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Population-based, Age- and Gender- Stratified Sero-Survey Study for SARS-CoV-2 in Uganda

Results of population-based age stratified seroepidemiological investigation in Uganda

Seroprevalence of immunoglobulin G antibodies against SARS-CoV-2 in Cyprus

Four vaccines that have been authorized in the European Union offer different levels of protection against SARS-CoV-2 by generating immune responses against the spike receptor-binding domain (RBD) of the virus. Monitoring the levels of IgG antibodies against the SARS-CoV-2 is important during the coronavirus disease 2019 (COVID-19) pandemic to plan an adequate and evidence-based public health response. We compared the levels of serum IgG antibodies against SARS-CoV-2 spike protein in three groups: i) individuals without evidence of prior infection with SARS-CoV-2 who received one or two doses of either an mRNA-based (Comirnaty BNT162b2/Pfizer-BioNTech or Spikevax mRNA-1273/Moderna) or an adenoviral-based vaccine (Vaxzervia ChAdOx1 nCoV-19 /Oxford-Astra Zeneca) (n=227), ii) unvaccinated individuals with evidence of prior infection with SARS-CoV-2 (n=109), and iii) individuals with evidence of prior infection with SARS-CoV-2 who received at least one dose of a vaccine (n=30). Unvaccinated individuals without evidence of prior infection with SARS-CoV-2 were used as a control group (n=211). Our results indicate that vaccine-induced responses lead to higher levels of IgG antibodies compared to those produced following infection with the virus. In agreement with previous studies, our results suggest that among individuals previously infected with SARS-CoV-2, even a single dose of a vaccine is adequate to elicit high levels of humoral immunity.

Molecular Dynamics of hACE2 Receptor and SARS-CoV-2 Omicron-RBD (Receptor Binding Domain) in Electrostatics View

Molecular Dynamics of hACE2 Receptor and SARS-CoV-2 Omicron-RBD (Receptor Binding Domain) in Electrostatics View. Molecular Dynamics performed with NAMD in Frontera supercomputer for 8 nanoseconds at 37 degrees Celsius. Electrostatics is visualized with ChimeraX (red is negative and blue is positive). By Victor Padilla-Sanchez, PhD; Texas Advanced Computing Center.

SARS-CoV-2 antigen exposure history shapes phenotypes and specificity of memory CD8 T cells

This dataset contains aggregated CellRanger output for six 10x Genomics (5'GEX+abTCR+Feature barcoding) experiments from the study by Minervina, Pogorelyy et al (<a href="https://www.medrxiv.org/content/10.1101/2021.07.12.21260227v3">medrxiv</a>).  The scripts to process it further are available at github (<a href="https://github.com/pogorely/COVID_vax_CD8">repository</a>).  Raw sequencing data is available at SRA (acc. PRJNA744851)

opencc-by-4.0Aug 2021View details →

Epistasis at the SARS-CoV-2 RBD Interface and the Propitiously Boring Implications for Vaccine Escape

This repository includes:   SI Appendix GISAID Acknowledgements An example resfile RosettaScripts .xml files Complex conformations (50 each) for WT/Delta/Gamma/Omicron; antibody (NAb) and receptor (ACE2)

Interaction of Surface Glycoprotein of SARS-CoV-2 Variants of Concern with Potential Drug Candidates: A Molecular Docking Study

This dataset contains additional docking images of SARS-CoV-2 Variants of Concern with drugs under study. It also contains a spreadsheet containing binding residues with different types of bonds. Further it includes the raw spike protein sequences, 3D model of spike proteins of VOCs (variant of concern) and potential drugs used in this study.

opencc-by-4.0Mar 2022View details →

Molecular Genetic Analysis of SARS-CoV-2 Lineages in Armenia - additional data

Sequencing of SARS-CoV-2 provides essential information on viral evolution, transmission, and epidemiology. In this study, we performed whole-genome sequencing of SARS-CoV-2 using nanopore and Illumina short-read sequencing to describe the circulation of the virus lineage in Armenia. This dataset contains Nextstrain configuration files, the auspice JSON file, BEAST output logs, and trees files, and resulting log and tree files as well as R scripts and data files used in phylogenetic and functional analyses.

dryad36/100

Data from: SARS-CoV-2 antibody dynamics in blood donors and COVID-19 epidemiology in eight Brazilian state capitals

The COVID-19 situation in Brazil is complex due to large differences in the shape and size of regional epidemics. Here we tested monthly blood donation samples for IgG antibodies from March 2020 to March 2021 in eight of Brazil's most populous cities. The inferred attack rate of SARS-CoV-2 adjusted for seroreversion in December 2020, before the Gamma VOC was dominant, ranged from 19.3% (95% CrI 17.5% - 21.2%) in Curitiba to 75.0% (95% CrI 70.8% - 80.3%) in Manaus. Seroprevalence was consistently smaller in women and donors older than 55 years. The age-specific infection fatality rate (IFR) differed between cities and consistently increased with age. The infection hospitalisation rate (IHR) increased significantly during the Gamma-dominated second wave in Manaus, suggesting increased morbidity of the Gamma VOC compared to previous variants circulating in Manaus. The higher disease penetrance associated with the health system's collapse increased the overall IFR by a minimum factor of 2.91 (95% CrI 2.43 – 3.53). These results highlight the utility of blood donor serosurveillance to track epidemic maturity and demonstrate demographic and spatial heterogeneity in SARS-CoV-2 spread.

opencc-zeroApr 2022View details →

opencc-by-4.0Jun 2021View details →

Dataset: Macro-Level Drivers of SARS-CoV-2 Transmission

Data-set for research article: Macro-Level Drivers of SARS-CoV-2 Transmission: A Data-Driven Analysis of Factors Contributing to Epidemic Growth During the First Wave of outbreaks in the United States

dryad36/100

Data from: Detection of silent SARS-CoV-2 infection (S1 File)

Background: To control COVID-19 pandemic is of critical importance to the global public health. To capture the prevalence in an accurate and timely manner and to understand the mode of nosocomial infection are essential for its preventive measure. Methods: We recruited 685 healthcare workers (HCW's) at Tokyo Shinagawa Hospital prior to the vaccination with COVID-19 vaccine. Sera of the subjects were tested by assays for the titer of IgG against S protein's receptor binding domain (IgG (RBD)) or IgG against nucleocapsid protein (IgG (N)) of SARS-CoV-2. Together with PCR data, the positive rates by these methods were evaluated. Results: Overall positive rates among HCW's by PCR, IgG (RBD), IgG (N) with a cut-off of 1.4 S/C (IgG (N)1.4), and IgG (N) with a cut-off of 0.2 S/C (IgG (N)0.2) were 3.5%, 9.5%, 6.1%, and 27.7%, respectively. Positive rates of HCW's working in COVID-19 ward were significantly higher than those of HCW's working in non-COVID-19 ward by all the four methods. Concordances of IgG (RBD), IgG (N)1.4, and IgG (N)0.2 against PCR were 97.1%, 71.4%, and 88.6%, respectively. By subtracting the positive rates of PCR from that of IgG (RBD), the rate of overall silent infection and that of HCW's in COVID-19 ward were estimated to be 6.0% and 21.1%, respectively. Conclusions: For the prevention of nosocomial infection of SARS-CoV-2, identification of silent infection is essential. For the detection of ongoing infection, periodical screening with IgG (RBD) in addition to PCR would be an effective measure. For the surveillance of morbidity in the population, on the other hand, IgG (N)0.2 could be the most reliable indicator among the three serological tests.

opencc-zeroApr 2022View details →

opencc-by-4.0May 2022View details →

Dataset for the manuscript: Modelling the within-host spread of SARS-CoV-2 infection, and the subsequent immune response, using a hybrid, multiscale, individual-based model. Part I: Macrophages.

Dataset for the manuscript: Modelling the within-host spread of SARS-CoV-2 infection, and the subsequent immune response, using a hybrid, multiscale, individual-based model. Part I: Macrophages. preprint, bioRxiv, 2022. DOI: 10.1101/2022.05.06.490883 Each zip file contains the raw computational data (as a gzip compressed tarball), YAML input files, as well as Python plotting scripts. The Python plotting scripts have dependencies on the packages: tarfile, multiprocessing, numpy, scipy, and matplotlib. Note that the Python plotting scripts plot directly from the gzip compressed tarballs. The corresponding code can be found on GitHub: https://github.com/Ruth-Bowness-Group/CAModel

opencc-by-4.0May 2022View details →

Supplementary data to Analyzing and Modeling the Spread of SARS-CoV-2 Omicron Lineages BA.1 and BA.2, France, September 2021–February 2022

ZIP folder containing supplementary files to the article entitled Analyzing and Modeling the Spread of SARS-CoV-2 Omicron Lineages BA.1 and BA.2, France, September 2021–February 2022 and published in Emerging Infectious Diseases with doi <a href="https://dx.doi.org/10.3201/eid2807.220033">10.3201/eid2807.220033</a> <ul> <li>Script_EID_1.R is the R script analysing the data_EID1.csv screening test data file (Figure 1 and Suppl Figure F1, and Tables 1 and 3).</li> <li>Script_EID_2.R is the R script analysing the data_EID2.csv screening test data file (Figures 2, 3, 5, and Suppl Figure F2, and Table 2).</li> <li>Script_EID_sequencing_raw.R is the R script analysing the data_EID_sequencing.csv sequencing data file (Figures 4, 5, and Suppl Figure F3).</li> </ul>

opencc-by-4.0May 2022View details →

Supplementary information, datasets and fluorescence images related to the article "The role of NSP6 in the biogenesis of the SARS-CoV-2 replication organelle"

Supplementary information, datasets and fluorescence images related to the article "The role of NSP6 in the biogenesis of the SARS-CoV-2 replication organelle". The PDF file entitled "Supplementary material" contains the uncropped original western blots and autoradiographs published in the article. The PDF files entitled "Extended Data Fig.2,6,7,9,10 all panels" and "Figure 1,4 all panels" contain the original full-size confocal immunofluorescence images from which specific ROIs are published in the article. The Excel files "Source Data Principal Figures" and "Source Data Extended Figures" contain all the original datasets used for calculation and graphical representation of data published in the article.

Quantification of SARS-CoV-2 RNA in Wastewater Treatment Plants Mirrors the Pandemic Trend in Hong Kong

The dataset included the SARS-CoV-2 and PMMoV virus concentration of WWTPs from December 24, 2020 to June 30, 2021 in Hong Kong, China.

Length-dependent motions of SARS-CoV-2 frameshifting RNA pseudoknot and alternative conformations suggest avenues for frameshifting suppression

Supplementary dataset for manuscript "Length-dependent motions of SARS-CoV-2 frameshifting RNA pseudoknot and alternative conformations suggest avenues for frameshifting suppression"

Quantifying the importance and location of SARS-CoV-2 transmission events in large metropolitan areas

Networks used in the paper Quantifying the importance and location of SARS-CoV-2 transmission events in large metropolitan areas.

Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy – data set 03

We developed a sedimentation method using desktop ultracentrifugation (see description below) to visualize SARS-CoV-2 particles in suspensions from oro- and/or nasopharyngeal swabs by thin section electron microscopy. A detailed description of the methods and the data set is provided in the download container. Data set 03 is a stitched image montage recorded from an area of a thin section through the sediment obtained from a swab sample which was positive by quantitative PCR (delta variant). One infected ciliated cell is visible in the center of the recorded area. Virus particles are visible within membrane-bound compartments of the cytoplasm. Spike visibility is poor and some virus particles appear compressed. Related publication: Laue M, Hoffmann T, Michel J, Nitsche A. Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy. Virol J. 2023 Feb 6;20(1):21. doi: 10.1186/s12985-023-01981-9. PMID: 36747188; PMCID: PMC9901382.

Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy – data set 04

We developed a sedimentation method using desktop ultracentrifugation (see description below) to visualize SARS-CoV-2 particles in suspensions from oro- and/or nasopharyngeal swabs by thin section electron microscopy. A detailed description of the methods and the data set is provided in the download container. Data set 04 is a stitched image montage recorded from an area of a thin section through the sediment obtained from a swab sample  which was negative by quantitative PCR (negative control). The recorded area shows the profiles of four keratinocytes which are surrounded by heterogenous material (e.g. membrane lamella, needle-like crystals, round profiles with a fine-fibrous matrix). Virus partricles are not visible. Related publication: Laue M, Hoffmann T, Michel J, Nitsche A. Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy. Virol J. 2023 Feb 6;20(1):21. doi: 10.1186/s12985-023-01981-9. PMID: 36747188; PMCID: PMC9901382.

Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy – data set 01

We developed a sedimentation method using desktop ultracentrifugation (see description below) to visualize SARS-CoV-2 particles in suspensions from oro- and/or nasopharyngeal swabs by thin section electron microscopy. A detailed description of the methods and the data set is provided in the download container. Data set 01 is a stitched image montage recorded from an area of a thin section through the sediment obtained from a swab sample which was positive by quantitative PCR (delta variant). Two, more or less, intact ciliated cells are visible and surrounded by other cells or cellular debris. The ciliated cell in the upper right corner is infected with SARS-CoV-2. Virus particles are visible within membrane-bound compartments of the cytoplasm. Several double-membrane vesicles, which are typical compartments of the coronavirus replication machinery, are also detectable. Related publication: Laue M, Hoffmann T, Michel J, Nitsche A. Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy. Virol J. 2023 Feb 6;20(1):21. doi: 10.1186/s12985-023-01981-9. PMID: 36747188; PMCID: PMC9901382.

Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy – data set 02

We developed a sedimentation method using desktop ultracentrifugation (see description below) to visualize SARS-CoV-2 particles in suspensions from oro- and/or nasopharyngeal swabs by thin section electron microscopy. A detailed description of the methods and the data set is provided in the download container. Data set 02 is a stitched image montage recorded from an area of a thin section through the sediment obtained from a swab sample which was positive by quantitative PCR (delta variant). One ciliated cell is visible and surrounded by cellular debris. The ciliated cell is infected with SARS-CoV-2. Few virus particles are visible within membrane-bound compartments of the cytoplasm. Numerous virus particles are located at the cell surface intermingled between the cilia. The virus particles of this cell appear deformed and deviate from the oval/circular profile which is usually present. Related publication: Laue M, Hoffmann T, Michel J, Nitsche A. Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy. Virol J. 2023 Feb 6;20(1):21. doi: 10.1186/s12985-023-01981-9. PMID: 36747188; PMCID: PMC9901382.