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Dataset results
17 results for “Viral evolution”
Data and code from: Viral outbreak dynamics and evolution in wildlife at the interface with humans
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Data from: Inferring epidemiologic dynamics from viral evolution: 2014–2015 Eurasian/North American highly pathogenic avian influenza viruses exceed transmission threshold, R0 = 1, in wild birds and poultry in North America
Highly pathogenic avian influenza virus (HPAIV) is a multi-host pathogen with lineages that pose health risks for domestic birds, wild birds, and humans. One mechanism of intercontinental HPAIV spread is through wild bird reservoirs and wild birds were the likely sources of a Eurasian (EA) lineage HPAIV into North America in 2014. The introduction resulted in several reassortment events with North American (NA) lineage low pathogenic avian influenza viruses and the reassortant EA/NA H5N2 went on to cause one of the largest HPAIV poultry outbreaks in North America. We evaluated three hypotheses about novel HPAIV introduced into wild and domestic bird hosts: (i) transmission of novel HPAIVs in wild birds was restricted by mechanisms associated with highly-pathogenic phenotypes; (ii) the HPAIV poultry outbreak was not self-sustaining and required viral input from wild birds; (iii) reassortment of the EA H5N8 generated reassortant EA/NA AIVs with a fitness advantage over fully Eurasian lineages in North American wild birds. We used a time-rooted phylodynamic model that explicitly incorporated viral population dynamics with evolutionary dynamics to estimate the basic reproductive number (R0) and viral migration among host types in domestic and wild birds, as well as between the EA H5N8 and EA/NA H5N2 in wild birds. We did not find evidence to support hypothesis (i) or (ii) as our estimates of the transmission parameters suggested that the HPAIV outbreak met or exceeded the threshold for persistence in wild birds (R0 > 1) and poultry (R0 ≈ 1) with minimal estimated transmission among host types. There was also no evidence to support hypothesis (iii) because R0 values were similar among EA H5N8 and EA/NA H5N2 in wild birds. Our results suggest that this novel HPAIV and reassortments did not encounter any transmission barriers sufficient to prevent persistence when introduced to wild or domestic birds.
Isolation may select for earlier and higher peak viral load but shorter duration in SARS-CoV-2 evolution
<p>Supplementary figures and additional graphs described in "Isolation may select for earlier and higher peak viral load but shorter duration in SARS-CoV-2 evolution". (version 2)</p>
Source Code: Isolation may select for earlier and higher peak viral load but shorter duration in SARS-CoV-2 evolution
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Prospective Analysis of Seasonal Influenza - Viral Transmission and Evolution in the City of Basel, Switzerland
ClinicalTrials.gov study NCT03010007. IPD Sharing: NO. Countries: 1. Publications: 1.
Data from: Inferring epidemiologic dynamics from viral evolution: 2014–2015 Eurasian/North American highly pathogenic avian influenza viruses exceed transmission threshold, R0 = 1, in wild birds and poultry in North America
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Data from: Multiplicity of infection does not accelerate infectivity evolution of viral parasites in laboratory microcosms
Coinfection with multiple parasite genotypes (multiplicity of infection) creates within-host competition and opportunities for parasite recombination, and is therefore predicted to be important for both parasite and host evolution. We tested for a difference in the infectivity of viral parasites (lytic phage Φ2) and resistance of their bacterial hosts (Pseudomonas fluorescens SBW25) under both high and low multiplicity of infection (MOI) during coevolution in laboratory microcosms. Results show that MOI has no effect on infectivity and resistance evolution during coevolution over approximately 80 generations of host growth, and this is true when the experiment is initiated with wild-type viruses and hosts, or with viruses and hosts that have already been coevolving for ~330 generations. This suggests that MOI does not have a net effect of accelerating parasite adaptation to hosts through recombination, or retarding adaptation to hosts through between-parasite conflict in this system.
Data from: Evolution and diversity of the Microviridae viral family through a collection of 81 new complete genomes assembled from virome reads.
Recent studies suggest that members of the Microviridae (a family of ssDNA bacteriophages) might play an important role in a broad spectrum of environments, as they were found dominant among the viral fraction from seawater and human gut samples. 24 completely sequenced Microviridae have been described so far, divided into three distinct groups named Microvirus, Gokushovirinae and Alpavirinae, this last group being only composed of prophages. In this study, we present the analysis of 81 new complete Microviridae genomes, assembled from viral metagenomes originating from various ecosystems. The phylogenetic analysis of the core genes concludes to the existence of four groups, confirming the three sub-families described so far and exhibiting a new group, named Pichovirinae. The genomic organizations of these viruses are strikingly coherent with their phylogeny, the Pichovirinae being the only group of this family with a different organization of the three core genes. Analysis of the structure of the major capsid protein reveals the presence of mushroom-like insertions conserved within all the groups except for the Microvirus. In addition, a peptidase gene was found in 11 Microviridae and its analysis concludes to a horizontal gene transfer that occurred several times between these viruses and their bacterial hosts. This is the first report of such gene transfer in microviruses. Finally, searches against viral metagenomes revealed the presence of highly similar sequences in a variety of biomes indicating that Microviridae probably have both an important role in these ecosystems and an ancient origin.
Data from: Multiplicity of infection does not accelerate infectivity evolution of viral parasites in laboratory microcosms
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Data from: Evolution and diversity of the Microviridae viral family through a collection of 81 new complete genomes assembled from virome reads.
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Bacteriophage lambda overcomes a perturbation in its host‐viral genetic network through mutualism and evolution of life history traits
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Data for "Learning the language of viral evolution and escape"
<p>Training data from:</p> <ul> <li>Influenza A HA protein sequences from the NIAID Influenza Research Database (IRD) (<a href="http://www.fludb.org">http://www.fludb.org</a>)</li> <li>HIV-1 Env protein sequences from the Los Alamos National Laboratory (LANL) HIV database (<a href="https://www.hiv.lanl.gov">https://www.hiv.lanl.gov</a>)</li> <li><em>Coronavidae</em> spike protein sequences from the Virus Pathogen Resource (ViPR) database (<a href="https://www.viprbrc.org/brc/home.spg?decorator=corona">https://www.viprbrc.org/brc/home.spg?decorator=corona</a>)</li> <li>SARS-CoV-2 Spike protein sequences from NCBI Virus (<a href="https://www.ncbi.nlm.nih.gov/labs/virus/vssi/">https://www.ncbi.nlm.nih.gov/labs/virus/vssi/</a>)</li> <li>SARS-CoV-2 Spike and other Betacoronavirus spike protein sequences from GISAID (<a href="https://www.gisaid.org/">https://www.gisaid.org/</a>)</li> </ul> <p>Datasets for fitness and escape validation:</p> <ul> <li>Fitness single-residue DMS of HA H1 WSN33 from Doud and Bloom (2016)</li> <li>Fitness combinatorial DMS of antigenic site B in six HA H3 strains from Wu et al. (2020)</li> <li>Fitness single-residue DMS of Env BF520 and BG505 from Haddox et al. (2018)</li> <li>ACE2 binding affinity combinatorial DMS of Spike from Starr et al. (2020)</li> <li>Escape single-residue DMS of HA H1 WSN33 from Doud et al. (2018)</li> <li>Escape single-residue DMS of HA H3 Perth09 from Lee et al. (2019)</li> <li>Escape single-residue DMS of Env BG505 from Dingens et al. (2019)</li> <li>Escape mutations of Spike from Baum et al. (2020)</li> <li>Escape single-residue DMS of Spike from Greaney et al. (2020)</li> </ul>
Evolution of Cellular and Viral Resistance in HIV-infected Patients With Lymphoma
ClinicalTrials.gov study NCT01330342. IPD Sharing: Not stated. Countries: 1. Publications: 0.
MMF Influence on HCV Viral Evolution After Liver Transplantation
ClinicalTrials.gov study NCT00170131. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Viral Epidemiology of Bronchiolitis After Nirsevimab Implementation and Respiratory Evolution in Infants
ClinicalTrials.gov study NCT06636955. IPD Sharing: NO. Countries: 1. Publications: 0.
Assessment of the Predictive Value of Anti-beta1AR and Anti-L-CaC Antibodies in the Evolution to Dilated Cardiomyopathy in Patients With Acute Viral Myocarditis
ClinicalTrials.gov study NCT06742008. IPD Sharing: NO. Countries: 1. Publications: 0.
Evolution of the PRD1-adenovirus lineage (Varidnaviria): a viral tree of life incongruent with the cellular universal tree of life(data)
<p>Additional data for the manuscript "Evolution of the PRD1-adenovirus lineage (<em>Varidnaviria</em>): a viral tree of life incongruent with the cellular universal tree of life"</p>
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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.