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46 results for “Flavivirus”
Flavivirus NS1 protein models
<p>Four <em>Flavivirus</em> NS1 protein models based on ZIKV-UG (Zika virus from Uganda), ZIKV-BR (Zika virus from Brazil), DENV2 (Dengue virus variant 2), and WNV (West Nile Virus). Due to the crystals for these four NS1 are having missing regions (i.e., X-ray structures with PDB ids 5K6K, 5GS6, 4O6B, and 4O6D, respectively) a homology protocol was applied. Models were built using Modeller 9.24 and default parameters and were selected the structures with the best DOPE score. NS1<sub>ZIKV-UG</sub> and NS1<sub>ZIKV-BR</sub> models are based on the templates with PDB ids 5K6K and 5GS6, respectively. For NS1<sub>DENV2</sub> three templates were used the two complete structures from NS1<sub>ZIKV-UG</sub> and NS1<sub>ZIKV-BR</sub>, and the crystal PDB id 4O6B. For NS1<sub>WNV</sub>, was followed the same strategy as for NS1<sub>DENV2</sub>, but the third template was changed for the crystal PDB id 4O6D.</p> <p>For more details check the SI of <a href="https://doi.org/10.1016/j.virusres.2022.198838">https://doi.org/10.1016/j.virusres.2022.198838</a>.</p>
Phylogenetic analysis of policistronic amino-acid sequences encoded by 116 flavivirus genomes
<p><span>Recently, Genome Biology and Evolution (11:3341-3352) published three statistical tests for testing whether alignments of sequence data violate the phylogenetic assumption of evolution under homogeneous conditions. The tests extend the matched-pairs tests of symmetry, marginal symmetry, and internal symmetry for pairs of aligned homologous sequences to the case where a whole alignment is considered. Here we reveal that the new tests are misleading. We explain why this is so, reveal how the tests of whole alignments may be done, and release new bioinformatics tools that implement statistically sound methods of dealing with multiple comparisons (i.e., by controlling the family-wise error rate or the false discovery rate). Using the new software to analyse an alignment of amino acids encoded by 116 flavivirus genomes, we reveal, for the first time, that these genomes are unlikely to have evolved under stationary, reversible, and homogeneous Markovian conditions.</span></p>
Protein Structure Files and Galaxy Workflows for Conducting Molecular Dynamics Simulations of Flavivirus Helicases
<p>The files included here are a set of Galaxy workflows and starting structure files (PDB, mol2, and frcmod) for the simulation of flavivirus helicases in the apo and drug-bound state. The inhibitors include the 4th highest ranking compound from a virtual screening of more than 12.7 million drug-like molecules.</p>
Immunogenicity and Safety of Tetravalent Dengue Vaccine Candidate (TDV) in Flavivirus-Naïve and Dengue-Immune Adults
ClinicalTrials.gov study NCT03746015. IPD Sharing: YES. Countries: 1. Publications: 1.
Protein Structure Files and Galaxy Workflows for Conducting Molecular Dynamics Simulations of Flavivirus Helicases -- Output Files
<p>These are the output files generated using the input files and Galaxy workflows for flavivirus helicase simulations, from: </p> <pre>https://doi.org/10.5281/zenodo.7493015</pre>
A Phase I/II Trial of Tetravalent Live Attenuated Dengue Vaccine in Flavivirus Antibody Naive Infants
ClinicalTrials.gov study NCT00322049. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
A Phase I/II Trial of a Tetravalent Live Attenuated Dengue Vaccine in Flavivirus Antibody Naïve Children
ClinicalTrials.gov study NCT00384670. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Safety, Tolerability, and Immunogenicity of Zika Vaccine mRNA-1893 in Healthy Flavivirus Seropositive and Seronegative Adults
ClinicalTrials.gov study NCT04064905. IPD Sharing: NO. Countries: 2. Publications: 1.
A naturally isolated symbiotic bacterium suppresses flavivirus transmission by Aedes mosquitoes
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Data from: Screening test for neutralizing antibodies against yellow fever virus, based on a flavivirus pseudotype
Given the possibility of yellow fever virus reintroduction in epidemiologically receptive geographic areas, the risk of vaccine supply disruption is a serious issue. New strategies to reduce the doses of injected vaccines should be evaluated very carefully in terms of immunogenicity. The plaque reduction test for the determination of neutralizing antibodies (PRNT) is particularly time-consuming and requires the use of a confinement laboratory. We have developed a new test based on the use of a non-infectious pseudovirus (WN/YF17D). The presence of a reporter gene allows sensitive determination of neutralizing antibodies by flow cytometry. This WN/YF17D test was as sensitive as PRNT for the follow-up of yellow fever vaccinees. Both tests lacked specificity with sera from patients hospitalized for acute Dengue virus infection. Conversely, both assays were strictly negative in adults never exposed to flavivirus infection or vaccination, and in patients sampled some time after acute Dengue infection. This WN/YF17D test will be particularly useful for large epidemiological studies and for screening for neutralizing antibodies against yellow fever virus.
A Phase 1, First-in-human, Double-blinded, Randomized, Placebo-controlled Trial of a Zika Virus Purified Inactivated Vaccine (ZPIV) With Alum Adjuvant in Healthy Flavivirus-naive and Flavivirus-Primed
ClinicalTrials.gov study NCT02963909. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Safety and Immunogenicity of Formulations of Dengue Vaccines in Healthy Flavivirus-Naïve Adults
ClinicalTrials.gov study NCT00740155. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Data from: Screening test for neutralizing antibodies against yellow fever virus, based on a flavivirus pseudotype
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Data from: First dating of a recombination event in mammalian tick-borne flaviviruses
The mammalian tick-borne flavivirus group (MTBFG) contains viruses associated with important human and animal diseases such as encephalitis and hemorrhagic fever. In contrast to mosquito-borne flaviviruses where recombination events are frequent, the evolutionary dynamic within the MTBFG was believed to be essentially clonal. This assumption was challenged with the recent report of several homologous recombinations within the Tick-borne encephalitis virus TBEV. We performed a thorough analysis of publicly available genomes in this group and found no compelling evidence for the previously identified recombinations. However, our results show for the first time that demonstrable recombination (i.e., with large statistical support and strong phylogenetic evidences) has occurred in the MTBFG, more specifically within the Louping ill virus lineage. Putative parents, recombinant strains and breakpoints were further tested for statistical significance using phylogenetic methods. We investigated the time of divergence between the recombinant and parental strains in a Bayesian framework. The recombination was estimated to have occurred during a window period of 282 to 76 years before the present. By unravelling the temporal setting of the event, we adduce hypotheses
Safety and Immunogenicity of the Live Attenuated Zika Vaccine rZIKV/D4Δ30-713 in Flavivirus-naïve Adults
ClinicalTrials.gov study NCT03611946. IPD Sharing: Not stated. Countries: 1. Publications: 0.
A Phase I/II Trial of a Tetravalent Live Attenuated DEN Vaccine in Flavivirus Antibody Naive Children
ClinicalTrials.gov study NCT01843621. IPD Sharing: YES. Countries: 1. Publications: 0.
Flavivirus Cross-priming Potential of IMOJEV
ClinicalTrials.gov study NCT03920111. IPD Sharing: NO. Countries: 1. Publications: 0.
A Study of Zika Vaccine mRNA-1893 in Adult Participants Living in Endemic and Non-Endemic Flavivirus Areas
ClinicalTrials.gov study NCT04917861. IPD Sharing: Not stated. Countries: 2. Publications: 0.
Data from: First dating of a recombination event in mammalian tick-borne flaviviruses
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Oligodendrocyte-derived IL-33 functions as a microglial survival factor during neuroinvasive flavivirus infection
GEO Series GSE241804. Mus musculus. 11 samples. Type: Expression profiling by high throughput sequencing.
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