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Willekens, S. M. A., Morini, F., Mediavilla, T., Nilsson, E., Orädd, G., Hahn, M., . . . Marcellino, D. (2024). An MR-based brain template and atlas for optical projection tomography and light sheet fluorescence microscopy in neuroscience. Frontiers in Neuroscience, 18, Article ID 1328815.
Open this publication in new window or tab >>An MR-based brain template and atlas for optical projection tomography and light sheet fluorescence microscopy in neuroscience
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2024 (English)In: Frontiers in Neuroscience, ISSN 1662-4548, E-ISSN 1662-453X, Vol. 18, article id 1328815Article in journal (Refereed) Published
Abstract [en]

Introduction: Optical Projection Tomography (OPT) and light sheet fluorescence microscopy (LSFM) are high resolution optical imaging techniques, ideally suited for ex vivo 3D whole mouse brain imaging. Although they exhibit high specificity for their targets, the anatomical detail provided by tissue autofluorescence remains limited.

Methods: T1-weighted images were acquired from 19 BABB or DBE cleared brains to create an MR template using serial longitudinal registration. Afterwards, fluorescent OPT and LSFM images were coregistered/normalized to the MR template to create fusion images.

Results: Volumetric calculations revealed a significant difference between BABB and DBE cleared brains, leading to develop two optimized templates, with associated tissue priors and brain atlas, for BABB (OCUM) and DBE (iOCUM). By creating fusion images, we identified virus infected brain regions, mapped dopamine transporter and translocator protein expression, and traced innervation from the eye along the optic tract to the thalamus and superior colliculus using cholera toxin B. Fusion images allowed for precise anatomical identification of fluorescent signal in the detailed anatomical context provided by MR.

Discussion: The possibility to anatomically map fluorescent signals on magnetic resonance (MR) images, widely used in clinical and preclinical neuroscience, would greatly benefit applications of optical imaging of mouse brain. These specific MR templates for cleared brains enable a broad range of neuroscientific applications integrating 3D optical brain imaging.

Place, publisher, year, edition, pages
Frontiers Media S.A., 2024
Keywords
brain template, LSFM, mesoscopic imaging, MRI, neuroimaging, OPT
National Category
Neurosciences Radiology, Nuclear Medicine and Medical Imaging
Identifiers
urn:nbn:se:umu:diva-223641 (URN)10.3389/fnins.2024.1328815 (DOI)001198866200001 ()38601090 (PubMedID)2-s2.0-85189910322 (Scopus ID)
Funder
The Kempe FoundationsSwedish Research Council, 2020-06224Swedish Research Council, 2018-05851Swedish Research Council, 2020-02300Novo Nordisk FoundationFamiljen Erling-Perssons Stiftelse
Available from: 2024-04-24 Created: 2024-04-24 Last updated: 2024-04-24Bibliographically approved
Garvanska, D. H., Alvarado, R. E., Mundt, F. O., Lindquist, R., Duel, J. K., Coscia, F., . . . Nilsson, J. (2024). The NSP3 protein of SARS-CoV-2 binds fragile X mental retardation proteins to disrupt UBAP2L interactions. EMBO Reports, 25(2), 902-926
Open this publication in new window or tab >>The NSP3 protein of SARS-CoV-2 binds fragile X mental retardation proteins to disrupt UBAP2L interactions
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2024 (English)In: EMBO Reports, ISSN 1469-221X, E-ISSN 1469-3178, Vol. 25, no 2, p. 902-926Article in journal (Refereed) Published
Abstract [en]

Viruses interact with numerous host factors to facilitate viral replication and to dampen antiviral defense mechanisms. We currently have a limited mechanistic understanding of how SARS-CoV-2 binds host factors and the functional role of these interactions. Here, we uncover a novel interaction between the viral NSP3 protein and the fragile X mental retardation proteins (FMRPs: FMR1, FXR1-2). SARS-CoV-2 NSP3 mutant viruses preventing FMRP binding have attenuated replication in vitro and reduced levels of viral antigen in lungs during the early stages of infection. We show that a unique peptide motif in NSP3 binds directly to the two central KH domains of FMRPs and that this interaction is disrupted by the I304N mutation found in a patient with fragile X syndrome. NSP3 binding to FMRPs disrupts their interaction with the stress granule component UBAP2L through direct competition with a peptide motif in UBAP2L to prevent FMRP incorporation into stress granules. Collectively, our results provide novel insight into how SARS-CoV-2 hijacks host cell proteins and provides molecular insight into the possible underlying molecular defects in fragile X syndrome.

Place, publisher, year, edition, pages
Springer Nature, 2024
Keywords
Fragile X Syndrome, NSP3, SARS-CoV-2, Stress Granules, UBAP2L
National Category
Infectious Medicine Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-221660 (URN)10.1038/s44319-023-00043-z (DOI)38177924 (PubMedID)2-s2.0-85185482825 (Scopus ID)
Funder
Swedish Research Council, 2018-05851
Available from: 2024-03-04 Created: 2024-03-04 Last updated: 2024-03-04Bibliographically approved
Wigren, J., Vikström, L., Rosendal, E., Gröning, R., Gwon, Y.-D., Nilsson, E., . . . Forsell, M. N. E. (2023). At-home sampling to meet geographical challenges for serological assessment of SARS-CoV-2 exposure in a rural region of northern Sweden, March to May 2021: a retrospective cohort study. Eurosurveillance, 28(13), Article ID 2200432.
Open this publication in new window or tab >>At-home sampling to meet geographical challenges for serological assessment of SARS-CoV-2 exposure in a rural region of northern Sweden, March to May 2021: a retrospective cohort study
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2023 (English)In: Eurosurveillance, ISSN 1025-496X, E-ISSN 1560-7917, Vol. 28, no 13, article id 2200432Article in journal (Refereed) Published
Abstract [en]

Background: The current SARS-CoV-2 pandemic has highlighted a need for easy and safe blood sampling in combination with accurate serological methodology. Venipuncture for testing is usually performed by trained staff at healthcare centres. Long travel distances to healthcare centres in rural regions may introduce a bias of testing towards relatively large communities with closer access. Rural regions are therefore often not represented in population-based data.

Aim: The aim of this retrospective cohort study was to develop and implement a strategy for at-home testing in a rural region of Sweden during spring 2021, and to evaluate its role to provide equal health care for its inhabitants.

Methods: We developed a sensitive method to measure antibodies to the S-protein of SARS-CoV-2 and optimised this assay for clinical use together with a strategy of at-home capillary blood sampling.

Results: We demonstrated that our ELISA gave comparable results after analysis of capillary blood or serum from SARS-CoV-2-experienced individuals. We demonstrated stability of the assay under conditions that reflected temperature and humidity during winter or summer. By assessment of capillary blood samples from 4,122 individuals, we could show both feasibility of the strategy and that implementation shifted the geographical spread of testing in favour of rural areas.

Conclusion: Implementation of at-home sampling enabled citizens living in remote rural areas access to centralised and sensitive laboratory antibody tests. The strategy for testing used here could therefore enable disease control authorities to get rapid access to information concerning immunity to infectious diseases, even across vast geographical distance.

Place, publisher, year, edition, pages
European Centre for Disease Control and Prevention (ECDC), 2023
Keywords
coronavirus disease (COVID-19), laboratory, surveillance, Sweden
National Category
Infectious Medicine Microbiology in the medical area
Identifiers
urn:nbn:se:umu:diva-206673 (URN)10.2807/1560-7917.ES.2023.28.13.2200432 (DOI)000971868200003 ()36995373 (PubMedID)2-s2.0-85151573640 (Scopus ID)
Available from: 2023-04-14 Created: 2023-04-14 Last updated: 2023-09-05Bibliographically approved
Mihalič, F., Benz, C., Kassa, E., Lindquist, R., Simonetti, L., Inturi, R., . . . Ivarsson, Y. (2023). Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets. Nature Communications, 14(1), Article ID 5636.
Open this publication in new window or tab >>Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets
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2023 (English)In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 5636Article in journal (Refereed) Published
Abstract [en]

The virus life cycle depends on host-virus protein-protein interactions, which often involve a disordered protein region binding to a folded protein domain. Here, we used proteomic peptide phage display (ProP-PD) to identify peptides from the intrinsically disordered regions of the human proteome that bind to folded protein domains encoded by the SARS-CoV-2 genome. Eleven folded domains of SARS-CoV-2 proteins were found to bind 281 peptides from human proteins, and affinities of 31 interactions involving eight SARS-CoV-2 protein domains were determined (K D ∼ 7-300 μM). Key specificity residues of the peptides were established for six of the interactions. Two of the peptides, binding Nsp9 and Nsp16, respectively, inhibited viral replication. Our findings demonstrate how high-throughput peptide binding screens simultaneously identify potential host-virus interactions and peptides with antiviral properties. Furthermore, the high number of low-affinity interactions suggest that overexpression of viral proteins during infection may perturb multiple cellular pathways.

Place, publisher, year, edition, pages
Nature Publishing Group, 2023
National Category
Infectious Medicine
Identifiers
urn:nbn:se:umu:diva-214614 (URN)10.1038/s41467-023-41312-8 (DOI)37704626 (PubMedID)2-s2.0-85171182010 (Scopus ID)
Funder
Swedish Foundation for Strategic Research, SB16-0039Swedish Research Council, 2020-03380Swedish Research Council, 2020-04395Swedish Research Council, 2018-05851Knut and Alice Wallenberg Foundation, KAW 2020.0241Knut and Alice Wallenberg Foundation, V-2020-0699
Available from: 2023-09-27 Created: 2023-09-27 Last updated: 2023-09-27Bibliographically approved
Mihalič, F., Simonetti, L., Giudice, G., Sander, M. R., Lindquist, R., Peters, M. B., . . . Ivarsson, Y. (2023). Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs. Nature Communications, 14(1), Article ID 2409.
Open this publication in new window or tab >>Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs
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2023 (English)In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 2409Article in journal (Refereed) Published
Abstract [en]

Viruses mimic host short linear motifs (SLiMs) to hijack and deregulate cellular functions. Studies of motif-mediated interactions therefore provide insight into virus-host dependencies, and reveal targets for therapeutic intervention. Here, we describe the pan-viral discovery of 1712 SLiM-based virus-host interactions using a phage peptidome tiling the intrinsically disordered protein regions of 229 RNA viruses. We find mimicry of host SLiMs to be a ubiquitous viral strategy, reveal novel host proteins hijacked by viruses, and identify cellular pathways frequently deregulated by viral motif mimicry. Using structural and biophysical analyses, we show that viral mimicry-based interactions have similar binding strength and bound conformations as endogenous interactions. Finally, we establish polyadenylate-binding protein 1 as a potential target for broad-spectrum antiviral agent development. Our platform enables rapid discovery of mechanisms of viral interference and the identification of potential therapeutic targets which can aid in combating future epidemics and pandemics.

Place, publisher, year, edition, pages
Springer Nature, 2023
National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:umu:diva-208216 (URN)10.1038/s41467-023-38015-5 (DOI)000979744000013 ()37100772 (PubMedID)2-s2.0-85153911486 (Scopus ID)
Funder
Swedish Research Council, 2018-05851Swedish Research Council, 2020-03380Swedish Research Council, 2020-04395Knut and Alice Wallenberg Foundation, 2020.0182Swedish Foundation for Strategic Research, SB16-0039
Available from: 2023-05-12 Created: 2023-05-12 Last updated: 2023-09-05Bibliographically approved
Pulkkinen, L. I., Barrass, S. V., Lindgren, M., Pace, H., Överby, A. K., Anastasina, M., . . . Butcher, S. J. (2023). Simultaneous membrane and RNA binding by tick-borne encephalitis virus capsid protein. PLoS Pathogens, 19(2), Article ID e1011125.
Open this publication in new window or tab >>Simultaneous membrane and RNA binding by tick-borne encephalitis virus capsid protein
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2023 (English)In: PLoS Pathogens, ISSN 1553-7366, E-ISSN 1553-7374, Vol. 19, no 2, article id e1011125Article in journal (Refereed) Published
Abstract [en]

Tick-borne encephalitis virus is an enveloped, pathogenic, RNA virus in the family Flaviviridae, genus Flavivirus. Viral particles are formed when the nucleocapsid, consisting of an RNA genome and multiple copies of the capsid protein, buds through the endoplasmic reticulum membrane and acquires the viral envelope and the associated proteins. The coordination of the nucleocapsid components to the sites of assembly and budding are poorly understood. Here, we investigate the interactions of the wild-type and truncated capsid proteins with membranes with biophysical methods and model membrane systems. We show that capsid protein initially binds membranes via electrostatic interactions with negatively-charged lipids, which is followed by membrane insertion. Additionally, we show that membrane-bound capsid protein can recruit viral genomic RNA. We confirm the biological relevance of the biophysical findings by using mass spectrometry to show that purified virions contain negatively-charged lipids. Our results suggest that nucleocapsid assembly is coordinated by negatively-charged membrane patches on the endoplasmic reticulum and that the capsid protein mediates direct contacts between the nucleocapsid and the membrane.

Place, publisher, year, edition, pages
Public Library of Science, 2023
National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:umu:diva-205497 (URN)10.1371/journal.ppat.1011125 (DOI)000966733300001 ()36787339 (PubMedID)2-s2.0-85149054055 (Scopus ID)
Available from: 2023-03-14 Created: 2023-03-14 Last updated: 2023-09-05Bibliographically approved
Chotiwan, N., Rosendal, E., Willekens, S. M. A., Schexnaydre, E., Nilsson, E., Lindquist, R., . . . Överby, A. K. (2023). Type I interferon shapes brain distribution and tropism of tick-borne flavivirus. Nature Communications, 14(1), Article ID 2007.
Open this publication in new window or tab >>Type I interferon shapes brain distribution and tropism of tick-borne flavivirus
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2023 (English)In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 2007Article in journal (Refereed) Published
Abstract [en]

Viral tropism within the brain and the role(s) of vertebrate immune response to neurotropic flaviviruses infection is largely understudied. We combine multimodal imaging (cm-nm scale) with single nuclei RNA-sequencing to study Langat virus in wildtype and interferon alpha/beta receptor knockout (Ifnar-/-) mice to visualize viral pathogenesis and define molecular mechanisms. Whole brain viral infection is imaged by Optical Projection Tomography coregistered to ex vivo MRI. Infection is limited to grey matter of sensory systems in wildtype mice, but extends into white matter, meninges and choroid plexus in Ifnar-/- mice. Cells in wildtype display strong type I and II IFN responses, likely due to Ifnb expressing astrocytes, infiltration of macrophages and Ifng-expressing CD8+ NK cells, whereas in Ifnar-/-, the absence of this response contributes to a shift in cellular tropism towards non-activated resident microglia. Multimodal imaging-transcriptomics exemplifies a powerful way to characterize mechanisms of viral pathogenesis and tropism.

Place, publisher, year, edition, pages
Springer Nature, 2023
National Category
Microbiology in the medical area Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy) Neurosciences
Identifiers
urn:nbn:se:umu:diva-206780 (URN)10.1038/s41467-023-37698-0 (DOI)000967732600009 ()37037810 (PubMedID)2-s2.0-85152115180 (Scopus ID)
Funder
The Kempe Foundations, SMK-1532Knut and Alice Wallenberg Foundation, KAW2015.0284Swedish Research Council, 2018-05851Swedish Research Council, 2017-01307Swedish Research Council, 2020-06224Swedish Research Council, 2021-06602
Available from: 2023-04-24 Created: 2023-04-24 Last updated: 2023-09-05Bibliographically approved
Welén, K., Rosendal, E., Gisslén, M., Lenman, A., Freyhult, E., Fonseca Rodriguez, O., . . . Josefsson, A. (2022). A Phase 2 Trial of the Effect of Antiandrogen Therapy on COVID-19 Outcome: No Evidence of Benefit, Supported by Epidemiology and In Vitro Data. European Urology, 81(3), 285-293
Open this publication in new window or tab >>A Phase 2 Trial of the Effect of Antiandrogen Therapy on COVID-19 Outcome: No Evidence of Benefit, Supported by Epidemiology and In Vitro Data
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2022 (English)In: European Urology, ISSN 0302-2838, E-ISSN 1873-7560, Vol. 81, no 3, p. 285-293Article in journal (Refereed) Published
Abstract [en]

Background: Men are more severely affected by COVID-19. Testosterone may influence SARS-CoV-2 infection and the immune response.

Objective: To clinically, epidemiologically, and experimentally evaluate the effect of antiandrogens on SARS-CoV-2 infection.

Designs, settings, and participants: A randomized phase 2 clinical trial (COVIDENZA) enrolled 42 hospitalized COVID-19 patients before safety evaluation. We also conducted a population-based retrospective study of 7894 SARS-CoV-2–positive prostate cancer patients and an experimental study using an air-liquid interface three-dimensional culture model of primary lung cells.

Intervention: In COVIDENZA, patients were randomized 2:1 to 5 d of enzalutamide or standard of care.

Outcome measurements: The primary outcomes in COVIDENZA were the time to mechanical ventilation or discharge from hospital. The population-based study investigated risk of hospitalization, intensive care, and death from COVID-19 after androgen inhibition.

Results and limitations: Enzalutamide-treated patients required longer hospitalization (hazard ratio [HR] for discharge from hospital 0.43, 95% confidence interval [CI] 0.20–0.93) and the trial was terminated early. In the epidemiological study, no preventive effects were observed. The frail population of patients treated with androgen deprivation therapy (ADT) in combination with abiraterone acetate or enzalutamide had a higher risk of dying from COVID-19 (HR 2.51, 95% CI 1.52–4.16). In vitro data showed no effect of enzalutamide on virus replication. The epidemiological study has limitations that include residual confounders.

Conclusions: The results do not support a therapeutic effect of enzalutamide or preventive effects of bicalutamide or ADT in COVID-19. Thus, these antiandrogens should not be used for hospitalized COVID-19 patients or as prevention for COVID-19. Further research on these therapeutics in this setting are not warranted.

Patient summary: We studied whether inhibition of testosterone could diminish COVID-19 symptoms. We found no evidence of an effect in a clinical study or in epidemiological or experimental investigations. We conclude that androgen inhibition should not be used for prevention or treatment of COVID-19.

Place, publisher, year, edition, pages
Elsevier, 2022
Keywords
COVID-19, SARS-CoV-2, Antiandrogen, Randomized trial, Enzalutamide, Bicalutamide, Androgen deprivation therapy
National Category
Cancer and Oncology Public Health, Global Health, Social Medicine and Epidemiology Urology and Nephrology Infectious Medicine
Identifiers
urn:nbn:se:umu:diva-190911 (URN)10.1016/j.eururo.2021.12.013 (DOI)000809752100020 ()2-s2.0-85122412349 (Scopus ID)
Funder
Knut and Alice Wallenberg Foundation, 2020.0182ProstatacancerförbundetSwedish Cancer Society, 2017/478Swedish Cancer Society, 20 1055 PjFSwedish Heart Lung Foundation, 20200385Region Västerbotten, RV-836351Region Västerbotten, RV-939769
Available from: 2022-01-02 Created: 2022-01-02 Last updated: 2023-04-25Bibliographically approved
Lindquist, R., Benz, C., Sereikaite, V., Maassen, L., Laursen, L., Jemth, P., . . . Överby, A. K. (2022). A syntenin inhibitor blocks endosomal entry of SARS-CoV-2 and a panel of RNA viruses. Viruses, 14(10), Article ID 2202.
Open this publication in new window or tab >>A syntenin inhibitor blocks endosomal entry of SARS-CoV-2 and a panel of RNA viruses
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2022 (English)In: Viruses, E-ISSN 1999-4915, Vol. 14, no 10, article id 2202Article in journal (Refereed) Published
Abstract [en]

Viruses are dependent on host factors in order to efficiently establish an infection and replicate. Targeting the interactions of such host factors provides an attractive strategy to develop novel antivirals. Syntenin is a protein known to regulate the architecture of cellular membranes by its involvement in protein trafficking and has previously been shown to be important for human papilloma virus (HPV) infection. Here, we show that a highly potent and metabolically stable peptide inhibitor that binds to the PDZ1 domain of syntenin inhibits severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection by blocking the endosomal entry of the virus. Furthermore, we found that the inhibitor also hampered chikungunya infection and strongly reduced flavivirus infection, which is completely dependent on receptor-mediated endocytosis for their entry. In conclusion, we have identified a novel broad spectrum antiviral inhibitor that efficiently targets a broad range of RNA viruses.

Place, publisher, year, edition, pages
MDPI, 2022
Keywords
CHIKV, flavivirus, peptide inhibitor, SARS-CoV-2, syntenin
National Category
Infectious Medicine Microbiology in the medical area
Identifiers
urn:nbn:se:umu:diva-200890 (URN)10.3390/v14102202 (DOI)000873879700001 ()36298757 (PubMedID)2-s2.0-85140802544 (Scopus ID)
Available from: 2022-11-09 Created: 2022-11-09 Last updated: 2024-01-17Bibliographically approved
Ljungquist, O., Lundgren, M., Iliachenko, E., Månsson, F., Böttiger, B., Landin-Olsson, M., . . . Holm, K. (2022). Convalescent plasma treatment in severely immunosuppressed patients hospitalized with COVID-19: an observational study of 28 cases. Infectious Diseases, 54(4), 283-291
Open this publication in new window or tab >>Convalescent plasma treatment in severely immunosuppressed patients hospitalized with COVID-19: an observational study of 28 cases
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2022 (English)In: Infectious Diseases, ISSN 2374-4235, E-ISSN 2374-4243, Vol. 54, no 4, p. 283-291Article in journal (Refereed) Published
Abstract [en]

Background: Immunosuppressed patients are particularly vulnerable to severe infection from the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), risking prolonged viremia and symptom duration. In this study we describe clinical and virological treatment outcomes in a heterogeneous group of patients with severe immunosuppression due to various causes suffering from COVID-19 infection, who were all treated with convalescent plasma (CCP) along with standard treatment.

Methods: We performed an observational, retrospective case series between May 2020 to March 2021 at three sites in Skåne, Sweden, with a population of nearly 1.4 million people. All patients hospitalized for COVID-19 who received CCP with the indication severe immunosuppression as defined by the treating physician were included in the study (n = 28).

Results: In total, 28 severely immunocompromised patients, half of which previously had been treated with rituximab, who had received in-hospital convalescent plasma treatment of COVID-19 were identified. One week after CCP treatment, 13 of 28 (46%) patients had improved clinically defined as a decrease of at least one point at the WHO-scale. Three patients had increased score points of whom two had died. For 12 patients, the WHO-scale was unchanged.

Conclusion: As one of only few studies on CCP treatment of COVID-19 in hospitalized patients with severe immunosuppression, this study adds descriptive data. The study design prohibits conclusions on safety and efficacy, and the results should be interpreted with caution. Prospective, randomized trials are needed to investigate this further.

Place, publisher, year, edition, pages
Taylor & Francis Group, 2022
Keywords
Antibodies, convalescent plasma, COVID-19, immunosuppression, lymphoma, pandemic, PCR, rituximab, SARS-CoV-2
National Category
Infectious Medicine
Identifiers
urn:nbn:se:umu:diva-190857 (URN)10.1080/23744235.2021.2013528 (DOI)000728648300001 ()34878955 (PubMedID)2-s2.0-85121359656 (Scopus ID)
Available from: 2021-12-29 Created: 2021-12-29 Last updated: 2023-04-25Bibliographically approved
Projects
Viperin vs. flaviviruses: mechanisms of a potent antiviral protein [2011-02795_VR]; Umeå UniversityAntiviral defense mechanisms in the portal to the brain [2017-02438_VR]; Umeå UniversityMultimodal imaging and proteomics to study flavivirus replication and molecular disease mechanisms [2018-05851_VR]; Umeå University
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0001-6553-0940

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