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Data highlights : COVID-19

The Data Highlights section showcases recently published datasets relevant to pandemic preparedness research by researchers affiliated with a Swedish research institute. Specifically, in our case we write about e.g. COVID-19 and SARS-CoV-2, infectious diseases in general, and antibiotic resistance. The goal is to highlight openly shared data that can potentially be used by many other researchers to make further discoveries.

Topic: COVID-19

CoViMAPP – analysing changes in the soluble blood proteome due to COVID-19
January 19, 2024
CoViMAPP – analysing changes in the soluble blood proteome due to COVID-19
Babačić and colleagues expanded the coverage of the soluble blood proteome using mass spectrometry. In order to support further research in this area, their results have been added to an open-access app.
COVID-19
METTL3 localisation during SARS-CoV-2 infection could highlight new novel antiviral strategy
June 2, 2023
METTL3 localisation during SARS-CoV-2 infection could highlight new novel antiviral strategy
Vaid and Mendez, and collaborators, studied how the gene expression profile of m6A mRNA is affected both during and after COVID-19 infection. All sequencing data and the source code for analysis are shared.
COVID-19 Infectious diseases
Variability in IGH antibody genes influences the response to SARS-CoV-2
May 5, 2023
Variability in IGH antibody genes influences the response to SARS-CoV-2
Pushparaj and colleagues use genotyping and haplotype analysis to show high genetic diversity in IGH genes among humans, which may influence our response to infections. Data, and IgDiscover software shared.
COVID-19 Infectious diseases
A wider variety of data sources contribute to better spatio-temporal predictions of COVID-19 test positivity
November 22, 2022
A wider variety of data sources contribute to better spatio-temporal predictions of COVID-19 test positivity
Van Zoest et al (2022) developed and evaluated the performance of four different statistical single models and one ensemble model to predict trends in COVID-19 test positivity. Data are shared openly in GitHub.
COVID-19 Infectious diseases
Data-driven research shows that Neanderthal gene connected to severity of COVID-19 (Update)
October 3, 2022
Data-driven research shows that Neanderthal gene connected to severity of COVID-19 (Update)
Study by Hugo Zeberg and Svante Pääbo fully based on openly available data published open access in Nature.

Now a Nobel Prize winner!!
COVID-19 Infectious diseases
Direct RT-PCR used to monitor Omicron BA.1/BA.2 variant transition in Sweden (Update)
August 15, 2022
Direct RT-PCR used to monitor Omicron BA.1/BA.2 variant transition in Sweden (Update)
Lentini and collegues used direct RT-PCR to show the transition from Omicron BA.1 to sub-variant BA.2 in Sweden Jan-March 2022. New Preprint from Reinius lab which shares data and code.
COVID-19 Infectious diseases
Large scale immunofluorescence to explore the host cell response to SARS-CoV-2 infection
April 25, 2022
Large scale immunofluorescence to explore the host cell response to SARS-CoV-2 infection
Expression of 602 host proteins were evaluated in populations of infected and non-infected cells using immunofluorescence. ≈75,000 images have been published as a resource for further studies.
COVID-19 Infectious diseases
Interactions between fragments and SARS-CoV-2 nsp10 provide insight into the viral replications
March 1, 2022
Interactions between fragments and SARS-CoV-2 nsp10 provide insight into the viral replications
Interactions between fragments and SARS-CoV-2 nsp10 have been successfully identified and characterised by Kozielski and colleagues. Data shared on the Protein Data Bank and Zenodo.
COVID-19 Infectious diseases
Study provides important insights for future predictions of SARS CoV-2 infection
February 21, 2022
Study provides important insights for future predictions of SARS CoV-2 infection
Mangsbo and colleagues investigated sensitivity and specificity of a SARS-CoV-2 T-cell assay. Research warrants further research into that future T-cell receptor sequencing as future tools for prediction of previous infections.
COVID-19 Infectious diseases
Newly discovered Fu2 nanobody hold potential for future antiviral development
February 17, 2022
Newly discovered Fu2 nanobody hold potential for future antiviral development
In this study, Hanke and colleagues discovered a new nanobody. The new RBD-specific Fu2 nanobody was found to utilize a unique neutralization mechanism. Data was shared openly in, eg. The Electron Microscopy Data Bank.
COVID-19 Infectious diseases
OAS1 splicing found to be associated with risk of severe COVID-19
February 9, 2022
OAS1 splicing found to be associated with risk of severe COVID-19
In this article, Huffman et al studied individuals across different ancestry groups and discusses the association between OAS1 splicing and severity of COVID-19. Data related to this study is shared publicly.
COVID-19 Infectious diseases
Mass spectrometry suggested as a future essential analytical contribution to Covid-19 pandemic readiness
January 20, 2022
Mass spectrometry suggested as a future essential analytical contribution to Covid-19 pandemic readiness
Hober et al. present how LC-MRM/MS could form the basis of a scalable method that should facilitate future pandemic preparedness. The data has been openly shared.
COVID-19 Infectious diseases
Host factor interaction between human G3BP proteins and SARS-CoV-2 N-protein could represent an antiviral target
November 24, 2021
Host factor interaction between human G3BP proteins and SARS-CoV-2 N-protein could represent an antiviral target
Kruse and Benz et al. describe a scalable method of investigating virus-host interactions that can be used as a means of identifying potential targets for novel antiviral drugs. All data from the study have been shared publicly.
COVID-19 Infectious diseases
Drug repurposing identifies Fostamatinib as a drug with potentially high efficacy in COVID-19 treatment
November 19, 2021
Drug repurposing identifies Fostamatinib as a drug with potentially high efficacy in COVID-19 treatment
Recent study finds that drug repurposing can offer an average of an 11-fold increase in disease coverage and demonstrates its value for COVID-19. All data and code that support the findings have been made publicly available.
COVID-19 Infectious diseases
Clues to the genetic factors underlying greater susceptibility to severe COVID-19 in men
November 3, 2021
Clues to the genetic factors underlying greater susceptibility to severe COVID-19 in men
The COVID Human Genetic Efforts consortium published a study on genetic factors underlying greater susceptibility to the severe COVID-19 in men. Relevant RNA-seq data were shared in Gene Expression Omnibus (GEO).
COVID-19 Infectious diseases
Reliable profiling of IgG and IgM levels in home-sampled dried blood spots
October 18, 2021
Reliable profiling of IgG and IgM levels in home-sampled dried blood spots
Roxhed et al. demonstrate how self sampling at home can be effective by profiling IgG and IgM levels against several versions of SARS-CoV-2 proteins (S, RBD, N) in home-sampled dried blood spots. Metadata records and the analysis scripts used in the study are shared.
COVID-19 Infectious diseases
Metabolic perturbation of SARS-CoV-2 as a potential future therapeutic target
October 7, 2021
Metabolic perturbation of SARS-CoV-2 as a potential future therapeutic target
Krishnan et al. showed that the SARS-CoV-2 virus can use and rewire metabolic pathways to their benefit in replication. Their findings indicate that host metabolic perturbation could be an attractive strategy to limit replication. Code and data from the study have been shared pubicly.
COVID-19 Infectious diseases
Human genetic mapping can provide insight about COVID-19 pathogenesis and drug development
August 10, 2021
Human genetic mapping can provide insight about COVID-19 pathogenesis and drug development
Researchers in the COVID-19 Host Genetics initiative performed genome-wide association meta-analyses to examine the loci involved in the variation of COVID-19 disease severity and susceptibility between individuals. The data and code used in the project have been made available.
COVID-19 Infectious diseases
New phenomics method for antiviral drug discovery may help to fight COVID-19
August 2, 2021
New phenomics method for antiviral drug discovery may help to fight COVID-19
Rietdijk and colleagues used a new phenomics approach to aid in the discovery of both novel drugs and drugs that could potentially be repurposed to fight COVID-19. Both data and code are published.
COVID-19 Infectious diseases
Interferon signatures in SARS-CoV-2 infected liver cells could provide knowledge for new antiviral therapies
July 6, 2021
Interferon signatures in SARS-CoV-2 infected liver cells could provide knowledge for new antiviral therapies
Chen and Saccon et al. used a proteomics-based approach to study how SARS-CoV-2 infection affected Type-1 interferon signalling in liver cells. Both data and code are published.
COVID-19 Infectious diseases
Cost-effective COVseq method could be used for large-scale genomic surveillance of VOCs
July 1, 2021
Cost-effective COVseq method could be used for large-scale genomic surveillance of VOCs
Simonetti, Zhang, and Harbers et al. have shared a cost-effective, scalable and versatile method (alongside associated data and code) that could facilitate large-scale genomic surveillance of variants of concern (VOCs).
COVID-19 Infectious diseases
Quantitative proteomic provides important knowledge about cellular response against SARS CoV-2
May 19, 2021
Quantitative proteomic provides important knowledge about cellular response against SARS CoV-2
Saccon and colleagues studied changes in protein abundance caused by SARS-CoV-2 virus in susceptible cell lines using quantitative proteomics. All proteomics were made data openly available in different repositories.
COVID-19 Infectious diseases
Proteomic profiling in COVID-19 patients as biomarkers to monitor disease severity
April 13, 2021
Proteomic profiling in COVID-19 patients as biomarkers to monitor disease severity
Recent study examined a large number of inflammatory, immune response, cardiovascular, and neurological markers in the blood of patients variously impacted by COVID-19. Data and analysis code were shared in public repositories.
COVID-19 Infectious diseases
Swedish COVID-19 symptom data contribute to accelerating research about pandemic
March 29, 2021
Swedish COVID-19 symptom data contribute to accelerating research about pandemic
COVID Symptom Study Sweden collects data through a smartphone app to investigate prevalence, risk factors, and symptoms associated with COVID-19. To date, over 200.000 volunteers have enrolled in the study.
COVID-19 Infectious diseases
Neanderthal gene protecting against severe COVID-19 could be potential new drug target
March 10, 2021
Neanderthal gene protecting against severe COVID-19 could be potential new drug target
A new study largely relying on existing data re-use identified circulating proteins influencing COVID-19 susceptibility and severity. Based on these results, work on repurposing relevant existing drugs work can now be launched.
COVID-19 Infectious diseases
Bevacizumab treatment beneficial for patients with severe COVID-19
February 18, 2021
Bevacizumab treatment beneficial for patients with severe COVID-19
A recently published clinical study investigating bevacizumab, a humanized anti-VEGF monoclonal antibody, offers promising results in fighting severe COVID-19. Treatment progress data and analysis code were shared publicly.
COVID-19 Infectious diseases
Nanobodies promising new therapeutics for treatment of SARS CoV-2
February 16, 2021
Nanobodies promising new therapeutics for treatment of SARS CoV-2
A recently published study characterizes the mechanisms by which nanobodies neutralize or prevent of infection in molecular detail. Crystallographic coordinates, cryo-EM density maps, and atomic coordinates were deposited to public databases.
COVID-19 Infectious diseases
Mechanism of entry used by human species D adenoviruses proving important for COVID-19 vaccine development
January 18, 2021
Mechanism of entry used by human species D adenoviruses proving important for COVID-19 vaccine development
New study identifies a noncanonical entry mechanism used by human adenoviruses, important for development of adenovirus-based vaccine vectors. The reported X-ray structural data was made available through the Protein Data Bank.
COVID-19 Infectious diseases
A novel approach to discover and characterize broad-spectrum antivirals
December 18, 2020
A novel approach to discover and characterize broad-spectrum antivirals
Newly discovered antiviral compounds showed broad-range antiviral activity against pathogenic RNA viruses such as SARS-CoV-2. The authors share data freely in open repositories.
COVID-19 Infectious diseases
Pathogenesis of hyperinflammatory syndrome associated with COVID-19 in children
December 7, 2020
Pathogenesis of hyperinflammatory syndrome associated with COVID-19 in children
Multiple autoantibodies and specific cytokines could be involved in the pathogenesis of MIS-C associated with COVID-19. Data and code made available in open repositories.
COVID-19 Infectious diseases
An alpaca-derived nanobody can potently neutralize SARS-CoV-2
November 27, 2020
An alpaca-derived nanobody can potently neutralize SARS-CoV-2
Leo Hanke and colleagues identified a SARS-CoV-2 RBD-specific single domain antibody fragment, Ty1, that potently neutralizes the virus. Ty1 should now be further investigated as a candidate for antiviral therapy.
COVID-19 Infectious diseases
Synthetic nanobodies are easy to produce and can effectively neutralize SARS-CoV-2
November 24, 2020
Synthetic nanobodies are easy to produce and can effectively neutralize SARS-CoV-2
Recently published study demonstrates that it is possible to select highly specific binders with neutralizing activity against SARS-CoV-2 from a synthetic nanobody library in a short timeframe.
COVID-19 Infectious diseases
MAIT cell activation and dynamics studied in relation to COVID-19 disease severity
November 18, 2020
MAIT cell activation and dynamics studied in relation to COVID-19 disease severity
Tiphaine Parrot and colleagues studied changes in conventional and unconventional T cell subsets in patients with various disease severity using flow cytometry. The results were published along with the data.
COVID-19 Infectious diseases
Crystal structure of SARS CoV-2 nsp-10 - a potential drug target for COVID-19
November 3, 2020
Crystal structure of SARS CoV-2 nsp-10 - a potential drug target for COVID-19
A study by Rogstam and colleagues published along with the crystal structure of SARS CoV-2 non-structural protein 10 in the Protein Data Bank provides a starting point for structure-guided drug discovery and design.
COVID-19 Infectious diseases
Bayesian model for estimating the impact of mobility patterns on COVID-19 infection
October 23, 2020
Bayesian model for estimating the impact of mobility patterns on COVID-19 infection
Patrick Bryant and Arne Elofsson shared code and instructions for modelling COVID-19 development using MCMC simulations based on mobile phone mobility data from Google mobility reports.
COVID-19 Infectious diseases
First study using data collected as part of the large-scale serology testing at SciLifeLab published
October 15, 2020
First study using data collected as part of the large-scale serology testing at SciLifeLab published
This study used only a fraction of the large volume of serology data continuously collected by the ScilifeLab Autoimmunity and Serology profiling facility.
COVID-19 Infectious diseases
Method circumventing RNA extraction in RT-PCR COVID-19 testing published along with data
October 1, 2020
Method circumventing RNA extraction in RT-PCR COVID-19 testing published along with data
Study by Björn Reinius and co-workers published open access in Nature Communications along with source data and the computational code.
COVID-19 Infectious diseases