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opencc-by-4.0Mar 2024View details →

Early and late consequences of damage to the stem cell compartment following SARS-CoV-2 infection

This application has been reviewed in a previous cycle and we would like to thank reviews for very positive comment. However, to our surprise one reviewer stated that this proposal is not based on our original hypothesis. To address this misunderstanding the role of Nlrp3 inflammasome as a trigger of cytokine storms COVID19 was proposed in the literature for a first time by our team (Ratajczak MZ, Kucia M. SARS-CoV-2 infection and overactivation of Nlrp3 inflammasome as a trigger of cytokine "storm" and risk factor for damage of hematopoietic stem cells. Leukemia. 2020 Jul;34(7):1726-1729. doi: 10.1038/s41375-020-0887-9) and subsequently several groups confirmed this hypothesis and highly cited our initial report. COVID19 or SARS-CoV-2 virus is single-stranded RNA virus, whose infection can be asymptomatic or lead to damage of several vital organs and a fatal complication involving “cytokine storm”, which results in uncontrolled hyperactivation of the immune response by innate immunity cells. The major concern is that we still cannot foresee late complications of this infection including direct or indirect effects on stem cell compartment. SARS-CoV-2 may enter human cells after binding to the angiotensin-converting enzyme 2 (ACE2) receptor and utilizes its surface spike protein (SP) for attachment and entry into the target cells. It has been demonstrated that ACE2 receptor is highly expressed on hematopoietic stem cells (HSCs) and endothelial progenitors (EPCs) isolated from adult hematopoietic organs as well on developmental early precursors of these cells. Its expression increases with more primitive phenotype of cells and it may explain that our group noticed its high expression in addition to HSC and EPC on human very small CD133+CD34+Lin-CD45– cells, which can be specified as reported by us and others into functional HSCs and EPCs. COVID19 after binding to ACE2 may hyperactivate Nlrp3 inflammasome as we recently demonstrated in cells at different level of specification into hematopoietic and endothelial lineage. This may lead to pyroptotic death of the cells exposed to virus SP. Moreover, this could lead also as we postulated of an initiation of “cytokine storm” by innate immunity cells. Evidence accumulates that COVID19 infection despite a fact that it manifests primarily as a respiratory syndrome has significant impact on other organs including the hematopoietic system and endothelium leading to several complications. To support this a large percentage of infected patients, suffer from lymphopenia and thrombocytopenia as well as from damage of endothelium that promotes hypercoagulability. Nevertheless, there are still not very well-known mechanisms how virus affect human stem cells and damage them by productive or abortive infection. It is well known that the innate immune response and activation of the Nlrp3 inflammasome are important defense mechanisms during the first days of infection, until acquired immunity responds with the production of antibodies. However, as mentioned above hyperactivation of this intracellular protein complex in innate cells may induce a cytokine storm or may lead to their death of other cells in mechanism of pyroptosis. Virus may also damage cells by lysis or theoretically what we hypothesize may stay after entry into long living stem cells in a latent form and become activated when immune system becomes impaired. Our group postulated a possibility that damage of stem cells for hemato/endothelial lineage may occur mainly by hyperactivation of Nlrp3 inflammasome after binding of viral SP to ACE2 expressed on these cells. Similar role may play interaction of SP with Toll like receptor-4 (TLR4). Our group and group of Dr. Hal Broxmeyer has demonstrated that exposure of umbilical cord blood-derived HSCs to SP protein decreases viability and in vitro clonogenicity of these cells. We also observed similar effect on proliferation of human EPC. Based on this a central hypothesis of our proposal is that COVID19 infection may damage by SP-ACE2 or SP-TLR4 interaction stem cells from hematopoietic/endothelial lineage which contributes to early and late consequences of this infection. Project was supported by the Polish National Center OPUS grant UM-2021/41/BNZ6/01590 RNAseq database  Patient COVID - PRJNA1167900 - <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1167900">https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1167900</a> scRNA-seq of VSELs: PRJNA1126429 (<a title="https://www.ncbi.nlm.nih.gov/sra/PRJNA1126429" href="https://www.ncbi.nlm.nih.gov/sra/PRJNA1126429" target="_blank" rel="noopener">https://www.ncbi.nlm.nih.gov/sra/PRJNA1126429</a>) scRNA-seq of HSC: PRJNA1128409 (<a title="https://www.ncbi.nlm.nih.gov/sra/PRJNA1128409" href="https://www.ncbi.nlm.nih.gov/sra/PRJNA1128409" target="_blank" rel="noopener">https://www.ncbi.nlm.nih.gov/sra/PRJNA1128409</a>).

opencc-by-4.0Mar 2024View details →

Molecular docking and quantum-chemical characterization of inhibitory activity of procyanidins and flavonol glucosides from Graptopetalum paraguayense E. Walther against nonstructural proteins of SARS-Cov-2

The dataset includes: <ol> <li>Optimized geometries of all ligands, NSPs and their complexes in gas phase</li> <li>Total energies (a.u.) and interaction energies (a.u. and kcal mol-1) of the complexes, ligands and NSPs in gas phase and in argon</li> <li>Mass spectra (full ms) and product ion spectra (ms2) of standards and identified components from GP. </li> <li>Output files from quantum-chemical calculations.</li> <li>pdb files of NSPs</li> <li>mol files of all complexes</li> </ol>

opencc-by-4.0Oct 2024View details →

SCoV2-VAR: A light-weighted, customizable, and open-source database of 12 million SARS-CoV-2 genomes

<pre>Explosive accumulation of SARS-CoV-2 variants is posing a challenge to monitoring virus mutation and other data dealing, particularly based on centralized databases. The present study aimed to establish a light-weighted, customizable, and open-source database for SARS-CoV-2 genomes and annotations, without any access limit. The database, named SCoV2-VAR, was constructed, based on the variations (VAR) of the full-length SARS-CoV-2 (SCoV2) data uploaded on websites. All sequence samples were subject to quality control, single nucleotide polymorphism (SNP) annotation, format conversion, and final compression before appending to SCoV2-VAR. The final version of SCoV2-VAR (up to Feb 2024) contained more than 12 million SARS-CoV-2 records, with full genome and annotations. SCoV2-VAR was extremely light-weighted, with a storage size of 937 Mb for all 12 million sequences, post a 1: 596 compression. SCoV2-VAR is capable of timely updating, quickly querying, and customizable outputting SARS-CoV-2 sequences and their annotations. Additionally, the present study provided an overview of all 12 million SARS-CoV-2 samples, for both sequences and annotations. </pre>

opencc-by-nc-nd-4.0Sep 2023View details →

Robust detection of SARS-CoV-2 exposure in population using T-cell repertoire profiling

The dataset contains processed T-cell receptor repertoire sequencing data from >1200 individuals of different sex and age. Note that only samples with good sequencing coverage are published (>10^5 reads per file).  The main aim of our study is to find TCR sequence biomarkers and develop a bioinformatic pipeline that allows building an accurate and robust classifier that distinguishes COVID-19-convalescent donors from unexposed individuals. We performed immunosequencing of the rearranged TCR α and β regions for PBMCs. For the cohort described in this study (Cohort-I) we sequence both chains of the TCR heterodimer as both of these chains are required to properly predict antigen recognition26. We ran conventional T-cell repertoire data analysis and pre-processed data to remove low-coverage samples.  Of samples in Cohort-I which passed read count threshold, 383/377 TCR α/β samples were from healthy donors (SARS-CoV-2 PCR test negative or obtained prior to pandemic) and 890/848 were from COVID-19-positive patients. The majority of samples were accompanied by information on HLA class I and II alleles. Samples were prepared and sequenced in nine batches. The metadata for both TCR alpha and beta repertoires contains the following information: <div> <ul> <li>sequencing_date - date when seguencing was performed</li> <li>batch_name - one of the 9 unique batch identifiers</li> <li>sample_id, patient_id - information on sample identifier and donor identifier</li> <li>COVID_status, COVID_IgG, COVID_IgM, COVID_PCR - information on COVID-19 status</li> <li>HLA-A.1, HLA-A.2, HLA-B.1, HLA-B.2, HLA-C.1, HLA-C.2 - MHC class I alleles</li> <li>HLA-DPB1.1, HLA-DPB1.2, HLA-DQB1.1, HLA-DQB1.2, HLA-DRB1.1, HLA-DRB1.2 - MHC class II alleles</li> <li>file_name - name of the corresponding file in fmba_clonotype_usage_tables.zip archive</li> </ul> </div> Each file in fmba_clonotype_usage_tables.zip archive stores the information on either TCR alpha or beta repertoire. Each line in a file corresponds to the unique clonotype and each clonotype is accompanied with the following information: <ul> <li>count - number of reads where the clonotype was detected</li> <li>freq - count of reads with the clonotype divided by thw whole number of reads in a sample</li> <li>cdr3nt, cdr3aa - nucleotide and amino acid sequences of TCR's CDR3 sequence</li> <li>v, d, j - the V/D/J segment name which was used for the clonotype's rearrangement</li> <li>VEnd, DStart, DEnd, JStart - information on VDJ junction positions </li> </ul> We proceed with selecting a set of CDR3 sequences that can serve as biomarkers and form a feature list for COVID-19 status classifier. We also validate the resulting set of clonotypes in several ways. Co-occurence of specific TCR α and β clonotypes can serve as an independent validation for biomarkers and their co-association with some specific pathogen. Additional information on donor HLAs is provided to filter the set of biomarkers based on HLA restriction: association with donor HLA serves as an additional evidence for TCR specificity to a specific set of antigens presented in a given donor and allows detecting the fingerprint of past and present infection. Furthermore, clonotypes with similar sequences can be aggregated into 'metaclonotype' biomarkers based on clonotype graph analysis. Finally, we train various COVID-19 status classifiers on selected batches from Cohort-I data using different algorithms and incorporating different feature sets. Verification of the robustness of our results was performed using independent batches of the Cohort-I and data from Cohort-II published previously.

opencc-by-4.0Oct 2021View details →

RNA extraction alternative method for SARS-CoV-2 molecular diagnosis

The devastating outbreak of COVID-19 has posed serious challenges for the diagnostics laboratories, often facing global shortage of reagents and equipment. This study aimed at evaluating an additional RNA extraction method respect to those already recommended by WHO and CDC. A new protocol for RNA extraction from nasopharyngeal swab was set up, adapting the Qiagen RNeasy 96 plate for cell lines, and validated on a set of 96 clinical samples analyzed in parallel by a recommended method. The internal control and target genes analysis showed a good agreement between the two extraction methods, indicating that the two approaches can be considered equivalent for the SARS-CoV-2 diagnostics. The addition of this extraction method can help in increasing the throughput for SARS-CoV-2 molecular test, even in a low automation setting. The data set published in Zenodo is the full data analysed in the paper.

Population-based Age-stratified Seroprevalence Investigation on SARS-CoV-2 Virus in Selected States of High and Low Burden of Disease in Nigeria

Results of population-based age stratified seroepidemiological investigation in Nigeria

opencc-by-4.0Dec 2020View details →

SARS-CoV-2 exposure in Malawian blood donors: an analysis of seroprevalence and variant dynamics between January 2020 and July 2021

Results of population-based age stratified seroepidemiological investigation in Malawi.

High prevalence of SARS-CoV-2 antibodies in pregnant women in the inner city of Johannesburg, Gauteng Province, South Africa

Results of population-based age stratified seroepidemiological investigation in South Africa.

Seroprevalence of SARS-CoV-2 in 10 Regional Capitals of Cameroon

Results of population-based age stratified seroepidemiological investigation in Cameroon

Age-stratified sero-surveillance for SARS-CoV-2 infections in four cities in Thailand

Results of population-based age stratified seroepidemiological investigation in Thailand

Effectiveness of Inactivated SARS-CoV-2 Vaccine (CoronaVac) on Survival at Intensive Care Unit: A Cross-sectional Study

Background: This study compared the course of COVID-19 in vaccinated and unvaccinated patients admitted to an intensive care unit (ICU) and evaluated the effect of vaccination with CoronaVac on admission to ICU. Methods: Patients admitted to ICU due to COVID-19 between 1 April 2021 and 15 May 2021 were enrolled to the study. Clinical, laboratory, radiological parameters, hospital and intensive care unit mortality were compared between vaccinated patients and eligible but unvaccinated patients. Patients over 65 years old were the target population of the study due to the national vaccination schedule. Results: Data from 90 patients were evaluated. Of these, 36 (40.0%) were vaccinated. All patients had the CoronaVac vaccine. Lactate dehydrogenase and ferritin levels were higher in unvaccinated group than vaccinated group (p=0.021 and 0.008, respectively). SpO2 from the first arterial blood gas at ICU was 83.71±19.50 % in vaccinated, 92.36±6.59 % in unvaccinated patients (p=0.003). Length of ICU and hospital stay were not different (p=0.204, 0.092, respectively).  ICU and hospital mortality were similar between groups (p=0.11 and 0.70, respectively). Conclusions: CoronaVac vaccine had no effect on survival from COVID-19. CoronaVac’s protective effect, especially on new genetic variants, should be investigated further.

Public attitudes to a human challenge study with SARS-CoV-2: a mixed-methods study

Human challenge studies involve the deliberate exposure of healthy volunteers to an infectious micro-organism in a highly controlled and monitored way. They are used to understand infectious diseases and have contributed to the development of vaccines. In early 2020, the UK started exploring the feasibility of establishing a human challenge study with SARS-CoV-2. Given the significant public interest and the complexity of the potential risks and benefits, it is vital that public views are considered in the design and approval of any such study and that investigators and ethics boards remain accountable to the public. We conducted a mixed methods study comprising online surveys conducted with 2,441 UK adults and in-depth virtual focus groups with 57 UK adults during October 2020 to explore the public’s attitudes to a human challenge study with SARS-CoV-2 taking place in the UK. This depositary includes: <ul> <li>Documentation relating to the online surveys; <ul> <li>Survey</li> <li>Animation that survey participants were asked to view</li> <li>Survey wrappers (invitations, participant information sheet and consent, end of survey messages)</li> <li>Survey data (demographic information not included)</li> </ul> </li> <li>Documentation relating to focus groups: <ul> <li>Participant Information Sheet</li> <li>Focus Group Discussion guide</li> </ul> </li> </ul>

Simulations from 'Estimating the relative proportions of SARS-CoV-2 strains from wastewater samples'

Simulations used in "Estimating the relative proportions of SARS-CoV-2 strains from wastewater samples"

Virtual screening of the Janssen compound collection against SARS-CoV-2 Mpro

This short report describes the most relevant results of virtually screening the Janssen Pharmaceutica compound collection for potential activity against SARS-CoV-2 Mpro and confirmation of potential hits in a VeroE6 cell-based anti-SARS-CoV-2 assay.

Virtual screening of the Enamine REAL database against SARS-CoV-2 RdRP

This short report describes the most relevant results of virtually screening the Enamine REAL database for potential activity against SARS-CoV-2 RdRP and confirmation of potential hits in a VeroE6 cell-based anti-SARS-CoV-2 assay.

Virtual screening of 2629 Janssen compounds against SARS-CoV-2 RdRP

This short report describes the most relevant results of virtually screening the Janssen Pharmaceutica compound collection for potential activity against SARS-CoV-2 RdRP and confirmation of potential hits in a VeroE6 cell-based anti-SARS-CoV-2 assay.

Structural dynamics of SARS-CoV-2 nucleocapsid protein induced by RNA binding

This dataset contains files of the molecular dynamics simulations performed in "Structural dynamics of SARS-CoV-2 nucleocapsid protein induced by RNA binding" study. Further information in presented in README.md file and the abstract of the study is presented below: "The nucleocapsid (N) protein of the SARS-CoV-2 virus, the causal agent of COVID-19, is a multifunction phosphoprotein that plays critical roles in the virus life cycle, including transcription and packaging of the viral RNA. To play such diverse roles, the N protein has two globular RNA-binding modules, the N- (NTD) and C-terminal (CTD) domains, which are connected by an intrinsically disordered region. Despite the wealth of structural data available for the isolated NTD and CTD, how these domains are arranged in the full-length protein and how the oligomerization of N influences its RNA-binding activity remains largely unclear. Herein, using experimental data from electron microscopy and biochemical/biophysical techniques combined with molecular modeling and molecular dynamics simulations, we showed that, in the absence of RNA, the N protein formed structurally dynamic dimers, with the NTD and CTD arranged in extended conformations. However, in the presence of RNA, the N protein assumed a more compact conformation where the NTD and CTD are packed together. We also provided an octameric model for the full-length N bound to RNA that was consistent with electron microscopy images of the N protein in the presence of RNA. Together, our results shed new light on the dynamics and higher-order oligomeric structure of this versatile protein."

SARS-CoV-2 Seroprevalence in a Rural and Urban Household Cohort, South Africa, July 2020–September 2021

Early results of the PHIRST-C study seroprevalence results in South Africa

opencc-by-4.0Feb 2022View details →

Serial seroprevalence study: follow-up of immunity to SARS-Cov-2 infection and monitoring of effective vaccination coverage, in three Chilean cities

Population-based serosurvey in Santiago, Talca, and Coquimbo–La Serena