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Platen L, Liao BH, Tellenbach M, Cheng CC, Holzmann-Littig C, Christa C, Dächert C, Kappler V, Bester R, Werz ML, Schönhals E, Platen E, Eggerer P, Tréguer L, Küchle C, Schmaderer C, Heemann U, Keppler OT, Renders L, Braunisch MC, Protzer U. Longitudinal SARS-CoV-2 neutralization of Omicron BA.1, BA.5 and BQ.1.1 after four vaccinations and the impact of breakthrough infections in haemodialysis patients. Clin Kidney J 2023; 16:2447-2460. [PMID: 38046025 PMCID: PMC10689143 DOI: 10.1093/ckj/sfad147] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Indexed: 12/05/2023] Open
Abstract
Background Individuals on haemodialysis (HD) are more vulnerable to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection than the general population due to end-stage kidney disease-induced immunosuppression. Methods A total of 26 HD patients experiencing SARS-CoV-2 infection after a third vaccination were matched 1:1 with 26 of 92 SARS-CoV-2-naïve patients by age, sex, dialysis vintage and immunosuppressive drugs receiving a fourth vaccination with a messenger RNA-based vaccine. A competitive surrogate neutralization assay was used to monitor vaccination success. To determine infection neutralization titres, Vero-E6 cells were infected with SARS-CoV-2 variants of concern (VoCs), Omicron sublineage BA.1, BA.5 and BQ.1.1. The 50% inhibitory concentration (IC50, serum dilution factor 1:x) was determined before, 4 weeks after and 6 months after the fourth vaccination. Results A total of 52 HD patients received four coronavirus disease 2019 (COVID-19) vaccinations and were followed up for a median of 6.3 months. Patient characteristics did not differ between the matched cohorts. Patients without a SARS-CoV-2 infection had a significant reduction of real virus neutralization capacity for all Omicron sublineages after 6 months (P < .001 each). Those patients with a virus infection did not experience a reduction in real virus neutralization capacity after 6 months. Compared with the other Omicron VoC, the BQ.1.1 sublineage had the lowest virus neutralization capacity. Conclusions SARS-CoV-2-naïve HD patients had significantly decreased virus neutralization capacity 6 months after the fourth vaccination, whereas patients with a SARS-CoV-2 infection had no change in neutralization capacity. This was independent of age, sex, dialysis vintage and immunosuppression. Therefore, in infection-naïve HD patients a fifth COVID-19 vaccination might be reasonable 6 months after the fourth vaccination.
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Affiliation(s)
- Louise Platen
- Department of Nephrology, University Hospital rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Bo-Hung Liao
- Institute of Virology, Technical University of Munich, School of Medicine, Munich, Germany
| | - Myriam Tellenbach
- Department of Nephrology, University Hospital rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Cho-Chin Cheng
- Institute of Virology, Technical University of Munich, School of Medicine, Munich, Germany
| | - Christopher Holzmann-Littig
- Institute of Virology, Technical University of Munich, School of Medicine, Munich, Germany
- TUM Medical Education Center, Technical University of Munich, School of Medicine, Munich, Germany
| | - Catharina Christa
- Institute of Virology, Technical University of Munich, School of Medicine, Munich, Germany
| | - Christopher Dächert
- Max von Pettenkofer Institute & Gene Center, Virology, Ludwig Maximilian University of Munich, Munich, Germany
| | - Verena Kappler
- Department of Nephrology, University Hospital rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Romina Bester
- Institute of Virology, Technical University of Munich, School of Medicine, Munich, Germany
| | - Maia Lucia Werz
- Department of Nephrology, University Hospital rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Emely Schönhals
- Department of Nephrology, University Hospital rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Eva Platen
- Kidney Center Eifel Dialyse, Mechernich, Germany
| | - Peter Eggerer
- KfH Kidney Center Harlaching, Munich-Harlaching, Germany
| | - Laëtitia Tréguer
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
| | - Claudius Küchle
- Department of Nephrology, University Hospital rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Christoph Schmaderer
- Department of Nephrology, University Hospital rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Uwe Heemann
- Department of Nephrology, University Hospital rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
| | - Oliver T Keppler
- Max von Pettenkofer Institute & Gene Center, Virology, Ludwig Maximilian University of Munich, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
| | - Lutz Renders
- Department of Nephrology, University Hospital rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
- KfH Kidney Center, Traunstein, Germany
| | - Matthias Christoph Braunisch
- Department of Nephrology, University Hospital rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Ulrike Protzer
- Institute of Virology, Technical University of Munich, School of Medicine, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
- Institute of Virology, Helmholtz Munich, Munich, Germany
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2
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Zaderer V, Abd El Halim H, Wyremblewsky AL, Lupoli G, Dächert C, Muenchhoff M, Graf A, Blum H, Lass-Flörl C, Keppler OT, Huber LA, Posch W, Wilflingseder D. Omicron subvariants illustrate reduced respiratory tissue penetration, cell damage and inflammatory responses in human airway epithelia. Front Immunol 2023; 14:1258268. [PMID: 37915577 PMCID: PMC10616953 DOI: 10.3389/fimmu.2023.1258268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/02/2023] [Indexed: 11/03/2023] Open
Abstract
Introduction To explore whether the reported lower pathogenicity in infected individuals of variant of concern (VoC) Omicron and its current subvariants compared to VoC Delta may be related to fundamental differences in the initial virus-tissue interaction, we assessed their ability to penetrate, replicate and cause damage in a human 3D respiratory model. Methods For this, we used TEER measurements, real-time PCR, LDH, cytokine and complex confocal imaging analyses. Results and discussion We observed that Delta readily penetrated deep into the respiratory epithelium and this was associated with major tissue destruction, high LDH activity, high viral loads and pronounced innate immune activation as observed by intrinsic C3 activation and IL-6 release at infection sites. In contrast, Omicron subvariants BA.5, BQ.1.1 and BF7 remained superficially in the mucosal layer resulting merely in outward-directed destruction of cells, maintenance of epithelial integrity, minimal LDH activity and low basolateral release of virus at infection sites, as well as significantly smaller areas of complement activation and lower IL-6 secretion. Interestingly, also within Omicron subvariants differences were observed with newer Omicron subvariants BQ.1.1 and BF.7 illustrating significantly reduced viral loads, IL-6 release and LDH activity compared to BA.5. Our data indicate that earliest interaction events after SARS-CoV-2 transmission may have a role in shaping disease severity.
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Affiliation(s)
- Viktoria Zaderer
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Hussam Abd El Halim
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Anna-Lena Wyremblewsky
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Gaia Lupoli
- Virology, Max von Pettenkofer Institute and Gene Center, Ludwig-Maximilians-Universität (LMU), Munich, Germany
| | - Christopher Dächert
- Virology, Max von Pettenkofer Institute and Gene Center, Ludwig-Maximilians-Universität (LMU), Munich, Germany
| | - Maximilian Muenchhoff
- Virology, Max von Pettenkofer Institute and Gene Center, Ludwig-Maximilians-Universität (LMU), Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians-Universität (LMU), Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians-Universität (LMU), Munich, Germany
| | - Cornelia Lass-Flörl
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Oliver T. Keppler
- Virology, Max von Pettenkofer Institute and Gene Center, Ludwig-Maximilians-Universität (LMU), Munich, Germany
| | - Lukas A. Huber
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
- ADSI - Austrian Drug Screening Institute GmbH, Innsbruck, Austria
| | - Wilfried Posch
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Doris Wilflingseder
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
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3
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Osterman A, Krenn F, Iglhaut M, Badell I, Lehner A, Späth PM, Stern M, Both H, Bender S, Muenchhoff M, Graf A, Krebs S, Blum H, Grimmer T, Durner J, Czibere L, Dächert C, Grzimek-Koschewa N, Protzer U, Kaderali L, Baldauf HM, Keppler OT. Automated antigen assays display a high heterogeneity for the detection of SARS-CoV-2 variants of concern, including several Omicron sublineages. Med Microbiol Immunol 2023; 212:307-322. [PMID: 37561226 PMCID: PMC10501957 DOI: 10.1007/s00430-023-00774-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 07/11/2023] [Indexed: 08/11/2023]
Abstract
Diagnostic tests for direct pathogen detection have been instrumental to contain the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) pandemic. Automated, quantitative, laboratory-based nucleocapsid antigen (Ag) tests for SARS-CoV-2 have been launched alongside nucleic acid-based test systems and point-of-care (POC) lateral-flow Ag tests. Here, we evaluated four commercial Ag tests on automated platforms for the detection of different sublineages of the SARS-CoV-2 Omicron variant of concern (VoC) (B.1.1.529) in comparison with "non-Omicron" VoCs. A total of 203 Omicron PCR-positive respiratory swabs (53 BA.1, 48 BA.2, 23 BQ.1, 39 XBB.1.5 and 40 other subvariants) from the period February to March 2022 and from March 2023 were examined. In addition, tissue culture-expanded clinical isolates of Delta (B.1.617.2), Omicron-BA.1, -BF.7, -BN.1 and -BQ.1 were studied. These results were compared to previously reported data from 107 clinical "non-Omicron" samples from the end of the second pandemic wave (February to March 2021) as well as cell culture-derived samples of wildtype (wt) EU-1 (B.1.177), Alpha VoC (B.1.1.7) and Beta VoC (B.1.351)). All four commercial Ag tests were able to detect at least 90.9% of Omicron-containing samples with high viral loads (Ct < 25). The rates of true-positive test results for BA.1/BA.2-positive samples with intermediate viral loads (Ct 25-30) ranged between 6.7% and 100.0%, while they dropped to 0 to 15.4% for samples with low Ct values (> 30). This heterogeneity was reflected also by the tests' 50%-limit of detection (LoD50) values ranging from 44,444 to 1,866,900 Geq/ml. Respiratory samples containing Omicron-BQ.1/XBB.1.5 or other Omicron subvariants that emerged in 2023 were detected with enormous heterogeneity (0 to 100%) for the intermediate and low viral load ranges with LoD50 values between 23,019 and 1,152,048 Geq/ml. In contrast, detection of "non-Omicron" samples was more sensitive, scoring positive in 35 to 100% for the intermediate and 1.3 to 32.9% of cases for the low viral loads, respectively, corresponding to LoD50 values ranging from 6181 to 749,792 Geq/ml. All four assays detected cell culture-expanded VoCs Alpha, Beta, Delta and Omicron subvariants carrying up to six amino acid mutations in the nucleocapsid protein with sensitivities comparable to the non-VoC EU-1. Overall, automated quantitative SARS-CoV-2 Ag assays are not more sensitive than standard rapid antigen tests used in POC settings and show a high heterogeneity in performance for VoC recognition. The best of these automated Ag tests may have the potential to complement nucleic acid-based assays for SARS-CoV-2 diagnostics in settings not primarily focused on the protection of vulnerable groups. In light of the constant emergence of new Omicron subvariants and recombinants, most recently the XBB lineage, these tests' performance must be regularly re-evaluated, especially when new VoCs carry mutations in the nucleocapsid protein or immunological and clinical parameters change.
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Affiliation(s)
- Andreas Osterman
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Franziska Krenn
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Maximilian Iglhaut
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Irina Badell
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Andreas Lehner
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Patricia M Späth
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Marcel Stern
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Hanna Both
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Sabine Bender
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Maximilian Muenchhoff
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
- COVID‑19 Registry of the LMU Munich (CORKUM), University Hospital, LMU München, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Timo Grimmer
- Department of Psychiatry and Psychotherapy, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Jürgen Durner
- Labor Becker MVZ GbR, Munich, Germany
- Department of Conservative Dentistry and Periodontology, University Hospital, LMU München, Munich, Germany
| | | | - Christopher Dächert
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Natascha Grzimek-Koschewa
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
| | - Ulrike Protzer
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum München, Munich, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Hanna-Mari Baldauf
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.
| | - Oliver T Keppler
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany.
- COVID‑19 Registry of the LMU Munich (CORKUM), University Hospital, LMU München, Munich, Germany.
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4
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Krenn F, Dächert C, Badell I, Lupoli G, Öztan GN, Feng T, Schneider N, Huber M, Both H, Späth PM, Muenchhoff M, Graf A, Krebs S, Blum H, Durner J, Czibere L, Kaderali L, Keppler OT, Baldauf HM, Osterman A. Ten rapid antigen tests for SARS-CoV-2 widely differ in their ability to detect Omicron-BA.4 and -BA.5. Med Microbiol Immunol 2023; 212:323-337. [PMID: 37561225 PMCID: PMC10501931 DOI: 10.1007/s00430-023-00775-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 07/11/2023] [Indexed: 08/11/2023]
Abstract
Since late 2021, the variant landscape of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been dominated by the variant of concern (VoC) Omicron and its sublineages. We and others have shown that the detection of Omicron-BA.1 and -BA.2-positive respiratory specimens by rapid antigen tests (RATs) is impaired compared to Delta VoC-containing samples. Here, in a single-center retrospective laboratory study, we evaluated the performance of ten most commonly used RATs for the detection of Omicron-BA.4 and -BA.5 infections. We used 171 respiratory swab specimens from SARS-CoV-2 RNA-positive patients, of which 71 were classified as BA.4 and 100 as BA.5. All swabs were collected between July and September 2022. 50 SARS-CoV-2 PCR-negative samples from healthy individuals, collected in October 2022, showed high specificity in 9 out of 10 RATs. When assessing analytical sensitivity using clinical specimens, the 50% limit of detection (LoD50) ranged from 7.6 × 104 to 3.3 × 106 RNA copies subjected to the RATs for BA.4 compared to 6.8 × 104 to 3.0 × 106 for BA.5. Overall, intra-assay differences for the detection of these two Omicron subvariants were not significant for both respiratory swabs and tissue culture-expanded virus isolates. In contrast, marked heterogeneity was observed among the ten RATs: to be positive in these point-of-care tests, up to 443-fold (BA.4) and up to 56-fold (BA.5) higher viral loads were required for the worst performing RAT compared to the best performing RAT. True-positive rates for Omicron-BA.4- or -BA.5-containing specimens in the highest viral load category (Ct values < 25) ranged from 94.3 to 34.3%, dropping to 25.6 to 0% for samples with intermediate Ct values (25-30). We conclude that the high heterogeneity in the performance of commonly used RATs remains a challenge for the general public to obtain reliable results in the evolving Omicron subvariant-driven pandemic.
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Affiliation(s)
- Franziska Krenn
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Christopher Dächert
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
| | - Irina Badell
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Gaia Lupoli
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Gamze Naz Öztan
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Tianle Feng
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Nikolas Schneider
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Melanie Huber
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Hanna Both
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Patricia M. Späth
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Maximilian Muenchhoff
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU München, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | | | | | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Oliver T. Keppler
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU München, Munich, Germany
| | - Hanna-Mari Baldauf
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Andreas Osterman
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
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5
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Diem G, Dichtl S, Zaderer V, Lass-Flörl C, Reindl M, Lupoli G, Dächert C, Muenchhoff M, Graf A, Blum H, Keppler OT, Wilflingseder D, Posch W. Salivary antibodies induced by BA.4/BA.5-convalescence or bivalent booster Immunoglobulin vaccination protect against novel SARS-COV-2 variants of concern. Microbiol Spectr 2023; 11:e0179323. [PMID: 37551989 PMCID: PMC10581068 DOI: 10.1128/spectrum.01793-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/28/2023] [Indexed: 08/09/2023] Open
Abstract
Currently, SARS-CoV-2 Omicron BA.5 subvariants BF.7 and BQ.1.1 are rapidly emerging worldwide. To evaluate the SARS-CoV-2-neutralizing capacity of sera and saliva from triple vaccinated individuals, either boosted with an adapted bivalent COVID-19 vaccine or recovered from BA.4/BA.5 infection, we analyzed the sensitivity of replication-competent SARS-CoV-2 Omicron subvariants BA.4/5, BQ.1.1 and BF.7 to neutralization. Analysis of SARS-CoV-2-specific IgGs and IgAs showed increased serum IgG titers in the vaccinated group, while the serum and salivary IgA levels were comparable. Similar and efficient serum neutralization against the ancestral strain of SARS-CoV-2 and Omicron BA.4/BA.5 was detected in both cohorts, but critically reduced for BQ.1.1 and BF.7. In contrast, salivary neutralization against BA.4/BA.5 was increased in the convalescent compared to the vaccinated group, while salivary neutralizing capacity against BQ.1.1 and BF.7 was comparable in these groups. Further, personalized protective effects studied in a human 3D respiratory model revealed the importance of salivary protection against different Omicron subvariants. IMPORTANCE In BA.4/BA.5-convalescent versus vaccinated groups, salivary neutralization capacity increased against SARS-CoV-2 Omicron BA.4/BA.5. In contrast, it neutralized novel Omicron subvariants BQ.1.1 and BF.7 similarly. Salivary protection against various Omicron subvariants was even more evident when tested in a personalized approach using highly differentiated respiratory human 3D models.
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Affiliation(s)
- Gabriel Diem
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Stefanie Dichtl
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Viktoria Zaderer
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Cornelia Lass-Flörl
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Markus Reindl
- Clinical Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Gaia Lupoli
- Max von Pettenkofer Institute and Gene Center, Virology, LMU München, Munich, Germany
| | - Christopher Dächert
- Max von Pettenkofer Institute and Gene Center, Virology, LMU München, Munich, Germany
| | - Maximilian Muenchhoff
- Max von Pettenkofer Institute and Gene Center, Virology, LMU München, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Oliver T. Keppler
- Max von Pettenkofer Institute and Gene Center, Virology, LMU München, Munich, Germany
| | - Doris Wilflingseder
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Wilfried Posch
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
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6
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Dichtl S, Diem G, Jäger M, Zaderer V, Lupoli G, Dächert C, Muenchhoff M, Graf A, Blum H, Keppler OT, Lass-Flörl C, Weiss G, Wilflingseder D, Posch W. Antiviral drugs block replication of highly immune-evasive Omicron subvariants ex vivo, but fail to reduce tissue inflammation. Antiviral Res 2023; 213:105581. [PMID: 36965526 PMCID: PMC10033493 DOI: 10.1016/j.antiviral.2023.105581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 02/20/2023] [Accepted: 03/15/2023] [Indexed: 03/25/2023]
Abstract
The identification of the SARS-CoV-2 Omicron variants BA.4/BA.5, BF.7 and BQ.1.1 immediately raised concerns regarding the efficacy of currently used monoclonal antibody therapies. Here we examined the activity of monoclonal antibody therapies and antiviral drugs against clinical specimens for SARS-CoV-2 Omicron BA.4/BA.5, BF.7 and BQ.1.1 employing an immunofluorescence neutralization assay. Further we explored treatment of BA.4/BA.5 infections with efficient antiviral drugs and monoclonal antibodies in a 3D model of primary human bronchial epithelial cells. We found that the antiviral drugs Molnupiravir, Nirmatrelvir and Remdesivir efficiently inhibit BA.4/BA.5, BF.7 and BQ.1.1 replication. In contrast, only the monoclonal antibody Cilgavimab exerted an inhibitory effect, while Tixagevimab, Regdanvimab and Sotrovimab lost their efficacy against BA.4/BA.5. We found that only the prophylactic treatment with Cilgavimab impacted on tissue inflammation by reducing intracellular complement component 3 (C3) activation following BA.4/BA.5 infection in primary human airway epithelial grown in air-liquid-interphase, which was not the case when using antiviral drugs or Cilgavimab after establishment of infection. Of note, all tested monoclonal antibodies had no neutralizing activity during infection by BF.7 and BQ.1.1 variants. Our results suggest that despite a marked reduction of viral replication, potent antiviral drugs fail to reduce tissue levels of inflammatory compounds such as C3, which can still result in tissue destruction.
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Affiliation(s)
- Stefanie Dichtl
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Gabriel Diem
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Michael Jäger
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Viktoria Zaderer
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Gaia Lupoli
- Max von Pettenkofer Institute and Gene Center, Virology, LMU München, Munich, Germany
| | - Christopher Dächert
- Max von Pettenkofer Institute and Gene Center, Virology, LMU München, Munich, Germany
| | - Maximilian Muenchhoff
- Max von Pettenkofer Institute and Gene Center, Virology, LMU München, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Oliver T Keppler
- Max von Pettenkofer Institute and Gene Center, Virology, LMU München, Munich, Germany
| | - Cornelia Lass-Flörl
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Günter Weiss
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Doris Wilflingseder
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria.
| | - Wilfried Posch
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria.
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7
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Zitzmann C, Dächert C, Schmid B, van der Schaar H, van Hemert M, Perelson AS, van Kuppeveld FJM, Bartenschlager R, Binder M, Kaderali L. Mathematical modeling of plus-strand RNA virus replication to identify broad-spectrum antiviral treatment strategies. PLoS Comput Biol 2023; 19:e1010423. [PMID: 37014904 PMCID: PMC10104377 DOI: 10.1371/journal.pcbi.1010423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 04/14/2023] [Accepted: 03/09/2023] [Indexed: 04/05/2023] Open
Abstract
Plus-strand RNA viruses are the largest group of viruses. Many are human pathogens that inflict a socio-economic burden. Interestingly, plus-strand RNA viruses share remarkable similarities in their replication. A hallmark of plus-strand RNA viruses is the remodeling of intracellular membranes to establish replication organelles (so-called "replication factories"), which provide a protected environment for the replicase complex, consisting of the viral genome and proteins necessary for viral RNA synthesis. In the current study, we investigate pan-viral similarities and virus-specific differences in the life cycle of this highly relevant group of viruses. We first measured the kinetics of viral RNA, viral protein, and infectious virus particle production of hepatitis C virus (HCV), dengue virus (DENV), and coxsackievirus B3 (CVB3) in the immuno-compromised Huh7 cell line and thus without perturbations by an intrinsic immune response. Based on these measurements, we developed a detailed mathematical model of the replication of HCV, DENV, and CVB3 and showed that only small virus-specific changes in the model were necessary to describe the in vitro dynamics of the different viruses. Our model correctly predicted virus-specific mechanisms such as host cell translation shut off and different kinetics of replication organelles. Further, our model suggests that the ability to suppress or shut down host cell mRNA translation may be a key factor for in vitro replication efficiency, which may determine acute self-limited or chronic infection. We further analyzed potential broad-spectrum antiviral treatment options in silico and found that targeting viral RNA translation, such as polyprotein cleavage and viral RNA synthesis, may be the most promising drug targets for all plus-strand RNA viruses. Moreover, we found that targeting only the formation of replicase complexes did not stop the in vitro viral replication early in infection, while inhibiting intracellular trafficking processes may even lead to amplified viral growth.
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Affiliation(s)
- Carolin Zitzmann
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Christopher Dächert
- Research Group "Dynamics of Early Viral Infection and the Innate Antiviral Response", Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bianca Schmid
- Dept of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Hilde van der Schaar
- Division of infectious Diseases and Immunology, Virology Section, Dept of Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Martijn van Hemert
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Alan S Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Frank J M van Kuppeveld
- Division of infectious Diseases and Immunology, Virology Section, Dept of Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Ralf Bartenschlager
- Division of infectious Diseases and Immunology, Virology Section, Dept of Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
- Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Center for Infection Research (DZIF), Heidelberg partner site, Heidelberg, Germany
| | - Marco Binder
- Research Group "Dynamics of Early Viral Infection and the Innate Antiviral Response", Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
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8
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Osterman A, Badell I, Dächert C, Schneider N, Kaufmann AY, Öztan GN, Huber M, Späth PM, Stern M, Autenrieth H, Muenchhoff M, Graf A, Krebs S, Blum H, Czibere L, Durner J, Kaderali L, Baldauf HM, Keppler OT. Variable detection of Omicron-BA.1 and -BA.2 by SARS-CoV-2 rapid antigen tests. Med Microbiol Immunol 2023; 212:13-23. [PMID: 36370197 PMCID: PMC9660148 DOI: 10.1007/s00430-022-00752-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 10/22/2022] [Indexed: 11/15/2022]
Abstract
During 2022, the COVID-19 pandemic has been dominated by the variant of concern (VoC) Omicron (B.1.1.529) and its rapidly emerging subvariants, including Omicron-BA.1 and -BA.2. Rapid antigen tests (RATs) are part of national testing strategies to identify SARS-CoV-2 infections on site in a community setting or to support layman's diagnostics at home. We and others have recently demonstrated an impaired RAT detection of infections caused by Omicron-BA.1 compared to Delta. Here, we evaluated the performance of five SARS-CoV-2 RATs in a single-centre laboratory study examining a total of 140 SARS-CoV-2 PCR-positive respiratory swab samples, 70 Omicron-BA.1 and 70 Omicron-BA.2, as well as 52 SARS-CoV-2 PCR-negative swabs collected from March 8th until April 10th, 2022. One test did not meet minimal criteria for specificity. In an assessment of the analytical sensitivity in clinical specimen, the 50% limit of detection (LoD50) ranged from 4.2 × 104 to 9.2 × 105 RNA copies subjected to the RAT for Omicron-BA.1 compared to 1.3 × 105 to 1.5 × 106 for Omicron-BA.2. Overall, intra-assay differences for the detection of Omicron-BA.1-containing and Omicron-BA.2-containing samples were non-significant, while a marked overall heterogeneity among the five RATs was observed. To score positive in these point-of-care tests, up to 22-fold (LoD50) or 68-fold (LoD95) higher viral loads were required for the worst performing compared to the best performing RAT. The rates of true-positive test results for these Omicron subvariant-containing samples in the highest viral load category (Ct values < 25) ranged between 44.7 and 91.1%, while they dropped to 8.7 to 22.7% for samples with intermediate Ct values (25-30). In light of recent reports on the emergence of two novel Omicron-BA.2 subvariants, Omicron-BA.2.75 and BJ.1, awareness must be increased for the overall reduced detection rate and marked differences in RAT performance for these Omicron subvariants.
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Affiliation(s)
- Andreas Osterman
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Irina Badell
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Christopher Dächert
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Nikolas Schneider
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Anna-Yasemin Kaufmann
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Gamze Naz Öztan
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Melanie Huber
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Patricia M Späth
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Marcel Stern
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Hanna Autenrieth
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Maximilian Muenchhoff
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU München, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | | | - Jürgen Durner
- Labor Becker MVZ GbR, Munich, Germany
- Department of Conservative Dentistry and Periodontology, University Hospital, LMU München, Munich, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Hanna-Mari Baldauf
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.
| | - Oliver T Keppler
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany.
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU München, Munich, Germany.
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9
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Keppler-Hafkemeyer A, Greil C, Wratil PR, Shoumariyeh K, Stern M, Hafkemeyer A, Ashok D, Hollaus A, Lupoli G, Priller A, Bischof ML, Ihorst G, Engelhardt M, Marks R, Finke J, Bertrand H, Dächert C, Muenchhoff M, Badell I, Emmerich F, Halder H, Spaeth PM, Knolle PA, Protzer U, von Bergwelt-Baildon M, Duyster J, Hartmann TN, Moosmann A, Keppler OT. Potent high-avidity neutralizing antibodies and T cell responses after COVID-19 vaccination in individuals with B cell lymphoma and multiple myeloma. Nat Cancer 2023; 4:81-95. [PMID: 36543907 PMCID: PMC9886553 DOI: 10.1038/s43018-022-00502-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 11/24/2022] [Indexed: 12/24/2022]
Abstract
Individuals with hematologic malignancies are at increased risk for severe coronavirus disease 2019 (COVID-19), yet profound analyses of COVID-19 vaccine-induced immunity are scarce. Here we present an observational study with expanded methodological analysis of a longitudinal, primarily BNT162b2 mRNA-vaccinated cohort of 60 infection-naive individuals with B cell lymphomas and multiple myeloma. We show that many of these individuals, despite markedly lower anti-spike IgG titers, rapidly develop potent infection neutralization capacities against several severe acute respiratory syndrome coronavirus 2 variants of concern (VoCs). The observed increased neutralization capacity per anti-spike antibody unit was paralleled by an early step increase in antibody avidity between the second and third vaccination. All individuals with hematologic malignancies, including those depleted of B cells and individuals with multiple myeloma, exhibited a robust T cell response to peptides derived from the spike protein of VoCs Delta and Omicron (BA.1). Consistently, breakthrough infections were mainly of mild to moderate severity. We conclude that COVID-19 vaccination can induce broad antiviral immunity including ultrapotent neutralizing antibodies with high avidity in different hematologic malignancies.
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Affiliation(s)
- Andrea Keppler-Hafkemeyer
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Christine Greil
- grid.5963.9Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Paul R. Wratil
- grid.5252.00000 0004 1936 973XMax von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany ,grid.452463.2German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany
| | - Khalid Shoumariyeh
- grid.5963.9Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), partner site Freiburg, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marcel Stern
- grid.5252.00000 0004 1936 973XMax von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Annika Hafkemeyer
- grid.5963.9Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Driti Ashok
- grid.5963.9Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Alexandra Hollaus
- grid.5252.00000 0004 1936 973XMedizinische Klinik und Poliklinik III, LMU Klinikum, LMU München, Munich, Germany
| | - Gaia Lupoli
- grid.5252.00000 0004 1936 973XMax von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Alina Priller
- grid.6936.a0000000123222966Institute of Molecular Immunology and Experimental Oncology, University Hospital rechts der Isar, Technical University of Munich (TUM) School of Medicine, Munich, Germany
| | - Marie L. Bischof
- grid.5252.00000 0004 1936 973XMax von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Gabriele Ihorst
- grid.5963.9Clinical Trials Unit, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Monika Engelhardt
- grid.5963.9Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Reinhard Marks
- grid.5963.9Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jürgen Finke
- grid.5963.9Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Hannah Bertrand
- grid.5963.9Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Christopher Dächert
- grid.5252.00000 0004 1936 973XMax von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany ,grid.452463.2German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany
| | - Maximilian Muenchhoff
- grid.5252.00000 0004 1936 973XMax von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany ,grid.452463.2German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany
| | - Irina Badell
- grid.5252.00000 0004 1936 973XMax von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany ,grid.452463.2German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany
| | - Florian Emmerich
- grid.5963.9Institute for Transfusion Medicine and Gene Therapy, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Hridi Halder
- grid.5252.00000 0004 1936 973XMedizinische Klinik und Poliklinik III, LMU Klinikum, LMU München, Munich, Germany
| | - Patricia M. Spaeth
- grid.5252.00000 0004 1936 973XMax von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Percy A. Knolle
- grid.452463.2German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany ,grid.6936.a0000000123222966Institute of Molecular Immunology and Experimental Oncology, University Hospital rechts der Isar, Technical University of Munich (TUM) School of Medicine, Munich, Germany
| | - Ulrike Protzer
- grid.452463.2German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany ,Helmholtz Munich, Munich, Germany ,grid.6936.a0000000123222966Institute of Virology, Technical University of Munich School of Medicine/Helmholtz Munich, Munich, Germany
| | - Michael von Bergwelt-Baildon
- grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), partner site Freiburg, and German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.5252.00000 0004 1936 973XMedizinische Klinik und Poliklinik III, LMU Klinikum, LMU München, Munich, Germany
| | - Justus Duyster
- grid.5963.9Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tanja N. Hartmann
- grid.5963.9Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Andreas Moosmann
- grid.452463.2German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), partner site Freiburg, and German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.5252.00000 0004 1936 973XMedizinische Klinik und Poliklinik III, LMU Klinikum, LMU München, Munich, Germany ,Helmholtz Munich, Munich, Germany
| | - Oliver T. Keppler
- grid.5252.00000 0004 1936 973XMax von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany ,grid.452463.2German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany
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10
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Maier BD, Aguilera LU, Sahle S, Mutz P, Kalra P, Dächert C, Bartenschlager R, Binder M, Kummer U. Stochastic dynamics of Type-I interferon responses. PLoS Comput Biol 2022; 18:e1010623. [PMID: 36269758 PMCID: PMC9629604 DOI: 10.1371/journal.pcbi.1010623] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 11/02/2022] [Accepted: 09/30/2022] [Indexed: 11/07/2022] Open
Abstract
Interferon (IFN) activates the transcription of several hundred of IFN stimulated genes (ISGs) that constitute a highly effective antiviral defense program. Cell-to-cell variability in the induction of ISGs is well documented, but its source and effects are not completely understood. The molecular mechanisms behind this heterogeneity have been related to randomness in molecular events taking place during the JAK-STAT signaling pathway. Here, we study the sources of variability in the induction of the IFN-alpha response by using MxA and IFIT1 activation as read-out. To this end, we integrate time-resolved flow cytometry data and stochastic modeling of the JAK-STAT signaling pathway. The complexity of the IFN response was matched by fitting probability distributions to time-course flow cytometry snapshots. Both, experimental data and simulations confirmed that the MxA and IFIT1 induction circuits generate graded responses rather than all-or-none responses. Subsequently, we quantify the size of the intrinsic variability at different steps in the pathway. We found that stochastic effects are transiently strong during the ligand-receptor activation steps and the formation of the ISGF3 complex, but negligible for the final induction of the studied ISGs. We conclude that the JAK-STAT signaling pathway is a robust biological circuit that efficiently transmits information under stochastic environments. We investigate the impact of intrinsic and extrinsic noise on the reliability of interferon signaling. Information must be transduced robustly despite existing biochemical variability and at the same time the system has to allow for cellular variability to tune it against changing environments. Getting insights into stochasticity in signaling networks is crucial to understand cellular dynamics and decision-making processes. To this end, we developed a detailed stochastic computational model based on single cell data. We are able to show that reliability is achieved despite high noise at the receptor level.
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Affiliation(s)
- Benjamin D. Maier
- Department of Modeling of Biological Processes, COS Heidelberg / Bioquant, Heidelberg University, Heidelberg, Germany
| | - Luis U. Aguilera
- Department of Modeling of Biological Processes, COS Heidelberg / Bioquant, Heidelberg University, Heidelberg, Germany
| | - Sven Sahle
- Department of Modeling of Biological Processes, COS Heidelberg / Bioquant, Heidelberg University, Heidelberg, Germany
| | - Pascal Mutz
- Division Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department for Infectious Diseases, Molecular Virology, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Priyata Kalra
- Department of Modeling of Biological Processes, COS Heidelberg / Bioquant, Heidelberg University, Heidelberg, Germany
| | - Christopher Dächert
- Research Group “Dynamics of early viral infection and the innate antiviral response”, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department for Infectious Diseases, Molecular Virology, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Ralf Bartenschlager
- Division Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department for Infectious Diseases, Molecular Virology, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Marco Binder
- Research Group “Dynamics of early viral infection and the innate antiviral response”, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ursula Kummer
- Department of Modeling of Biological Processes, COS Heidelberg / Bioquant, Heidelberg University, Heidelberg, Germany
- * E-mail:
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11
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Zitzmann C, Dächert C, Schmid B, van der Schaar H, van Hemert M, Perelson AS, van Kuppeveld FJ, Bartenschlager R, Binder M, Kaderali L. Mathematical modeling of plus-strand RNA virus replication to identify broad-spectrum antiviral treatment strategies. bioRxiv 2022:2022.07.25.501353. [PMID: 35923314 PMCID: PMC9347285 DOI: 10.1101/2022.07.25.501353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Plus-strand RNA viruses are the largest group of viruses. Many are human pathogens that inflict a socio-economic burden. Interestingly, plus-strand RNA viruses share remarkable similarities in their replication. A hallmark of plus-strand RNA viruses is the remodeling of intracellular membranes to establish replication organelles (so-called "replication factories"), which provide a protected environment for the replicase complex, consisting of the viral genome and proteins necessary for viral RNA synthesis. In the current study, we investigate pan-viral similarities and virus-specific differences in the life cycle of this highly relevant group of viruses. We first measured the kinetics of viral RNA, viral protein, and infectious virus particle production of hepatitis C virus (HCV), dengue virus (DENV), and coxsackievirus B3 (CVB3) in the immuno-compromised Huh7 cell line and thus without perturbations by an intrinsic immune response. Based on these measurements, we developed a detailed mathematical model of the replication of HCV, DENV, and CVB3 and show that only small virus-specific changes in the model were necessary to describe the in vitro dynamics of the different viruses. Our model correctly predicted virus-specific mechanisms such as host cell translation shut off and different kinetics of replication organelles. Further, our model suggests that the ability to suppress or shut down host cell mRNA translation may be a key factor for in vitro replication efficiency which may determine acute self-limited or chronic infection. We further analyzed potential broad-spectrum antiviral treatment options in silico and found that targeting viral RNA translation, especially polyprotein cleavage, and viral RNA synthesis may be the most promising drug targets for all plus-strand RNA viruses. Moreover, we found that targeting only the formation of replicase complexes did not stop the viral replication in vitro early in infection, while inhibiting intracellular trafficking processes may even lead to amplified viral growth. Author summary Plus-strand RNA viruses comprise a large group of related and medically relevant viruses. The current global pandemic of COVID-19 caused by the SARS-coronavirus-2 as well as the constant spread of diseases such as dengue and chikungunya fever show the necessity of a comprehensive and precise analysis of plus-strand RNA virus infections. Plus-strand RNA viruses share similarities in their life cycle. To understand their within-host replication strategies, we developed a mathematical model that studies pan-viral similarities and virus-specific differences of three plus-strand RNA viruses, namely hepatitis C, dengue, and coxsackievirus. By fitting our model to in vitro data, we found that only small virus-specific variations in the model were required to describe the dynamics of all three viruses. Furthermore, our model predicted that ribosomes involved in viral RNA translation seem to be a key player in plus-strand RNA replication efficiency, which may determine acute or chronic infection outcome. Furthermore, our in-silico drug treatment analysis suggests that targeting viral proteases involved in polyprotein cleavage, in combination with viral RNA replication, may represent promising drug targets with broad-spectrum antiviral activity.
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Affiliation(s)
- Carolin Zitzmann
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Christopher Dächert
- Research Group “Dynamics of Early Viral Infection and the Innate Antiviral Response”, Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bianca Schmid
- Dept of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Hilde van der Schaar
- Division of infectious Diseases and Immunology, Virology Section, Dept of Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Martijn van Hemert
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Alan S. Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Frank J.M. van Kuppeveld
- Division of infectious Diseases and Immunology, Virology Section, Dept of Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Ralf Bartenschlager
- Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Dept of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
- German Center for Infection Research (DZIF), Heidelberg partner site, Heidelberg, Germany
| | - Marco Binder
- Research Group “Dynamics of Early Viral Infection and the Innate Antiviral Response”, Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
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12
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Osterman A, Badell I, Basara E, Stern M, Kriesel F, Eletreby M, Öztan GN, Huber M, Autenrieth H, Knabe R, Späth PM, Muenchhoff M, Graf A, Krebs S, Blum H, Durner J, Czibere L, Dächert C, Kaderali L, Baldauf HM, Keppler OT. Impaired detection of omicron by SARS-CoV-2 rapid antigen tests. Med Microbiol Immunol 2022; 211:105-117. [PMID: 35187580 PMCID: PMC8858605 DOI: 10.1007/s00430-022-00730-z] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 02/12/2022] [Indexed: 01/25/2023]
Abstract
Since autumn 2020, rapid antigen tests (RATs) have been implemented in several countries as an important pillar of the national testing strategy to rapidly screen for infections on site during the SARS-CoV-2 pandemic. The current surge in infection rates around the globe is driven by the variant of concern (VoC) omicron (B.1.1.529). Here, we evaluated the performance of nine SARS-CoV-2 RATs in a single-centre laboratory study. We examined a total of 115 SARS-CoV-2 PCR-negative and 166 SARS-CoV-2 PCR-positive respiratory swab samples (101 omicron, 65 delta (B.1.617.2)) collected from October 2021 until January 2022 as well as cell culture-expanded clinical isolates of both VoCs. In an assessment of the analytical sensitivity in clinical specimen, the 50% limit of detection (LoD50) ranged from 1.77 × 106 to 7.03 × 107 RNA copies subjected to the RAT for omicron compared to 1.32 × 105 to 2.05 × 106 for delta. To score positive in these point-of-care tests, up to 10-fold (LoD50) or 101-fold (LoD95) higher virus loads were required for omicron- compared to delta-containing samples. The rates of true positive test results for omicron samples in the highest virus load category (Ct values < 25) ranged between 31.4 and 77.8%, while they dropped to 0-8.3% for samples with intermediate Ct values (25-30). Of note, testing of expanded virus stocks suggested a comparable RAT sensitivity of both VoCs, questioning the predictive value of this type of in vitro-studies for clinical performance. Given their importance for national test strategies in the current omicron wave, awareness must be increased for the reduced detection rate of omicron infections by RATs and a short list of suitable RATs that fulfill the minimal requirements of performance should be rapidly disclosed.
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Affiliation(s)
- Andreas Osterman
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - Irina Badell
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - Elif Basara
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - Marcel Stern
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - Fabian Kriesel
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - Marwa Eletreby
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - Gamze Naz Öztan
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - Melanie Huber
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - Hanna Autenrieth
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - Ricarda Knabe
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - Patricia M Späth
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - Maximilian Muenchhoff
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Jürgen Durner
- Labor Becker MVZ GbR, Munich, Germany
- Department of Conservative Dentistry and Periodontology, University Hospital, LMU München, Goethestr. 70, 80336, Munich, Germany
| | | | - Christopher Dächert
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475, Greifswald, Germany.
| | - Hanna-Mari Baldauf
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany.
| | - Oliver T Keppler
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany.
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany.
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.
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Dächert C, Muenchhoff M, Graf A, Autenrieth H, Bender S, Mairhofer H, Wratil PR, Thieme S, Krebs S, Grzimek-Koschewa N, Blum H, Keppler OT. Rapid and sensitive identification of omicron by variant-specific PCR and nanopore sequencing: paradigm for diagnostics of emerging SARS-CoV-2 variants. Med Microbiol Immunol 2022; 211:71-77. [PMID: 35061086 PMCID: PMC8780046 DOI: 10.1007/s00430-022-00728-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 01/08/2022] [Indexed: 12/19/2022]
Abstract
On November 26, 2021, the World Health Organization classified B.1.1.529 as a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant of concern (VoC), named omicron. Spike-gene dropouts in conventional SARS-CoV-2 PCR systems have been reported over the last weeks as indirect diagnostic evidence for the identification of omicron. Here, we report the combination of PCRs specific for heavily mutated sites in the spike gene and nanopore-based full-length genome sequencing for the rapid and sensitive identification of the first four COVID-19 patients diagnosed in Germany to be infected with omicron on November 28, 2021. This study will assist the unambiguous laboratory-based diagnosis and global surveillance for this highly contagious VoC with an unprecedented degree of humoral immune escape. Moreover, we propose that specialized diagnostic laboratories should continuously update their assays for variant-specific PCRs in the spike gene of SARS-CoV-2 to readily detect and diagnose emerging variants of interest and VoCs. The combination with established nanopore sequencing procedures allows both the rapid confirmation by whole genome sequencing as well as the sensitive identification of newly emerging variants of this pandemic β-coronavirus in years to come.
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Affiliation(s)
- Christopher Dächert
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Pettenkoferstr. 9a, 80336, Munich, Germany
| | - Maximilian Muenchhoff
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Pettenkoferstr. 9a, 80336, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Alexander Graf
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Pettenkoferstr. 9a, 80336, Munich, Germany
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Hanna Autenrieth
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Pettenkoferstr. 9a, 80336, Munich, Germany
| | - Sabine Bender
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Pettenkoferstr. 9a, 80336, Munich, Germany
| | - Helga Mairhofer
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Pettenkoferstr. 9a, 80336, Munich, Germany
| | - Paul R Wratil
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Pettenkoferstr. 9a, 80336, Munich, Germany
| | - Susanne Thieme
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Natascha Grzimek-Koschewa
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Pettenkoferstr. 9a, 80336, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Oliver T Keppler
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Pettenkoferstr. 9a, 80336, Munich, Germany.
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14
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Kok F, Rosenblatt M, Teusel M, Nizharadze T, Gonçalves Magalhães V, Dächert C, Maiwald T, Vlasov A, Wäsch M, Tyufekchieva S, Hoffmann K, Damm G, Seehofer D, Boettler T, Binder M, Timmer J, Schilling M, Klingmüller U. Disentangling molecular mechanisms regulating sensitization of interferon alpha signal transduction. Mol Syst Biol 2020; 16:e8955. [PMID: 32696599 PMCID: PMC7373899 DOI: 10.15252/msb.20198955] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/29/2020] [Accepted: 06/16/2020] [Indexed: 12/20/2022] Open
Abstract
Tightly interlinked feedback regulators control the dynamics of intracellular responses elicited by the activation of signal transduction pathways. Interferon alpha (IFNα) orchestrates antiviral responses in hepatocytes, yet mechanisms that define pathway sensitization in response to prestimulation with different IFNα doses remained unresolved. We establish, based on quantitative measurements obtained for the hepatoma cell line Huh7.5, an ordinary differential equation model for IFNα signal transduction that comprises the feedback regulators STAT1, STAT2, IRF9, USP18, SOCS1, SOCS3, and IRF2. The model-based analysis shows that, mediated by the signaling proteins STAT2 and IRF9, prestimulation with a low IFNα dose hypersensitizes the pathway. In contrast, prestimulation with a high dose of IFNα leads to a dose-dependent desensitization, mediated by the negative regulators USP18 and SOCS1 that act at the receptor. The analysis of basal protein abundance in primary human hepatocytes reveals high heterogeneity in patient-specific amounts of STAT1, STAT2, IRF9, and USP18. The mathematical modeling approach shows that the basal amount of USP18 determines patient-specific pathway desensitization, while the abundance of STAT2 predicts the patient-specific IFNα signal response.
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Affiliation(s)
- Frédérique Kok
- Division Systems Biology of Signal TransductionGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Faculty of BiosciencesHeidelberg UniversityHeidelbergGermany
| | - Marcus Rosenblatt
- Institute of PhysicsUniversity of FreiburgFreiburgGermany
- FDM ‐ Freiburg Center for Data Analysis and ModelingUniversity of FreiburgFreiburgGermany
| | - Melissa Teusel
- Division Systems Biology of Signal TransductionGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Faculty of BiosciencesHeidelberg UniversityHeidelbergGermany
| | - Tamar Nizharadze
- Division Systems Biology of Signal TransductionGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Faculty of BiosciencesHeidelberg UniversityHeidelbergGermany
| | - Vladimir Gonçalves Magalhães
- Research Group “Dynamics of Early Viral Infection and the Innate Antiviral Response”Division Virus‐Associated CarcinogenesisGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Christopher Dächert
- Faculty of BiosciencesHeidelberg UniversityHeidelbergGermany
- Research Group “Dynamics of Early Viral Infection and the Innate Antiviral Response”Division Virus‐Associated CarcinogenesisGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Tim Maiwald
- Institute of PhysicsUniversity of FreiburgFreiburgGermany
| | - Artyom Vlasov
- Division Systems Biology of Signal TransductionGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Faculty of BiosciencesHeidelberg UniversityHeidelbergGermany
| | - Marvin Wäsch
- Division Systems Biology of Signal TransductionGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Silvana Tyufekchieva
- Department of General, Visceral and Transplantation SurgeryRuprecht Karls University HeidelbergHeidelbergGermany
| | - Katrin Hoffmann
- Department of General, Visceral and Transplantation SurgeryRuprecht Karls University HeidelbergHeidelbergGermany
| | - Georg Damm
- Department of Hepatobiliary Surgery and Visceral TransplantationUniversity of LeipzigLeipzigGermany
| | - Daniel Seehofer
- Department of Hepatobiliary Surgery and Visceral TransplantationUniversity of LeipzigLeipzigGermany
| | - Tobias Boettler
- Department of Medicine IIUniversity Hospital Freiburg—Faculty of MedicineUniversity of FreiburgFreiburgGermany
| | - Marco Binder
- Research Group “Dynamics of Early Viral Infection and the Innate Antiviral Response”Division Virus‐Associated CarcinogenesisGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Jens Timmer
- Institute of PhysicsUniversity of FreiburgFreiburgGermany
- FDM ‐ Freiburg Center for Data Analysis and ModelingUniversity of FreiburgFreiburgGermany
- Signalling Research Centres BIOSS and CIBSSUniversity of FreiburgFreiburgGermany
- Center for Biological Systems Analysis (ZBSA)University of FreiburgFreiburgGermany
| | - Marcel Schilling
- Division Systems Biology of Signal TransductionGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Ursula Klingmüller
- Division Systems Biology of Signal TransductionGerman Cancer Research Center (DKFZ)HeidelbergGermany
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15
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Urban C, Welsch H, Heine K, Wüst S, Haas DA, Dächert C, Pandey A, Pichlmair A, Binder M. Persistent Innate Immune Stimulation Results in IRF3-Mediated but Caspase-Independent Cytostasis. Viruses 2020; 12:v12060635. [PMID: 32545331 PMCID: PMC7354422 DOI: 10.3390/v12060635] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 06/09/2020] [Accepted: 06/09/2020] [Indexed: 01/19/2023] Open
Abstract
Persistent virus infection continuously produces non-self nucleic acids that activate cell-intrinsic immune responses. However, the antiviral defense evolved as a transient, acute phase response and the effects of persistently ongoing stimulation onto cellular homeostasis are not well understood. To study the consequences of long-term innate immune activation, we expressed the NS5B polymerase of Hepatitis C virus (HCV), which in absence of viral genomes continuously produces immune-stimulatory RNAs. Surprisingly, within 3 weeks, NS5B expression declined and the innate immune response ceased. Proteomics and functional analyses indicated a reduced proliferation of those cells most strongly stimulated, which was independent of interferon signaling but required mitochondrial antiviral signaling protein (MAVS) and interferon regulatory factor 3 (IRF3). Depletion of MAVS or IRF3, or overexpression of the MAVS-inactivating HCV NS3/4A protease not only blocked interferon responses but also restored cell growth in NS5B expressing cells. However, pan-caspase inhibition could not rescue the NS5B-induced cytostasis. Our results underline an active counter selection of cells with prolonged innate immune activation, which likely constitutes a cellular strategy to prevent persistent virus infections.
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Affiliation(s)
- Christian Urban
- Institute of Virology, School of Medicine, Technical University of Munich, 81675 Munich, Germany; (C.U.); (D.A.H.)
| | - Hendrik Welsch
- Research Group “Dynamics of Early Viral Infection and the Innate Antiviral Response”, Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (H.W.); (K.H.); (S.W.); (C.D.); (A.P.)
- Faculty of Biosciences, Heidelberg University, 69117 Heidelberg, Germany
| | - Katharina Heine
- Research Group “Dynamics of Early Viral Infection and the Innate Antiviral Response”, Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (H.W.); (K.H.); (S.W.); (C.D.); (A.P.)
| | - Sandra Wüst
- Research Group “Dynamics of Early Viral Infection and the Innate Antiviral Response”, Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (H.W.); (K.H.); (S.W.); (C.D.); (A.P.)
| | - Darya A. Haas
- Institute of Virology, School of Medicine, Technical University of Munich, 81675 Munich, Germany; (C.U.); (D.A.H.)
| | - Christopher Dächert
- Research Group “Dynamics of Early Viral Infection and the Innate Antiviral Response”, Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (H.W.); (K.H.); (S.W.); (C.D.); (A.P.)
- Faculty of Biosciences, Heidelberg University, 69117 Heidelberg, Germany
| | - Aparna Pandey
- Research Group “Dynamics of Early Viral Infection and the Innate Antiviral Response”, Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (H.W.); (K.H.); (S.W.); (C.D.); (A.P.)
| | - Andreas Pichlmair
- Institute of Virology, School of Medicine, Technical University of Munich, 81675 Munich, Germany; (C.U.); (D.A.H.)
- German Center for Infection Research (DZIF), Munich Partner Site, 81675 Munich, Germany
- Correspondence: (A.P.); (M.B.)
| | - Marco Binder
- Research Group “Dynamics of Early Viral Infection and the Innate Antiviral Response”, Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (H.W.); (K.H.); (S.W.); (C.D.); (A.P.)
- Correspondence: (A.P.); (M.B.)
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16
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Dirmeier S, Dächert C, van Hemert M, Tas A, Ogando NS, van Kuppeveld F, Bartenschlager R, Kaderali L, Binder M, Beerenwinkel N. Host factor prioritization for pan-viral genetic perturbation screens using random intercept models and network propagation. PLoS Comput Biol 2020; 16:e1007587. [PMID: 32040506 PMCID: PMC7034926 DOI: 10.1371/journal.pcbi.1007587] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 02/21/2020] [Accepted: 12/05/2019] [Indexed: 12/16/2022] Open
Abstract
Genetic perturbation screens using RNA interference (RNAi) have been conducted successfully to identify host factors that are essential for the life cycle of bacteria or viruses. So far, most published studies identified host factors primarily for single pathogens. Furthermore, often only a small subset of genes, e.g., genes encoding kinases, have been targeted. Identification of host factors on a pan-pathogen level, i.e., genes that are crucial for the replication of a diverse group of pathogens has received relatively little attention, despite the fact that such common host factors would be highly relevant, for instance, for devising broad-spectrum anti-pathogenic drugs. Here, we present a novel two-stage procedure for the identification of host factors involved in the replication of different viruses using a combination of random effects models and Markov random walks on a functional interaction network. We first infer candidate genes by jointly analyzing multiple perturbations screens while at the same time adjusting for high variance inherent in these screens. Subsequently the inferred estimates are spread across a network of functional interactions thereby allowing for the analysis of missing genes in the biological studies, smoothing the effect sizes of previously found host factors, and considering a priori pathway information defined over edges of the network. We applied the procedure to RNAi screening data of four different positive-sense single-stranded RNA viruses, Hepatitis C virus, Chikungunya virus, Dengue virus and Severe acute respiratory syndrome coronavirus, and detected novel host factors, including UBC, PLCG1, and DYRK1B, which are predicted to significantly impact the replication cycles of these viruses. We validated the detected host factors experimentally using pharmacological inhibition and an additional siRNA screen and found that some of the predicted host factors indeed influence the replication of these pathogens.
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Affiliation(s)
- Simon Dirmeier
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Christopher Dächert
- Research Group “Dynamics of Early Viral Infection and the Innate Antiviral Response” (division F170), German Cancer Research Center, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Martijn van Hemert
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ali Tas
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Natacha S. Ogando
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Frank van Kuppeveld
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Ralf Bartenschlager
- Department for Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
- Division Virus-Associated Carcinogenesis, German Cancer Research Center, Heidelberg, Germany
| | - Lars Kaderali
- University Medicine Greifswald, Institute of Bioinformatics, Greifswald, Germany
| | - Marco Binder
- Research Group “Dynamics of Early Viral Infection and the Innate Antiviral Response” (division F170), German Cancer Research Center, Heidelberg, Germany
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
- * E-mail:
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17
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Dächert C, Gladilin E, Binder M. Gene Expression Profiling of Different Huh7 Variants Reveals Novel Hepatitis C Virus Host Factors. Viruses 2019; 12:v12010036. [PMID: 31905685 PMCID: PMC7019296 DOI: 10.3390/v12010036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/18/2019] [Accepted: 12/27/2019] [Indexed: 02/06/2023] Open
Abstract
Chronic Hepatitis C virus (HCV) infection still constitutes a major global health problem with almost half a million deaths per year. To date, the human hepatoma cell line Huh7 and its derivatives is the only cell line that robustly replicates HCV. However, even different subclones and passages of this single cell line exhibit tremendous differences in HCV replication efficiency. By comparative gene expression profiling using a multi-pronged correlation analysis across eight different Huh7 variants, we identified 34 candidate host factors possibly affecting HCV permissiveness. For seven of the candidates, we could show by knock-down studies their implication in HCV replication. Notably, for at least four of them, we furthermore found that overexpression boosted HCV replication in lowly permissive Huh7 cells, most prominently for the histone-binding transcriptional repressor THAP7 and the nuclear receptor NR0B2. For NR0B2, our results suggest a finely balanced expression optimum reached in highly permissive Huh7 cells, with even higher levels leading to a nearly complete breakdown of HCV replication, likely due to a dysregulation of bile acid and cholesterol metabolism. Our unbiased expression-profiling approach, hence, led to the identification of four host cellular genes that contribute to HCV permissiveness in Huh7 cells. These findings add to an improved understanding of the molecular underpinnings of the strict host cell tropism of HCV.
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Affiliation(s)
- Christopher Dächert
- Research Group “Dynamics of Early Viral Infection and the Innate Antiviral Response”, Division Virus-associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany;
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Evgeny Gladilin
- Division Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany;
- BioQuant, Heidelberg University, 69120 Heidelberg, Germany
| | - Marco Binder
- Research Group “Dynamics of Early Viral Infection and the Innate Antiviral Response”, Division Virus-associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany;
- Correspondence: ; Tel.: +49-622-142-4974
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18
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Mutz P, Metz P, Lempp FA, Bender S, Qu B, Schöneweis K, Seitz S, Tu T, Restuccia A, Frankish J, Dächert C, Schusser B, Koschny R, Polychronidis G, Schemmer P, Hoffmann K, Baumert TF, Binder M, Urban S, Bartenschlager R. HBV Bypasses the Innate Immune Response and Does Not Protect HCV From Antiviral Activity of Interferon. Gastroenterology 2018; 154:1791-1804.e22. [PMID: 29410097 DOI: 10.1053/j.gastro.2018.01.044] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 01/22/2018] [Accepted: 01/25/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Hepatitis C virus (HCV) infection is sensitive to interferon (IFN)-based therapy, whereas hepatitis B virus (HBV) infection is not. It is unclear whether HBV escapes detection by the IFN-mediated immune response or actively suppresses it. Moreover, little is known on how HBV and HCV influence each other in coinfected cells. We investigated interactions between HBV and the IFN-mediated immune response using HepaRG cells and primary human hepatocytes (PHHs). We analyzed the effects of HBV on HCV replication, and vice versa, at the single-cell level. METHODS PHHs were isolated from liver resection tissues from HBV-, HCV-, and human immunodeficiency virus-negative patients. Differentiated HepaRG cells overexpressing the HBV receptor sodium taurocholate cotransporting polypeptide (dHepaRGNTCP) and PHHs were infected with HBV. Huh7.5 cells were transfected with circular HBV DNA genomes resembling viral covalently closed circular DNA (cccDNA), and subsequently infected with HCV; this served as a model of HBV and HCV coinfection. Cells were incubated with IFN inducers, or IFNs, and antiviral response and viral replication were analyzed by immune fluorescence, reverse-transcription quantitative polymerase chain reaction, enzyme-linked immunosorbent assays, and flow cytometry. RESULTS HBV infection of dHepaRGNTCP cells and PHHs neither activated nor inhibited signaling via pattern recognition receptors. Incubation of dHepaRGNTCP cells and PHHs with IFN had little effect on HBV replication or levels of cccDNA. HBV infection of these cells did not inhibit JAK-STAT signaling or up-regulation of IFN-stimulated genes. In coinfected cells, HBV did not prevent IFN-induced suppression of HCV replication. CONCLUSIONS In dHepaRGNTCP cells and PHHs, HBV evades the induction of IFN and IFN-induced antiviral effects. HBV infection does not rescue HCV from the IFN-mediated response.
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Affiliation(s)
- Pascal Mutz
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany; Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany; HBIGS graduate school, Heidelberg, Germany
| | - Philippe Metz
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Florian A Lempp
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany; German Centre for Infection Research (DZIF), partner site Heidelberg, Heidelberg, Germany
| | - Silke Bender
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany; Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bingqian Qu
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Katrin Schöneweis
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany; German Centre for Infection Research (DZIF), partner site Heidelberg, Heidelberg, Germany
| | - Stefan Seitz
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Thomas Tu
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Agnese Restuccia
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany; Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jamie Frankish
- Research Group "Dynamics of early viral infection and the innate antiviral response", Division Virus-associated carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christopher Dächert
- Research Group "Dynamics of early viral infection and the innate antiviral response", Division Virus-associated carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Benjamin Schusser
- Reproductive Biotechnology, School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Ronald Koschny
- Department of Gastroenterology, Infection and Intoxication, University Hospital Heidelberg, Heidelberg, Germany
| | - Georgios Polychronidis
- Department of General-, Visceral- and Transplant Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Peter Schemmer
- Department of General-, Visceral- and Transplant Surgery, University Hospital Heidelberg, Heidelberg, Germany; Division of Transplant Surgery, Medical University of Graz, Graz, Austria
| | - Katrin Hoffmann
- Department of General-, Visceral- and Transplant Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Thomas F Baumert
- Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Université de Strasbourg, Institut Hospitalo-Universitaire, Pôle Hépato-digestif, Nouvel Hôpital Civil, Strasbourg, France
| | - Marco Binder
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany; Research Group "Dynamics of early viral infection and the innate antiviral response", Division Virus-associated carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stephan Urban
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany; German Centre for Infection Research (DZIF), partner site Heidelberg, Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany; Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany; HBIGS graduate school, Heidelberg, Germany; German Centre for Infection Research (DZIF), partner site Heidelberg, Heidelberg, Germany.
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