Find research datasets worth reusing

opencc-by-4.0Mar 2023View details →

SARS-CoV-2 vaccine breakthrough infections by Omicron and Delta variants in healthcare workers

An observational prospective cohort study was conducted in vaccinated employees with acute SARS-CoV-2 infection between October 2021 and February 2022. Serological and molecular testing was performed to determine SARS-CoV-2 viral load, lineage, antibody levels, and neutral-ising antibody titres. A total of 571 (9.7%) employees experienced SARS-CoV-2 breakthrough infections during the enrolment period, of which 81 were included. The majority (n=79, 97.5%) was symptomatic and most (n=75, 92.6%) showed Ct-values < 30 in RT-PCR assays. Twenty-four (30%) remained PCR-positive for > 15 days. Neutralizing antibody titres were strongest for the wildtype, intermediate for Delta and lowest for Omicron variants. Omicron infections occurred at higher anti-RBD-IgG serum levels (p= 0.00001) and showed a trend for higher viral loads (p=0.14, median Ct-difference 4.3, 95% CI [-2.5-10.5]). For both variants, viral loads were signifi-cantly higher in participants with lower anti-RBD-IgG serum levels (p=0.02).

opencc-zeroDec 2022View details →

Data from: Genome-wide epitope mapping reveals significant diversity in antibody responses to Coxiella burnetii vaccination and infection

Coxiella burnetii is an important zoonotic bacterial pathogen of global importance, causing the disease Q fever in a wide range of animal hosts. Ruminant livestock, in particular sheep and goats, are considered the main reservoir of infection. Vaccination is a key control measure and two commercial vaccines based on formalin-inactivated C. burnetii bacterins are currently available. However, their deployment is limited due to significant reactogenicity in individuals previously sensitized to C. burnetii antigens. Furthermore, these vaccines interfere with available serodiagnostic tests which are also based on C. burnetii bacterin preparations. Subunit vaccines based on recombinant proteins offer significant advantages, as they can be designed to reduce reactogenicity and can be co-designed with defined antigen serodiagnostic tests to allow discrimination between vaccinated and infected individuals. This study aimed to investigate the diversity of antibody responses to C. burnetii vaccination and/or infection in cattle, goats, humans, and sheep through genome-wide linear epitope mapping to identify candidate vaccine and diagnostic antigens within the predicted bacterial proteome. Using high-density peptide microarrays, we analyzed the seroreactivity in 156 serum samples from vaccinated and infected individuals to peptides derived from 2,092 ORFs in the C. burnetii genome. We found significant diversity in the antibody responses within and between species and across different C. burnetii exposure statuses. However, C. burnetii exposure did result in more uniform seroreactivity across species. Through the implementation of three different vaccine candidate methods, we identified 493 candidate protein antigens for protein subunit vaccine design or serodiagnostic, out of which 65 have been previously described. This is the first study to investigate seroreactivity against the entire C. burnetii genome presented as overlapping linear peptides and provides the basis for selection of antigen targets for next generation Q fever vaccines and diagnostic tests.

opencc-zeroApr 2023View details →

Data for: Evaluation of antibody kinetics and durability in health individuals vaccinated with inactivated COVID-19 vaccine (CoronaVac): a cross-sectional and cohort study in Zhejiang, China

Background: Although inactivated COVID-19 vaccines are proven to be safe and effective in the general population, the dynamic response and duration of antibodies after vaccination in the real world should be further assessed. Methods: We enrolled 1067 volunteers who had been vaccinated with one or two doses of CoronaVac in Zhejiang Province, China. Another 90 healthy adults without previous vaccinations were recruited and vaccinated with three doses of CoronaVac, 28 days and 6 months apart. Serum samples were collected from multiple timepoints and analyzed for specific IgM/IgG and neutralizing antibodies (NAbs) for immunogenicity evaluation. Antibody responses to the Delta and Omicron variants were measured by pseudovirus-based neutralization tests. Results: Our results revealed that binding antibody IgM peaked 14–28 days after one dose of CoronaVac, while IgG and NAbs peaked approximately 1 month after the second dose and then declined slightly over time. Antibody responses had waned by month 6 after vaccination and became undetectable in the majority of individuals at 12 months. Levels of NAbs to live SARS-CoV-2 were correlated with anti-SARS-CoV-2 IgG and NAbs to pseudovirus, but not IgM. Homologous booster around 6 months after primary vaccination activated anamnestic immunity and raised NAbs 25.5-fold. The neutralized fraction subsequently rose to 36.0% for Delta (p=0.03) and 4.3% for Omicron (p=0.004), and the response rate for Omicron rose from 7.9% (7/89) to 17.8% (16/90). Conclusions: Two doses of CoronaVac vaccine resulted in limited protection over a short duration. The inactivated vaccine booster can reverse the decrease of antibody levels to prime strain, but it does not elicit potent neutralization against Omicron; therefore, the optimization of booster procedures is vital.

opencc-by-4.0Apr 2023View details →

Perennial malaria chemoprevention with and without malaria vaccination to reduce malaria burden in young children: a modeling analysis

Simulation input and processed output files accompanying publication on "Perennial malaria chemoprevention with and without malaria vaccination to reduce malaria burden in young children: a modelling analysis" https://malariajournal.biomedcentral.com/articles/10.1186/s12936-023-04564-9

opencc-zeroDec 2022View details →

Understanding the incidence and timing of rabies cases in domestic animals and wildlife in south-east Tanzania in the presence of widespread domestic dog vaccination campaigns

The "Zero by 30" strategic plan aims to eliminate human deaths from dog-mediated rabies by 2030, and domestic dog vaccination is a vital component of this strategic plan. In areas where domestic dog vaccination has been implemented, it is important to assess the impact of this intervention. Additionally, understanding temporal and seasonal trends in the incidence of animal rabies cases may assist in optimizing such interventions. Data on the incidence of probable rabies cases in domestic and wild animals were collected between January 2011 and December 2018 in thirteen districts of south-east Tanzania where jackals comprise over 40% of reported rabies cases. Vaccination coverage was estimated over this period, as five domestic dog vaccination campaigns took place in all thirteen districts between 2011 and 2016. Negative binomial generalized linear models were used to explore the impact of domestic dog vaccination on the annual incidence of animal rabies cases, whilst generalized additive models were used to investigate the presence of temporal and/or seasonal trends. Increases in domestic dog vaccination coverage were significantly associated with a decreased incidence of rabies cases in both domestic dogs and jackals. A 35% increase in vaccination coverage was associated with a reduction in the incidence of probable dog rabies cases of between 78.0 and 85.5% (95% confidence intervals ranged from 61.2 to 92.2%) and a reduction in the incidence of probable jackal rabies cases of between 75.3 and 91.2% (95% confidence intervals ranged from 53.0 to 96.1%). A statistically significant common seasonality was identified in the monthly incidence of probable rabies cases in both domestic dogs and jackals with the highest incidence from February to August and lowest incidence from September to January. These results align with evidence supporting the use of domestic dog vaccination as part of control strategies aimed at reducing animal rabies cases in both domestic dogs and jackals in this region. The presence of a common seasonal trend requires further investigation but may have implications for the timing of future vaccination campaigns.

opencc-by-4.0May 2023View details →

Effects of Covid-19 Vaccines on the Menstrual Cycle: A Cross-Sectional Study

Background: Prior clinical studies that sought to investigate the safety and efficacy of Covid-19 vaccines did not list menstrual cycle changes as a side-effect. However, following reported cases of menstrual cycle disturbances after vaccination, this study sought to examine the link between Covid-19 vaccination and post-vaccine menstrual cycle abnormalities in pre- and post-menopausal women. Methods: A cross-sectional research design approach using online surveys was employed to investigate the link between vaccination and changes in menstrual cycle. The participants consisted of a cohort of 657 pre- and post-menopausal women with the majority drawn from the reproductive age group (25-44 years). The inclusion criteria was that participants must have received any type of Covid-19 vaccine, not be pregnant and those that did not have a negative diagnosis in any gynecologic condition. Of the eligible sample size, only 344 participants met the inclusion criteria. The sociodemographic and menstrual cycle data was collected from an online survey. Data was analyzed using descriptive, inferential chi-square tests, logistic regression, and correlation. Results: The results partially confirmed the findings from prior studies that Covid-19 vaccination is associated with significant changes in the women’s menstrual cycle flow and menstrual period length even after controlling for age, Body Mass Index, and ethnicity. Other menstrual cycle disturbances such as missed periods, cycle regularity, and spotting/vaginal bleeding were noted to be less significant. However, the extent of menstrual cycle changes was less severe and decreased after the second dose vaccination. It was found that 11.1% and 37.5% of post-menopausal women reported menstrual symptoms after the first and the second dose cycle respectively. Conclusion: The study concludes that although Covid-19 vaccines tend to adversely affect women’s menstrual cycle, these changes are short-lived. The findings have important implications in enhancing the success of Covid-19 vaccination programs by reducing cases of vaccine hesitancy among reproductive-age women.

opencc-zeroJun 2023View details →

Supporting data and code for: Phylogenetic identification of influenza virus candidates for seasonal vaccines

The seasonal influenza (flu) vaccine is designed to protect against those influenza viruses predicted to circulate during the upcoming flu season, but identifying which viruses are likely to circulate is challenging. We use features from phylogenetic trees reconstructed from hemagglutinin (HA) and neuraminidase (NA) sequences, together with a support vector machine, to predict future circulation. We obtain accuracies of 0.75–0.89 (Area under the curve AUC 0.83–0.91) over 2016–2020. We explore ways to select potential candidates for a seasonal vaccine and find that the machine learning model has a moderate ability to select strains that are close to future populations. However, consensus sequences among the most recent three years also do well at this task. We identify similar candidate strains to those proposed by the World Health Organization, suggesting that this approach can help inform vaccine strain selection.

opencc-by-4.0Jul 2023View details →

Data from "Optimizing the baiting strategy for oral vaccine delivery to wild boar"

Data from the paper "Optimization of the baiting strategy for the administration of oral vaccines to wild boar". These data are from experiments done in field work based on the baiting preference of different animal species.

opencc-by-4.0Aug 2023View details →

Search strategies for herpes zoster vaccination for adults

The dataset includes the complete, reproducible search strategies for all literature databases searched during this project. The search strategies were designed to answer the following research questions: <ul> <li>RQ 1 – What is the clinical efficacy and effectiveness of the currently licensed and approved recombinant vaccine for the prevention of herpes zoster and associated complications, in adults aged 50 years and older and in adults aged 18 and over who are at increased risk of herpes zoster?</li> <li>RQ 2 – What is the safety profile of the currently licensed and approved recombinant vaccine for the prevention of herpes zoster in adults aged 50 years and older and in adults aged 18 and over who are at increased risk of herpes zoster?</li> </ul>

opencc-zeroAug 2023View details →

Dataset for: mRNA vaccine quality analysis using RNA sequencing

The success of mRNA vaccines has been realised, in part, by advances in manufacturing that enabled billions of doses to be produced at sufficient quality and safety. However, mRNA vaccines must be rigorously analysed to measure their integrity and detect contaminants that reduce their effectiveness and induce side-effects. Currently, mRNA vaccines and therapies are analysed using a range of time-consuming and costly methods. Here we describe a streamlined method to analyse mRNA vaccines and therapies using long-read nanopore sequencing. Compared to other industry-standard techniques, VAX-seq can comprehensively measure key mRNA vaccine quality attributes, including sequence, length, integrity, and purity. We also show how direct RNA sequencing can analyse mRNA chemistry, including the detection of nucleoside modifications. To support this approach, we provide supporting software to automatically report on mRNA and plasmid template quality and integrity. Given these advantages, we anticipate that RNA sequencing methods, such as VAX-seq, will become central to the development and manufacture of mRNA drugs.

opencc-by-4.0Jan 2023View details →

COVID-19 vaccination single cell datasets

The datasets presented here comprise the sequencing data featured in the research paper titled: "Multimodal single-cell datasets characterize antigen-specific CD8+ T cells across SARS-CoV-2 vaccination and infection": https://www.nature.com/articles/s41590-023-01608-9 Peripheral Blood Mononuclear Cell (PBMC) samples utilized for both CITE-seq and ASAP-seq were systematically collected at four distinct time intervals: <ul> <li>Pre-vaccination (Day 0)</li> <li>Post-primary vaccination (Day 2 and Day 10.</li> <li>Seven days post-boost vaccination (Day 28).</li> </ul> The count matrix folder contains count matrices for each experimental type, specifically CITE-seq, ASAP-seq, and ECCITE-seq. In addition, we have included the fully integrated, processed Seurat objects for downstream analysis. Details of the content within the count matrix folder are as follows: <ul> <li>The RNA, ATAC, and TCR modality outputs were generated using the 10x Cellranger pipeline.</li> <li>HTO and ADT modalities were mapped with Alevin.</li> </ul> Outlined below are the three processed single-cell datasets: <ol> <li>PBMC_vaccine_CITE.rds: 3' RNA and surface proteins (173 TotalSeq-A antibodies)</li> <li>PBMC_vaccine_ASAP.rds: Chromatin accessibility and surface proteins (173 TotalSeq-A antibodies)</li> <li>PBMC_vaccine_ECCITE_TCR.rds: 5' RNA, surface proteins (137 TotalSeq-C antibodies), TCR and dextramer loaded with peptides of SARS-CoV-2 spike protein.</li> </ol> <ul> <li>antigen_module_genes.rds: This file contains the vaccine-induced gene sets.</li> <li>antigen_module_peaks.rds: This file contains the DE peaks specific for vaccine-induced cells. </li> </ul> To map the scRNA-seq query dataset onto our CITE-seq reference: <pre><code>library(Seurat) PBMC_CITE <- readRDS("/zenedo/PBMC_vaccine_CITE.rds") query_scRNA <- readRDS("/home/xx/your_own_data.rds") anchors <- FindTransferAnchors( reference = PBMC_CITE, query = query_scRNA, normalization.method = "SCT", k.anchor = 5, reference.reduction = "spca", dims = 1:50) query_scRNA <- MapQuery( anchorset = anchors, query = query_scRNA, reference = PBMC_CITE, refdata = list( l1 = "celltypel1", l2 = "celltypel2", l3 = "celltypel3"), reference.reduction = "spca", reduction.model = "wnn.umap") </code></pre> To use the scATAC-seq data, please run the commands below to update the path of the fragment file for the object.   <pre><code>Vaccine_ASAP <- readRDS("PBMC_vaccine_ASAP.rds") # remove fragment file information Fragments(Vaccine_ASAP) <- NULL # Update the path of the fragment file Fragments(Vaccine_ASAP) <- CreateFragmentObject(path = "download/PBMC_vaccine_ASAP_fragments.tsv.gz", cells = Cells(Vaccine_ASAP))</code></pre>

opencc-by-4.0Sep 2023View details →

Identifying viral and host genetic determinants of vaccine efficacy

This dataset includes summary statistics results from genetic analyses testing the hypothesis that germline genetic variants are associated with COVID-19 mRNA vaccine efficacy.    These genetic studies include GWAS, HLA-WAS and rare variant gene burden tests.

restrictedIPD-UNDECIDEDFeb 2026View details →

Study Evaluating Pneumococcal Vaccine in Healthy Infants

ClinicalTrials.gov study NCT00205803. IPD Sharing: Not stated. Countries: 1. Publications: 1.

restrictedIPD-UNDECIDEDFeb 2026View details →

A Study Evaluating Safety And Immunogenicity Of Meningococcal B Rlp2086 Vaccine In Adolescents

ClinicalTrials.gov study NCT00808028. IPD Sharing: Not stated. Countries: 3. Publications: 4.

restrictedIPD-UNDECIDEDFeb 2026View details →

Safety Study of ChimeriVax™-JE Vaccine to Prevent Japanese Encephalitis.

ClinicalTrials.gov study NCT00314132. IPD Sharing: Not stated. Countries: 2. Publications: 1.

HPV Vaccine Immunity in High-risk Women

ClinicalTrials.gov study NCT04590521. IPD Sharing: YES. Countries: 1. Publications: 1.

closedIPD-NOFeb 2026View details →

A Phase 2 Influenza A Challenge Study Following Oral Administration of an H1N1 HA Ad-Vector Seasonal Flu Vaccine

ClinicalTrials.gov study NCT02918006. IPD Sharing: NO. Countries: 1. Publications: 2.

Immunogenicity and Safety Study of GlaxoSmithKline (GSK) Biologicals' Boostrix™ Vaccine in Pregnant Women

ClinicalTrials.gov study NCT02377349. IPD Sharing: YES. Countries: 6. Publications: 1.

Adherence to Guidelines VAccination in Type 1 DIabetes Mellitus Patients (AVADI-1).

ClinicalTrials.gov study NCT03478254. IPD Sharing: YES. Countries: 1. Publications: 6.

Safety, Immunogenicity, and Relative Efficacy of H1N1 Vaccines in Adults Aged 18 Years and Older

ClinicalTrials.gov study NCT00979602. IPD Sharing: YES. Countries: 2. Publications: 1.