| 1. |
- Castro Dopico, Xaquin, et al.
(författare)
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Probabilistic classification of anti-SARS-CoV-2 antibody responses improves seroprevalence estimates
- 2022
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Ingår i: Clinical & Translational Immunology (CTI). - : John Wiley & Sons. - 2050-0068. ; 11:3
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Tidskriftsartikel (refereegranskat)abstract
- Objectives: Population-level measures of seropositivity are critical for understanding the epidemiology of an emerging pathogen, yet most antibody tests apply a strict cutoff for seropositivity that is not learnt in a data-driven manner, leading to uncertainty when classifying low-titer responses. To improve upon this, we evaluated cutoff-independent methods for their ability to assign likelihood of SARS-CoV-2 seropositivity to individual samples. Methods: Using robust ELISAs based on SARS-CoV-2 spike (S) and the receptor-binding domain (RBD), we profiled antibody responses in a group of SARS-CoV-2 PCR+ individuals (n = 138). Using these data, we trained probabilistic learners to assign likelihood of seropositivity to test samples of unknown serostatus (n = 5100), identifying a support vector machines-linear discriminant analysis learner (SVM-LDA) suited for this purpose. Results: In the training data from confirmed ancestral SARS-CoV-2 infections, 99% of participants had detectable anti-S and -RBD IgG in the circulation, with titers differing > 1000-fold between persons. In data of otherwise healthy individuals, 7.2% (n = 367) of samples were of uncertain serostatus, with values in the range of 3-6SD from the mean of pre-pandemic negative controls (n = 595). In contrast, SVM-LDA classified 6.4% (n = 328) of test samples as having a high likelihood (> 99% chance) of past infection, 4.5% (n = 230) to have a 50–99% likelihood, and 4.0% (n = 203) to have a 10–49% likelihood. As different probabilistic approaches were more consistent with each other than conventional SD-based methods, such tools allow for more statistically-sound seropositivity estimates in large cohorts. Conclusion: Probabilistic antibody testing frameworks can improve seropositivity estimates in populations with large titer variability.
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| 2. |
- Devi, Priya
(författare)
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Molecular characterization of the hepatitis C virus core protein
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Hepatitis C virus (HCV) is an RNA virus that causes chronic infection, which can lead to hepatocellular carcinomas in humans. Besides liver diseases, the chronic HCV infection causes a broad spectrum of extrahepatic complications such as lymphoproliferative, metabolic and autoimmune disorders. Notably, HCV encoded core (C) protein is the major virion component that is involved in the oncogenesis and immune subversion. Therefore, detailed molecular characterization of the C protein provides a rational starting point for identification of novel countermeasures against pathogenic HCV infections. In this thesis we have investigated the suppressive effect of the C protein on T cell functions in immortalized cell lines and clinical samples.In paper I, we found that the expression of the C protein enhanced overall tyrosine phosphorylation in immortalized T cells. Interestingly, stable expression of the C protein specifically reduced accumulation of the tyrosine phosphatase SHP-1 mRNA. Our detailed bisulfite sequencing (BS) studies revealed that the SHP-1 P2 promoter was particularly hypermethylated at CpG1 and proximal islands in these cells. In paper II, we presented a new high-throughput next generation bisulfite sequencing (NGS-BS) protocol for the analysis of locus specific CpG methylation in HCV-infected cells using SHP-1 P2 as a model promoter. In line with our data from the BS, the NGS-BS method showed similar methylation profile at CpG1 island in immortalized cells. Strikingly, peripheral blood mononuclear cells (PBMCs) isolated from healthy controls and HCV-positive (HCV+) patients, showed much lower levels of methylation at the CpG1 island with no significant difference in DNA methylation pattern. In paper III, we investigated the mechanism of the C protein-mediated release of Ca2+ from intracellular stores. We identified two distinct regions in the N- and C-terminal parts of the protein that were essential for activation of the Ca2+/NFAT pathway. Of these, the N-terminal region was required for self-association of the C protein into nucleocapsid-like structures whereas the C-terminal part is essential for anchoring the protein to the ER-membrane. In paper IV, we presented a PCR based diagnostic method for the specific detection of positive and negative strand HCV RNA using primers with a non-viral tag. The method was evaluated by analysing the plasma and PBMC samples from chronic HCV+ patients.Taken together, our studies provide more detailed molecular characterization of the HCV C protein functions in immortalized as well as in HCV+ T cells. Importantly, specific DNA methylation pattern of the SHP-1 gene promoter may function as a potential prognostic marker for the disease progression in HCV-induced tumors. In addition, our updated PCR-based HCV diagnostic method may provide a more specific tool to monitor HCV infections in minor reservoirs.
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| 3. |
- Gupta, Govind, et al.
(författare)
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Silver nanoparticles with excellent biocompatibility block pseudotyped SARS-CoV-2 in the presence of lung surfactant
- 2022
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Ingår i: Frontiers in Bioengineering and Biotechnology. - : Frontiers Media SA. - 2296-4185. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Silver (Ag) is known to possess antimicrobial properties which is commonly attributed to soluble Ag ions. Here, we showed that Ag nanoparticles (NPs) potently inhibited SARS-CoV-2 infection using two different pseudovirus neutralization assays. We also evaluated a set of Ag nanoparticles of different sizes with varying surface properties, including polyvinylpyrrolidone (PVP)-coated and poly (ethylene glycol) (PEG)-modified Ag nanoparticles, and found that only the bare (unmodified) nanoparticles were able to prevent virus infection. For comparison, TiO2 nanoparticles failed to intercept the virus. Proteins and lipids may adsorb to nanoparticles forming a so-called bio-corona; however, Ag nanoparticles pre-incubated with pulmonary surfactant retained their ability to block virus infection in the present model. Furthermore, the secondary structure of the spike protein of SARS-CoV-2 was perturbed by the Ag nanoparticles, but not by the ionic control (AgNO3) nor by the TiO2 nanoparticles. Finally, Ag nanoparticles were shown to be non-cytotoxic towards the human lung epithelial cell line BEAS-2B and this was confirmed by using primary human nasal epithelial cells. These results further support that Ag nanoparticles may find use as anti-viral agents.
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| 4. |
- Kruse, Thomas, et al.
(författare)
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Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 specific mechanisms and vulnerabilities
- 2021
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- Viral proteins make extensive use of short peptide interaction motifs to hijack cellular host factors. However, most current large-scale methods do not identify this important class of protein-protein interactions. Uncovering peptide mediated interactions provides both a molecular understanding of viral interactions with their host and the foundation for developing novel antiviral reagents. Here we describe a viral peptide discovery approach covering 23 coronavirus strains that provides high resolution information on direct virus-host interactions. We identify 269 peptide-based interactions for 18 coronaviruses including a specific interaction between the human G3BP1/2 proteins and an ΦxFG peptide motif in the SARS-CoV-2 nucleocapsid (N) protein. This interaction supports viral replication and through its ΦxFG motif N rewires the G3BP1/2 interactome to disrupt stress granules. A peptide-based inhibitor disrupting the G3BP1/2-N interaction dampened SARS-CoV-2 infection showing that our results can be directly translated into novel specific antiviral reagents.
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| 5. |
- Pushparaj, Pradeepa, et al.
(författare)
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Immunoglobulin germline gene polymorphisms influence the function of SARS-CoV-2 neutralizing antibodies
- 2023
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Ingår i: Immunity. - : Elsevier BV. - 1074-7613 .- 1097-4180. ; 56:1, s. 7-206
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Tidskriftsartikel (refereegranskat)abstract
- The human immunoglobulin heavy-chain (IGH) locus is exceptionally polymorphic, with high levels of allelic and structural variation. Thus, germline IGH genotypes are personal, which may influence responses to infection and vaccination. For an improved understanding of inter-individual differences in antibody responses, we isolated SARS-CoV-2 spike-specific monoclonal antibodies from convalescent health care workers, focusing on the IGHV1-69 gene, which has the highest level of allelic variation of all IGHV genes. The IGHV1-69∗20-using CAB-I47 antibody and two similar antibodies isolated from an independent donor were critically dependent on allele usage. Neutralization was retained when reverting the V region to the germline IGHV1-69∗20 allele but lost when reverting to other IGHV1-69 alleles. Structural data confirmed that two germline-encoded polymorphisms, R50 and F55, in the IGHV1-69 gene were required for high-affinity receptor-binding domain interaction. These results demonstrate that polymorphisms in IGH genes can influence the function of SARS-CoV-2 neutralizing antibodies.
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| 6. |
- Roxhed, Niclas, et al.
(författare)
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Multianalyte serology in home-sampled blood enables an unbiased assessment of the immune response against SARS-CoV-2
- 2021
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- Serological testing is essential to curb the consequences of the COVID-19 pandemic. However, most assays are still limited to single analytes and samples collected within healthcare. Thus, we establish a multianalyte and multiplexed approach to reliably profile IgG and IgM levels against several versions of SARS-CoV-2 proteins (S, RBD, N) in home-sampled dried blood spots (DBS). We analyse DBS collected during spring of 2020 from 878 random and undiagnosed individuals from the population in Stockholm, Sweden, and use classification approaches to estimate an accumulated seroprevalence of 12.5% (95% CI: 10.3%-14.7%). This includes 5.4% of the samples being IgG(+)IgM(+) against several SARS-CoV-2 proteins, as well as 2.1% being IgG(-)IgM(+) and 5.0% being IgG(+)IgM(-) for the virus' S protein. Subjects classified as IgG(+) for several SARS-CoV-2 proteins report influenza-like symptoms more frequently than those being IgG(+) for only the S protein (OR=6.1; p<0.001). Among all seropositive cases, 30% are asymptomatic. Our strategy enables an accurate individual-level and multiplexed assessment of antibodies in home-sampled blood, assisting our understanding about the undiagnosed seroprevalence and diversity of the immune response against the coronavirus. Here, Roxhed et al. develop a multiplexed approach to screen IgG and IgM levels against several SARS-CoV-2 proteins in home-sampled dried blood spots and estimate seroprevalence of 12.5% in Stockholm in spring of 2020.
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| 7. |
- Rudberg, Ann-Sofie, et al.
(författare)
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SARS-CoV-2 exposure, symptoms and seroprevalence in healthcare workers in Sweden.
- 2020
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- SARS-CoV-2 may pose an occupational health risk to healthcare workers. Here, we report the seroprevalence of SARS-CoV-2 antibodies, self-reported symptoms and occupational exposure to SARS-CoV-2 among healthcare workers at a large acute care hospital in Sweden. The seroprevalence of IgG antibodies against SARS-CoV-2 was 19.1% among the 2149 healthcare workers recruited between April 14th and May 8th 2020, which was higher than the reported regional seroprevalence during the same time period. Symptoms associated with seroprevalence were anosmia (odds ratio (OR) 28.4, 95% CI 20.6-39.5) and ageusia (OR 19.2, 95% CI 14.3-26.1). Seroprevalence was also associated with patient contact (OR 2.9, 95% CI 1.9-4.5) and covid-19 patient contact (OR 3.3, 95% CI 2.2-5.3). These findings imply an occupational risk for SARS-CoV-2 infection among healthcare workers. Continued measures are warranted to assure healthcare workers safety and reduce transmission from healthcare workers to patients and to the community.
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| 8. |
- Schlegel, Jan, et al.
(författare)
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A Multiparametric and High-Throughput Platform for Host-Virus Binding Screens
- 2023
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Ingår i: Nano Letters. - : American Chemical Society (ACS). - 1530-6984 .- 1530-6992. ; 23:9, s. 3701-3707
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Tidskriftsartikel (refereegranskat)abstract
- Speed is key during infectious disease outbreaks. It is essential, for example, to identify critical host binding factors to pathogens as fast as possible. The complexity of host plasma membrane is often a limiting factor hindering fast and accurate determination of host binding factors as well as high-throughput screening for neutralizing antimicrobial drug targets. Here, we describe a multiparametric and high-throughput platform tackling this bottleneck and enabling fast screens for host binding factors as well as new antiviral drug targets. The sensitivity and robustness of our platform were validated by blocking SARS-CoV-2 particles with nanobodies and IgGs from human serum samples.
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| 9. |
- Schulte, Tim, et al.
(författare)
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Caprin-1 binding to the critical stress granule protein G3BP1 is influenced by pH
- 2023
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Ingår i: Open Biology. - : The Royal Society. - 2046-2441. ; 13:5
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Tidskriftsartikel (refereegranskat)abstract
- G3BP is the central node within stress-induced protein-RNA interaction networks known as stress granules (SGs). The SG-associated proteins Caprin-1 and USP10 bind mutually exclusively to the NTF2 domain of G3BP1, promoting and inhibiting SG formation, respectively. Herein, we present the crystal structure of G3BP1-NTF2 in complex with a Caprin-1-derived short linear motif (SLiM). Caprin-1 interacts with His-31 and His-62 within a third NTF2-binding site outside those covered by USP10, as confirmed using biochemical and biophysical-binding assays. Nano-differential scanning fluorimetry revealed reduced thermal stability of G3BP1-NTF2 at acidic pH. This destabilization was counterbalanced significantly better by bound USP10 than Caprin-1. The G3BP1/USP10 complex immunoprecipated from human U2OS cells was more resistant to acidic buffer washes than G3BP1/Caprin-1. Acidification of cellular condensates by approximately 0.5 units relative to the cytosol was detected by ratiometric fluorescence analysis of pHluorin2 fused to G3BP1. Cells expressing a Caprin-1/FGDF chimera with higher G3BP1-binding affinity had reduced Caprin-1 levels and slightly reduced condensate sizes. This unexpected finding may suggest that binding of the USP10-derived SLiM to NTF2 reduces the propensity of G3BP1 to enter condensates.
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| 10. |
- Simonetti, Leandro, et al.
(författare)
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SLiM-binding pockets : an attractive target for broad-spectrum antivirals
- 2023
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Ingår i: TIBS -Trends in Biochemical Sciences. Regular ed.. - : Elsevier. - 0968-0004 .- 1362-4326. ; 48:5, s. 420-427
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Forskningsöversikt (refereegranskat)abstract
- Short linear motif (SLiM)-mediated interactions offer a unique strategy for viral intervention due to their compact interfaces, ease of convergent evolution, and key functional roles. Consequently, many viruses extensively mimic host SLiMs to hijack or deregulate cellular pathways and the same motif-binding pocket is often targeted by numerous unrelated viruses. A toolkit of therapeutics targeting commonly mimicked SLiMs could provide prophylactic and therapeutic broadspectrum antivirals and vastly improve our ability to treat ongoing and future viral outbreaks. In this opinion article, we discuss the therapeutic relevance of SLiMs, advocating their suitability as targets for broad-spectrum antiviral inhibitors.
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