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23 results for “virus surveillance”
Datasets underlying the publication "A new lineage nomenclature to aid genomic surveillance of dengue virus"
<p>These datasets are underlying the scientific publication titled "A new lineage nomenclature to aid genomic surveillance of dengue virus", published in the <a href="https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002834#abstract0">PLOS Biology</a> journal. </p> <p>All sequences used to design the lineage system are from Genbank and GISAID, with accession numbers listed in the tables. Custom scripts and alignments of representative sequences from Genbank can be found on the github of the publication authors (<a href="https://github.com/DENV-lineages/lineages-paper">https://github.com/DENV-lineages/lineages-paper</a>).</p> <p>Sequences for the Vietnam case study can be found on Genbank under accession numbers PP269455-PP270050, in bioproject PRJNA1072696. For the case study from Tanzania, sequences can be found on Genbank under accession numbers OM920035-OM920066 for DENV-3 and OM920075-OM920415 for DENV-1. Sequences for the Brazil case study can be found on GISAID under accession numbers EPI_ISL_17733558 ‐ EPI_ISL_191469691.<br><br>The provided information in the datasets are further discussed and interpreted in detail, as well as their subsequent results, in the scientific publication.</p> <p>VIRTIGATION partner EMWEB contributed to this publication with findings from the VIRTIGATION project, a project which is part of the EU Open Research Data pilot. This project has received funding from the European Union's Horizon 2020 research and innovation program under grant agreement No. 101000570.</p>
Dataset accompanying the article: West Nile virus surveillance using sentinel birds: results of eleven years of West Nile virus testing in corvids in a region of Northern Italy
<p>In this dataset are resumed the results of West Nile virus surveillance in sentinel corvids in the Emilia-Romagna region, Northern Italy. Overall, 15,632 European magpies (<em>Pica pica</em>), 4670 Hooded crows (<em>Corvus cornix</em>), and 2012 Eurasian jays (<em>Garrulus glandarius</em>) were collected between May and October 2013-2023. In the nine provinces of the region, birds were shot or captured using Larsen traps and killed by trained hunters by cervical dislocation in accordance with the provisions of the national legislation on animal welfare (Council Regulation (EC) 1099/2009). Sampling was carried out on a voluntary basis under the supervision of the official veterinary services, which ensured rapid delivery of the birds to the laboratory in charge of testing.</p> <p>From each sampled bird, heart, brain, kidney, and spleen were pooled, mechanically homogenized and tested by real-time PCRs to detect WNV RNA (Del Amo et al., 2013; Eiden et al., 2010; Tang et al., 2006). All tests were performed in the same laboratory (Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna; IZSLER, Reggio Emilia site).</p> <p>The following data are available for statistical analysis: bird species, sampling date, sampling province, date of delivery to the laboratory, testing start date, test result, date of notification of positive result.</p> <p>In the same dataset are reported some data about incidence of human cases of disease due to West Nile virus infection (neurological disease or fever), per year, week, and province.</p> <p>The record trace is described in Table 1.</p> <p>References</p> <p>1. Del Amo, J., Sotelo, E., Fernández-Pinero, J., Gallardo, C., Llorente, F., Agüero, M., Jiménez-Clavero, M.A., 2013. A novel quantitative multiplex real-time RT-PCR for the simultaneous detection and differentiation of West Nile virus lineages 1 and 2, and of Usutu virus. J Virol Methods 189, 321–327. https://doi.org/10.1016/j.jviromet.2013.02.019</p> <p>2. Eiden, M., Vina-Rodriguez, A., Hoffmann, B., Ziegler, U., Groschup, M.H., 2010. Two new real-time quantitative reverse transcription polymerase chain reaction assays with unique target sites for the specific and sensitive detection of lineages 1 and 2 West Nile virus strains. J Vet Diagn Invest 22, 748–753. https://doi.org/10.1177/104063871002200515 </p> <p>3. Tang, Y., Anne Hapip, C., Liu, B., Fang, C.T., 2006. Highly sensitive TaqMan RT-PCR assay for detection and quantification of both lineages of West Nile virus RNA. J Clin Virol 36, 177–182. <a href="https://doi.org/10.1016/j.jcv.2006.02.008">https://doi.org/10.1016/j.jcv.2006.02.008</a></p> <p> </p> <p>Table 1. Dataset record trace</p> <table> <tbody> <tr> <td> <p><strong>Field_name</strong></p> </td> <td> <p><strong>Description</strong></p> </td> </tr> <tr> <td> <p>Year</p> </td> <td> <p>Year of sampling</p> </td> </tr> <tr> <td> <p>province_CODE</p> </td> <td> <p>Italian code of the province of sampling</p> </td> </tr> <tr> <td> <p>BIRD_species</p> </td> <td> <p>Bird species collected: magpie (Pica pica), hooded crow (Corvus cornix); jay (Garrulus glandarius)</p> </td> </tr> <tr> <td> <p>N_birds_collected</p> </td> <td> <p>Number of birds collected</p> </td> </tr> <tr> <td> <p>Sampling_ID</p> </td> <td> <p>Sampling code</p> </td> </tr> <tr> <td> <p>dt_sampling</p> </td> <td> <p>Sampling date of birds</p> </td> </tr> <tr> <td> <p>dt_delivery</p> </td> <td> <p>Date of delivery to the lab (birds)</p> </td> </tr> <tr> <td> <p>dt_registration</p> </td> <td> <p>Date of registration of the lab (birds)</p> </td> </tr> <tr> <td> <p>dt_analysis</p> </td> <td> <p>Date of analysis (birds)</p> </td> </tr> <tr> <td> <p>dt_notification</p> </td> <td> <p>Date of result notification (birds)</p> </td> </tr> <tr> <td> <p>WNV_PCR_Positive</p> </td> <td> <p>Number of birds with WNV Positive result (PCR)</p> </td> </tr> <tr> <td> <p>WNV_PCR_tested</p> </td> <td> <p>Number of birds tested (PCR)</p> </td> </tr> <tr> <td> <p>WNV_PCR_not_tested</p> </td> <td> <p>Number of birds not tested</p> </td> </tr> <tr> <td> <p>WNV_PCR_Negative</p> </td> <td> <p>Number of birds with WNV Negative result (PCR)</p> </td> </tr> <tr> <td> <p>sampling_week_corvids</p> </td> <td> <p>Number of week of sampling (birds)</p> </td> </tr> <tr> <td> <p>notification_week_corvids</p> </td> <td> <p>Number of week of result notification (birds)</p> </td> </tr> <tr> <td> <p>num_WNhuman_cases</p> </td> <td> <p>Number of WN disease human cases</p> </td> </tr> <tr> <td> <p>first_human_notification_dt</p> </td> <td> <p>Date of notification of the first human disease case</p> </td> </tr> <tr> <td> <p>province_pop</p> </td> <td> <p>Province population</p> </td> </tr> <tr> <td> <p>human_inc</p> </td> <td> <p>Incidence of human cases (x100,000)</p> </td> </tr> <tr> <td> <p>flag_season_human_cases</p> </td> <td> <p>Occurrence of WN human cases (1=Yes; 0=No)</p> </td> </tr> <tr> <td> <p>week_first human_case</p> </td> <td> <p>Number of week of notification of the first human disease case</p> </td> </tr> <tr> <td> <p>early_detection_code</p> </td> <td> <p>Early detection code (1=first detection in birds; 0=first detection in human beings; 9=No case detection in human beings)</p> </td> </tr> <tr> <td> <p>province_sup_km2</p> </td> <td> <p>Province surface (km2)</p> </td> </tr> <tr> <td> <p>delta_sampling_lab</p> </td> <td> <p>Days from sampling to delivery to the lab (birds)</p> </td> </tr> <tr> <td> <p>delta_lab_testing</p> </td> <td> <p>Days from lab registration to test (birds)</p> </td> </tr> <tr> <td> <p>delta_testing_notification</p> </td> <td> <p>Days from testing to result notification (birds)</p> </td> </tr> <tr> <td> <p>delta_sampling_notification</p> </td> <td> <p>Days from sampling to result notification (birds)</p> </td> </tr> </tbody> </table> <p> </p>
Use-Results Surveillance Study of Harvoni® in Japanese Patients With Chronic Genotype 1 Hepatitis C Virus Infection
ClinicalTrials.gov study NCT02591277. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Circulating Human Papilloma Virus (HPV) DNA for the Screening and Surveillance of Gynecologic Cancers
ClinicalTrials.gov study NCT05606133. IPD Sharing: NO. Countries: 1. Publications: 6.
Serial Epstein-Barr Virus DNA Surveillance in Nasopharyngeal Carcinoma Patients
ClinicalTrials.gov study NCT03855020. IPD Sharing: NO. Countries: 1. Publications: 0.
Data from: Inference of Japanese encephalitis virus ecological and evolutionary dynamics from passive and active virus surveillance
A comprehensive monitoring strategy is vital for tracking the spread of mosquito-borne Japanese encephalitis virus (JEV), the leading cause of viral encephalitis in Asia. Virus detection consists of passive surveillance of primarily humans and swine, and/or active surveillance in mosquitoes, which may be a valuable proxy in providing insights into ecological processes underlying the spread and persistence of JEV. However, it has not been well characterized whether passive surveillance alone can capture the circulating genetic diversity to make reasonable inferences. Here, we develop phylogenetic models to infer JEV host changes, spatial diffusion patterns, and evolutionary dynamics from data collected through active and passive surveillance. We evaluate the feasibility of using JEV sequence data collected from mosquitoes to estimate the migration histories of genotypes GI and GIII. We show that divergence times estimated from this dataset were comparable to estimates from all available data. Increasing the amount of data collected from active surveillance improved time of most recent common ancestor estimates and reduced uncertainty. Phylogenetic estimates using all available data and only mosquito data from active surveillance produced similar results, showing that GI epidemics were widespread and diffused significantly faster between regions than GIII. In contrast, GIII outbreaks were highly structured and unlinked suggesting localized, unsampled infectious sources. Our results show that active surveillance of mosquitoes can sufficiently capture circulating genetic diversity of JEV to confidently estimate spatial and evolutionary patterns. While surveillance of other hosts could contribute to more detailed disease tracking and evaluation, comprehensive JEV surveillance programs should include systematic surveillance in mosquitoes to infer the most complete patterns for epidemiology, and risk assessment.
Repeated Cross Sectional Surveillance Study To Determine the Respiratory Syncytial Virus (RSV) Immunization Rates in German Infants
ClinicalTrials.gov study NCT06824207. IPD Sharing: YES. Countries: 1. Publications: 0.
Prospective Surveillance of Respiratory Syncytial Virus Disease in Infants and Toddlers
ClinicalTrials.gov study NCT05964582. IPD Sharing: YES. Countries: 7. Publications: 0.
Data from: Inference of Japanese encephalitis virus ecological and evolutionary dynamics from passive and active virus surveillance
Open the record for dataset details and reuse information.
A Surveillance Program for the Detection of Hepatitis B Virus (HBV) Resistance to Tenofovir in HIV-HBV co-Infected Patients
ClinicalTrials.gov study NCT00660361. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Virus Surveillance in Pediatric Solid Organ Transplant Recipients
ClinicalTrials.gov study NCT00886158. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Surveillance of Influenza Virus Shedding and Immunologic Response in Immunocompromised Children and Young Adults
ClinicalTrials.gov study NCT00998803. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Use-Results Surveillance Study of Sovaldi® Plus Rebetol® in Japanese Patients With Chronic Genotype 2 Hepatitis C Virus Infection
ClinicalTrials.gov study NCT02562742. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Surveillance of Respiratory Viruses in Healthcare and Animal Workers
ClinicalTrials.gov study NCT07156890. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Prospective Surveillance For Respiratory Virus Infections In Children Undergoing Hematopoietic Stem Cell Transplantation
ClinicalTrials.gov study NCT00667303. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Surveillance Study of Respiratory Syncytial Virus Infection (RSV) in Subjects < 24 Months of Age
ClinicalTrials.gov study NCT01754428. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Use-Results Surveillance Study of Sovaldi® Plus Copegus® in Japanese Patients With Chronic Genotype 2 Hepatitis C Virus Infection
ClinicalTrials.gov study NCT02537379. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Surveillance of Influenza Virus Among Children With Febrile Respiratory Complaints Attending the Pediatric Clinic of the First Affiliated Hospital, Shantou University Medical College, Shantou, Guangdo
ClinicalTrials.gov study NCT00760500. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Post-marketing Safety Surveillance Program in Human Immunodeficiency Virus (HIV)-Infected Children Exposed to Atazanavir in Europe
ClinicalTrials.gov study NCT01389310. IPD Sharing: Not stated. Countries: 7. Publications: 0.
DNA Microarray Platform for Detection and Surveillance of Viruses Transmitted by Small Mammals and Arthropods
GEO Series GSE81392. dengue virus type 2; Aedes albopictus; Chikungunya virus; dengue virus type 1; dengue virus type 3; Viruses; dengue virus type 4; Zika virus. 7 samples. Type: Expression profiling by array.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.