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2,562 results for “SARS CoV 2”
Detection of SARS-CoV-2 variants by genomic analysis of wastewater metatranscriptomic samples (Galaxy Training Material)
<p>The tutorial aims to train how to run workflows to analyze lineages abundances in SAR-CoV-2 wastewater metatranscriptomic samples. (https://training.galaxyproject.org/training-material/)</p>
Data for: Oligonucleotide mapping via mass spectrometry to enable comprehensive primary structure characterization of an mRNA vaccine against SARS-CoV-2
<p>Oligonucleotide mapping via liquid chromatography mass spectrometry mass spectrometry (LC-MS/MS) was recently developed to support development of Comirnaty®, the world's first commercial mRNA vaccine which immunizes against the SARS-CoV-2 virus. Analogous to peptide mapping of therapeutic protein modalities, oligonucleotide mapping described here provides direct primary structure characterization of mRNA, through enzymatic digestion, accurate mass determinations, and optimized collisionally-induced fragmentation. Sample preparation for oligonucleotide mapping is a rapid, one-pot, one-enzyme digestion. The digest is analyzed via LC-MS/MS with an extended gradient and resulting data analysis employs semi-automated software. In a single method, oligonucleotide mapping readouts include a highly reproducible and completely annotated UV chromatogram with >98% sequence coverage and a microheterogeneity assessment of 5´ terminus capping and 3´ terminus poly(A) tail length. Oligonucleotide mapping was pivotal to ensure the quality, safety, and efficacy of mRNA vaccines by providing: confirmation of construct identity and primary structure and assessment of product comparability following manufacturing process changes. More broadly, this technique may be used to directly interrogate the primary structure of RNA molecules in general.</p>
Nature and well-being: The association of nature engagement and well-being during the SARS-CoV-2 pandemic
<p><span>1. </span><span>Numerous studies have shown the positive association between nature engagement and well-being. During the early phases of the SARS-CoV-2 pandemic, nature engagement changed dramatically as mental health and well-being declined across the globe.</span></p> <p><span>2. </span><span>This study examines how psychological connection to nature and engagement with nature in various forms is associated with well-being during the SARS-CoV-2 pandemic. Specifically, we examine which types of nature engagement (i.e., with nearby nature, through nature excursions, and media-based) are more strongly associated with well-being based on measures of loneliness, rumination, pandemic emotional impact, and mental health.</span></p> <p><span>3. </span><span>We employed a cross-sectional online survey of adults (N=3,282) residing in the United States, 25% of whom report seldom spending time in nature.</span></p> <p><span>4. </span><span>Our findings revealed that the psychological construct of connection to nature was associated with less loneliness and greater mental health. Overall, nature engagement was a consistent predictor of well-being, but different types of activities predicted varying outcomes on our four dependent variables. Greater engagement with nearby nature during the pandemic was associated with less rumination, less pandemic emotional impact, and better mental health while nature excursions (e.g., camping, backpacking) and media-based nature engagement were associated with greater loneliness, more emotional impact from the pandemic, and worse mental health. Additionally, nature engagement via media was associated with greater rumination.</span></p> <p><span>5. </span><span>Our findings suggest that promoting opportunities to increase engagement with and access to nearby nature is associated with better human well-being, especially during challenging events, and should be part of a </span>multi-pronged approach for coping with the next public health crisis<span>.</span></p>
Raw Data for the article: Analysis of the Specific Immune Response after the Third Dose of mRNA COVID-19 Vaccines in Organ Transplant Recipients: Possible Spike-S1 Reactive IgA Signature in Protection from SARS-CoV-2 Infection
<p><strong>Background:</strong> Several studies have indicated that anti-SARS-CoV-2 mRNA vaccinations are less effective in inducing robust immune responses among solid organ transplant recipients (SOTRs) compared with the immunocompetent. The third dose of vaccine in SOTRs showed promising results of immunogenicity, even though clinical studies have suggested that immunocompromised subjects are less likely to build a protective immune response against SARS-CoV-2 resulting in lower vaccine efficacy for the prevention of severe COVID-19. <strong>Methods:</strong> Serological IgG and IgA were analyzed through CLIA or ELISA, respectively, while Spike-specific T cells were detected by ELISpot assay after the second and third dose of vaccine in 43 SOTRs. <strong>Results:</strong> The third dose induced an improvement in antibody response against SARS-CoV-2. We also reported a strong correlation between specific humoral and cellular responses after the third dose, even though we did not see significant changes in the magnitude of the SARS-CoV-2-specific T cell response. SOTRs who contracted the SARS-CoV-2 infection after the third dose, despite eliciting a positive IgG response, failed to mount an anti-Spike-S1 IgA response, both after the third dose and after SARS-CoV-2 infection. <strong>Conclusions:</strong> We can conclude that serum IgA detection can be helpful, along with IgG detection, for the evaluation of vaccine efficacy, principally in fragile subjects at high risk of infection.</p>
Data for: Single versus serial dilution SARS-CoV-2 IgG
<p>Reliable and scalable seroepidemiology methods are needed to estimate SARS-CoV-2 incidence and monitor the dynamics of population-level immunity as the pandemic evolves. We aimed to evaluate the reliability of SARS-CoV-2 normalized ELISA optical density (nOD) at a single dilution compared to titers derived from serial dilutions. We conducted serial serosurveys within a community-based cohort in Salvador, Brazil. Anti-S IgG ELISA (Euroimmun AG) was performed with five serial 3-fold dilutions of paired sera from 54 participants. Changes in nOD reliably predicted increases and decreases in titers (98.1% agreement, <span>κ </span>= 95.8%). Fitting the relationship between nOD and interpolated titers to a log-log curve yields highly accurate predictions of titers (r<sup>2</sup> = 0.995) and changes in titers (r<sup>2</sup> = 0.975), using only one to two dilutions. This approach can significantly reduce the time, labor and resources needed for large-scale serosurveys to ascertain population-level changes in exposure and immunity.</p>
SARS-COV-2 genomic sequences used as references for the NASCarD method
<p>A set of 9 SARS-CoV-2 genome sequences used as reference in the NASCarD process.</p>
Data for: Charting the spatial dynamics of early SARS-CoV-2 transmission in Washington state
<p>All code and data necessary to reproduce results and figures in the publication "Charting the spatial dynamics of early SARS-CoV-2 transmission in Washington state".</p>
Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin
<p>The Papain-like protease (PLpro) is a domain of a multi-functional, non-structural protein 3 of coronaviruses. PLpro cleaves viral polyproteins and posttranslational conjugates with poly-ubiquitin and protective ISG15, composed of two ubiquitin-like (UBL) domains. Across coronaviruses, PLpro showed divergent selectivity for recognition and cleavage of posttranslational conjugates despite sequence conservation. We show that SARS-CoV-2 PLpro binds human ISG15 and K48-linked di-ubiquitin (K48-Ub<sub>2</sub>) with nanomolar affinity and detect alternate weaker-binding modes. Crystal structures of untethered PLpro complexes with ISG15 and K48-Ub<sub>2</sub> combined with solution NMR and cross-linking mass spectrometry revealed how the two domains of ISG15 or K48-Ub<sub>2</sub> are differently utilized in interactions with PLpro. Analysis of protein interface energetics predicted differential binding stabilities of the two UBL/Ub domains that were validated experimentally. We emphasize how substrate recognition can be tuned to cleave specifically ISG15 or K48-Ub<sub>2</sub> modifications while retaining capacity to cleave mono-Ub conjugates. These results highlight alternative druggable surfaces that would inhibit PLpro function.</p>
Multiplexed On-Yeast Serological Assay for Immune Escape Screening of SARS-CoV-2 Variants
<p>Experimental data and scripts used for the development of a Yeast-based serological Assay:</p> <ol> <li>The<strong> Python scripts</strong> folder includes all scripts used in this study to analyze sera titers and plotting data.</li> <li>The<strong> Raw data</strong> folder includes: <ol> <li>The Y<strong>east Immunoassay development</strong> folder includes the flow cytometric data for serum depletion and reduction of ligand depletion effects.</li> <li>The <strong>Yeast serological data folder</strong> includes the raw data of all tested sera and related data for their analyses.</li> </ol> </li> <li>The <strong>Snapgene plasmid maps </strong>folder includes the plasmid maps for the three SARS-CoV-2 VOCs for Snapgene.</li> </ol> <p> </p> <p> </p>
SARS-CoV-2 vaccine breakthrough infections by Omicron and Delta variants in healthcare workers
<p>An observational prospective cohort study was conducted in vaccinated employees with acute SARS-CoV-2 infection between October 2021 and February 2022. Serological and molecular testing was performed to determine SARS-CoV-2 viral load, lineage, antibody levels, and neutral-ising antibody titres. A total of 571 (9.7%) employees experienced SARS-CoV-2 breakthrough infections during the enrolment period, of which 81 were included. The majority (n=79, 97.5%) was symptomatic and most (n=75, 92.6%) showed Ct-values < 30 in RT-PCR assays. Twenty-four (30%) remained PCR-positive for > 15 days. Neutralizing antibody titres were strongest for the wildtype, intermediate for Delta and lowest for Omicron variants. Omicron infections occurred at higher anti-RBD-IgG serum levels (p= 0.00001) and showed a trend for higher viral loads (p=0.14, median Ct-difference 4.3, 95% CI [-2.5-10.5]). For both variants, viral loads were signifi-cantly higher in participants with lower anti-RBD-IgG serum levels (p=0.02). </p>
Supplementary Data for: "The principles of SARS-CoV-2 inter-variant competition are exemplified in the pre-Omicron era of the Colombian epidemic"
<p>Supplementary data files, including BEAST XMLs and logs from the study "The principles of SARS-CoV-2 inter-variant competition are exemplified in the pre-Omicron era of the Colombian epidemic".</p>
Data set: genetic variants related to SARS-CoV-2 viremia
<p>Data set generated to evaluate the association between SNPs from genes related to SARS-CoV-2 pathogenesis and the presence of viremia.</p>
Validation of a SARS-CoV-2 surrogate neutralization test detecting neutralizing antibodies against the major variants of concern
<p>SARS-CoV-2 infection and/or vaccination elicit a broad range of neutralizing antibody responses against the different variants of concern (VOC). We established a new variant-adapted surrogate neutralization test (sVNT) and assessed the neutralization activity against the ancestral B.1 (WT) as well as VOC Delta, Omicron BA.1, BA.2 and BA.5. Performances were compared to the reference virus neutralization test (VNT) against the respective VOC using three different cohorts collected during the COVID waves. Pre-COVID samples confirmed 100% specificity of the sVNT. Correlation analyses showed moderate to strong correlation for Omicron sub-variants (Spearman’s r=0.7081 for BA.1, r=0.7205 for BA.2 and r=0.6042 for BA.5), and for WT (r=0.8458) and Delta-sVNT (r=0.8158), respectively. Comparison of the WT-sVNT performance with two CE-IVD commercial kits “Icosagen SARS-CoV-2 Neutralizing Antibody ELISA kit” and “Genscript cPass kit” revealed an overall good correlation ranging from 0.8673 to -0.8773 and a midway profile between both commercial kits with 87.76% sensitivity and 90.48% clinical specificity resulting in a Youden Index of 78.24. This midway trend was further confirmed on 100 double-vaccinated individuals. The BA.2-sVNT performance was similar to that of the Genscript test. Finally, sVNT ability to assess neutralizing antibodies against Omicron BA.5 was validated on a double-vaccinated cohort (n=100) and an Omicron-breakthrough infection cohort (n=91). Correlation analysis revealed a strong association (r=0.8583) between BA.5-sVNT and VNT. Accurate classification was confirmed by receiving operating characteristic (ROC) analysis reporting an area under the curve (AUC) of 0.9543. In conclusion, the sVNT allows for efficient prediction of immune protection against the various VOCs.</p>
Dataset for a study:Clinical characteristics of SARS-CoV-2 delta variant infection in Xiamen
<p>This retrospective study aims to identify the clinical and demographic features of patients infected with the SARS-CoV-2 delta variant at a single institution in Xiamen, China.</p>
SARS-CoV-2 Viral Samples and Reference Genome for Galaxy Training Network SARS with Galaxy on AnVIL Tutorial
<p>In the lab activity, we'll see if there are genomic differences in the collected sample compared to the original SARS-CoV-2 genome (the reference). We need three files to do this:</p> <ul> <li><strong>SARS-CoV-2_reference_genome.fasta</strong> : the reference genome</li> <li><strong>VA_sample_forward_reads.fastq.gz</strong>: 1 of 2 raw read data files</li> <li><strong>VA_sample_reverse_reads.fastq.gz</strong>: 2 of 2 raw read data files</li> </ul> <p>The sample for this activity was derived from data collected at Virginia Commonwealth University in Richmond, VA. The researchers collected the sample with the goal of being able to track the spread and evolution of this virus state-wide, nationally, and internationally. You can download the original data <a href="https://www.ncbi.nlm.nih.gov/sra/?term=XGTK449087">here</a>.</p> <p>You can download the reference genome <a href="https://www.ncbi.nlm.nih.gov/nuccore/1798174254">here</a>.</p>
Data from: Serosurvey of SARS-COV-2 at a large public university
<p><strong>Objective</strong>: This study investigated the seroprevalence of SARS-CoV-2 antibodies among adults over 18 years.</p> <p><strong>Design</strong>: Prospective cohort study.</p> <p><strong>Settings</strong>: a population-based study among the big university community.</p> <p><strong>Participants</strong>: This study took volunteers over five days and recruited adult 1064 participants.</p> <p><strong>Primary outcome measures</strong>: We conducted a seroprevalence in our community with SARS-CoV-2-specific antibodies due to previous exposure to SARS-CoV-2 and/or vaccination.</p> <p><strong>Results</strong>: The seroprevalence of the anti-receptor binding domain (RBD) antibody was 90% by a lateral flow assay and 88% by a semi-quantitative chemiluminescent immunoassay. The seroprevalence for anti-nucleocapsid (NC) was 20%. In addition, individuals with previous natural COVID infection plus vaccination had higher anti-RBD antibody levels compared to those who had vaccination only or infection only. Individuals who had a breakthrough infection had the highest anti-RBD antibody levels.</p> <p><strong>Conclusion</strong>: Accurate estimates of the cumulative incidence of SARS-CoV-2 infection can inform the development of university risk mitigation protocols such as encouraging booster shots, extending mask mandates, or reverting to online classes. It could help us to have clear guidance to act at the first sign of the next surge as well, especially since there is a surge of COVID subvariant infections.</p>
Data from: Phenotypic evolution of SARS-CoV-2: A statistical inference approach
<p>Since its emergence in late 2019, the SARS-CoV-2 virus has spread globally, causing the ongoing COVID-19 pandemic. In the fall of 2020, the Alpha variant (lineage B.1.1.7) was detected in England and spread rapidly, outcompeting the previous lineage. Yet, very little is known about the underlying modifications of the infection process that can explain this selective advantage. Here, we try to quantify how the Alpha variant differed from its predecessor on two phenotypic traits: the transmission rate and the duration of infectiousness. To this end, we analysed the joint epidemiological and evolutionary dynamics as a function of the Stringency Index, a measure of the amount of Non-Pharmaceutical Interventions. Assuming that these control measures reduce contact rates and transmission, we developed a two-step approach based on SEIR models and the analysis of a combination of epidemiological and evolutionary information. First, we quantify the link between the Stringency Index and the reduction in viral transmission. Secondly, based on a novel theoretical derivation of the selection gradient in an SEIR model, we infer the phenotype of the Alpha variant from its frequency changes. We show that its selective advantage is more likely to result from a higher transmission than from a longer infectious period. Our work illustrates how the analysis of the joint epidemiological and evolutionary dynamics of infectious diseases can help understand the phenotypic evolution driving pathogen adaptation.</p>
Evaluation of oxidative stress markers in Rwanda during the SARS-CoV-2 pandemic: a cross-sectional study
<p>SARS-CoV-2 is mainly described as endothelial dysfunction, and due to the bidirectional link between oxidative stress and endothelial dysfunction, we initiated a program directed to the evaluation of the oxidative status of the population of Rwanda by measuring spectrophotometrically their plasma Reactive Oxygen Metabolites (dROMs) and Plasma Antioxidant Potential (PAT). The reference population was chosen to reflect the absence of actual or past SARS-CoV-2 infections as well as other clinically established infective status and reference intervals for d-ROM and PAT were identified.</p> <p>The average d-ROM was 378.6 UCARR with a standard deviation of 105.2. The average PAT value was 2853.6, with a standard deviation of 635.7 UCOR. On the basis of the published values for the Caucasian and East Asian populations, the average value of d-ROM obtained in Rwanda was significantly higher than expected. Conversely, the average PAT value was at the upper limit according to the averaged values for healthy Caucasian populations. The results of this study, the first so far reported on a sub-Saharan population, can effectively be used as a baseline value for clinical management of inflammatory conditions, for the stratification of at-risk individuals and to inform recommendations for effective use of public health resources.</p>
SARS CoV 2 ORF10KO paper raw data
<p>Raw seq data for ORF10KO paper</p>
Raw data for " Unnatural evolutionary processes of SARS-CoV-2 variants and possibility of deliberate natural selection" DOI 10.5281/zenodo.8248320
<p>Compressed raw data for " Unnatural evolutionary processes of SARS-CoV-2 variants and possibility of deliberate natural selection" </p> <p>DOI 10.5281/zenodo.8248320</p>
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