hBO were infected with SARS-CoV-2, remarkable amplification of the viral genome and the expression of spike protein of the virus was confirmed. In addition, cytotoxicity and pyknosis cells were observed due to the virus infection. Furthermore, treatment with camostat, an inhibitor of TMPRSS2, reduced the viral copy number to 2% of the control group. RNA-seq analyses revealed genes whose expression was altered by SARS-CoV-2 infection and camostat treatment. These results suggest that our hBO are acceptable for SARS-CoV-2 infection and replication, but also can be used as a model for COVID-19 drug discovery.
2020-05-26 | GSE150819 | GEO
Project description: Not available
| S-BSST379 | biostudies-other
Project description:Durable cell-mediated immune responses require efficient innate immune signaling and the release of pro-inflammatory cytokines. How precisely mRNA vaccines trigger innate immune cells for shaping antigen specific adaptive immunity remains unknown. Here we show that SARS-CoV-2 mRNA vaccination primes human monocyte derived macrophages for activation of the NLRP3 inflammasome. Spike protein exposed macrophages undergo NLRP3 driven pyroptotic cell death and subsequently secrete mature interleukin-1β. These effects depend on activation of spleen tyrosine kinase (SYK) coupled to C-type lectin receptors. Using autologous co-cultures, we show that SYK and NLRP3 orchestrate macrophage driven activation of effector memory T cells. Furthermore, vaccination induced macrophage priming can be enhanced with repetitive antigen exposure providing a rationale for prime-boost concepts to augment innate immune signaling in SARS-CoV-2 vaccination. Collectively, these findings identify SYK as a regulatory node capable of differentiating between primed and unprimed macrophages, which modulate spike protein specific T cell responses.
| S-SCDT-EMM-2022-15888P | biostudies-other
Project description:In the initial process of COVID-19, SARS-CoV-2 infects respiratory epithelial cells and then transfers to other organs via the blood vessels. It is believed that SARS-CoV-2 can pass the vascular wall by altering the endothelial barrier using an unknown mechanism. In this study, we investigated the effect of SARS-CoV-2 on the endothelial barrier using an airway-on-a-chip that mimics respiratory organs and found that SARS-CoV-2 produced from infected epithelial cells disrupts the barrier by decreasing Claudin-5 (CLDN5), a tight junction protein, and disrupting vascular endothelial cadherin (VE-cadherin)-mediated adherens junctions. Consistently, the gene and protein expression levels of CLDN5 in a COVID-19 patient’s lungs were decreased. CLDN5 overexpression or Fluvastatin treatment could rescue the SARS-CoV-2-induced respiratory endothelial barrier disruption. We therefore concluded that the downregulation of CLDN5 expression is a pivotal mechanism for SARS-CoV-2-induced endothelial barrier disruption in respiratory organs and that inducing CLDN5 expression is a novel therapeutic strategy against COVID-19.
2022-09-22 | GSE196113 | GEO
Project description:The focus on treatment of COVID19 patients during the Sars-CoV-2 outbreak has most likely implications for the extent and quality of diagnosis and treatment of non-COVID19 patients. Medical care of cancer patients is a particularly sensitive area. To draw holistic conclusions, it is necessary to analyze the provision of healthcare as broadly as possible with regard to the dimensions of access, processes and outcome during the Sars-CoV-2 pandemic. This will be implemented exemplarily for the early detection, diagnosis and treatment of colorectal cancer (CRC) and pancreatic cancer (PaCa) in Saxony. Patients with diagnosis, treatment or early detection measures for type 2 diabetes (T2D), coronary heart disease (CHD) and multiple sclerosis (MS) serve as comparison groups.
| 2743388 | ecrin-mdr-crc
Project description:Bioinformatics has been playing a crucial role in the scientific progress to fight against the pandemic of the coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The advances in novel algorithms, mega data technology, artificial intelligence and deep learning assisted the development of novel bioinformatics tools to analyze daily increasing SARS-CoV-2 data in the past years. These tools were applied in genomic analyses, evolutionary tracking, epidemiological analyses, protein structure interpretation, studies in virus-host interaction and clinical performance. To promote the in-silico analysis in the future, we conducted a review which summarized the databases, web services and software applied in SARS-CoV-2 research. Those digital resources applied in SARS-CoV-2 research may also potentially contribute to the research in other coronavirus and non-coronavirus viruses.
| S-EPMC10568291 | biostudies-literature
Project description:IntroductionNational Immunization Survey-Child data are used widely to assess childhood vaccination coverage in the U.S. This study compares National Immunization Survey-Child coverage estimates with estimates using other supplementary data sources.MethodsRetrospective analyses in 2021 assessed vaccination coverage of privately insured children for vaccines recommended by the Advisory Committee on Immunization Practices by age 2 years, using the 2015-2018 MarketScan Commercial Claims and Encounters databases and the 2018-2019 Healthcare Effectiveness Data and Information Set. The coverage estimates were compared statistically with those using the 2016-2018 National Immunization Survey-Child.ResultsEstimated coverage ranged from 69.9% (≥2 doses of influenza vaccine) to 95.0% (≥3 doses of diphtheria, tetanus toxoids, and acellular pertussis vaccine) using the MarketScan Commercial Claims and Encounters data and from 68.0% (≥2 doses of influenza vaccine) to 92.2% (≥1 dose of measles, mumps, and rubella vaccine) using the Healthcare Effectiveness Data and Information Set. The difference between the MarketScan Commercial Claims and Encounters and National Immunization Survey-Child estimates ranged from 0.1 to 4.3 percentage points and was statistically significant for 6 of the 13 assessed vaccines/doses and percentage of children receiving no vaccinations. The difference between the Healthcare Effectiveness Data and Information Set and National Immunization Survey-Child estimates ranged from 0.4 to 7.2 percentage points and was statistically significant for 6 of the 10 assessed vaccines/doses.ConclusionsFor certain vaccines and populations of interest, the National Immunization Survey-Child, MarketScan Commercial Claims and Encounters, and Healthcare Effectiveness Data and Information Set data might give comparable coverage of privately insured children.
| S-EPMC9996641 | biostudies-literature