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Esser E, Schulte EC, Graf A, Karollus A, Smith NH, Michler T, Dvoretskii S, Angelov A, Sonnabend M, Peter S, Engesser C, Radonic A, Thürmer A, von Kleist M, Gebhardt F, da Costa CP, Busch DH, Muenchhoff M, Blum H, Keppler OT, Gagneur J, Protzer U. Viral genome sequencing to decipher in-hospital SARS-CoV-2 transmission events. Sci Rep 2024; 14:5768. [PMID: 38459123 PMCID: PMC10923895 DOI: 10.1038/s41598-024-56162-7] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 03/02/2024] [Indexed: 03/10/2024] Open
Abstract
The SARS-CoV-2 pandemic has highlighted the need to better define in-hospital transmissions, a need that extends to all other common infectious diseases encountered in clinical settings. To evaluate how whole viral genome sequencing can contribute to deciphering nosocomial SARS-CoV-2 transmission 926 SARS-CoV-2 viral genomes from 622 staff members and patients were collected between February 2020 and January 2021 at a university hospital in Munich, Germany, and analysed along with the place of work, duration of hospital stay, and ward transfers. Bioinformatically defined transmission clusters inferred from viral genome sequencing were compared to those inferred from interview-based contact tracing. An additional dataset collected at the same time at another university hospital in the same city was used to account for multiple independent introductions. Clustering analysis of 619 viral genomes generated 19 clusters ranging from 3 to 31 individuals. Sequencing-based transmission clusters showed little overlap with those based on contact tracing data. The viral genomes were significantly more closely related to each other than comparable genomes collected simultaneously at other hospitals in the same city (n = 829), suggesting nosocomial transmission. Longitudinal sampling from individual patients suggested possible cross-infection events during the hospital stay in 19.2% of individuals (14 of 73 individuals). Clustering analysis of SARS-CoV-2 whole genome sequences can reveal cryptic transmission events missed by classical, interview-based contact tracing, helping to decipher in-hospital transmissions. These results, in line with other studies, advocate for viral genome sequencing as a pathogen transmission surveillance tool in hospitals.
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Affiliation(s)
- Elisabeth Esser
- Institute of Virology, School of Medicine & Health, Technical University of Munich/Helmholtz Munich, Munich, Germany
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Eva C Schulte
- Institute of Virology, School of Medicine & Health, Technical University of Munich/Helmholtz Munich, Munich, Germany
- Department of Psychiatry, University Hospital, LMU Munich, Munich, Germany
- Institute of Psychiatric Phenomics and Genomics, University Hospital, LMU Munich, Munich, Germany
- Department of Psychiatry, University Hospital, Medical Faculty, University of Bonn, Bonn, Germany
- Institute of Human Genetics, University Hospital, Medical Faculty, University of Bonn, Bonn, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Alexander Karollus
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Nicholas H Smith
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Thomas Michler
- Institute of Virology, School of Medicine & Health, Technical University of Munich/Helmholtz Munich, Munich, Germany
- Institute of Laboratory Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Stefan Dvoretskii
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Angel Angelov
- NGS Competence Center, University of Tübingen, Tübingen, Germany
| | | | - Silke Peter
- NGS Competence Center, University of Tübingen, Tübingen, Germany
| | | | - Aleksandar Radonic
- Method development, Research Infrastructure & IT (MFI), Robert-Koch Institute (RKI), Berlin, Germany
| | - Andrea Thürmer
- Method development, Research Infrastructure & IT (MFI), Robert-Koch Institute (RKI), Berlin, Germany
| | - Max von Kleist
- Department of Mathematics and Computer Science, Freie Universität (FU) Berlin, Berlin, Germany
- Project Groups, Robert-Koch Institute (RKI), Berlin, Germany
| | - Friedemann Gebhardt
- Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich, Munich, Germany
| | - Clarissa Prazeres da Costa
- Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich, Munich, Germany
- German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich, Munich, Germany
- German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany
| | - Maximilian Muenchhoff
- German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Oliver T Keppler
- German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Julien Gagneur
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.
- Institute of Human Genetics, School of Medicine & Health, Technical University of Munich, Munich, Germany.
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany.
| | - Ulrike Protzer
- Institute of Virology, School of Medicine & Health, Technical University of Munich/Helmholtz Munich, Munich, Germany.
- German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany.
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Agi E, Reifenstein ET, Wit C, Schneider T, Kauer M, Kehribar M, Kulkarni A, von Kleist M, Hiesinger PR. Axonal self-sorting without target guidance in Drosophila visual map formation. Science 2024; 383:1084-1092. [PMID: 38452066 DOI: 10.1126/science.adk3043] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 02/01/2024] [Indexed: 03/09/2024]
Abstract
The idea of guidance toward a target is central to axon pathfinding and brain wiring in general. In this work, we show how several thousand axonal growth cones self-pattern without target-dependent guidance during neural superposition wiring in Drosophila. Ablation of all target lamina neurons or loss of target adhesion prevents the stabilization but not the development of the pattern. Intravital imaging at the spatiotemporal resolution of growth cone dynamics in intact pupae and data-driven dynamics simulations reveal a mechanism by which >30,000 filopodia do not explore potential targets, but instead simultaneously generate and navigate a dynamic filopodial meshwork that steers growth directions. Hence, a guidance mechanism can emerge from the interactions of the axons being guided, suggesting self-organization as a more general feature of brain wiring.
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Affiliation(s)
- Egemen Agi
- Division of Neurobiology, Free University of Berlin, 14195 Berlin, Germany
| | - Eric T Reifenstein
- Department of Mathematics, Free University of Berlin, 14195 Berlin, Germany
| | - Charlotte Wit
- Division of Neurobiology, Free University of Berlin, 14195 Berlin, Germany
| | - Teresa Schneider
- Division of Neurobiology, Free University of Berlin, 14195 Berlin, Germany
| | - Monika Kauer
- Division of Neurobiology, Free University of Berlin, 14195 Berlin, Germany
| | - Melinda Kehribar
- Division of Neurobiology, Free University of Berlin, 14195 Berlin, Germany
| | - Abhishek Kulkarni
- Division of Neurobiology, Free University of Berlin, 14195 Berlin, Germany
| | - Max von Kleist
- Department of Mathematics, Free University of Berlin, 14195 Berlin, Germany
| | - P Robin Hiesinger
- Division of Neurobiology, Free University of Berlin, 14195 Berlin, Germany
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3
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Zhang L, Iannuzzi S, Chaturvedula A, Irungu E, Haberer JE, Hendrix CW, von Kleist M. Model-based predictions of protective HIV pre-exposure prophylaxis adherence levels in cisgender women. Nat Med 2023; 29:2753-2762. [PMID: 37957377 PMCID: PMC10667095 DOI: 10.1038/s41591-023-02615-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 04/03/2023] [Accepted: 09/26/2023] [Indexed: 11/15/2023]
Abstract
Most human immunodeficiency virus (HIV) infections occur in cisgender women in resource-limited settings. In women, self-protection with emtricitabine/tenofovir disoproxil fumarate pre-exposure prophylaxis (FTC/TDF-PrEP) constitutes a major pillar of HIV prevention. However, clinical trials in women had inconsistent outcomes, sparking uncertainty about adherence requirements and reluctance in evaluating on-demand regimens. We analyzed data from published FTC/TDF-PrEP trials to establish efficacy ranges in cisgender women. In a 'bottom-up' approach, we modeled hypotheses in the context of risk-group-specific, adherence-efficacy profiles and challenged those hypotheses with clinical data. We found that different clinical outcomes were related to the proportion of women taking the product, allowing coherent interpretation of the data. Our analysis showed that 90% protection was achieved when women took some product. We found that hypotheses of putative male/female differences were either not impactful or statistically inconsistent with clinical data. We propose that differing clinical outcomes could arise from pill-taking behavior rather than biological factors driving specific adherence requirements in cisgender women.
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Affiliation(s)
- Lanxin Zhang
- Project group 5 'Systems Medicine of Infectious Diseases', Robert Koch Institute, Berlin, Germany
| | - Sara Iannuzzi
- Project group 5 'Systems Medicine of Infectious Diseases', Robert Koch Institute, Berlin, Germany
- International Max-Planck Research School 'Biology and Computation', Max-Planck Institute for Molecular Genetics, Berlin, Germany
| | - Ayyappa Chaturvedula
- Department of Pharmacotherapy, University of North Texas Health Science Center, Fort Worth, TX, USA
| | | | - Jessica E Haberer
- Center for Global Health, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Craig W Hendrix
- Division of Clinical Pharmacology, Johns Hopkins University, Baltimore, MD, USA
| | - Max von Kleist
- Project group 5 'Systems Medicine of Infectious Diseases', Robert Koch Institute, Berlin, Germany.
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany.
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Bunse T, Koerber N, Wintersteller H, Schneider J, Graf A, Radonic A, Thuermer A, von Kleist M, Blum H, Spinner CD, Bauer T, Knolle PA, Protzer U, Schulte EC. T-Cell-Dominated Immune Response Resolves Protracted SARS-CoV-2 Infection in the Absence of Neutralizing Antibodies in an Immunocompromised Individual. Microorganisms 2023; 11:1562. [PMID: 37375064 DOI: 10.3390/microorganisms11061562] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/01/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Immunocompromised individuals are at higher risk of developing protracted and severe COVID-19, and understanding individual disease courses and SARS-CoV-2 immune responses in these individuals is of the utmost importance. For more than two years, we followed an immunocompromised individual with a protracted SARS-CoV-2 infection that was eventually cleared in the absence of a humoral neutralizing SARS-CoV-2 antibody response. By conducting an in-depth examination of this individual's immune response and comparing it to a large cohort of convalescents who spontaneously cleared a SARS-CoV-2 infection, we shed light on the interplay between B- and T-cell immunity and how they interact in clearing SARS-CoV-2 infection.
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Affiliation(s)
- Till Bunse
- Institute of Virology, School of Medicine, Technical University of Munich, 81675 Munich, Germany
- Institute of Virology, Helmholtz Munich, Trogerstrasse 30, 81675 Munich, Germany
| | - Nina Koerber
- Institute of Virology, School of Medicine, Technical University of Munich, 81675 Munich, Germany
- Institute of Virology, Helmholtz Munich, Trogerstrasse 30, 81675 Munich, Germany
| | - Hannah Wintersteller
- Institute of Molecular Immunology and Experimental Oncology, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Jochen Schneider
- Department of Internal Medicine II, University Hospital Rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, 81377 Munich, Germany
| | - Aleksandar Radonic
- Method Development, Research Infrastructure & IT (MFI), Robert-Koch Institute (RKI), 13353 Berlin, Germany
| | - Andrea Thuermer
- Method Development, Research Infrastructure & IT (MFI), Robert-Koch Institute (RKI), 13353 Berlin, Germany
| | - Max von Kleist
- Department of Mathematics and Computer Science, Freie Universität (FU) Berlin, 14195 Berlin, Germany
- Project Groups, Robert-Koch Institute (RKI), 13353 Berlin, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, 81377 Munich, Germany
| | - Christoph D Spinner
- Department of Internal Medicine II, University Hospital Rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany
- German Center for Infection Research (DZIF), Munich Partner Site, 81675 Munich, Germany
| | - Tanja Bauer
- Institute of Virology, School of Medicine, Technical University of Munich, 81675 Munich, Germany
- Institute of Virology, Helmholtz Munich, Trogerstrasse 30, 81675 Munich, Germany
- German Center for Infection Research (DZIF), Munich Partner Site, 81675 Munich, Germany
| | - Percy A Knolle
- Institute of Molecular Immunology and Experimental Oncology, School of Medicine, Technical University of Munich, 81675 Munich, Germany
- German Center for Infection Research (DZIF), Munich Partner Site, 81675 Munich, Germany
| | - Ulrike Protzer
- Institute of Virology, School of Medicine, Technical University of Munich, 81675 Munich, Germany
- Institute of Virology, Helmholtz Munich, Trogerstrasse 30, 81675 Munich, Germany
- German Center for Infection Research (DZIF), Munich Partner Site, 81675 Munich, Germany
| | - Eva C Schulte
- Institute of Virology, School of Medicine, Technical University of Munich, 81675 Munich, Germany
- Institute of Virology, Helmholtz Munich, Trogerstrasse 30, 81675 Munich, Germany
- Department of Psychiatry, University Hospital, LMU Munich, 80336 Munich, Germany
- Institute of Psychiatric Phenomics and Genomics, University Hospital, LMU Munich, 80336 Munich, Germany
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5
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Zhang L, Iannuzzi S, Chaturvedula A, Haberer JE, Hendrix CW, von Kleist M. Synthesis of protective oral PrEP adherence levels in cisgender women using convergent clinical- and bottom-up modeling. Res Sq 2023:rs.3.rs-2772765. [PMID: 37131701 PMCID: PMC10153398 DOI: 10.21203/rs.3.rs-2772765/v1] [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] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Globally, most HIV infections occur in heterosexual women in resource-limited settings. In these settings, female self-protection with generic emtricitabine/tenofovir disoproxil fumarate pre-exposure prophylaxis (FTC/TDF-PrEP) may constitute a major pillar of the HIV prevention portfolio. However, clinical trials in women had inconsistent outcomes, sparking uncertainty regarding risk-group specific adherence requirements and causing reluctance in testing and recommending on-demand regimen in women. We analyzed all FTC/TDF-PrEP trials to establish PrEP efficacy ranges in women. In a 'bottom-up' approach, we modeled hypotheses corroborating risk-group specific adherence-efficacy profiles. Finally, we used the clinical efficacy ranges to (in-)validate hypotheses. We found that different clinical outcomes could solely be explained by the proportion of enrolled participants not taking the product, allowing, for the first time, to unify clinical observations. This analysis showed that 90% protection was achieved, when women took some of the product. Using 'bottom-up' modelling, we found that hypotheses of putative male/female differences were either irrelevant, or statistically inconsistent with clinical data. Furthermore, our multiscale modelling indicated that 90% protection was achieved if oral FTC/TDF was taken at least twice weekly.
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Affiliation(s)
- Lanxin Zhang
- Project group 5 “Systems Medicine of Infectious Disease”, Robert Koch Institute, Berlin, Germany
| | - Sara Iannuzzi
- Project group 5 “Systems Medicine of Infectious Disease”, Robert Koch Institute, Berlin, Germany
- International Max-Planck Research School “Biology and Computation” (IMPRS-BAC), Max-Planck Institute for Molecular Genetics, Berlin, Germany
| | - Ayyappa Chaturvedula
- The University of North Texas; Health Science Center, Fort Worth, United States
- Pumas-AI Inc
| | - Jessica E. Haberer
- Center for Global Health, Massachusetts General Hospital, Boston, United States
- Department of Medicine, Harvard Medical School, Boston, United States
| | - Craig W. Hendrix
- Division of Clinical Pharmacology, Johns-Hopkins University, Baltimore, United States
| | - Max von Kleist
- Project group 5 “Systems Medicine of Infectious Disease”, Robert Koch Institute, Berlin, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
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Ye L, Gribling-Burrer AS, Bohn P, Kibe A, Börtlein C, Ambi UB, Ahmad S, Olguin-Nava M, Smith M, Caliskan N, von Kleist M, Smyth RP. Author Correction: Short- and long-range interactions in the HIV-1 5' UTR regulate genome dimerization and packaging. Nat Struct Mol Biol 2023; 30:403. [PMID: 36828979 PMCID: PMC10023560 DOI: 10.1038/s41594-023-00946-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Affiliation(s)
- Liqing Ye
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Anne-Sophie Gribling-Burrer
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Patrick Bohn
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Anuja Kibe
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Charlene Börtlein
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Uddhav B Ambi
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Shazeb Ahmad
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Marco Olguin-Nava
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Maureen Smith
- P5 Systems Medicine of Infectious Disease, Robert Koch-Institute, Berlin, Germany
| | - Neva Caliskan
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany.,Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Max von Kleist
- P5 Systems Medicine of Infectious Disease, Robert Koch-Institute, Berlin, Germany
| | - Redmond P Smyth
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany. .,Faculty of Medicine, University of Würzburg, Würzburg, Germany.
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Oh DY, Hölzer M, Paraskevopoulou S, Trofimova M, Hartkopf F, Budt M, Wedde M, Richard H, Haldemann B, Domaszewska T, Reiche J, Keeren K, Radonić A, Calderón JPR, Smith MR, Brinkmann A, Trappe K, Drechsel O, Klaper K, Hein S, Hildt E, Haas W, Calvignac-Spencer S, Semmler T, Dürrwald R, Thürmer A, Drosten C, Fuchs S, von Kleist M, Kröger S, Wolff T. 1358. Establishing Genomic SARS-CoV-2 Surveillance at the National Level: Germany, 2021. Open Forum Infect Dis 2022. [PMCID: PMC9752442 DOI: 10.1093/ofid/ofac492.1187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Background The COVID-19 pandemic has demonstrated the importance of pathogen genomic surveillance. At RKI, the German National Institute of Public Health, we established the Integrated Molecular Surveillance for SARS-CoV-2 (IMS-SC2) network to perform SARS-CoV-2 genomic surveillance. Methods SARS-CoV-2 positive samples from laboratories distributed across Germany regularly undergo whole-genome sequencing at RKI. This surveillance instrument enables (i) almost-real-time monitoring of SARS-CoV-2 genomic diversity and evolution, (ii) in vitro assessment of vaccine coverage against emerging variants and (iii) genome-based estimates of SARS-CoV-2-incidences. Results We report the results of our analyses of 3623 SARS-CoV-2 genomes collected between 12/1/2020 and 12/31/2021. All variants of concern were identified, at ratios equivalent to those in the 100-fold larger German GISAID sequence dataset from the same time period. Lineage distributions fluctuated over time, covering the rise of the Alpha and Delta, as well as the emergence of Omicron. Phylogenetic analysis confirmed variant assignments. Multiple mutations of concern emerged during the observation period. To model vaccine effectiveness in vitro, we employed authentic-virus neutralization assays, confirming that both the Beta and Zeta variants are capable of immune evasion. The IMS-SC2 sequence dataset facilitated an estimate of the SARS-CoV-2 incidence based on genetic evolution rates. Together with modelled vaccine efficacies, Delta-specific incidence estimation indicated that the German vaccination campaign contributed substantially to a deceleration of the nascent German Delta wave. Conclusion This example illustrates that pathogen genomics enables a proactive approach to controlling a pandemic as the virus evolves. Molecular and genomic SARS-CoV-2 surveillance will be crucial during the post-pandemic future, informing public health policies including vaccination strategies. Of note, the IMS-SC2 infrastructure can be adapted to many other pathogens, serving as a blueprint for future efforts to increase genomic pathogen surveillance. Disclosures All Authors: No reported disclosures.
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Affiliation(s)
- Djin-Ye Oh
- Robert Koch Institute (RKI), Berlin, Berlin, Germany
| | - Martin Hölzer
- Robert Koch Institute (RKI), Berlin, Berlin, Germany
| | | | | | | | - Matthias Budt
- Robert Koch Institute (RKI), Berlin, Berlin, Germany
| | | | | | | | | | - Janine Reiche
- Robert Koch Institute (RKI), Berlin, Berlin, Germany
| | | | | | | | | | | | | | | | | | - Sascha Hein
- Paul Ehrlich Institute, Berlin, Berlin, Germany
| | | | - Walter Haas
- Robert Koch Institute (RKI), Berlin, Berlin, Germany
| | | | | | - Ralf Dürrwald
- Robert Koch Institute (RKI), Berlin, Berlin, Germany
| | | | - Christian Drosten
- Institute of Virology, Charité-University Medicine Berlin, Berlin, Berlin, Germany
| | - Stephan Fuchs
- Robert Koch Institute (RKI), Berlin, Berlin, Germany
| | | | - Stefan Kröger
- Robert Koch Institute (RKI), Berlin, Berlin, Germany
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8
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Oh DY, Hölzer M, Paraskevopoulou S, Trofimova M, Hartkopf F, Budt M, Wedde M, Richard H, Haldemann B, Domaszewska T, Reiche J, Keeren K, Radonić A, Ramos Calderón JP, Smith MR, Brinkmann A, Trappe K, Drechsel O, Klaper K, Hein S, Hildt E, Haas W, Calvignac-Spencer S, Semmler T, Dürrwald R, Thürmer A, Drosten C, Fuchs S, Kröger S, von Kleist M, Wolff T. Advancing Precision Vaccinology by Molecular and Genomic Surveillance of Severe Acute Respiratory Syndrome Coronavirus 2 in Germany, 2021. Clin Infect Dis 2022; 75:S110-S120. [PMID: 35749674 PMCID: PMC9278222 DOI: 10.1093/cid/ciac399] [Citation(s) in RCA: 8] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Comprehensive pathogen genomic surveillance represents a powerful tool to complement and advance precision vaccinology. The emergence of the Alpha variant in December 2020 and the resulting efforts to track the spread of this and other severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern led to an expansion of genomic sequencing activities in Germany. METHODS At Robert Koch Institute (RKI), the German National Institute of Public Health, we established the Integrated Molecular Surveillance for SARS-CoV-2 (IMS-SC2) network to perform SARS-CoV-2 genomic surveillance at the national scale, SARS-CoV-2-positive samples from laboratories distributed across Germany regularly undergo whole-genome sequencing at RKI. RESULTS We report analyses of 3623 SARS-CoV-2 genomes collected between December 2020 and December 2021, of which 3282 were randomly sampled. All variants of concern were identified in the sequenced sample set, at ratios equivalent to those in the 100-fold larger German GISAID sequence dataset from the same time period. Phylogenetic analysis confirmed variant assignments. Multiple mutations of concern emerged during the observation period. To model vaccine effectiveness in vitro, we employed authentic-virus neutralization assays, confirming that both the Beta and Zeta variants are capable of immune evasion. The IMS-SC2 sequence dataset facilitated an estimate of the SARS-CoV-2 incidence based on genetic evolution rates. Together with modeled vaccine efficacies, Delta-specific incidence estimation indicated that the German vaccination campaign contributed substantially to a deceleration of the nascent German Delta wave. CONCLUSIONS SARS-CoV-2 molecular and genomic surveillance may inform public health policies including vaccination strategies and enable a proactive approach to controlling coronavirus disease 2019 spread as the virus evolves.
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Affiliation(s)
- Djin Ye Oh
- Correspondence: D.-Y. Oh Robert Koch Institute, Dept. of Infectious Diseases, Seestr. 10, 13353 Berlin, Germany ()
| | | | - Sofia Paraskevopoulou
- Methodology and Research Infrastructure, Bioinformatics and Systems Biology (MF1), Robert Koch Institute, Berlin, Germany
| | - Maria Trofimova
- Systems Medicine of Infectious Disease (P5), Robert Koch Institute, Berlin, Germany
| | - Felix Hartkopf
- Methodology and Research Infrastructure, Genome Sequencing and Genomic Epidemiology (MF2), Robert Koch Institute, Berlin, Germany
| | - Matthias Budt
- Influenza and Other Respiratory Viruses (FG17), Robert Koch Institute, Berlin, Germany
| | - Marianne Wedde
- Influenza and Other Respiratory Viruses (FG17), Robert Koch Institute, Berlin, Germany
| | - Hugues Richard
- Methodology and Research Infrastructure, Bioinformatics and Systems Biology (MF1), Robert Koch Institute, Berlin, Germany
| | - Berit Haldemann
- Methodology and Research Infrastructure, Bioinformatics and Systems Biology (MF1), Robert Koch Institute, Berlin, Germany
| | | | - Janine Reiche
- Influenza and Other Respiratory Viruses (FG17), Robert Koch Institute, Berlin, Germany
| | - Kathrin Keeren
- Gastroenteritis and Hepatitis Pathogens and Enteroviruses (FG15), Robert Koch Institute, Berlin, Germany
| | - Aleksandar Radonić
- Methodology and Research Infrastructure, Genome Sequencing and Genomic Epidemiology (MF2), Robert Koch Institute, Berlin, Germany
| | | | | | - Annika Brinkmann
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS1), Robert Koch Institute, Berlin, Germany
| | - Kathrin Trappe
- Methodology and Research Infrastructure, Bioinformatics and Systems Biology (MF1), Robert Koch Institute, Berlin, Germany
| | - Oliver Drechsel
- Methodology and Research Infrastructure, Bioinformatics and Systems Biology (MF1), Robert Koch Institute, Berlin, Germany
| | - Kathleen Klaper
- Methodology and Research Infrastructure, Genome Sequencing and Genomic Epidemiology (MF2), Robert Koch Institute, Berlin, Germany,Sexually Transmitted Bacterial Pathogens and HIV (FG18), Robert Koch Institute, Berlin, Germany
| | - Sascha Hein
- Division of Virology, Paul Ehrlich Institute, Langen, Germany
| | - Eberhardt Hildt
- Division of Virology, Paul Ehrlich Institute, Langen, Germany
| | - Walter Haas
- Gastroenteritis and Hepatitis Pathogens and Enteroviruses (FG15), Robert Koch Institute, Berlin, Germany
| | - Sébastien Calvignac-Spencer
- Epidemiology of Highly Pathogenic Microorganisms (P3), Viral Evolution, Robert Koch Institute, Berlin, Germany
| | - Torsten Semmler
- Methodology and Research Infrastructure, Genome Sequencing and Genomic Epidemiology (MF2), Robert Koch Institute, Berlin, Germany
| | - Ralf Dürrwald
- Influenza and Other Respiratory Viruses (FG17), Robert Koch Institute, Berlin, Germany
| | - Andrea Thürmer
- Methodology and Research Infrastructure, Genome Sequencing and Genomic Epidemiology (MF2), Robert Koch Institute, Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Charité-University Medicine Berlin, Berlin, Germany
| | - Stephan Fuchs
- Methodology and Research Infrastructure, Bioinformatics and Systems Biology (MF1), Robert Koch Institute, Berlin, Germany
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9
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Baumgarte S, Hartkopf F, Hölzer M, von Kleist M, Neitz S, Kriegel M, Bollongino K. Investigation of a Limited but Explosive COVID-19 Outbreak in a German Secondary School. Viruses 2022; 14:v14010087. [PMID: 35062291 PMCID: PMC8780098 DOI: 10.3390/v14010087] [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] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/24/2021] [Accepted: 12/27/2021] [Indexed: 12/22/2022] Open
Abstract
The role of schools as a source of infection and driver in the coronavirus-pandemic has been controversial and is still not completely clarified. To prevent harm and disadvantages for children and adolescents, but also adults, detailed data on school outbreaks is needed, especially when talking about open schools employing evidence-based safety concepts. Here, we investigated the first significant COVID-19 school outbreak in Hamburg, Germany, after the re-opening of schools in 2020. Using clinical, laboratory, and contact data and spatial measures for epidemiological and environmental studies combined with whole-genome sequencing (WGS) analysis, we examined the causes and the course of the secondary school outbreak. The potential index case was identified by epidemiological tracking and the lessons in classrooms with presumably high virus spreading rates and further infection chains in the setting. Sequence analysis of samples detected one sample of a different virus lineage and 25 virus genomes with almost identical sequences, of which 21 showed 100% similarity. Most infections occurred in connection with two lesson units of the primary case. Likely, 31 students (12–14 years old), two staff members, and three family members were infected in the school or the typical household. Sequence analysis revealed an outbreak cluster with a single source that was epidemiologically identified as a member of the educational staff. In lesson units, two superspreading events of varying degrees with airborne transmission took place. These were influenced by several parameters including the exposure times, the use of respiratory masks while speaking and spatial or structural conditions at that time.
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Affiliation(s)
- Sigrid Baumgarte
- Infection Protection, Local Health Authority Hamburg-Nord, 20249 Hamburg, Germany; (S.N.); (K.B.)
- Correspondence:
| | - Felix Hartkopf
- Methodology and Research Infrastructure, Genome Sequencing and Genomic Epidemiology, Robert Koch Institute, 13353 Berlin, Germany;
| | - Martin Hölzer
- Methodology and Research Infrastructure, Bioinformatics, Robert Koch Institute, 13353 Berlin, Germany;
| | - Max von Kleist
- Systems Medicine of Infectious Disease, Robert Koch Institute, 13353 Berlin, Germany;
| | - Sabine Neitz
- Infection Protection, Local Health Authority Hamburg-Nord, 20249 Hamburg, Germany; (S.N.); (K.B.)
| | - Martin Kriegel
- Herrmann Rietschel-Institute, Technical University of Berlin, 10587 Berlin, Germany;
| | - Kirsten Bollongino
- Infection Protection, Local Health Authority Hamburg-Nord, 20249 Hamburg, Germany; (S.N.); (K.B.)
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10
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Ye L, Gribling-Burrer AS, Bohn P, Kibe A, Börtlein C, Ambi UB, Ahmad S, Olguin-Nava M, Smith M, Caliskan N, von Kleist M, Smyth RP. Short- and long-range interactions in the HIV-1 5' UTR regulate genome dimerization and packaging. Nat Struct Mol Biol 2022; 29:306-319. [PMID: 35347312 PMCID: PMC9010304 DOI: 10.1038/s41594-022-00746-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 02/14/2022] [Indexed: 11/09/2022]
Abstract
RNA dimerization is the noncovalent association of two human immunodeficiency virus-1 (HIV-1) genomes. It is a conserved step in the HIV-1 life cycle and assumed to be a prerequisite for binding to the viral structural protein Pr55Gag during genome packaging. Here, we developed functional analysis of RNA structure-sequencing (FARS-seq) to comprehensively identify sequences and structures within the HIV-1 5' untranslated region (UTR) that regulate this critical step. Using FARS-seq, we found nucleotides important for dimerization throughout the HIV-1 5' UTR and identified distinct structural conformations in monomeric and dimeric RNA. In the dimeric RNA, key functional domains, such as stem-loop 1 (SL1), polyadenylation signal (polyA) and primer binding site (PBS), folded into independent structural motifs. In the monomeric RNA, SL1 was reconfigured into long- and short-range base pairings with polyA and PBS, respectively. We show that these interactions disrupt genome packaging, and additionally show that the PBS-SL1 interaction unexpectedly couples the PBS with dimerization and Pr55Gag binding. Altogether, our data provide insights into late stages of HIV-1 life cycle and a mechanistic explanation for the link between RNA dimerization and packaging.
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Affiliation(s)
- Liqing Ye
- grid.498164.6Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Anne-Sophie Gribling-Burrer
- grid.498164.6Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Patrick Bohn
- grid.498164.6Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Anuja Kibe
- grid.498164.6Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Charlene Börtlein
- grid.498164.6Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Uddhav B. Ambi
- grid.498164.6Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Shazeb Ahmad
- grid.498164.6Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Marco Olguin-Nava
- grid.498164.6Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Maureen Smith
- grid.13652.330000 0001 0940 3744P5 Systems Medicine of Infectious Disease, Robert Koch-Institute, Berlin, Germany
| | - Neva Caliskan
- grid.498164.6Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany ,grid.8379.50000 0001 1958 8658Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Max von Kleist
- grid.13652.330000 0001 0940 3744P5 Systems Medicine of Infectious Disease, Robert Koch-Institute, Berlin, Germany
| | - Redmond P. Smyth
- grid.498164.6Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany ,grid.8379.50000 0001 1958 8658Faculty of Medicine, University of Würzburg, Würzburg, Germany
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11
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Zhang L, Wang J, von Kleist M. Numerical approaches for the rapid analysis of prophylactic efficacy against HIV with arbitrary drug-dosing schemes. PLoS Comput Biol 2021; 17:e1009295. [PMID: 34941864 PMCID: PMC8741042 DOI: 10.1371/journal.pcbi.1009295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 07/06/2021] [Revised: 01/07/2022] [Accepted: 12/03/2021] [Indexed: 11/18/2022] Open
Abstract
Pre-exposure prophylaxis (PrEP) is an important pillar to prevent HIV transmission. Because of experimental and clinical shortcomings, mathematical models that integrate pharmacological, viral- and host factors are frequently used to quantify clinical efficacy of PrEP. Stochastic simulations of these models provides sample statistics from which the clinical efficacy is approximated. However, many stochastic simulations are needed to reduce the associated sampling error. To remedy the shortcomings of stochastic simulation, we developed a numerical method that allows predicting the efficacy of arbitrary prophylactic regimen directly from a viral dynamics model, without sampling. We apply the method to various hypothetical dolutegravir (DTG) prophylaxis scenarios. The approach is verified against state-of-the-art stochastic simulation. While the method is more accurate than stochastic simulation, it is superior in terms of computational performance. For example, a continuous 6-month prophylactic profile is computed within a few seconds on a laptop computer. The method’s computational performance, therefore, substantially expands the horizon of feasible analysis in the context of PrEP, and possibly other applications. Pre-exposure prophylaxis (PrEP) is an important tool to prevent HIV transmission. However, experimental identification of parameters that determine prophylactic efficacy is extremely difficult. Clues about these parameters could prove essential for the design of next-generation PrEP compounds. Integrative mathematical models can fill this void: Based on stochastic simulation, a sample statistic can be generated, from which the prophylactic efficacy is estimated. However, for this sample statistic to be accurate, many simulations need to be performed. Here, we introduce a numerical method to directly compute the prophylactic efficacy from a viral dynamics model, without the need for sampling. Based on several examples with dolutegravir (DTG) -based short- and long-term PrEP, as well as post-exposure prophylaxis we demonstrate the correctness of the new method and its outstanding computational performance. Due to the method’s computational performance, a number of analyses, including formal sensitivity analysis, are becoming feasible with the proposed method.
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Affiliation(s)
- Lanxin Zhang
- Project group 5 “Systems Medicine of Infectious Disease”, Robert Koch Institute, Berlin, Germany
| | - Junyu Wang
- Project group 5 “Systems Medicine of Infectious Disease”, Robert Koch Institute, Berlin, Germany
| | - Max von Kleist
- Project group 5 “Systems Medicine of Infectious Disease”, Robert Koch Institute, Berlin, Germany
- * E-mail:
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12
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Kiral FR, Dutta SB, Linneweber GA, Hilgert S, Poppa C, Duch C, von Kleist M, Hassan BA, Hiesinger PR. Brain connectivity inversely scales with developmental temperature in Drosophila. Cell Rep 2021; 37:110145. [PMID: 34936868 DOI: 10.1016/j.celrep.2021.110145] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 10/04/2021] [Accepted: 11/29/2021] [Indexed: 11/17/2022] Open
Abstract
Variability of synapse numbers and partners despite identical genes reveals the limits of genetic determinism. Here, we use developmental temperature as a non-genetic perturbation to study variability of brain wiring and behavior in Drosophila. Unexpectedly, slower development at lower temperatures increases axo-dendritic branching, synapse numbers, and non-canonical synaptic partnerships of various neurons, while maintaining robust ratios of canonical synapses. Using R7 photoreceptors as a model, we show that changing the relative availability of synaptic partners using a DIPγ mutant that ablates R7's preferred partner leads to temperature-dependent recruitment of non-canonical partners to reach normal synapse numbers. Hence, R7 synaptic specificity is not absolute but based on the relative availability of postsynaptic partners and presynaptic control of synapse numbers. Behaviorally, movement precision is temperature robust, while movement activity is optimized for the developmentally encountered temperature. These findings suggest genetically encoded relative and scalable synapse formation to develop functional, but not identical, brains and behaviors.
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Affiliation(s)
- Ferdi Ridvan Kiral
- Division of Neurobiology, Institute for Biology, Freie Universität Berlin, 14195 Berlin, Germany
| | - Suchetana B Dutta
- Division of Neurobiology, Institute for Biology, Freie Universität Berlin, 14195 Berlin, Germany
| | - Gerit Arne Linneweber
- Division of Neurobiology, Institute for Biology, Freie Universität Berlin, 14195 Berlin, Germany
| | - Selina Hilgert
- Institute of Developmental Biology and Neurobiology (iDN), Hanns-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Caroline Poppa
- Division of Neurobiology, Institute for Biology, Freie Universität Berlin, 14195 Berlin, Germany
| | - Carsten Duch
- Institute of Developmental Biology and Neurobiology (iDN), Hanns-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Max von Kleist
- MF1 Bioinformatics, Robert Koch-Institute, 13353 Berlin, Germany
| | - Bassem A Hassan
- Division of Neurobiology, Institute for Biology, Freie Universität Berlin, 14195 Berlin, Germany; Institut du Cerveau - Paris Brain Institute - ICM, Sorbonne Université, Inserm, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - P Robin Hiesinger
- Division of Neurobiology, Institute for Biology, Freie Universität Berlin, 14195 Berlin, Germany.
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13
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Smith MR, Trofimova M, Weber A, Duport Y, Kühnert D, von Kleist M. Rapid incidence estimation from SARS-CoV-2 genomes reveals decreased case detection in Europe during summer 2020. Nat Commun 2021; 12:6009. [PMID: 34650062 PMCID: PMC8517019 DOI: 10.1038/s41467-021-26267-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 05/25/2021] [Accepted: 09/24/2021] [Indexed: 12/24/2022] Open
Abstract
By October 2021, 230 million SARS-CoV-2 diagnoses have been reported. Yet, a considerable proportion of cases remains undetected. Here, we propose GInPipe, a method that rapidly reconstructs SARS-CoV-2 incidence profiles solely from publicly available, time-stamped viral genomes. We validate GInPipe against simulated outbreaks and elaborate phylodynamic analyses. Using available sequence data, we reconstruct incidence histories for Denmark, Scotland, Switzerland, and Victoria (Australia) and demonstrate, how to use the method to investigate the effects of changing testing policies on case ascertainment. Specifically, we find that under-reporting was highest during summer 2020 in Europe, coinciding with more liberal testing policies at times of low testing capacities. Due to the increased use of real-time sequencing, it is envisaged that GInPipe can complement established surveillance tools to monitor the SARS-CoV-2 pandemic. In post-pandemic times, when diagnostic efforts are decreasing, GInPipe may facilitate the detection of hidden infection dynamics.
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Affiliation(s)
- Maureen Rebecca Smith
- Systems Medicine of Infectious Disease (P5), Robert Koch Institute, Berlin, Germany.
- Bioinformatics (MF1), Robert Koch Institute, Berlin, Germany.
| | - Maria Trofimova
- Systems Medicine of Infectious Disease (P5), Robert Koch Institute, Berlin, Germany
- Bioinformatics (MF1), Robert Koch Institute, Berlin, Germany
| | - Ariane Weber
- Transmission, Infection, Diversification and Evolution Group, Max-Planck Institute for the Science of Human History, Jena, Germany
| | - Yannick Duport
- Systems Medicine of Infectious Disease (P5), Robert Koch Institute, Berlin, Germany
- Bioinformatics (MF1), Robert Koch Institute, Berlin, Germany
| | - Denise Kühnert
- Transmission, Infection, Diversification and Evolution Group, Max-Planck Institute for the Science of Human History, Jena, Germany
- German COVID Omics Initiative (deCOI), Bonn, Germany
| | - Max von Kleist
- Systems Medicine of Infectious Disease (P5), Robert Koch Institute, Berlin, Germany.
- Bioinformatics (MF1), Robert Koch Institute, Berlin, Germany.
- German COVID Omics Initiative (deCOI), Bonn, Germany.
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14
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Raharinirina NA, Peppert F, von Kleist M, Schütte C, Sunkara V. Inferring gene regulatory networks from single-cell RNA-seq temporal snapshot data requires higher-order moments. Patterns (N Y) 2021; 2:100332. [PMID: 34553172 PMCID: PMC8441581 DOI: 10.1016/j.patter.2021.100332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 02/23/2021] [Accepted: 07/22/2021] [Indexed: 11/30/2022]
Abstract
Single-cell RNA sequencing (scRNA-seq) has become ubiquitous in biology. Recently, there has been a push for using scRNA-seq snapshot data to infer the underlying gene regulatory networks (GRNs) steering cellular function. To date, this aspiration remains unrealized due to technical and computational challenges. In this work we focus on the latter, which is under-represented in the literature. We took a systemic approach by subdividing the GRN inference into three fundamental components: data pre-processing, feature extraction, and inference. We observed that the regulatory signature is captured in the statistical moments of scRNA-seq data and requires computationally intensive minimization solvers to extract it. Furthermore, current data pre-processing might not conserve these statistical moments. Although our moment-based approach is a didactic tool for understanding the different compartments of GRN inference, this line of thinking—finding computationally feasible multi-dimensional statistics of data—is imperative for designing GRN inference methods. Single-cell RNA-seq temporal snapshot data for detecting regulation Challenges in data pre-processing, feature extraction, and network inference for GRNs Encoding of regulatory information in higher-order raw moments Non-linear least-squares inference for temporal scRNA-seq snapshot data
Single-cell RNA sequencing (scRNA-seq) has become ubiquitous in biology. Recently, there has been a push for using scRNA-seq snapshot data to infer the underlying gene regulatory networks (GRNs) steering cellular function. A recent benchmark of 12 GRN methods demonstrated that the algorithms struggled to predict the ground-truth GRNs and speculated that the low performance was due to the insufficient resolution in the scRNA-seq data. Rather than proposing another method, this paper focuses on how to decompose a GRN problem into three subproblems (pre-processing, feature extraction, and inference), so that the gene regulatory information is preserved in each step. Subsequently, we discuss how to best approach each of the three subproblems.
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Affiliation(s)
| | - Felix Peppert
- Explainable A.I. for Biology, Zuse Institute Berlin, 14195 Berlin, Germany
| | - Max von Kleist
- MF1 Bioinformatics, Methods Development and Research Infrastructure, Robert Koch Institute, 13353 Berlin, Germany
| | - Christof Schütte
- Mathematics of Complex Systems, Zuse Institute Berlin, 14195 Berlin, Germany.,Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany
| | - Vikram Sunkara
- Mathematics of Complex Systems, Zuse Institute Berlin, 14195 Berlin, Germany.,Explainable A.I. for Biology, Zuse Institute Berlin, 14195 Berlin, Germany
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15
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Calvignac-Spencer S, Budt M, Huska M, Richard H, Leipold L, Grabenhenrich L, Semmler T, von Kleist M, Kröger S, Wolff T, Hölzer M. Rise and Fall of SARS-CoV-2 Lineage A.27 in Germany. Viruses 2021; 13:1491. [PMID: 34452356 PMCID: PMC8402818 DOI: 10.3390/v13081491] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 07/08/2021] [Revised: 07/23/2021] [Accepted: 07/24/2021] [Indexed: 01/01/2023] Open
Abstract
Here, we report on the increasing frequency of the SARS-CoV-2 lineage A.27 in Germany during the first months of 2021. Genomic surveillance identified 710 A.27 genomes in Germany as of 2 May 2021, with a vast majority identified in laboratories from a single German state (Baden-Wuerttemberg, n = 572; 80.5%). Baden-Wuerttemberg is located near the border with France, from where most A.27 sequences were entered into public databases until May 2021. The first appearance of this lineage based on sequencing in a laboratory in Baden-Wuerttemberg can be dated to early January '21. From then on, the relative abundance of A.27 increased until the end of February but has since declined-meanwhile, the abundance of B.1.1.7 increased in the region. The A.27 lineage shows a mutational pattern typical of VOIs/VOCs, including an accumulation of amino acid substitutions in the Spike glycoprotein. Among those, L18F, L452R and N501Y are located in the epitope regions of the N-terminal- (NTD) or receptor binding domain (RBD) and have been suggested to result in immune escape and higher transmissibility. In addition, A.27 does not show the D614G mutation typical for all VOIs/VOCs from the B lineage. Overall, A.27 should continue to be monitored nationally and internationally, even though the observed trend in Germany was initially displaced by B.1.1.7 (Alpha), while now B.1.617.2 (Delta) is on the rise.
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Affiliation(s)
| | - Matthias Budt
- Influenza and other Respiratory Viruses, Robert Koch Institute, 13353 Berlin, Germany; (M.B.); (T.W.)
| | - Matthew Huska
- Methodology and Research Infrastructure, Bioinformatics, Robert Koch Institute, 13353 Berlin, Germany; (M.H.); (H.R.)
| | - Hugues Richard
- Methodology and Research Infrastructure, Bioinformatics, Robert Koch Institute, 13353 Berlin, Germany; (M.H.); (H.R.)
| | - Luca Leipold
- Methodology and Research Infrastructure, Information and Research Data Management, Robert Koch Institute, 13353 Berlin, Germany; (L.L.); (L.G.)
| | - Linus Grabenhenrich
- Methodology and Research Infrastructure, Information and Research Data Management, Robert Koch Institute, 13353 Berlin, Germany; (L.L.); (L.G.)
| | - Torsten Semmler
- Methodology and Research Infrastructure, Genome Sequencing and Genomic Epidemiology, Robert Koch Institute, 13353 Berlin, Germany;
| | - Max von Kleist
- Systems Medicine of Infectious Disease, Robert Koch Institute, 13353 Berlin, Germany;
| | - Stefan Kröger
- Infectious Disease Epidemiology, Robert Koch Institute, 13353 Berlin, Germany;
| | - Thorsten Wolff
- Influenza and other Respiratory Viruses, Robert Koch Institute, 13353 Berlin, Germany; (M.B.); (T.W.)
| | - Martin Hölzer
- Methodology and Research Infrastructure, Bioinformatics, Robert Koch Institute, 13353 Berlin, Germany; (M.H.); (H.R.)
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16
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Oh DY, Buda S, Biere B, Reiche J, Schlosser F, Duwe S, Wedde M, von Kleist M, Mielke M, Wolff T, Dürrwald R. Trends in respiratory virus circulation following COVID-19-targeted nonpharmaceutical interventions in Germany, January - September 2020: Analysis of national surveillance data. Lancet Reg Health Eur 2021; 6:100112. [PMID: 34124707 PMCID: PMC8183189 DOI: 10.1016/j.lanepe.2021.100112] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND During the initial COVID-19 response, Germany's Federal Government implemented several nonpharmaceutical interventions (NPIs) that were instrumental in suppressing early exponential spread of SARS-CoV-2. NPI effect on the transmission of other respiratory viruses has not been examined at the national level thus far. METHODS Upper respiratory tract specimens from 3580 patients with acute respiratory infection (ARI), collected within the nationwide German ARI Sentinel, underwent RT-PCR diagnostics for multiple respiratory viruses. The observation period (weeks 1-38 of 2020) included the time before, during and after a far-reaching contact ban. Detection rates for different viruses were compared to 2017-2019 sentinel data (15350 samples; week 1-38, 11823 samples). FINDINGS The March 2020 contact ban, which was followed by a mask mandate, was associated with an unprecedented and sustained decline of multiple respiratory viruses. Among these, rhinovirus was the single agent that resurged to levels equalling those of previous years. Rhinovirus rebound was first observed in children, after schools and daycares had reopened. By contrast, other nonenveloped viruses (i.e. gastroenteritis viruses reported at the national level) suppressed after the shutdown did not rebound. INTERPRETATION Contact restrictions with a subsequent mask mandate in spring may substantially reduce respiratory virus circulation. This reduction appears sustained for most viruses, indicating that the activity of influenza and other respiratory viruses during the subsequent winter season might be low,whereas rhinovirus resurgence, potentially driven by transmission in educational institutions in a setting of waning population immunity, might signal predominance of rhinovirus-related ARIs. FUNDING Robert Koch-Institute and German Ministry of Health.
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Affiliation(s)
- Djin-Ye Oh
- Unit 17: Influenza and Other Respiratory Viruses | German National Influenza Center, Department of Infectious Diseases, Robert Koch-Institute, D-13353 Berlin, Germany
- The Rockefeller University, New York, NY, United States
| | - Silke Buda
- Department of Infectious Diseases Epidemiology, Robert-Koch Institute, Germany
| | - Barbara Biere
- Unit 17: Influenza and Other Respiratory Viruses | German National Influenza Center, Department of Infectious Diseases, Robert Koch-Institute, D-13353 Berlin, Germany
| | - Janine Reiche
- Unit 17: Influenza and Other Respiratory Viruses | German National Influenza Center, Department of Infectious Diseases, Robert Koch-Institute, D-13353 Berlin, Germany
| | - Frank Schlosser
- Computational Epidemiology (P4), Robert Koch-Institute, Germany
- Institute for Theoretical Biology, Humboldt University of Berlin, D-10115 Berlin, Germany
| | - Susanne Duwe
- Unit 17: Influenza and Other Respiratory Viruses | German National Influenza Center, Department of Infectious Diseases, Robert Koch-Institute, D-13353 Berlin, Germany
| | - Marianne Wedde
- Unit 17: Influenza and Other Respiratory Viruses | German National Influenza Center, Department of Infectious Diseases, Robert Koch-Institute, D-13353 Berlin, Germany
| | - Max von Kleist
- Systems Medicine of Infectious Disease (P5), Robert Koch-Institute, Germany
| | - Martin Mielke
- Department of Infectious Diseases, Robert Koch-Institute, Germany
| | - Thorsten Wolff
- Unit 17: Influenza and Other Respiratory Viruses | German National Influenza Center, Department of Infectious Diseases, Robert Koch-Institute, D-13353 Berlin, Germany
| | - Ralf Dürrwald
- Unit 17: Influenza and Other Respiratory Viruses | German National Influenza Center, Department of Infectious Diseases, Robert Koch-Institute, D-13353 Berlin, Germany
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17
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van der Toorn W, Oh DY, von Kleist M. COVIDStrategyCalculator: A software to assess testing and quarantine strategies for incoming travelers, contact management, and de-isolation. Patterns (N Y) 2021; 2:100264. [PMID: 33899035 PMCID: PMC8057763 DOI: 10.1016/j.patter.2021.100264] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/01/2021] [Accepted: 04/15/2021] [Indexed: 12/27/2022]
Abstract
While large-scale vaccination campaigns against SARS-CoV-2 are rolled out at the time of writing, non-pharmaceutical interventions (NPIs), including the isolation of infected individuals and quarantine of exposed individuals, remain central measures to contain the spread of SARS-CoV-2. Strategies that combine NPIs with innovative SARS-CoV-2 testing strategies may increase containment efficacy and help to shorten quarantine durations. We developed a user-friendly software tool that implements a recently published stochastic within-host viral dynamics model that captures temporal attributes of the viral infection, such as test sensitivity, infectiousness, and the occurrence of symptoms. Based on this model, the software allows to evaluate the efficacy of user-defined, arbitrary NPI and testing strategies in reducing the transmission potential in different contexts. The software thus enables decision makers to explore NPI strategies and perform hypothesis testing, e.g., with regard to the utilization of novel diagnostics or with regard to containing novel virus variants.
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Affiliation(s)
- Wiep van der Toorn
- Systems Medicine of Infectious Disease (P5), Robert Koch Institute, Berlin, Germany
- Bioinformatics (MF1), Methodology and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | - Djin-Ye Oh
- FG17 Influenza and Other Respiratory Viruses, Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Max von Kleist
- Systems Medicine of Infectious Disease (P5), Robert Koch Institute, Berlin, Germany
- Bioinformatics (MF1), Methodology and Research Infrastructure, Robert Koch Institute, Berlin, Germany
- German COVID Omics Initiative (deCOI) Bonn, Germany
| | - the Working Group on SARS-CoV-2 Diagnostics at RKI
- Systems Medicine of Infectious Disease (P5), Robert Koch Institute, Berlin, Germany
- Bioinformatics (MF1), Methodology and Research Infrastructure, Robert Koch Institute, Berlin, Germany
- FG17 Influenza and Other Respiratory Viruses, Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
- German COVID Omics Initiative (deCOI) Bonn, Germany
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18
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van der Toorn W, Oh DY, Bourquain D, Michel J, Krause E, Nitsche A, von Kleist M. An intra-host SARS-CoV-2 dynamics model to assess testing and quarantine strategies for incoming travelers, contact management, and de-isolation. Patterns (N Y) 2021; 2:100262. [PMID: 33899034 PMCID: PMC8057735 DOI: 10.1016/j.patter.2021.100262] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/20/2021] [Accepted: 04/14/2021] [Indexed: 12/15/2022]
Abstract
Non-pharmaceutical interventions (NPIs) remain decisive tools to contain SARS-CoV-2. Strategies that combine NPIs with testing may improve efficacy and shorten quarantine durations. We developed a stochastic within-host model of SARS-CoV-2 that captures temporal changes in test sensitivities, incubation periods, and infectious periods. We used the model to simulate relative transmission risk for (1) isolation of symptomatic individuals, (2) contact person management, and (3) quarantine of incoming travelers. We estimated that testing travelers at entry reduces transmission risks to 21.3% ([20.7, 23.9], by PCR) and 27.9% ([27.1, 31.1], by rapid diagnostic test [RDT]), compared with unrestricted entry. We calculated that 4 (PCR) or 5 (RDT) days of pre-test quarantine are non-inferior to 10 days of quarantine for incoming travelers and that 8 (PCR) or 10 (RDT) days of pre-test quarantine are non-inferior to 14 days of post-exposure quarantine. De-isolation of infected individuals 13 days after symptom onset may reduce the transmission risk to <0.2% (<0.01, 6.0).
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Affiliation(s)
- Wiep van der Toorn
- Systems Medicine of Infectious Disease (P5), Robert Koch Institute, Berlin, Germany
- Bioinformatics (MF1), Methodology and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | - Djin-Ye Oh
- FG17 Influenza and Other Respiratory Viruses, Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Daniel Bourquain
- ZBS1 Highly Pathogenic Viruses, Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Janine Michel
- ZBS1 Highly Pathogenic Viruses, Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Eva Krause
- ZBS1 Highly Pathogenic Viruses, Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Andreas Nitsche
- ZBS1 Highly Pathogenic Viruses, Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Max von Kleist
- Systems Medicine of Infectious Disease (P5), Robert Koch Institute, Berlin, Germany
- Bioinformatics (MF1), Methodology and Research Infrastructure, Robert Koch Institute, Berlin, Germany
- German COVID Omics Initiative (deCOI), Bonn, Germany
| | - the Working Group on SARS-CoV-2 Diagnostics at RKI
- Systems Medicine of Infectious Disease (P5), Robert Koch Institute, Berlin, Germany
- Bioinformatics (MF1), Methodology and Research Infrastructure, Robert Koch Institute, Berlin, Germany
- FG17 Influenza and Other Respiratory Viruses, Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
- ZBS1 Highly Pathogenic Viruses, Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
- German COVID Omics Initiative (deCOI), Bonn, Germany
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19
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Goettsch W, Beerenwinkel N, Deng L, Dölken L, Dutilh BE, Erhard F, Kaderali L, von Kleist M, Marquet R, Matthijnssens J, McCallin S, McMahon D, Rattei T, Van Rij RP, Robertson DL, Schwemmle M, Stern-Ginossar N, Marz M. ITN-VIROINF: Understanding (Harmful) Virus-Host Interactions by Linking Virology and Bioinformatics. Viruses 2021; 13:v13050766. [PMID: 33925452 PMCID: PMC8145447 DOI: 10.3390/v13050766] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 03/05/2021] [Revised: 04/15/2021] [Accepted: 04/22/2021] [Indexed: 11/16/2022] Open
Abstract
Many recent studies highlight the fundamental importance of viruses. Besides their important role as human and animal pathogens, their beneficial, commensal or harmful functions are poorly understood. By developing and applying tailored bioinformatical tools in important virological models, the Marie Skłodowska-Curie Initiative International Training Network VIROINF will provide a better understanding of viruses and the interaction with their hosts. This will open the door to validate methods of improving viral growth, morphogenesis and development, as well as to control strategies against unwanted microorganisms. The key feature of VIROINF is its interdisciplinary nature, which brings together virologists and bioinformaticians to achieve common goals.
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Affiliation(s)
- Winfried Goettsch
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University, 07743 Jena, Germany;
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland;
| | - Li Deng
- Institute of Virology, Helmholtz Centre Munich and Technical University Munich, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany;
| | - Lars Dölken
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, 97078 Würzburg, Germany; (L.D.); (F.E.)
| | - Bas E. Dutilh
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Hugo R. Kruytgebouw, Padualaan 8, 3584 CH Utrecht, The Netherlands;
| | - Florian Erhard
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, 97078 Würzburg, Germany; (L.D.); (F.E.)
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, 17475 Greifswald, Germany;
| | - Max von Kleist
- MF1 Bioinformatics, Robert Koch-Institute, 13353 Berlin, Germany;
| | - Roland Marquet
- CNRS, Architecture et Réactivité de l’ARN, Université de Strasbourg, UPR 9002 Strasbourg, France;
| | - Jelle Matthijnssens
- Department of Microbiology and Immunology, Katholieke Universiteit Leuven, Herestraat 49 Box 1040, 3000 Leuven, Belgium;
| | - Shawna McCallin
- Department of Neuro-Urology, Balgrist University Hospital, University of Zürich, Forchstrasse 340, 8008 Zürich, Switzerland;
| | - Dino McMahon
- Institute of Biology, Freie Universität Berlin, Schwendenerstr. 1, 14195 Berlin, Germany;
| | - Thomas Rattei
- Division of Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstraße 14, 1090 Vienna, Austria;
| | - Ronald P. Van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands;
| | - David L. Robertson
- MRC, University of Glasgow Centre for Virus Research (CVR), 464 Bearsden Road, Glasgow G61 1QH, UK;
| | - Martin Schwemmle
- Institute of Virology, Medical Center—University of Freiburg, Hermann-Herder-Strasse 11, 79104 Freiburg, Germany;
| | - Noam Stern-Ginossar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel;
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University, 07743 Jena, Germany;
- FLI Leibniz Institute for Age Research, 07745 Jena, Germany
- Correspondence: ; Tel.: +49-3641-9-46480
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20
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Grote U, Arvand M, Brinkwirth S, Brunke M, Buchholz U, Eckmanns T, von Kleist M, Niebank M, Ruehe B, Schulze K, Stoliaroff-Pépin A, Thanheiser M, Schaade L, Said D, Haas W. [Measures to cope with the COVID-19 pandemic in Germany: nonpharmaceutical and pharmaceutical interventions]. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2021; 64:435-445. [PMID: 33787944 PMCID: PMC8010780 DOI: 10.1007/s00103-021-03306-z] [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] [Accepted: 03/05/2021] [Indexed: 12/15/2022]
Abstract
When the emerging novel SARS-CoV‑2 virus first appeared in December 2019, neither specific therapeutic options nor vaccinations were available. The role of nonpharmaceutical interventions (NPIs) became of central importance. At the Robert Koch Institute, a multilayer strategy consisting of population-based and individual preventive measures to control the pandemic was developed, which built upon existing influenza pandemic plans as well as generic plans. This paper explains the recommended NPIs and illustrates the pharmaceutical approaches developed in parallel.Among others, general contact bans, providing material for infection prevention and control, ban of events, closing educational institutions, and restricting travel are counted among population-based measures. Additional individual preventive measures are necessary, e.g., keeping a minimum distance, reducing contacts, and wearing a mouth-nose covering as well as quarantine and isolation. Measures within the health system are based on recommendations of the Commission on Hospital Hygiene and Infection Protection (Kommission für Krankenhaushygiene und Infektionsprävention (KRINKO)) and specified and implemented by professional societies. Since November 2020, an antiviral therapy with remdesivir and treatment with the glucocorticoid dexamethasone have been available as pharmaceutical interventions. Monoclonal antibodies are at this time not approved. Therapeutic anticoagulation is recommended.Recommendations are constantly adapted to the increasing knowledge on the pathogen and its means of transmission. A challenge is to strengthen the trust of the population. Many measures have to be applied on an individual basis in order to work together.
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Affiliation(s)
- Ulrike Grote
- Abteilung für Infektionsepidemiologie, Robert Koch-Institut, Berlin, Deutschland.
- ÖGD Kontaktstelle: Infektionsepidemiologisches Krisenmanagement, Ausbruchsuntersuchungen und Trainingsprogramme (Fachgebiet 38), Abteilung für Infektionsepidemiologie, Robert Koch-Institut, Seestraße 10, 13353, Berlin, Deutschland.
| | - Mardjan Arvand
- Abteilung für Infektionskrankheiten, Robert Koch-Institut, Berlin, Deutschland
| | - Simon Brinkwirth
- Abteilung für Infektionsepidemiologie, Robert Koch-Institut, Berlin, Deutschland
| | - Melanie Brunke
- Abteilung für Infektionskrankheiten, Robert Koch-Institut, Berlin, Deutschland
| | - Udo Buchholz
- Abteilung für Infektionsepidemiologie, Robert Koch-Institut, Berlin, Deutschland
| | - Tim Eckmanns
- Abteilung für Infektionsepidemiologie, Robert Koch-Institut, Berlin, Deutschland
| | - Max von Kleist
- MF Methodenentwicklung und Forschungsinfrastruktur, Robert Koch-Institut, Berlin, Deutschland
| | - Michaela Niebank
- Zentrum für Biologische Gefahren und Spezielle Pathogene (ZBS), Robert Koch-Institut, Berlin, Deutschland
| | - Bettina Ruehe
- Zentrum für Biologische Gefahren und Spezielle Pathogene (ZBS), Robert Koch-Institut, Berlin, Deutschland
| | - Kai Schulze
- Abteilung für Infektionsepidemiologie, Robert Koch-Institut, Berlin, Deutschland
| | | | - Marc Thanheiser
- Abteilung für Infektionskrankheiten, Robert Koch-Institut, Berlin, Deutschland
| | - Lars Schaade
- Zentrum für Biologische Gefahren und Spezielle Pathogene (ZBS), Robert Koch-Institut, Berlin, Deutschland
| | - Dunja Said
- Abteilung für Infektionsepidemiologie, Robert Koch-Institut, Berlin, Deutschland
| | - Walter Haas
- Abteilung für Infektionsepidemiologie, Robert Koch-Institut, Berlin, Deutschland
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21
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Hufsky F, Lamkiewicz K, Almeida A, Aouacheria A, Arighi C, Bateman A, Baumbach J, Beerenwinkel N, Brandt C, Cacciabue M, Chuguransky S, Drechsel O, Finn RD, Fritz A, Fuchs S, Hattab G, Hauschild AC, Heider D, Hoffmann M, Hölzer M, Hoops S, Kaderali L, Kalvari I, von Kleist M, Kmiecinski R, Kühnert D, Lasso G, Libin P, List M, Löchel HF, Martin MJ, Martin R, Matschinske J, McHardy AC, Mendes P, Mistry J, Navratil V, Nawrocki EP, O’Toole ÁN, Ontiveros-Palacios N, Petrov AI, Rangel-Pineros G, Redaschi N, Reimering S, Reinert K, Reyes A, Richardson L, Robertson DL, Sadegh S, Singer JB, Theys K, Upton C, Welzel M, Williams L, Marz M. Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. Brief Bioinform 2021; 22:642-663. [PMID: 33147627 PMCID: PMC7665365 DOI: 10.1093/bib/bbaa232] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [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: 05/27/2020] [Revised: 07/28/2020] [Accepted: 08/26/2020] [Indexed: 12/16/2022] Open
Abstract
SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causes the infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformatics tools designed explicitly for SARS-CoV-2 have only recently been developed as a rapid reaction to the need for fast detection, understanding and treatment of COVID-19. To control the ongoing COVID-19 pandemic, it is of utmost importance to get insight into the evolution and pathogenesis of the virus. In this review, we cover bioinformatics workflows and tools for the routine detection of SARS-CoV-2 infection, the reliable analysis of sequencing data, the tracking of the COVID-19 pandemic and evaluation of containment measures, the study of coronavirus evolution, the discovery of potential drug targets and development of therapeutic strategies. For each tool, we briefly describe its use case and how it advances research specifically for SARS-CoV-2. All tools are free to use and available online, either through web applications or public code repositories. Contact:evbc@unj-jena.de.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Christian Brandt
- Institute of Infectious Disease and Infection Control at Jena University Hospital, Germany
| | - Marco Cacciabue
- Consejo Nacional de Investigaciones Científicas y Tócnicas (CONICET) working on FMDV virology at the Instituto de Agrobiotecnología y Biología Molecular (IABiMo, INTA-CONICET) and at the Departamento de Ciencias Básicas, Universidad Nacional de Luján (UNLu), Argentina
| | | | - Oliver Drechsel
- bioinformatics department at the Robert Koch-Institute, Germany
| | | | - Adrian Fritz
- Computational Biology of Infection Research group of Alice C. McHardy at the Helmholtz Centre for Infection Research, Germany
| | - Stephan Fuchs
- bioinformatics department at the Robert Koch-Institute, Germany
| | - Georges Hattab
- Bioinformatics Division at Philipps-University Marburg, Germany
| | | | - Dominik Heider
- Data Science in Biomedicine at the Philipps-University of Marburg, Germany
| | | | | | - Stefan Hoops
- Biocomplexity Institute and Initiative at the University of Virginia, USA
| | - Lars Kaderali
- Bioinformatics and head of the Institute of Bioinformatics at University Medicine Greifswald, Germany
| | | | - Max von Kleist
- bioinformatics department at the Robert Koch-Institute, Germany
| | - Renó Kmiecinski
- bioinformatics department at the Robert Koch-Institute, Germany
| | | | - Gorka Lasso
- Chandran Lab, Albert Einstein College of Medicine, USA
| | | | | | | | | | | | | | - Alice C McHardy
- Computational Biology of Infection Research Lab at the Helmholtz Centre for Infection Research in Braunschweig, Germany
| | - Pedro Mendes
- Center for Quantitative Medicine of the University of Connecticut School of Medicine, USA
| | | | - Vincent Navratil
- Bioinformatics and Systems Biology at the Rhône Alpes Bioinformatics core facility, Universitó de Lyon, France
| | | | | | | | | | | | - Nicole Redaschi
- Development of the Swiss-Prot group at the SIB for UniProt and SIB resources that cover viral biology (ViralZone)
| | - Susanne Reimering
- Computational Biology of Infection Research group of Alice C. McHardy at the Helmholtz Centre for Infection Research
| | | | | | | | | | - Sepideh Sadegh
- Chair of Experimental Bioinformatics at Technical University of Munich, Germany
| | - Joshua B Singer
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, UK
| | | | - Chris Upton
- Department of Biochemistry and Microbiology, University of Victoria, Canada
| | | | | | - Manja Marz
- Friedrich Schiller University Jena, Germany
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22
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von Kleist M, García-Lerma JG, Liu A, Anderson PL. Editorial: Pharmacokinetics and Pharmacodynamics of Pre-Exposure Prophylaxis Against HIV. Front Pharmacol 2020; 11:1288. [PMID: 32982729 PMCID: PMC7479819 DOI: 10.3389/fphar.2020.01288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/04/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Max von Kleist
- MF1 Bioinformatics, Methods Development and Research Infrastructure (MF), Robert Koch Institute, Berlin, Germany.,Systems Pharmacology & Disease Control, Department of Mathematics, Freie Universität Berlin, Berlin, Germany
| | - J Gerardo García-Lerma
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Albert Liu
- Bridge HIV, San Francisco Department of Public Health, San Francisco, CA, United States
| | - Peter L Anderson
- Anschutz Medical Campus, University of Colorado, Denver, CO, United States
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23
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Richter AM, Possling A, Malysheva N, Yousef KP, Herbst S, von Kleist M, Hengge R. Local c-di-GMP Signaling in the Control of Synthesis of the E. coli Biofilm Exopolysaccharide pEtN-Cellulose. J Mol Biol 2020; 432:4576-4595. [PMID: 32534064 PMCID: PMC7397504 DOI: 10.1016/j.jmb.2020.06.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [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: 12/16/2019] [Revised: 05/20/2020] [Accepted: 06/08/2020] [Indexed: 12/17/2022]
Abstract
In many bacteria, the biofilm-promoting second messenger c-di-GMP is produced and degraded by multiple diguanylate cyclases (DGC) and phosphodiesterases (PDE), respectively. High target specificity of some of these enzymes has led to theoretical concepts of "local" c-di-GMP signaling. In Escherichia coli K-12, which has 12 DGCs and 13 PDEs, a single DGC, DgcC, is specifically required for the biosynthesis of the biofilm exopolysaccharide pEtN-cellulose without affecting the cellular c-di-GMP pool, but the mechanistic basis of this target specificity has remained obscure. DGC activity of membrane-associated DgcC, which is demonstrated in vitro in nanodiscs, is shown to be necessary and sufficient to specifically activate cellulose biosynthesis in vivo. DgcC and a particular PDE, PdeK (encoded right next to the cellulose operon), directly interact with cellulose synthase subunit BcsB and with each other, thus establishing physical proximity between cellulose synthase and a local source and sink of c-di-GMP. This arrangement provides a localized, yet open source of c-di-GMP right next to cellulose synthase subunit BcsA, which needs allosteric activation by c-di-GMP. Through mathematical modeling and simulation, we demonstrate that BcsA binding from the low cytosolic c-di-GMP pool in E. coli is negligible, whereas a single c-di-GMP molecule that is produced and released in direct proximity to cellulose synthase increases the probability of c-di-GMP binding to BcsA several hundred-fold. This local c-di-GMP signaling could provide a blueprint for target-specific second messenger signaling also in other bacteria where multiple second messenger producing and degrading enzymes exist.
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Affiliation(s)
- Anja M Richter
- Institute of Biology/Microbiology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany; Department of Materials and the Environment, Bundesanstalt für Materialforschung und -Prüfung, 12205 Berlin, Germany
| | - Alexandra Possling
- Institute of Biology/Microbiology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Nadezhda Malysheva
- Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany; MF1 Bioinformatics, Robert-Koch-Institut, 13353 Berlin, Germany
| | - Kaveh P Yousef
- Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany
| | - Susanne Herbst
- Institute of Biology/Microbiology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Max von Kleist
- Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany; MF1 Bioinformatics, Robert-Koch-Institut, 13353 Berlin, Germany
| | - Regine Hengge
- Institute of Biology/Microbiology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
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24
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Rettig A, Haase T, Pletnyov A, Kohl B, Ertel W, von Kleist M, Sunkara V. SLCV-a supervised learning-computer vision combined strategy for automated muscle fibre detection in cross-sectional images. PeerJ 2019; 7:e7053. [PMID: 31367478 PMCID: PMC6657690 DOI: 10.7717/peerj.7053] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 05/02/2019] [Indexed: 11/20/2022] Open
Abstract
Muscle fibre cross-sectional area (CSA) is an important biomedical measure used to determine the structural composition of skeletal muscle, and it is relevant for tackling research questions in many different fields of research. To date, time consuming and tedious manual delineation of muscle fibres is often used to determine the CSA. Few methods are able to automatically detect muscle fibres in muscle fibre cross-sections to quantify CSA due to challenges posed by variation of brightness and noise in the staining images. In this paper, we introduce the supervised learning-computer vision combined pipeline (SLCV), a robust semi-automatic pipeline for muscle fibre detection, which combines supervised learning (SL) with computer vision (CV). SLCV is adaptable to different staining methods and is quickly and intuitively tunable by the user. We are the first to perform an error analysis with respect to cell count and area, based on which we compare SLCV to the best purely CV-based pipeline in order to identify the contribution of SL and CV steps to muscle fibre detection. Our results obtained on 27 fluorescence-stained cross-sectional images of varying staining quality suggest that combining SL and CV performs significantly better than both SL-based and CV-based methods with regards to both the cell separation- and the area reconstruction error. Furthermore, applying SLCV to our test set images yielded fibre detection results of very high quality, with average sensitivity values of 0.93 or higher on different cluster sizes and an average Dice similarity coefficient of 0.9778.
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Affiliation(s)
- Anika Rettig
- Systems Pharmacology and Disease Control, Freie Universität Berlin, Berlin, Germany
| | - Tobias Haase
- Department of Traumatology and Reconstructive Surgery, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Alexandr Pletnyov
- Department of Traumatology and Reconstructive Surgery, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Benjamin Kohl
- Department of Traumatology and Reconstructive Surgery, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Wolfgang Ertel
- Department of Traumatology and Reconstructive Surgery, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Max von Kleist
- Systems Pharmacology and Disease Control, Freie Universität Berlin, Berlin, Germany
| | - Vikram Sunkara
- Systems Pharmacology and Disease Control, Freie Universität Berlin, Berlin, Germany.,Computational Medicine, Zuse Institute Berlin, Berlin, Germany
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25
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Özel MN, Kulkarni A, Hasan A, Brummer J, Moldenhauer M, Daumann IM, Wolfenberg H, Dercksen VJ, Kiral FR, Weiser M, Prohaska S, von Kleist M, Hiesinger PR. Serial Synapse Formation through Filopodial Competition for Synaptic Seeding Factors. Dev Cell 2019; 50:447-461.e8. [PMID: 31353313 DOI: 10.1016/j.devcel.2019.06.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 05/15/2019] [Accepted: 06/21/2019] [Indexed: 11/15/2022]
Abstract
Following axon pathfinding, growth cones transition from stochastic filopodial exploration to the formation of a limited number of synapses. How the interplay of filopodia and synapse assembly ensures robust connectivity in the brain has remained a challenging problem. Here, we developed a new 4D analysis method for filopodial dynamics and a data-driven computational model of synapse formation for R7 photoreceptor axons in developing Drosophila brains. Our live data support a "serial synapse formation" model, where at any time point only 1-2 "synaptogenic" filopodia suppress the synaptic competence of other filopodia through competition for synaptic seeding factors. Loss of the synaptic seeding factors Syd-1 and Liprin-α leads to a loss of this suppression, filopodial destabilization, and reduced synapse formation. The failure to form synapses can cause the destabilization and secondary retraction of axon terminals. Our model provides a filopodial "winner-takes-all" mechanism that ensures the formation of an appropriate number of synapses.
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Affiliation(s)
- M Neset Özel
- Division of Neurobiology, Institute for Biology, Freie Universität Berlin, 14195 Berlin, Germany; Neuroscience Graduate Program, UT Southwestern Medical Center Dallas, Dallas, TX 75390, USA
| | - Abhishek Kulkarni
- Division of Neurobiology, Institute for Biology, Freie Universität Berlin, 14195 Berlin, Germany
| | - Amr Hasan
- Division of Neurobiology, Institute for Biology, Freie Universität Berlin, 14195 Berlin, Germany
| | - Josephine Brummer
- Department of Visual Data Analysis, Zuse Institute Berlin, 14195 Berlin, Germany
| | - Marian Moldenhauer
- Computational Medicine and Numerical Mathematics, Zuse Institute Berlin, 14195 Berlin, Germany; Department of Mathematics and Informatics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Ilsa-Maria Daumann
- Division of Neurobiology, Institute for Biology, Freie Universität Berlin, 14195 Berlin, Germany
| | - Heike Wolfenberg
- Division of Neurobiology, Institute for Biology, Freie Universität Berlin, 14195 Berlin, Germany
| | - Vincent J Dercksen
- Department of Visual Data Analysis, Zuse Institute Berlin, 14195 Berlin, Germany
| | - F Ridvan Kiral
- Division of Neurobiology, Institute for Biology, Freie Universität Berlin, 14195 Berlin, Germany
| | - Martin Weiser
- Computational Medicine and Numerical Mathematics, Zuse Institute Berlin, 14195 Berlin, Germany
| | - Steffen Prohaska
- Department of Visual Data Analysis, Zuse Institute Berlin, 14195 Berlin, Germany
| | - Max von Kleist
- Department of Mathematics and Informatics, Freie Universität Berlin, 14195 Berlin, Germany.
| | - P Robin Hiesinger
- Division of Neurobiology, Institute for Biology, Freie Universität Berlin, 14195 Berlin, Germany.
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Duwal S, Seeler D, Dickinson L, Khoo S, von Kleist M. The Utility of Efavirenz-based Prophylaxis Against HIV Infection. A Systems Pharmacological Analysis. Front Pharmacol 2019; 10:199. [PMID: 30918485 PMCID: PMC6424904 DOI: 10.3389/fphar.2019.00199] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 02/18/2019] [Indexed: 11/13/2022] Open
Abstract
Pre-exposure prophylaxis (PrEP) is considered one of the five “pillars” by UNAIDS to reduce HIV transmission. Moreover, it is a tool for female self-protection against HIV, making it highly relevant to sub-Saharan regions, where women have the highest infection burden. To date, Truvada is the only medication for PrEP. However, the cost of Truvada limits its uptake in resource-constrained countries. Similarly, several currently investigated, patent-protected compounds may be unaffordable in these regions. We set out to explore the potential of the patent-expired antiviral efavirenz (EFV) as a cost-efficient PrEP alternative. A population pharmacokinetic model utilizing data from the ENCORE1 study was developed. The model was refined for metabolic autoinduction. We then explored EFV cellular uptake mechanisms, finding that it is largely determined by plasma protein binding. Next, we predicted the prophylactic efficacy of various EFV dosing schemes after exposure to HIV using a stochastic simulation framework. We predicted that plasma concentrations of 11, 36, 1287 and 1486ng/mL prevent 90% sexual transmissions with wild type and Y181C, K103N and G190S mutants, respectively. Trough concentrations achieved after 600 mg once daily dosing (median: 2017 ng/mL, 95% CI:445–9830) and after reduced dose (400 mg) efavirenz (median: 1349ng/mL, 95% CI: 297–6553) provided complete protection against wild-type virus and the Y181C mutant, and median trough concentrations provided about 90% protection against the K103N and G190S mutants. As reduced dose EFV has a lower toxicity profile, we predicted the reduction in HIV infection when 400 mg EFV-PrEP was poorly adhered to, when it was taken “on demand” and as post-exposure prophylaxis (PEP). Once daily EFV-PrEP provided 99% protection against wild-type virus, if ≥50% of doses were taken. PrEP “on demand” provided complete protection against wild-type virus and prevented ≥81% infections in the mutants. PEP could prevent >98% infection with susceptible virus when initiated within 24 h after virus exposure and continued for at least 9 days. We predict that 400 mg oral EFV may provide superior protection against wild-type HIV. However, further studies are warranted to evaluate EFV as a cost-efficient alternative to Truvada. Predicted prophylactic concentrations may guide release kinetics of EFV long-acting formulations for clinical trial design.
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Affiliation(s)
- Sulav Duwal
- Department of Mathematics and Computer Science, Systems Pharmacology and Disease Control, Institute of Bioinformatics, Freie Universität Berlin, Berlin, Germany
| | - Daniel Seeler
- Department of Mathematics and Computer Science, Systems Pharmacology and Disease Control, Institute of Bioinformatics, Freie Universität Berlin, Berlin, Germany
| | - Laura Dickinson
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, United Kingdom
| | - Saye Khoo
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, United Kingdom
| | - Max von Kleist
- Department of Mathematics and Computer Science, Systems Pharmacology and Disease Control, Institute of Bioinformatics, Freie Universität Berlin, Berlin, Germany
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Gupta P, Peter S, Jung M, Lewin A, Hemmrich-Stanisak G, Franke A, von Kleist M, Schütte C, Einspanier R, Sharbati S, Bruegge JZ. Analysis of long non-coding RNA and mRNA expression in bovine macrophages brings up novel aspects of Mycobacterium avium subspecies paratuberculosis infections. Sci Rep 2019; 9:1571. [PMID: 30733564 PMCID: PMC6367368 DOI: 10.1038/s41598-018-38141-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 12/18/2018] [Indexed: 12/12/2022] Open
Abstract
Paratuberculosis is a major disease in cattle that severely affects animal welfare and causes huge economic losses worldwide. Development of alternative diagnostic methods is of urgent need to control the disease. Recent studies suggest that long non-coding RNAs (lncRNAs) play a crucial role in regulating immune function and may confer valuable information about the disease. However, their role has not yet been investigated in cattle with respect to infection towards Paratuberculosis. Therefore, we investigated the alteration in genomic expression profiles of mRNA and lncRNA in bovine macrophages in response to Paratuberculosis infection using RNA-Seq. We identified 397 potentially novel lncRNA candidates in macrophages of which 38 were differentially regulated by the infection. A total of 820 coding genes were also significantly altered by the infection. Co-expression analysis of lncRNAs and their neighbouring coding genes suggest regulatory functions of lncRNAs in pathways related to immune response. For example, this included protein coding genes such as TNIP3, TNFAIP3 and NF-κB2 that play a role in NF-κB2 signalling, a pathway associated with immune response. This study advances our understanding of lncRNA roles during Paratuberculosis infection.
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Affiliation(s)
- Pooja Gupta
- Department of Mathematics and Informatics, Freie Universität Berlin, Berlin, Germany. .,Department of Mathematics for Life and Materials Sciences, Zuse Institute Berlin, Berlin, Germany.
| | - Sarah Peter
- Institute for the Reproduction of Farm Animals Schönow Inc, Bernau, Germany
| | - Markus Jung
- Institute for the Reproduction of Farm Animals Schönow Inc, Bernau, Germany
| | - Astrid Lewin
- Robert Koch-Institute, Department Infectious Diseases, Berlin, Germany
| | | | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Max von Kleist
- Department of Mathematics and Informatics, Freie Universität Berlin, Berlin, Germany
| | - Christof Schütte
- Department of Mathematics and Informatics, Freie Universität Berlin, Berlin, Germany.,Department of Mathematics for Life and Materials Sciences, Zuse Institute Berlin, Berlin, Germany
| | - Ralf Einspanier
- Institute of Veterinary Biochemistry, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Soroush Sharbati
- Institute of Veterinary Biochemistry, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Jennifer Zur Bruegge
- Institute of Veterinary Biochemistry, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
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Duwal S, Dickinson L, Khoo S, von Kleist M. Mechanistic framework predicts drug-class specific utility of antiretrovirals for HIV prophylaxis. PLoS Comput Biol 2019; 15:e1006740. [PMID: 30699105 PMCID: PMC6370240 DOI: 10.1371/journal.pcbi.1006740] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 12/22/2017] [Revised: 02/11/2019] [Accepted: 12/20/2018] [Indexed: 11/21/2022] Open
Abstract
Currently, there is no effective vaccine to halt HIV transmission. However, pre-exposure prophylaxis (PrEP) with the drug combination Truvada can substantially decrease HIV transmission in individuals at risk. Despite its benefits, Truvada-based PrEP is expensive and needs to be taken once-daily, which often leads to inadequate adherence and incomplete protection. These deficits may be overcome by next-generation PrEP regimen, including currently investigated long-acting formulations, or patent-expired drugs. However, poor translatability of animal- and ex vivo/in vitro experiments, and the necessity to conduct long-term (several years) human trials involving considerable sample sizes (N>1000 individuals) are major obstacles to rationalize drug-candidate selection. We developed a prophylaxis modelling tool that mechanistically considers the mode-of-action of all available drugs. We used the tool to screen antivirals for their prophylactic utility and identify lower bound effective concentrations that can guide dose selection in PrEP trials. While in vitro measurable drug potency usually guides PrEP trial design, we found that it may over-predict PrEP potency for all drug classes except reverse transcriptase inhibitors. While most drugs displayed graded concentration-prophylaxis profiles, protease inhibitors tended to switch between none- and complete protection. While several treatment-approved drugs could be ruled out as PrEP candidates based on lack-of-prophylactic efficacy, darunavir, efavirenz, nevirapine, etravirine and rilpivirine could more potently prevent infection than existing PrEP regimen (Truvada). Notably, some drugs from this candidate set are patent-expired and currently neglected for PrEP repurposing. A next step is to further trim this candidate set by ruling out compounds with ominous safety profiles, to assess different administration schemes in silico and to test the remaining candidates in human trials. Pre-exposure prophylaxis (PrEP) is a novel, promising strategy to halt HIV transmission. PrEP with Truvada can substantially decrease the risk of infection. However, individuals often inadequately adhere to the once-daily regimen and the drug is expensive. These shortcomings may be overcome by next-generation PrEP compounds, including long-acting formulations. However, poor translatability of animal- and ex vivo/in vitro experiments, and difficulties in conducting long-term trials involving considerable sample sizes (N > 1000 individuals) make drug-candidate selection and optimization of administration schemes costly and often infeasible. We developed a simulation tool that mechanistically considers the mode-of-action of all antivirals. We used the tool to screen all available antivirals for their prophylactic utility and identified lower bound effective concentrations for designing PrEP dosing regimen in clinical trials. We found that in vitro measured drug potency may over-predict PrEP potency, for all antiviral classes except reverse transcriptase inhibitors. We could rule out a number of antivirals for PrEP repurposing and predicted that darunavir, efavirenz, nevirapine, etravirine and rilpivirine provide complete protection at clinically relevant concentrations. Further trimming of this candidate set by compound-safety and by assessing different implementation schemes is envisaged.
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Affiliation(s)
- Sulav Duwal
- Department of Mathematics & Computer Science, Freie Universität Berlin, Germany
- * E-mail: (SD); (MvK)
| | - Laura Dickinson
- Institute of Translational Medicine, University of Liverpool, United Kingdom
| | - Saye Khoo
- Institute of Translational Medicine, University of Liverpool, United Kingdom
| | - Max von Kleist
- Department of Mathematics & Computer Science, Freie Universität Berlin, Germany
- * E-mail: (SD); (MvK)
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Duwal S, Dickinson L, Khoo S, von Kleist M. Hybrid stochastic framework predicts efficacy of prophylaxis against HIV: An example with different dolutegravir prophylaxis schemes. PLoS Comput Biol 2018; 14:e1006155. [PMID: 29902179 PMCID: PMC6001963 DOI: 10.1371/journal.pcbi.1006155] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 12/22/2017] [Accepted: 04/21/2018] [Indexed: 01/02/2023] Open
Abstract
To achieve the 90-90-90 goals set by UNAIDS, the number of new HIV infections needs to decrease to approximately 500,000 by 2020. One of the 'five pillars' to achieve this goal is pre-exposure prophylaxis (PrEP). Truvada (emtricitabine-tenofovir) is currently the only medication approved for PrEP. Despite its advantages, Truvada is costly and requires individuals to adhere to the once-daily regimen. To improve PrEP, many next-generation regimen, including long-acting formulations, are currently investigated. However, pre-clinical testing may not guide candidate selection, since it often fails to translate into clinical efficacy. On the other hand, quantifying prophylactic efficacy in the clinic is ethically problematic and requires to conduct long (years) and large (N>1000 individuals) trials, precluding systematic evaluation of candidates and deployment strategies. To prioritize- and help design PrEP regimen, tools are urgently needed that integrate pharmacological-, viral- and host factors determining prophylactic efficacy. Integrating the aforementioned factors, we developed an efficient and exact stochastic simulation approach to predict prophylactic efficacy, as an example for dolutegravir (DTG). Combining the population pharmacokinetics of DTG with the stochastic framework, we predicted that plasma concentrations of 145.18 and 722.23nM prevent 50- and 90% sexual transmissions respectively. We then predicted the reduction in HIV infection when DTG was used in PrEP, PrEP 'on demand' and post-exposure prophylaxis (PEP) before/after virus exposure. Once daily PrEP with 50mg oral DTG prevented 99-100% infections, and 85% of infections when 50% of dosing events were missed. PrEP 'on demand' prevented 79-84% infections and PEP >80% when initiated within 6 hours after virus exposure and continued for as long as possible. While the simulation framework can easily be adapted to other PrEP candidates, our simulations indicated that oral 50mg DTG is non-inferior to Truvada. Moreover, the predicted 90% preventive concentrations can guide release kinetics of currently developed DTG nano-formulations.
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Affiliation(s)
- Sulav Duwal
- Department of Mathematics & Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Laura Dickinson
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Saye Khoo
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Max von Kleist
- Department of Mathematics & Computer Science, Freie Universität Berlin, Berlin, Germany
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Meixenberger K, Yousef KP, Smith MR, Somogyi S, Fiedler S, Bartmeyer B, Hamouda O, Bannert N, von Kleist M, Kücherer C. Molecular evolution of HIV-1 integrase during the 20 years prior to the first approval of integrase inhibitors. Virol J 2017; 14:223. [PMID: 29137637 PMCID: PMC5686839 DOI: 10.1186/s12985-017-0887-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [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: 04/12/2017] [Accepted: 10/31/2017] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Detailed knowledge of the evolutionary potential of polymorphic sites in a viral protein is important for understanding the development of drug resistance in the presence of an inhibitor. We therefore set out to analyse the molecular evolution of the HIV-1 subtype B integrase at the inter-patient level in Germany during a 20-year period prior to the first introduction of integrase strand inhibitors (INSTIs). METHODS We determined 337 HIV-1 integrase subtype B sequences (amino acids 1-278) from stored plasma samples of antiretroviral treatment-naïve individuals newly diagnosed with HIV-1 between 1986 and 2006. Shannon entropy was calculated to determine the variability at each amino acid position. Time trends in the frequency of amino acid variants were identified by linear regression. Direct coupling analysis was applied to detect covarying sites. RESULTS Twenty-two time trends in the frequency of amino acid variants demonstrated either single amino acid exchanges or variation in the degree of polymorphy. Covariation was observed for 17 amino acid variants with a temporal trend. Some minor INSTI resistance mutations (T124A, V151I, K156 N, T206S, S230 N) and some INSTI-selected mutations (M50I, L101I, T122I, T124 N, T125A, M154I, G193E, V201I) were identified at overall frequencies >5%. Among these, the frequencies of L101I, T122I, and V201I increased over time, whereas the frequency of M154I decreased. Moreover, L101I, T122I, T124A, T125A, M154I, and V201I covaried with non-resistance-associated variants. CONCLUSIONS Time-trending, covarying polymorphisms indicate that long-term evolutionary changes of the HIV-1 integrase involve defined clusters of possibly structurally or functionally associated sites independent of selective pressure through INSTIs at the inter-patient level. Linkage between polymorphic resistance- and non-resistance-associated sites can impact the selection of INSTI resistance mutations in complex ways. Identification of these sites can help in improving genotypic resistance assays, resistance prediction algorithms, and the development of new integrase inhibitors.
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Affiliation(s)
| | - Kaveh Pouran Yousef
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Maureen Rebecca Smith
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Sybille Somogyi
- HIV and other Retroviruses, Robert Koch Institute, Berlin, Germany
| | - Stefan Fiedler
- HIV and other Retroviruses, Robert Koch Institute, Berlin, Germany
| | - Barbara Bartmeyer
- HIV/AIDS, STI and Blood-borne Infections, Robert Koch Institute, Berlin, Germany
| | - Osamah Hamouda
- HIV/AIDS, STI and Blood-borne Infections, Robert Koch Institute, Berlin, Germany
| | - Norbert Bannert
- HIV and other Retroviruses, Robert Koch Institute, Berlin, Germany
| | - Max von Kleist
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Claudia Kücherer
- HIV and other Retroviruses, Robert Koch Institute, Berlin, Germany
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Smith MR, Smyth RP, Marquet R, von Kleist M. MIMEAnTo: profiling functional RNA in mutational interference mapping experiments. Bioinformatics 2016; 32:3369-3370. [PMID: 27402903 DOI: 10.1093/bioinformatics/btw479] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 07/06/2016] [Indexed: 11/14/2022] Open
Abstract
The mutational interference mapping experiment (MIME) is a powerful method that, coupled to a bioinformatics analysis pipeline, allows the identification of domains and structures in RNA that are important for its function. In MIME, target RNAs are randomly mutated, selected by function, physically separated and sequenced using next-generation sequencing (NGS). Quantitative effects of each mutation at each position in the RNA can be recovered with statistical certainty using the herein developed user-friendly, cross-platform software MIMEAnTo (MIME Analysis Tool). AVAILABILITY AND IMPLEMENTATION MIMEAnTo is implemented in C ++ using the boost library as well as Qt for the graphical user interface and is distributed under GPL (http://www.gnu.org/licences/gpl). The libraries are statically linked in a stand alone executable and are not required on the system. The plots are generated with gnuplot. Gnuplot-iostream (https://github.com/dstahlke/gnuplot-iostream) serves as gnuplot interface. Standalone executables including examples and source code can be downloaded from https://github.com/maureensmith/MIMEAnTo CONTACTS: msmith@zedat.fu-berlin.de or vkleist@zedat.fu-berlin.deSupplementary information: Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Maureen R Smith
- Systems Pharmacology & Disease Control, Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Redmond P Smyth
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg, France
| | - Roland Marquet
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg, France
| | - Max von Kleist
- Systems Pharmacology & Disease Control, Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
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Duwal S, Winkelmann S, Schütte C, von Kleist M. Optimal Treatment Strategies in the Context of 'Treatment for Prevention' against HIV-1 in Resource-Poor Settings. PLoS Comput Biol 2015; 11:e1004200. [PMID: 25927964 PMCID: PMC4423987 DOI: 10.1371/journal.pcbi.1004200] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [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: 06/17/2014] [Accepted: 02/18/2015] [Indexed: 12/15/2022] Open
Abstract
An estimated 2.7 million new HIV-1 infections occurred in 2010. `Treatment-for-prevention’ may strongly prevent HIV-1 transmission. The basic idea is that immediate treatment initiation rapidly decreases virus burden, which reduces the number of transmittable viruses and thereby the probability of infection. However, HIV inevitably develops drug resistance, which leads to virus rebound and nullifies the effect of `treatment-for-prevention’ for the time it remains unrecognized. While timely conducted treatment changes may avert periods of viral rebound, necessary treatment options and diagnostics may be lacking in resource-constrained settings. Within this work, we provide a mathematical platform for comparing different treatment paradigms that can be applied to many medical phenomena. We use this platform to optimize two distinct approaches for the treatment of HIV-1: (i) a diagnostic-guided treatment strategy, based on infrequent and patient-specific diagnostic schedules and (ii) a pro-active strategy that allows treatment adaptation prior to diagnostic ascertainment. Both strategies are compared to current clinical protocols (standard of care and the HPTN052 protocol) in terms of patient health, economic means and reduction in HIV-1 onward transmission exemplarily for South Africa. All therapeutic strategies are assessed using a coarse-grained stochastic model of within-host HIV dynamics and pseudo-codes for solving the respective optimal control problems are provided. Our mathematical model suggests that both optimal strategies (i)-(ii) perform better than the current clinical protocols and no treatment in terms of economic means, life prolongation and reduction of HIV-transmission. The optimal diagnostic-guided strategy suggests rare diagnostics and performs similar to the optimal pro-active strategy. Our results suggest that ‘treatment-for-prevention’ may be further improved using either of the two analyzed treatment paradigms. HIV-1 continues to spread globally. Antiviral treatment cannot cure patients, but it slows disease progression and may prevent HIV transmission by decreasing the amount of transmittable viruses in treated individuals. ‘Treatment-for-prevention’ argues for immediate treatment initiation and may reduce transmission by 96% (CI: 73–99%), according to the results of a large clinical study (HPTN052). In order to ensure long-lasting treatment success, early therapy initiation demands more sophisticated treatment strategies & exceeding funds. However, countries facing the highest HIV burden are among the poorest. Within this work, we provide a mathematical framework that allows assessing different treatment paradigms using optimal control theory together with stochastic modelling of within-host viral dynamics and drug resistance development. We use this framework to compute and evaluate two distinct optimal long-term treatment strategies for resource-constrained settings: (i) a diagnostic-guided and (ii) a pro-active treatment strategy. The cost of a strategy is evaluated from a national economic perspective, valuating a severe patient health status in terms of an economic loss. The optimal strategies are compared with current clinical treatment protocols and no treatment in terms of costs, life expectation and reduction of secondary cases. Our simulations indicate that the pro-active treatment strategy performs comparably to the diagnostic-guided treatment strategy. Both strategies perform better than current clinical protocols, suggesting directions for improvement.
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Affiliation(s)
- Sulav Duwal
- Department of Mathematics and Computer Science, Freie Universität Berlin, Germany
- Junior Research Group “Systems Pharmacology & Disease Control”
| | - Stefanie Winkelmann
- Department of Mathematics and Computer Science, Freie Universität Berlin, Germany
| | - Christof Schütte
- Department of Mathematics and Computer Science, Freie Universität Berlin, Germany
- Zuse Institute Berlin, Germany
| | - Max von Kleist
- Department of Mathematics and Computer Science, Freie Universität Berlin, Germany
- Junior Research Group “Systems Pharmacology & Disease Control”
- * E-mail:
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Chen X, Pouran Yousef K, Duwe S, Karsch K, Grover S, Wählisch S, Obermeier P, Tief F, Mühlhans S, Seeber L, von Kleist M, Schweiger B, Rath B. Quantitative influenza follow-up testing (QIFT)--a novel biomarker for the monitoring of disease activity at the point-of-care. PLoS One 2014; 9:e92500. [PMID: 24658130 PMCID: PMC3962407 DOI: 10.1371/journal.pone.0092500] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [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: 12/21/2013] [Accepted: 02/21/2014] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Influenza infections induce considerable disease burden in young children. Biomarkers for the monitoring of disease activity at the point-of-care (POC) are currently lacking. Recent methodologies for fluorescence-based rapid testing have been developed to provide improved sensitivities with the initial diagnosis. The present study aims to explore the utility of second-generation rapid testing during longitudinal follow-up of influenza patients (Rapid Influenza Follow-up Testing = RIFT). Signal/control fluorescent readouts (Quantitative Influenza Follow-up Testing = QIFT) are evaluated as a potential biomarker for the monitoring of disease activity at the POC. METHODS AND FINDINGS RIFT (SOFIA) and QIFT were performed at the POC and compared to blinded RT-PCR at the National Reference Centre for Influenza. From 10/2011-4/2013, a total of 2048 paediatric cases were studied prospectively; 273 cases were PCR-confirmed for influenza. During follow-up, RIFT results turned negative either prior to PCR (68%), or simultaneously (30%). The first negative RIFT occurred after a median of 8 days with a median virus load (VL) of 5.6×10∧3 copies/ml and cycle threshold of 37, with no evidence of viral rebound. Binning analysis revealed that QIFT differentiated accurately between patients with low, medium and high viral titres. QIFT increase/decrease showed 88% agreement (sensitivity = 52%, specificity = 95%) with VL increase/decrease, respectively. QIFT-based viral clearance estimates showed similar values compared to PCR-based estimates. Variations in viral clearance rates were lower in treated compared to untreated patients. The study was limited by use of non-invasive, semi-quantitative nasopharyngeal samples. VL measurements below the limit of detection could not be quantified reliably. CONCLUSIONS During follow-up, RIFT provides a first surrogate measure for influenza disease activity. A "switch" from positive to negative values may indicate a drop in viral load below a critical threshold, where rebound is no longer expected. QIFT may provide a useful tool for the monitoring of disease burden and viral clearance at the POC.
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Affiliation(s)
- Xi Chen
- Department of Paediatrics, Division of Pneumonology-Immunology, Charité University Medical Centre, Berlin, Germany
| | - Kaveh Pouran Yousef
- AG systems Pharmacology & Disease Control, Department of Mathematics and Computer Science, Free University Berlin, Berlin, Germany
| | - Susanne Duwe
- Robert Koch Institute, Division 17 Influenza and Other Respiratory Viruses, National Reference Centre for Influenza, Berlin, Germany
| | - Katharina Karsch
- Department of Paediatrics, Division of Pneumonology-Immunology, Charité University Medical Centre, Berlin, Germany
| | - Sandeep Grover
- Department of Paediatrics, Division of Pneumonology-Immunology, Charité University Medical Centre, Berlin, Germany
| | - Stephanie Wählisch
- Robert Koch Institute, Division 17 Influenza and Other Respiratory Viruses, National Reference Centre for Influenza, Berlin, Germany
| | - Patrick Obermeier
- Department of Paediatrics, Division of Pneumonology-Immunology, Charité University Medical Centre, Berlin, Germany
| | - Franziska Tief
- Department of Paediatrics, Division of Pneumonology-Immunology, Charité University Medical Centre, Berlin, Germany
| | - Susann Mühlhans
- Department of Paediatrics, Division of Pneumonology-Immunology, Charité University Medical Centre, Berlin, Germany
| | - Lea Seeber
- Department of Paediatrics, Division of Pneumonology-Immunology, Charité University Medical Centre, Berlin, Germany
| | - Max von Kleist
- AG systems Pharmacology & Disease Control, Department of Mathematics and Computer Science, Free University Berlin, Berlin, Germany
| | - Brunhilde Schweiger
- Robert Koch Institute, Division 17 Influenza and Other Respiratory Viruses, National Reference Centre for Influenza, Berlin, Germany
| | - Barbara Rath
- Department of Paediatrics, Division of Pneumonology-Immunology, Charité University Medical Centre, Berlin, Germany
- * E-mail:
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Rath B, Tief F, Karsch K, Muehlhans S, Obermeier P, Adamou E, Chen X, Seeber L, Peiser C, Hoppe C, von Kleist M, Conrad T, Schweiger B. Towards a personalised approach to managing influenza infections in infants and children - food for thought and a note on oseltamivir. Infect Disord Drug Targets 2014; 13:25-33. [PMID: 23675924 DOI: 10.2174/18715265112129990005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 04/22/2013] [Indexed: 11/22/2022]
Abstract
Acute respiratory infections represent common diseases in childhood and a challenge to infection control, public heath, and the clinical management of patients and their families. Children are avid spreaders of respiratory viruses, and seasonal outbreaks of influenza create additional disease burden and healthcare cost. Infants under the age of two and children with chronic conditions are at high risk. The absence of pre-defined risk factors however, does not protect from serious disease. Immunisation rates remain low, and physical interventions are of limited value in young children. Children with influenza may be contagious prior to the onset of symptoms, and school closures have been shown to have a temporary effect at most. The timely detection of influenza in at-risk patients is important to prevent hospital-based transmission and influenza-associated morbidity and mortality. Guidelines issued by professional associations and public health agencies need to be translated into everyday clinical practice. Antiviral therapy should be initiated early and monitored closely, including virologic and clinical outcomes. The duration of treatment and the decision to readmit children to schools and kindergartens should be adjusted to the individual child patient using evidence-based clinical and virologic criteria. This article presents lessons learnt from a quality management program for infants and children with influenza-like illness at the Charite Department of Paediatrics in collaboration with the National Reference Centre for Influenza at the Robert Koch Institute, in Berlin, Germany. The Charité Influenza-Like Disease (ChILD) Cohort was established during the 2009 influenza pandemic and encompasses nearly 4000 disease episodes to date.
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Affiliation(s)
- Barbara Rath
- Department of Pediatrics, Division of Pneumonology-Immunology, Charité University Medical Center, Augustenburger Platz 1, 13353 Berlin,
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Rath BA, Yousef KP, Katzenstein DK, Shafer RW, Schütte C, von Kleist M, Merigan TC. In vitro HIV-1 evolution in response to triple reverse transcriptase inhibitors & in silico phenotypic analysis. PLoS One 2013; 8:e61102. [PMID: 23613794 PMCID: PMC3629221 DOI: 10.1371/journal.pone.0061102] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [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: 11/11/2012] [Accepted: 03/05/2013] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Effectiveness of ART regimens strongly depends upon complex interactions between the selective pressure of drugs and the evolution of mutations that allow or restrict drug resistance. METHODS Four clinical isolates from NRTI-exposed, NNRTI-naive subjects were passaged in increasing concentrations of NVP in combination with 1 µM 3 TC and 2 µM ADV to assess selective pressures of multi-drug treatment. A novel parameter inference procedure, based on a stochastic viral growth model, was used to estimate phenotypic resistance and fitness from in vitro combination passage experiments. RESULTS Newly developed mathematical methods estimated key phenotypic parameters of mutations arising through selective pressure exerted by 3 TC and NVP. Concentrations of 1 µM 3 TC maintained the M184V mutation, which was associated with intrinsic fitness deficits. Increasing NVP concentrations selected major NNRTI resistance mutations. The evolutionary pathway of NVP resistance was highly dependent on the viral genetic background, epistasis as well as stochasticity. Parameter estimation indicated that the previously unrecognized mutation L228Q was associated with NVP resistance in some isolates. CONCLUSION Serial passage of viruses in the presence of multiple drugs may resemble the selection of mutations observed among treated individuals and populations in vivo and indicate evolutionary preferences and restrictions. Phenotypic resistance estimated here "in silico" from in vitro passage experiments agreed well with previous knowledge, suggesting that the unique combination of "wet-" and "dry-lab" experimentation may improve our understanding of HIV-1 resistance evolution in the future.
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Affiliation(s)
- Barbara A. Rath
- Department of Pediatrics, Division of Pneumonology-Immunology, Charité University Medical Center, Berlin, Germany
- Center for AIDS Research, Stanford University Medical Center, Stanford, California, United States of America
| | - Kaveh Pouran Yousef
- Department of Mathematics and Computer Science, Free University, Berlin, Germany
| | - David K. Katzenstein
- Center for AIDS Research, Stanford University Medical Center, Stanford, California, United States of America
| | - Robert W. Shafer
- Center for AIDS Research, Stanford University Medical Center, Stanford, California, United States of America
| | - Christof Schütte
- Department of Mathematics and Computer Science, Free University, Berlin, Germany
| | - Max von Kleist
- Department of Mathematics and Computer Science, Free University, Berlin, Germany
| | - Thomas C. Merigan
- Center for AIDS Research, Stanford University Medical Center, Stanford, California, United States of America
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Duwal S, Schütte C, von Kleist M. Pharmacokinetics and pharmacodynamics of the reverse transcriptase inhibitor tenofovir and prophylactic efficacy against HIV-1 infection. PLoS One 2012; 7:e40382. [PMID: 22808148 PMCID: PMC3394807 DOI: 10.1371/journal.pone.0040382] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [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: 03/02/2012] [Accepted: 06/05/2012] [Indexed: 11/18/2022] Open
Abstract
Antiviral pre-exposure prophylaxis (PrEP) through daily drug administration can protect healthy individuals from HIV-1 infection. While PrEP was recently approved by the FDA, the potential long-term consequences of PrEP implementation remain entirely unclear. The aim of this study is to predict the efficacy of different prophylactic strategies with the pro-drug tenofovir-disoproxil-fumarate (TDF) and to assess the sensitivity towards timing- and mode of TDF administration (daily- vs. single dose), adherence and the number of transmitted viruses. We developed a pharmacokinetic model for TDF and its active anabolite tenofovir-diphosphate (TFV-DP) and validated it with data from 4 different trials, including 4 distinct dosing regimes. Pharmacokinetics were coupled to an HIV model and viral decay following TDF mono-therapy was predicted, consistent with available data. Subsequently, a stochastic approach was used to estimate the % infections prevented by (i) daily TDF-based PrEP, (ii) one week TDF started either shortly before, or -after viral exposure and (iii) a single dose oral TDF before viral challenge (sd-PrEP). Analytical solutions were derived to assess the relation between intracellular TFV-DP concentrations and prophylactic efficacy. The predicted efficacy of TDF was limited by a slow accumulation of active compound (TFV-DP) and variable TFV-DP half-life and decreased with increasing numbers of transmitted viruses. Once daily TDF-based PrEP yielded [Formula: see text]80% protection, if at least 40% of pills were taken. Sd-PrEP with 300 mg or 600 mg TDF could prevent [Formula: see text]50% infections, when given at least before virus exposure. The efficacy dropped to [Formula: see text]10%, when given 1 h before 24 h exposure. Efficacy could not be increased with increasing dosage or prolonged administration. Post-exposure prophylaxis poorly prevented infection. The use of drugs that accumulate more rapidly, or local application of tenofovir gel may overcome the need for drug administration long before virus exposure.
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Affiliation(s)
- Sulav Duwal
- Department of Mathematics and Computer Science, Free University Berlin, Berlin, Germany
| | - Christof Schütte
- Department of Mathematics and Computer Science, Free University Berlin, Berlin, Germany
| | - Max von Kleist
- Department of Mathematics and Computer Science, Free University Berlin, Berlin, Germany
- * E-mail:
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von Kleist M, Metzner P, Marquet R, Schütte C. HIV-1 polymerase inhibition by nucleoside analogs: cellular- and kinetic parameters of efficacy, susceptibility and resistance selection. PLoS Comput Biol 2012; 8:e1002359. [PMID: 22275860 PMCID: PMC3261923 DOI: 10.1371/journal.pcbi.1002359] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [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: 08/01/2011] [Accepted: 12/05/2011] [Indexed: 11/30/2022] Open
Abstract
Nucleoside analogs (NAs) are used to treat numerous viral infections and cancer. They compete with endogenous nucleotides (dNTP/NTP) for incorporation into nascent DNA/RNA and inhibit replication by preventing subsequent primer extension. To date, an integrated mathematical model that could allow the analysis of their mechanism of action, of the various resistance mechanisms, and their effect on viral fitness is still lacking. We present the first mechanistic mathematical model of polymerase inhibition by NAs that takes into account the reversibility of polymerase inhibition. Analytical solutions for the model point out the cellular- and kinetic aspects of inhibition. Our model correctly predicts for HIV-1 that resistance against nucleoside analog reverse transcriptase inhibitors (NRTIs) can be conferred by decreasing their incorporation rate, increasing their excision rate, or decreasing their affinity for the polymerase enzyme. For all analyzed NRTIs and their combinations, model-predicted macroscopic parameters (efficacy, fitness and toxicity) were consistent with observations. NRTI efficacy was found to greatly vary between distinct target cells. Surprisingly, target cells with low dNTP/NTP levels may not confer hyper-susceptibility to inhibition, whereas cells with high dNTP/NTP contents are likely to confer natural resistance. Our model also allows quantification of the selective advantage of mutations by integrating their effects on viral fitness and drug susceptibility. For zidovudine triphosphate (AZT-TP), we predict that this selective advantage, as well as the minimal concentration required to select thymidine-associated mutations (TAMs) are highly cell-dependent. The developed model allows studying various resistance mechanisms, inherent fitness effects, selection forces and epistasis based on microscopic kinetic data. It can readily be embedded in extended models of the complete HIV-1 reverse transcription process, or analogous processes in other viruses and help to guide drug development and improve our understanding of the mechanisms of resistance development during treatment. Nucleoside analogs (NAs) represent an important drug class for the treatment of viral infections and cancer. They inhibit DNA/RNA polymerization after being incorporated into nascent DNA/RNA, which prevents primer extension. Viruses are particularly versatile and frequently develop mutations enabling them to avert the effects of NAs. The mechanisms of resistance development are, however, still poorly understood. Through mathematical modeling, we assess the mechanisms by which HIV-1 can develop resistance against nucleoside analog reverse transcriptase inhibitors (NRTI). We quantify the effects of treatment and estimate the fitness of drug resistant mutants. We correctly predict that HIV-1 can develop resistance by decreasing NRTI incorporation rate, increasing its excision rate, or decreasing its affinity for the viral polymerase enzyme. Our model also allows quantification of the cell specific factors affecting NRTI efficacy. Resistance development also changes drug susceptibility distinctly and we show, for the first time, that selection of drug resistance can occur in particular target cells. This finding could provide an explanation of how clinically observed resistant viral mutants may arise. It also pin-points important parameters that may impact clinical efficacy of NAs used to treat other viruses.
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Affiliation(s)
- Max von Kleist
- Department of Mathematics and Computer Science, Free University Berlin, Berlin, Germany.
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von Kleist M, Menz S, Huisinga W. Drug-class specific impact of antivirals on the reproductive capacity of HIV. PLoS Comput Biol 2010; 6:e1000720. [PMID: 20361047 PMCID: PMC2845651 DOI: 10.1371/journal.pcbi.1000720] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [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: 09/02/2009] [Accepted: 02/23/2010] [Indexed: 11/18/2022] Open
Abstract
Predictive markers linking drug efficacy to clinical outcome are a key component in the drug discovery and development process. In HIV infection, two different measures, viral load decay and phenotypic assays, are used to assess drug efficacy in vivo and in vitro. For the newly introduced class of integrase inhibitors, a huge discrepancy between these two measures of efficacy was observed. Hence, a thorough understanding of the relation between these two measures of drug efficacy is imperative for guiding future drug discovery and development activities in HIV. In this article, we developed a novel viral dynamics model, which allows for a mechanistic integration of the mode of action of all approved drugs and drugs in late clinical trials. Subsequently, we established a link between in vivo and in vitro measures of drug efficacy, and extract important determinants of drug efficacy in vivo. The analysis is based on a new quantity-the reproductive capacity-that represents in mathematical terms the in vivo analog of the read-out of a phenotypic assay. Our results suggest a drug-class specific impact of antivirals on the total amount of viral replication. Moreover, we showed that the (drug-)target half life, dominated by immune-system related clearance processes, is a key characteristic that affects both the emergence of resistance as well as the in vitro-in vivo correlation of efficacy measures in HIV treatment. We found that protease- and maturation inhibitors, due to their target half-life, decrease the total amount of viral replication and the emergence of resistance most efficiently.
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Affiliation(s)
- Max von Kleist
- Hamilton Institute, Computational Physiology Group, National University of Ireland Maynooth, Kildare, Ireland.
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von Kleist M, Huisinga W. Physiologically based pharmacokinetic modelling: a sub-compartmentalized model of tissue distribution. J Pharmacokinet Pharmacodyn 2007; 34:789-806. [PMID: 17899329 DOI: 10.1007/s10928-007-9071-3] [Citation(s) in RCA: 26] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2007] [Accepted: 08/15/2007] [Indexed: 11/25/2022]
Abstract
We present a sub-compartmentalized model of drug distribution in tissue that extends existing approaches based on the well-stirred tissue model. It is specified in terms of differential equations that explicitly account for the drug concentration in erythrocytes, plasma, interstitial and cellular space. Assuming, in addition, steady state drug distribution and by lumping the different sub-compartments, established models to predict tissue-plasma partition coefficients can be derived in an intriguingly simple way. This direct link is exploited to explicitly construct and parameterize the sub-compartmentalized model for moderate to strong bases, acids, neutrals and zwitterions. The derivation highlights the contributions of the different tissue constituents and provides a simple and transparent framework for the construction of novel tissue distribution models.
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Affiliation(s)
- Max von Kleist
- Department of Mathematics and Computer Science, and DFG Research Center Matheon, Freie Universität Berlin, Berlin, Germany
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