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28 results for “virus community”
Impact of viruses on microbial communities and biogeochemical processes in agricultural soils
<p>The source data of microcosm experiment.</p>
Sharing pollinators and pollen-associated viruses: understanding the diversity of the pollen virome within a co-flowering community
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Data from: Diversity and composition of viral communities: coinfection of barley and cereal yellow dwarf viruses in California grasslands 2000 - 2005
Most species host multiple pathogens, yet field studies rarely examine the processes determining pathogen diversity within a single host or the effects of coinfection on pathogen dynamics in natural systems. Coinfection can affect pathogen transmission and virulence. In turn, coinfection can be regulated within hosts by interactions such as cross-protective immunity or at broader spatial scales via vector distributions. Using a general model, we demonstrate that coinfection by a group of vectored pathogens is highest with abundant generalist vectors and weak cross-protection and coinfection- induced mortality. Using these predictions, we investigate the distribution of five coexisting aphid-vectored, viral pathogens (barley and cereal yellow dwarf luteoviruses and poleroviruses) in a native perennial grass (Elymus glaucus) in both space (700 km) and time (4 years). Observed coinfection rates were much higher than expected at random, suggesting that within-host processes exerted weak effects on within-host pathogen diversity. Covariance among viruses in space and time was highest for viral species sharing a vector. Temporal correlation arose from the synchronous invasion of two viruses transmitted by a shared aphid species. On the basis of our modeling and empirical results, we expect that factors external to individual hosts may affect the coinfection dynamics in other communities hosting vectored pathogens.
Experimental parasite community perturbation reveals associations between Sin Nombre virus and gastrointestinal nematodes in a rodent reservoir host
<p>Individuals are often co-infected with several parasite species, yet measuring within-host interactions remains difficult in the wild. Consequently, the impact of such interactions on host fitness and epidemiology are often unknown. We used anthelmintic drugs to experimentally reduce nematode infection and measured the effects on both nematodes and the important zoonosis Sin Nombre virus (SNV) in its primary reservoir (<i>Peromyscus spp.</i>). Treatment significantly reduced nematode infection, but increased SNV seroprevalence. Furthermore, mice that were co-infected with both nematodes and SNV were in better condition and survived up to four times longer than uninfected or singly-infected mice. These results highlight the importance of investigating multiple parasites for understanding interindividual variation and epidemiological dynamics in reservoir populations with zoonotic transmission potential.</p>
Uptake of Human Papilloma Virus vaccine among young women living in fishing communities in Wakiso and Mukono districts, Uganda
<p>Human Papilloma Virus (HPV) is a preventable cause of cervical cancer, the most common cancer among women in Uganda. The Uganda Ministry of Health included the HPV vaccine in the free routine immunization schedule since 2015. Five years after this policy, we assessed the uptake of the HPV vaccine and associated socio-demographic factors among young women living in fishing communities in Central Uganda in 2020.</p> <p>We analyzed secondary data from 94 young women aged 9–25 years who were recruited from the two fishing communities (Kasenyi landing site and Koome Island) in a primary implementation study that aimed to promote awareness of maternal and childhood vaccines. We assessed uptake of the HPV vaccine as the proportion of participants who self-reported to have ever received at least one dose of the HPV vaccine. We assessed the socio-demographic factors associated with HPV vaccine uptake using a modified Poisson regression model adjusted for clustering by study site in STATA version 17.</p> <p>The mean (standard deviation) age of study participants was 21.1 (3.1) years and most (81.9%) of them were from Kasenyi landing site. The uptake of the HPV vaccine was 10.6% [95% Confidence Interval (CI) 5.6, 18.9]. After adjusting for covariates, being 20–25 years old (adjusted prevalence ratio [aPR] 0.18, 95%CI 0.06, 0.59) and of Catholic religion (aPR 5.55, 95%CI 1.53, 20.16) were significantly associated with HPV vaccine uptake. The HPV vaccine uptake was very low, despite the reported 99% national coverage of HPV vaccination program for the first dose at the end of 2019. Age and religion were shown to be important determinants of the HPV vaccine uptake. Reasons for very low uptake of HPV vaccinations need to be carefully assessed to find effective strategies to improve it.</p>
In silico mock communities for evaluation of taxonomic profilers across prokaryotes and viruses
<p><em>In silico </em>mock communities generated with CAMISIM for benchmarking the performance of taxonomic profilers across prokaryotic (50 communities), eukaryotic (30 communities), and viral communities (10 communities) of the human microbiome. Metagenomes were generated using CAMISIM (Fritz et al., 2019), which simulates 2.1 Gb of Illumina 2 ×150 bp paired end reads with the default HiSeq 2500 error profile and a mean insert size of 200 bp. To assess profiling performance for a range of sequencing depths, the 50 <em>in silico</em> metagenomes were also rarefied with seqtk (-s100) to sequencing depths of 20, 5, 2, 1, 0.5, 0.25 and 0.1 million read pairs. Counts are provided for rarefied metagenomes.</p> <p><strong>Prokaryotic communities<br></strong>For prokaryotic benchmarking, 10 body site-representative prokaryotic metagenomes were simulated for each of the following five body sites: adult gut, infant gut, oral, skin, and vagina. Genome accession ids for prokaryotic species found in each human body site were identified from published literature (Bäckhed et al., 2015; Proctor et al., 2019; Saheb Kashaf et al., 2021). </p> <p>Adult Gut: pro_gut_adult.zip<br>Infant Gut: pro_gut_infant.zip<br>Oral: pro_oral.zip<br>Skin: pro_skin_1.zip, pro_skin_2.zip, pro_skin_3.zip<br>Vaginal: pro_vaginal.zip</p> <p>Downsized counts: </p> <p><strong>Eukaryotic communities<br></strong>30 eukaryotic <em>in silico</em> metagenomes comprising up to 200 randomly sampled genomes from a set of 113 eukaryotic species (See Supplementary Table 2 from the paper) corresponding to the eukaryotic species within both CHAMP and MetaPhlAn 4 (Blanco-Míguez et al., 2023) databases.</p> <p>Eukaryotic data is deposited here: <a href="https://doi.org/10.5281/zenodo.12090449" target="_blank" rel="noopener">doi: 10.5281/zenodo.12090449</a></p> <p><strong>Viral communities</strong><br>10 viral communities were simulated with 95% of the reads from bacteria and 5% of the reads originating from phages. Each community consisted of 200 randomly selected bacterial genomes from GTDB with species-level annotation and 200 viral genomes from the Gut Phage Database (GPD, Camarillo-Guerrero et al., 2021). </p> <p>Counts: phage_communities_counts.zip<br>FastQ, forward reads: camisimu_[1-10].fq.1.gz<br>FastQ, reverse reads: camisimu_[1-10].fq.2.gz</p> <p><strong>References</strong></p> <p>Bäckhed, F., Roswall, J., Peng, Y., Feng, Q., Jia, H., Kovatcheva-Datchary, P., et al. (2015). Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life. <em>Cell Host Microbe</em> 17, 690–703. doi: 10.1016/J.CHOM.2015.04.004</p> <p>Blanco-Míguez, A., Beghini, F., Cumbo, F., McIver, L. J., Thompson, K. N., Zolfo, M., et al. (2023). Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4. <em>Nature Biotechnology 2023 41:11</em> 41, 1633–1644. doi: 10.1038/s41587-023-01688-w</p> <p>Camarillo-Guerrero, L. F., Almeida, A., Rangel-Pineros, G., Finn, R. D., and Lawley, T. D. (2021). Massive expansion of human gut bacteriophage diversity. <em>Cell</em> 184, 1098. doi: 10.1016/J.CELL.2021.01.029</p> <p>Fritz, A., Hofmann, P., Majda, S., Dahms, E., Dröge, J., Fiedler, J., et al. (2019). CAMISIM: Simulating metagenomes and microbial communities. <em>Microbiome</em> 7, 1–12. doi: 10.1186/S40168-019-0633-6/FIGURES/5</p> <p>Proctor, L. (2019). Priorities for the next 10 years of human microbiome research. <em>Nature 2021 569:7758</em> 569, 623–625. doi: 10.1038/d41586-019-01654-0</p> <p>Saheb Kashaf, S., Proctor, D. M., Deming, C., Saary, P., Hölzer, M., Mullikin, J., et al. (2021). Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions. <em>Nature Microbiology 2021 7:1</em> 7, 169–179. doi: 10.1038/s41564-021-01011-w</p>
Data from: Diversity and composition of viral communities: coinfection of barley and cereal yellow dwarf viruses in California grasslands
Most species host multiple pathogens, yet field studies rarely examine the processes determining pathogen diversity within a single host or the effects of coinfection on pathogen dynamics in natural systems. Coinfection can affect pathogen transmission and virulence. In turn, coinfection can be regulated within hosts by interactions such as cross-protective immunity or at broader spatial scales via vector distributions. Using a general model, we demonstrate that coinfection by a group of vectored pathogens is highest with abundant generalist vectors and weak cross-protection and coinfection- induced mortality. Using these predictions, we investigate the distribution of five coexisting aphid-vectored, viral pathogens (barley and cereal yellow dwarf luteoviruses and poleroviruses) in a native perennial grass (Elymus glaucus) in both space (700 km) and time (4 years). Observed coinfection rates were much higher than expected at random, suggesting that within-host processes exerted weak effects on within-host pathogen diversity. Covariance among viruses in space and time was highest for viral species sharing a vector. Temporal correlation arose from the synchronous invasion of two viruses transmitted by a shared aphid species. On the basis of our modeling and empirical results, we expect that factors external to individual hosts may affect the coinfection dynamics in other communities hosting vectored pathogens.
Tundra soil viruses mediate the responses of microbial communities to climate warming
<p>The dataset of this study contains the information of metagenomic data, environmental factors, GeoChip data, vOTUs table, mOTUs tables, and the viral and microbial sequences.</p> <p>If this study dataset is useful, please cite: Ji M, et al. Tundra Soil Viruses Mediate Responses of Microbial Communities to Climate Warming[J]. Mbio, 2023: e03009-22.</p> <p>For any other dataset/analysis inquiries, please contact me: jimengzhi@mail.sdu.edu.cn.</p>
Data from: Virus community structuring is shaped by habitat heterogeneity and resource utilisation strategies
<p><span>After decades of disconcerted research, we still recognise large gaps in the understanding of mechanisms that govern disease dynamics in complex biological communities. To determine how spatial structuring of plant communities caused by anthropic disturbance affects resource utilisation traits of viruses, we combine high-throughput, network, and metacommunity approaches. We find that the disturbance gradient corresponded to network modules and habitat specificity exhibited by a majority of viruses. Communities were connected through key hub species of either generalist viruses or high potential host reservoirs. Spatial dependencies were evident in regression models of species richness and correlations between metacommunity structure and both host range and transmission mode at finer spatial resolutions. We propose that virus community assembly is influenced by variation in niche opportunities. Distinctions in virus community composition caused by resource compartmentalisation can be used to track ecological traits important in forecasting transmission risk.</span></p>
This Study Will Describe the Burden of DENgue Fever Virus (DENV) Illness Among Household Members Aged 6 Months to 50 Years of Selected Communities in Latin America and Southeast Asia
ClinicalTrials.gov study NCT02766088. IPD Sharing: Not stated. Countries: 2. Publications: 2.
Data from: Diversity and composition of viral communities: coinfection of barley and cereal yellow dwarf viruses in California grasslands
Open the record for dataset details and reuse information.
Uptake of Human Papilloma Virus vaccine among young women living in fishing communities in Wakiso and Mukono districts, Uganda
Open the record for dataset details and reuse information.
Data from: Virus community structuring is shaped by habitat heterogeneity and resource utilisation strategies
Open the record for dataset details and reuse information.
Experimental parasite community perturbation reveals associations between Sin Nombre virus and gastrointestinal nematodes in a rodent reservoir host
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Data from: Pollinator community species richness dilutes prevalence of multiple viruses within multiple host species
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Data for: Metagenomics show high spatiotemporal virus diversity and ecological compartmentalisation: virus infections of melon, Cucumis melo, crops and adjacent wild communities
<p>Emergence of viral diseases results from novel transmission dynamics between wild and crop plant communities. The bias of studies towards pathogenic viruses of crops has distracted from knowledge of non-antagonistic symbioses in wild plants. Here we implemented a high throughput approach to compare the viromes of melon (<em>Cucumis melo</em>)<em>, </em>and wild plants of crop (Crop) and adjacent boundaries (Edge). Each of the 41-plant species examined was infected by at least one virus. The interactions of 104 virus operational taxonomic units (OTUs) with these hosts occurred largely within ecological compartments of either Crop or Edge, Edge having traits of a reservoir community. The positive correlation of virus and plant richness at each site, the tendency for increased specialist host use through seasons, and specialist host use by OTUs observed only in Melon, characterised local-scale patterns of infection. In this study of systematically sampled viromes of crop and adjacent wild communities most hosts showed no disease symptoms, suggesting non-antagonistic symbioses are common. The coexistence of viruses within species-rich ecological compartments of agro-systems might promote the evolution of a diversity of virus strategies for survival and transmission. These communities, including those suspected as reservoirs, are subject to sporadic changes in assemblages, and so too are the conditions that favour the emergence of disease.</p>
Human Papilloma Viruses (HPV) Vaccine Adherence Community Clinic Study
ClinicalTrials.gov study NCT01908517. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Clinical Significance of Community-acquired Respiratory Virus Infection and Longitudinal Analysis of the Lung Microbiome in Lung Transplantation
ClinicalTrials.gov study NCT03545919. IPD Sharing: UNDECIDED. Countries: 1. Publications: 8.
Assessment of Community Transmission of Sabin Type 2 Virus in Bangladesh
ClinicalTrials.gov study NCT02477046. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Data from: Long-term avian influenza virus epidemiology in a small Spanish wetland ecosystem is driven by the breeding Anseriformes community
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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.