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2,562 results for “SARS CoV 2”
Predicting reservoir hosts based on early SARS-CoV-2 samples and analyzing later world-wide pandemic
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Understanding shared variation in SARS-CoV-2 genomes
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Converting non-neutralizing SARS-CoV-2 antibodies targeting conserved epitopes into broad-spectrum inhibitors through receptor blockade
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Long COVID manifests with T cell dysregulation, inflammation, and an uncoordinated adaptive immune response to SARS-CoV-2
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Online phylogenetics using parsimony produces slightly better trees and is dramatically more efficient for large SARS-CoV-2 phylogenies than de novo and maximum-likelihood approaches
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Phosphoprotoemics for SARS COV 2 infected VeroE6 cells
<p>Vero cells infected with SARS CoV 2 at Bristol University March 2020 this phospho preoteome is matched with fastq data and a total proteome</p>
Vero cells infected with SARS CoV 2 no quantitation slices 1-10 of 20
<p>Slices 1 -10 of 20 slices from a gel. Vero cells infected with SARS CoV2 at Bristol University march 2020</p>
F I G U R E 2 in Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict potential intermediate hosts of SARS- CoV-2
F I G U R E 2 Phylogenetic analysis of sequences of coronavirus spike glycoproteins. The sequences of spike glycoproteins of SARS‐CoV‐2, bat SARS‐like CoV, pangolin SARS‐like CoV, and SARS‐CoV were analyzed. The red stars indicate pangolin SARS‐like CoV and bat SARS‐like CoV. Host flags are marked after the clusters. SARS‐CoV‐2, severe respiratory syndrome coronavirus‐2
Pairwise distance demarcation of species in the family Coronaviridae. a, Diagonal matrix of PPDs of 2,505 viruses clustered according to 49 coronavirus species, 39 established and 10 pending or tentative, and ordered from the most to least populous species, from left to right; green and white, PPDs smaller and larger than the inter-species threshold, respectively. Areas of the green squares along the diagonal are proportional to the virus sampling of the respective species, and virus prototypes of the five most sampled species are specified to the left; asterisks indicate species that include viruses whose intra-species PPDs crossed the inter-species threshold (threshold 'violators'). b, Maximal intra-species PPDs (x axis, linear scale) plotted against virus sampling (y axis, log scale) for 49 species (green dots) of the Coronaviridae. Indicated are the acronyms of virus prototypes of the seven most sampled species. Green and blue plot sections represent intra-species and intra-subgenera PPD ranges. The vertical black line indicates the inter-species threshold. c, Shown are the PDs of non-identical residues (y axis) for four viruses representing three major phylogenetic lineages (clades) of the species Severe acute respiratorysyndrome-related coronavirus (panel b) and all pairs of the 256 viruses of this species ('all pairs'). The PD values were derived from pairwise distances in the MSA that were calculated using an identity matrix. Panels a and b were adopted from the DEmARC v.1.4 output. in The species Severe acute respiratory syndromerelated coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2
Pairwise distance demarcation of species in the family Coronaviridae. a, Diagonal matrix of PPDs of 2,505 viruses clustered according to 49 coronavirus species, 39 established and 10 pending or tentative, and ordered from the most to least populous species, from left to right; green and white, PPDs smaller and larger than the inter-species threshold, respectively. Areas of the green squares along the diagonal are proportional to the virus sampling of the respective species, and virus prototypes of the five most sampled species are specified to the left; asterisks indicate species that include viruses whose intra-species PPDs crossed the inter-species threshold (threshold 'violators'). b, Maximal intra-species PPDs (x axis, linear scale) plotted against virus sampling (y axis, log scale) for 49 species (green dots) of the Coronaviridae. Indicated are the acronyms of virus prototypes of the seven most sampled species. Green and blue plot sections represent intra-species and intra-subgenera PPD ranges. The vertical black line indicates the inter-species threshold. c, Shown are the PDs of non-identical residues (y axis) for four viruses representing three major phylogenetic lineages (clades) of the species Severe acute respiratorysyndrome-related coronavirus (panel b) and all pairs of the 256 viruses of this species ('all pairs'). The PD values were derived from pairwise distances in the MSA that were calculated using an identity matrix. Panels a and b were adopted from the DEmARC v.1.4 output.
History of coronavirus naming during the three zoonotic outbreaks in relation to virus taxonomy and diseases caused by these viruses. According to the current international classification of diseases49, MERS and SARS are classified as 1D64 and 1D65, respectively. in The species Severe acute respiratory syndromerelated coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2
History of coronavirus naming during the three zoonotic outbreaks in relation to virus taxonomy and diseases caused by these viruses. According to the current international classification of diseases49, MERS and SARS are classified as 1D64 and 1D65, respectively.
Box 4 in The species Severe acute respiratory syndromerelated coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2
Box 4 | Classifying SARS-CoV-2 The species demarcation threshold (also known as demarcation limit) in the family Coronaviridae is defined by viruses whose PPD(s) may cross the inter-species demarcation PPD threshold (threshold 'violators'). Due to their minute share of ~10–4 of the to- tal number of all intra- and inter-species PPDs, these violators may not even be visually recognized in a conventional diagonal plot clus- tering viruses on a species basis (panel a of the figure in Box 4). Furthermore, they do not involve any virus of the species Severe acute respiratory syndrome-related coronavirus, as is evident from the analysis of maximal intraspecies PPDs of 2,505 viruses of all 49 coronavirus species (of which 39 are established and 10 are pending or tentative) (panel b of the figure in Box 4) and PDs of 256 viruses of this species (panel c of the figure in Box 4). Thus, the genomic variation of the known viruses of the species Severe acute respiratory syndrome-related coronavirus is smaller compared to that of other comparably well-sampled species—for example, those prototyped by MERS-CoV, human coronavirus OC43 (HCoV-OC43) and in- fectious bronchitis virus (IBV) (panel b of the figure in Box 4)—and this species is well separated from other known coronavirus species in the sequence space. Both of these characteristics facilitate the un- ambiguous assignment of SARS-CoV-2 to this species. Intra-species PDs of SARS-CoV-2 belong to the top 25% of this species and also include the largest PD between SARS-CoV-2 and an African bat virus isolate (SARSr-CoV_BtKY72)56 (panel c of the figure in Box 4), representing two basal lineages within the species Severe acute respiratory syndrome-related coronavirus that constitute very few known viruses (Fig. 2b,c). These relationships stand in contrast to the shallow branching of the most populous lineage of this species, which includes all the human SARS-CoV isolates collected during the 2002–2003 outbreak and the closely related bat viruses of Asian origin identified in the search for the potential zoonotic source of that epidemic57. This clade structure is susceptible to homologous recombination, which is common in this species44,58,59; to formalize clade definition, it must be revisited after the sampling of viruses representing the deep branches has improved sufficiently. The current sampling defines a very small median PD for human SARS-CoVs, which is approximately 15 times smaller than the median PD determined for SARS-CoV-2 (0.16% versus 2.6%; panel c of the figure in Box 4). This small median PD of human SARS-CoVs also dominates the species- wide PD distribution (0.25%; panel c of the figure in Box 4). Pairwise distance demarcation of species in the family Coronaviridae. a, Diagonal matrix of PPDs of 2,505 viruses clustered according to 49 coronavirus species, 39 established and 10 pending or tentative, and ordered from the most to least populous species, from left to right; green and white, PPDs smaller and larger than the inter-species threshold, respectively. Areas of the green squares along the diagonal are proportional to the virus sampling of the respective species, and virus prototypes of the five most sampled species are specified to the left; asterisks indicate species that include viruses whose intra-species PPDs crossed the inter-species threshold (threshold 'violators'). b, Maximal intra-species PPDs (x axis, linear scale) plotted against virus sampling (y axis, log scale) for 49 species (green dots) of the Coronaviridae. Indicated are the acronyms of virus prototypes of the seven most sampled species. Green and blue plot sections represent intra-species and intra-subgenera PPD ranges. The vertical black line indicates the inter-species threshold. c, Shown are the PDs of non-identical residues (y axis) for four viruses representing three major phylogenetic lineages (clades) of the species Severe acute respiratorysyndrome-related coronavirus (panel b) and all pairs of the 256 viruses of this species ('all pairs'). The PD values were derived from pairwise distances in the MSA that were calculated using an identity matrix. Panels a and b were adopted from the DEmARC v.1.4 output.
Fig. 2 in The species Severe acute respiratory syndromerelated coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2
Fig. 2 | Phylogeny of coronaviruses. a, Concatenated multiple sequence alignments (MSAs) of the protein domain combination44 used for phylogenetic and DEmARC analyses of the family Coronaviridae. Shown are the locations of the replicative domains conserved in the ordert Nidovirales in relation to several other ORF1a/b-encoded domains and other major ORFs in the SARS-CoV genome. 5d, 5 domains: nsp5A-3CLpro, two beta-barrel domains of the 3C-like protease; nsp12-NiRAN, nidovirus RdRp-associated nucleotidyltransferase; nsp12-RdRp, RNA-dependent RNA polymerase; nsp13-HEL1 core, superfamily 1 helicase with upstream Zn-binding domain (nsp13-ZBD); nt, nucleotide. b, The maximum-likelihood tree of SARS-CoV was reconstructed by IQ-TREE v.1.6.1 (ref. 45) using 83 sequences with the best fitting evolutionary model. Subsequently, the tree was purged from the most similar sequences and midpoint-rooted. Branch support was estimated using the Shimodaira–Hasegawa (SH)-like approximate likelihood ratio test with 1,000 replicates. GenBank IDs for all viruses except four are shown; SARS-CoV, AY274119.3; SARS-CoV-2, MN908947.3; SARSr-CoV_BtKY72, KY352407.1; SARS-CoV_PC4-227, AY613950.1. c, Shown is an IQ-TREE maximum-likelihood tree of single virus representatives of thirteen species and five representatives of the species Severe acute respiratory syndrome-related coronavirus of the genus Betacoronavirus. The tree is rooted with HCoV-NL63 and HCoV-229E, representing two species of the genus Alphacoronavirus. Purple text highlights zoonotic viruses with varying pathogenicity in humans; orange text highlights common respiratory viruses that circulate in humans. Asterisks indicate two coronavirus species whose demarcations and names are pending approval from the ICTV and, thus, these names are not italicized.
Inputs for Galaxy tutorial on molecular docking on SARS-CoV-2 MPro
<p>Inputs for Galaxy tutorial on molecular docking on SARS-CoV-2 main protease.</p>
Illumina reads SARS-Cov-2 using amplicon enrichment
<p>Testing data for <a href="https://github.com/nf-core/viralrecon">nf-core/viralrecon</a> pipeline</p> <p>.Here we share two samples with illumina reads obtained from a enrichment experiment using Artic network amplicons V1 for SARS-Cov-2 virus. We also share the fasta and bed file with the localization of the primers in the virus genome.</p> <p>The library has been constructed performing the next steps:</p> <p>- Amplicon creation.</p> <p>- Illumina library generation. No fragmentation, only adaptor and indexes.</p> <p>- MiSeq 2x300 sequencing.</p> <p> </p>
A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing
<p>The Krogan Laboratory used affinity-purification mass spectrometry to identify 332 high confidence SARS-CoV-2-human protein-protein interactions, including 67 druggable human proteins or host factors targeted by 69 known drugs. Results may be relevant to antiviral drug production.</p>
Variant analysis of SARS-CoV-2 genomes
<p>These are supplemental files accompanying a publication.</p>
Haruspex Analysis for SARS-CoV-2 surface_glycoprotein pdb entry 6m17 emdb 30039
Haruspex (version 1.0 190116) analysis for SARS-CoV-2 surface_glycoprotein , pdb entry 6m17 , emdb 30039. https://onlinelibrary.wiley.com/doi/10.1002/anie.202000421
Haruspex Analysis for SARS-CoV-2 surface_glycoprotein pdb entry 6vxx emdb 21452
<p>Haruspex (version 1.0 190116) analysis for SARS-CoV-2 surface_glycoprotein , pdb entry 6vxx , emdb 21452. https://onlinelibrary.wiley.com/doi/10.1002/anie.202000421</p>
Data from: Evolution and epidemic spread of SARS-CoV-2 in Brazil
Brazil currently has one of the fastest growing SARS-CoV-2 epidemics in the world. Owing to limited available data, assessments of the impact of non-pharmaceutical interventions (NPIs) on virus spread remain challenging. Using a mobility-driven transmission model, we show that NPIs reduced the reproduction number from >3 to 1–1.6 in São Paulo and Rio de Janeiro. Sequencing of 427 new genomes and analysis of a geographically representative genomic dataset identified >100 international virus introductions in Brazil. We estimate that most (76%) of the Brazilian strains fell in three clades that were introduced from Europe between 22 February11 March 2020. During the early epidemic phase, we found that SARS-CoV-2 spread mostly locally and within-state borders. After this period, despite sharp decreases in air travel, we estimated multiple exportations from large urban centers that coincided with a 25% increase in average travelled distances in national flights. This study sheds new light on the epidemic transmission and evolutionary trajectories of SARS-CoV-2 lineages in Brazil, and provide evidence that current interventions remain insufficient to keep virus transmission under control in the country.
Supplementary figure for: "UVA radiation could be a significant contributor to sunlight inactivation of SARS-CoV-2"
<p><strong>Supplementary Figure 1 for https://www.biorxiv.org/content/10.1101/2020.09.07.286666 </strong></p> <p><strong>Summary of sunlight inactivation mechanisms for viruses, based on <a href="https://paperpile.com/c/sh96XE/c05Xp+qSRra">[1,2]</a>. Solid yellow line: example of solar spectral irradiance reaching the Earth’s surface <a href="https://paperpile.com/c/sh96XE/KMpGD">[3]</a>. In principle, UVC light is most effective at damaging nucleic acid, leading to direct, endogenous inactivation; however, it is completely blocked by atmospheric ozone. Some UVB reaches the Earth’s surface, and may also damage nucleic acid. However, its effectiveness is lower than for UVC, and falls rapidly as wavelength increases (as shown by the white dashed line). Sunlight in the UVA range reaches the ground in larger amounts than for UVB, but does not interact directly with nucleic acid. However, UVA can be absorbed by natural or engineered sensitizers in the suspending medium, thereby creating photo-produced reactive intermediates that can damage viruses, leading to indirect, exogenous inactivation.</strong></p> <p><strong>* Corresponding author: pfegiz [at] ucsb [dot] edu</strong></p> <p><strong>1. <a href="http://paperpile.com/b/sh96XE/c05Xp">Nelson KL, Boehm AB, Davies-Colley RJ, et al. Sunlight-mediated inactivation of health-relevant microorganisms in water: a review of mechanisms and modeling approaches. Environ Sci Process Impacts. 2018; 20(8):1089–1122.</a></strong></p> <p><strong>2. <a href="http://paperpile.com/b/sh96XE/qSRra">Lytle CD, Sagripanti J-L. Predicted inactivation of viruses of relevance to biodefense by solar radiation. J Virol. 2005; 79(22):14244–14252.</a></strong></p> <p><strong>3. <a href="http://paperpile.com/b/sh96XE/KMpGD">Tropospheric Ultraviolet and Visible (TUV) Radiation Model [Internet]. [cited 2020 Sep 2]. Available from: </a><a href="https://www2.acom.ucar.edu/modeling/tropospheric-ultraviolet-and-visible-tuv-radiation-model">https://www2.acom.ucar.edu/modeling/tropospheric-ultraviolet-and-visible-tuv-radiation-model</a></strong></p> <p> </p> <p><strong>Funding statement:</strong></p> <p><strong>This work was supported by the University of California, Santa Barbara [Vice Chancellor for Research COVID-19 Seed Grant] and by the Army Research Office Multi University Research Initiative [W911NF-17-1-0306 to P.L.-F.].</strong></p>
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.