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Lungu C, Overmars RJ, Grundeken E, Boers PHM, van der Ende ME, Mesplède T, Gruters RA. Genotypic and Phenotypic Characterization of Replication-Competent HIV-2 Isolated from Controllers and Progressors. Viruses 2023; 15:2236. [PMID: 38005913 PMCID: PMC10675771 DOI: 10.3390/v15112236] [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: 09/29/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Although some individuals with HIV-2 develop severe immunodeficiency and AIDS-related complications, most may never progress to AIDS. Replication-competent HIV-2 isolated from asymptomatic long-term non-progressors (controllers) have lower replication rates than viruses from individuals who progress to AIDS (progressors). To investigate potential retroviral factors that correlate with disease progression in HIV-2, we sequenced the near full-length genomes of replication-competent viruses previously outgrown from controllers and progressors and used phylogeny to seek genotypic correlates of disease progression. We validated the integrity of all open reading frames and used cell-based assays to study the retroviral transcriptional activity of the long terminal repeats (LTRs) and Tat proteins of HIV-2 from controllers and progressors. Overall, we did not identify genotypic defects that may contribute to HIV-2 non-progression. Tat-induced, LTR-mediated transcription was comparable between viruses from controllers and progressors. Our results were obtained from a small number of participants and should be interpreted accordingly. Overall, they suggest that progression may be determined before or during integration of HIV-2.
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Affiliation(s)
- Cynthia Lungu
- Viroscience Department, Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands; (C.L.); (R.J.O.); (E.G.); (P.H.M.B.)
| | - Ronald J. Overmars
- Viroscience Department, Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands; (C.L.); (R.J.O.); (E.G.); (P.H.M.B.)
| | - Esmée Grundeken
- Viroscience Department, Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands; (C.L.); (R.J.O.); (E.G.); (P.H.M.B.)
| | - Patrick H. M. Boers
- Viroscience Department, Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands; (C.L.); (R.J.O.); (E.G.); (P.H.M.B.)
| | - Marchina E. van der Ende
- Department of Internal Medicine, Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands;
| | - Thibault Mesplède
- Viroscience Department, Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands; (C.L.); (R.J.O.); (E.G.); (P.H.M.B.)
| | - Rob A. Gruters
- Viroscience Department, Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands; (C.L.); (R.J.O.); (E.G.); (P.H.M.B.)
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Prins HAB, Crespo R, Lungu C, Rao S, Li L, Overmars RJ, Papageorgiou G, Mueller YM, Stoszko M, Hossain T, Kan TW, Rijnders BJA, Bax HI, van Gorp ECM, Nouwen JL, de Vries-Sluijs TEMS, Schurink CAM, de Mendonça Melo M, van Nood E, Colbers A, Burger D, Palstra RJ, van Kampen JJA, van de Vijver DAMC, Mesplède T, Katsikis PD, Gruters RA, Koch BCP, Verbon A, Mahmoudi T, Rokx C. The BAF complex inhibitor pyrimethamine reverses HIV-1 latency in people with HIV-1 on antiretroviral therapy. Sci Adv 2023; 9:eade6675. [PMID: 36921041 PMCID: PMC10017042 DOI: 10.1126/sciadv.ade6675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Reactivation of the latent HIV-1 reservoir is a first step toward triggering reservoir decay. Here, we investigated the impact of the BAF complex inhibitor pyrimethamine on the reservoir of people living with HIV-1 (PLWH). Twenty-eight PLWH on suppressive antiretroviral therapy were randomized (1:1:1:1 ratio) to receive pyrimethamine, valproic acid, both, or no intervention for 14 days. The primary end point was change in cell-associated unspliced (CA US) HIV-1 RNA at days 0 and 14. We observed a rapid, modest, and significant increase in (CA US) HIV-1 RNA in response to pyrimethamine exposure, which persisted throughout treatment and follow-up. Valproic acid treatment alone did not increase (CA US) HIV-1 RNA or augment the effect of pyrimethamine. Pyrimethamine treatment did not result in a reduction in the size of the inducible reservoir. These data demonstrate that the licensed drug pyrimethamine can be repurposed as a BAF complex inhibitor to reverse HIV-1 latency in vivo in PLWH, substantiating its potential advancement in clinical studies.
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Affiliation(s)
- Henrieke A. B. Prins
- Department of Internal Medicine, Section Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Raquel Crespo
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Cynthia Lungu
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Shringar Rao
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Letao Li
- Department of Pharmacy, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Ronald J. Overmars
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | | | - Yvonne M. Mueller
- Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Mateusz Stoszko
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Tanvir Hossain
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Tsung Wai Kan
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Pathology, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Urology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Bart J. A. Rijnders
- Department of Internal Medicine, Section Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Hannelore I. Bax
- Department of Internal Medicine, Section Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Eric C. M. van Gorp
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Jan L. Nouwen
- Department of Internal Medicine, Section Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Theodora E. M. S. de Vries-Sluijs
- Department of Internal Medicine, Section Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Carolina A. M. Schurink
- Department of Internal Medicine, Section Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Mariana de Mendonça Melo
- Department of Internal Medicine, Section Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Els van Nood
- Department of Internal Medicine, Section Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Angela Colbers
- Department of Pharmacy, Radboud Institute for Health Sciences, Radboud University Medical Center Nijmegen, Nijmegen, Netherlands
| | - David Burger
- Department of Pharmacy, Radboud Institute for Health Sciences, Radboud University Medical Center Nijmegen, Nijmegen, Netherlands
| | - Robert-Jan Palstra
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Pathology, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Urology, Erasmus University Medical Center, Rotterdam, Netherlands
| | | | | | - Thibault Mesplède
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Peter D. Katsikis
- Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Rob A. Gruters
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Birgit C. P. Koch
- Department of Pharmacy, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Annelies Verbon
- Department of Internal Medicine, Section Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Internal Medicine, University Medical Center, Utrecht, Netherlands
| | - Tokameh Mahmoudi
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Pathology, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Urology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Casper Rokx
- Department of Internal Medicine, Section Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
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Overmars RJ, Krullaars Z, Mesplède T. Investigational drugs for HIV: trends, opportunities and key players. Expert Opin Investig Drugs 2023; 32:127-139. [PMID: 36751107 DOI: 10.1080/13543784.2023.2178415] [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] [Indexed: 02/09/2023]
Abstract
INTRODUCTION Since the first antiretroviral drug was described, the field of HIV treatment and prevention has undergone two drug-based revolutions: the first one, enabled by the virtually concomitant discovery of non-nucleoside reverse transcriptase and protease inhibitors, was the inception of combined antiretroviral therapy. The second followed the creation of integrase strand-transfer inhibitors with improved safety, potency, and resistance profiles. Long-acting antiretroviral drugs, including broadly neutralizing antibodies, now offer the opportunity for a third transformational change in HIV management. AREAS COVERED Our review focused on HIV treatment and prevention with investigational drugs that offer the potential for infrequent dosing, including drugs not yet approved for clinical use. We also discussed approved drugs for which administration modalities or formulations are being optimized. We performed a literature search in published manuscripts, conference communications, and registered clinical trials. EXPERT OPINION While the field focuses on extending dosing intervals, we identify drug tissue penetration as an understudied opportunity to improve HIV care. We repeat that self-administration remains an essential milestone to reach the full potential of long-acting drugs. Treatments and prevention strategies based on broadly neutralizing antibodies require a deeper understanding of their antiretroviral properties.
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Affiliation(s)
- Ronald J Overmars
- Viroscience Department, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Zoë Krullaars
- Viroscience Department, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Thibault Mesplède
- Viroscience Department, Erasmus Medical Center, Rotterdam, The Netherlands
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van Kampen JJA, Pham HT, Yoo S, Overmars RJ, Lungu C, Mahmud R, Schurink CAM, van Boheemen S, Gruters RA, Fraaij PLA, Burger DM, Voermans JJC, Rokx C, van de Vijver DAMC, Mesplède T. HIV-1 resistance against dolutegravir fluctuates rapidly alongside erratic treatment adherence: a case report. J Glob Antimicrob Resist 2022; 31:323-327. [PMID: 36347497 DOI: 10.1016/j.jgar.2022.11.001] [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: 08/26/2022] [Revised: 10/26/2022] [Accepted: 11/02/2022] [Indexed: 11/08/2022] Open
Abstract
OBJECTIVES We report a case of incomplete HIV-1 suppression on a dolutegravir, lamivudine, and abacavir single-tablet regimen with the emergence of the H51Y and G118R integrase resistance mutations. METHODS Integrase sequencing was performed retrospectively by Sanger and next-generation sequencing. Rates of emergence and decline of resistance mutations were calculated using next-generation sequencing data. Dolutegravir plasma concentrations were measured by ultra-performance liquid chromatography-tandem mass spectrometry. The effects of H51Y and G118R on infectivity, fitness, and susceptibility to dolutegravir were quantified using cell-based assays. RESULTS During periods of non-adherence to treatment, mutations were retrospectively documented only by next-generation sequencing. Misdiagnosis by Sanger sequencing was caused by the rapid decline of mutant strains within the retroviral population. This observation was also true for a M184V lamivudine-resistant reverse transcriptase mutation found in association with integrase mutations on single HIV genomes. Resistance rebound upon treatment re-initiation was swift (>8000 copies per day). Next-generation sequencing indicated cumulative adherence to treatment. Compared to WT HIV-1, relative infectivity was 73%, 38%, and 43%; relative fitness was 100%, 35%, and 10% for H51Y, G118R, and H51Y+G118R viruses, respectively. H51Y did not change the susceptibility to dolutegravir, but G188R and H51Y+G118R conferred 7- and 28-fold resistance, respectively. CONCLUSION This case illustrates how poorly-fit drug-resistant viruses wax and wane alongside erratic treatment adherence and are easily misdiagnosed by Sanger sequencing. We recommend next-generation sequencing to improve the clinical management of incomplete virological suppression with dolutegravir.
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Affiliation(s)
| | - Hanh Thi Pham
- Department of Microbiology and Immunology, McGill University, Canada
| | - Sunbin Yoo
- Department of Microbiology and Immunology, McGill University, Canada
| | - Ronald J Overmars
- Viroscience department, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Cynthia Lungu
- Viroscience department, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Rizwan Mahmud
- Viroscience department, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Carolina A M Schurink
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, Rotterdam, The Netherlands; Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Rob A Gruters
- Viroscience department, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Pieter L A Fraaij
- Viroscience department, Erasmus Medical Center, Rotterdam, The Netherlands; Department of Pediatrics, Subdivision Infectious Diseases and Immunology, Sophia's Children Hospital, Erasmus Medical Center, Rotterdam, The Netherlands
| | - David M Burger
- Department of Pharmacy, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Casper Rokx
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, Rotterdam, The Netherlands; Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Thibault Mesplède
- Viroscience department, Erasmus Medical Center, Rotterdam, The Netherlands.
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Oude Munnink BB, Nieuwenhuijse DF, Stein M, O'Toole Á, Haverkate M, Mollers M, Kamga SK, Schapendonk C, Pronk M, Lexmond P, van der Linden A, Bestebroer T, Chestakova I, Overmars RJ, van Nieuwkoop S, Molenkamp R, van der Eijk AA, GeurtsvanKessel C, Vennema H, Meijer A, Rambaut A, van Dissel J, Sikkema RS, Timen A, Koopmans M. Author Correction: Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands. Nat Med 2020; 26:1802. [PMID: 33082576 PMCID: PMC7574672 DOI: 10.1038/s41591-020-1128-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Bas B Oude Munnink
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - David F Nieuwenhuijse
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Mart Stein
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Manon Haverkate
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Madelief Mollers
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Sandra K Kamga
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Claudia Schapendonk
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Mark Pronk
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Pascal Lexmond
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Anne van der Linden
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Theo Bestebroer
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Irina Chestakova
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Ronald J Overmars
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Stefan van Nieuwkoop
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Richard Molenkamp
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Annemiek A van der Eijk
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Corine GeurtsvanKessel
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Harry Vennema
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Adam Meijer
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Jaap van Dissel
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Reina S Sikkema
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Aura Timen
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Marion Koopmans
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands.
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Lungu C, Procopio FA, Overmars RJ, Beerkens RJJ, Voermans JJC, Rao S, Prins HAB, Rokx C, Pantaleo G, van de Vijver DAMC, Mahmoudi T, Boucher CAB, Gruters RA, van Kampen JJA. Inter-Laboratory Reproducibility of Inducible HIV-1 Reservoir Quantification by TILDA. Viruses 2020; 12:v12090973. [PMID: 32887284 PMCID: PMC7552071 DOI: 10.3390/v12090973] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 08/11/2020] [Revised: 08/29/2020] [Accepted: 08/31/2020] [Indexed: 12/16/2022] Open
Abstract
Substantial efforts to eliminate or reduce latent HIV-1 reservoirs are underway in clinical trials and have created a critical demand for sensitive, accurate, and reproducible tools to evaluate the efficacy of these strategies. Alternative reservoir quantification assays have been developed to circumvent limitations of the quantitative viral outgrowth assay. One such assay is tat/rev induced limiting dilution assay (TILDA), which measures the frequency of CD4+ T cells harboring inducible latent HIV-1 provirus. We modified pre-amplification reagents and conditions (TILDA v2.0) to improve assay execution and first internally validated assay performance using CD4+ T cells obtained from cART-suppressed HIV-1-infected individuals. Detection of tat/rev multiply spliced RNA was not altered by modifying pre-amplification conditions, confirming the robustness of the assay, and supporting the technique’s amenability to limited modifications to ensure better implementation for routine use in clinical studies of latent HIV-1 reservoirs. Furthermore, we cross-validated results of TILDA v2.0 and the original assay performed in two separate laboratories using samples from 15 HIV-1-infected individuals. TILDA and TILDA v2.0 showed a strong correlation (Lin’s Concordance Correlation Coefficient = 0.86). The low inter-laboratory variability between TILDAs performed at different institutes further supports use of TILDA for reservoir quantitation in multi-center interventional HIV-1 Cure trials.
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Affiliation(s)
- Cynthia Lungu
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (R.J.O.); (R.J.J.B.); (J.J.C.V.); (D.A.M.C.v.d.V.); (C.A.B.B.); (R.A.G.); (J.J.A.v.K.)
- Correspondence:
| | - Francesco A. Procopio
- Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland; (F.A.P.); (G.P.)
| | - Ronald J. Overmars
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (R.J.O.); (R.J.J.B.); (J.J.C.V.); (D.A.M.C.v.d.V.); (C.A.B.B.); (R.A.G.); (J.J.A.v.K.)
| | - Rob J. J. Beerkens
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (R.J.O.); (R.J.J.B.); (J.J.C.V.); (D.A.M.C.v.d.V.); (C.A.B.B.); (R.A.G.); (J.J.A.v.K.)
| | - Jolanda J. C. Voermans
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (R.J.O.); (R.J.J.B.); (J.J.C.V.); (D.A.M.C.v.d.V.); (C.A.B.B.); (R.A.G.); (J.J.A.v.K.)
| | - Shringar Rao
- Department of Biochemistry, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (S.R.); (T.M.)
| | - Henrieke A. B. Prins
- Department of Internal Medicine, Section of Infectious Diseases, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (H.A.B.P.); (C.R.)
| | - Casper Rokx
- Department of Internal Medicine, Section of Infectious Diseases, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (H.A.B.P.); (C.R.)
| | - Giuseppe Pantaleo
- Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland; (F.A.P.); (G.P.)
| | - David A. M. C. van de Vijver
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (R.J.O.); (R.J.J.B.); (J.J.C.V.); (D.A.M.C.v.d.V.); (C.A.B.B.); (R.A.G.); (J.J.A.v.K.)
| | - Tokameh Mahmoudi
- Department of Biochemistry, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (S.R.); (T.M.)
| | - Charles A. B. Boucher
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (R.J.O.); (R.J.J.B.); (J.J.C.V.); (D.A.M.C.v.d.V.); (C.A.B.B.); (R.A.G.); (J.J.A.v.K.)
| | - Rob A. Gruters
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (R.J.O.); (R.J.J.B.); (J.J.C.V.); (D.A.M.C.v.d.V.); (C.A.B.B.); (R.A.G.); (J.J.A.v.K.)
| | - Jeroen J. A. van Kampen
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (R.J.O.); (R.J.J.B.); (J.J.C.V.); (D.A.M.C.v.d.V.); (C.A.B.B.); (R.A.G.); (J.J.A.v.K.)
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7
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Oude Munnink BB, Nieuwenhuijse DF, Stein M, O'Toole Á, Haverkate M, Mollers M, Kamga SK, Schapendonk C, Pronk M, Lexmond P, van der Linden A, Bestebroer T, Chestakova I, Overmars RJ, van Nieuwkoop S, Molenkamp R, van der Eijk AA, GeurtsvanKessel C, Vennema H, Meijer A, Rambaut A, van Dissel J, Sikkema RS, Timen A, Koopmans M. Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands. Nat Med 2020; 26:1405-1410. [PMID: 32678356 DOI: 10.1038/s41591-020-0997-y] [Citation(s) in RCA: 208] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/26/2020] [Indexed: 11/09/2022]
Abstract
In late December 2019, a cluster of cases of pneumonia of unknown etiology were reported linked to a market in Wuhan, China1. The causative agent was identified as the species Severe acute respiratory syndrome-related coronavirus and was named SARS-CoV-2 (ref. 2). By 16 April the virus had spread to 185 different countries, infected over 2,000,000 people and resulted in over 130,000 deaths3. In the Netherlands, the first case of SARS-CoV-2 was notified on 27 February. The outbreak started with several different introductory events from Italy, Austria, Germany and France followed by local amplification in, and later also outside, the south of the Netherlands. The combination of near to real-time whole-genome sequence analysis and epidemiology resulted in reliable assessments of the extent of SARS-CoV-2 transmission in the community, facilitating early decision-making to control local transmission of SARS-CoV-2 in the Netherlands. We demonstrate how these data were generated and analyzed, and how SARS-CoV-2 whole-genome sequencing, in combination with epidemiological data, was used to inform public health decision-making in the Netherlands.
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Affiliation(s)
- Bas B Oude Munnink
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - David F Nieuwenhuijse
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Mart Stein
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Manon Haverkate
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Madelief Mollers
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Sandra K Kamga
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Claudia Schapendonk
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Mark Pronk
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Pascal Lexmond
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Anne van der Linden
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Theo Bestebroer
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Irina Chestakova
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Ronald J Overmars
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Stefan van Nieuwkoop
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Richard Molenkamp
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Annemiek A van der Eijk
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Corine GeurtsvanKessel
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Harry Vennema
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Adam Meijer
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Jaap van Dissel
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Reina S Sikkema
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Aura Timen
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Marion Koopmans
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands.
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Sikkema RS, Pas SD, Nieuwenhuijse DF, O'Toole Á, Verweij J, van der Linden A, Chestakova I, Schapendonk C, Pronk M, Lexmond P, Bestebroer T, Overmars RJ, van Nieuwkoop S, van den Bijllaardt W, Bentvelsen RG, van Rijen MML, Buiting AGM, van Oudheusden AJG, Diederen BM, Bergmans AMC, van der Eijk A, Molenkamp R, Rambaut A, Timen A, Kluytmans JAJW, Oude Munnink BB, Kluytmans van den Bergh MFQ, Koopmans MPG. COVID-19 in health-care workers in three hospitals in the south of the Netherlands: a cross-sectional study. Lancet Infect Dis 2020; 20:1273-1280. [PMID: 32622380 PMCID: PMC7332281 DOI: 10.1016/s1473-3099(20)30527-2] [Citation(s) in RCA: 175] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/01/2020] [Accepted: 06/09/2020] [Indexed: 01/05/2023]
Abstract
Background 10 days after the first reported case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in the Netherlands (on Feb 27, 2020), 55 (4%) of 1497 health-care workers in nine hospitals located in the south of the Netherlands had tested positive for SARS-CoV-2 RNA. We aimed to gain insight in possible sources of infection in health-care workers. Methods We did a cross-sectional study at three of the nine hospitals located in the south of the Netherlands. We screened health-care workers at the participating hospitals for SARS-CoV-2 infection, based on clinical symptoms (fever or mild respiratory symptoms) in the 10 days before screening. We obtained epidemiological data through structured interviews with health-care workers and combined this information with data from whole-genome sequencing of SARS-CoV-2 in clinical samples taken from health-care workers and patients. We did an in-depth analysis of sources and modes of transmission of SARS-CoV-2 in health-care workers and patients. Findings Between March 2 and March 12, 2020, 1796 (15%) of 12 022 health-care workers were screened, of whom 96 (5%) tested positive for SARS-CoV-2. We obtained complete and near-complete genome sequences from 50 health-care workers and ten patients. Most sequences were grouped in three clusters, with two clusters showing local circulation within the region. The noted patterns were consistent with multiple introductions into the hospitals through community-acquired infections and local amplification in the community. Interpretation Although direct transmission in the hospitals cannot be ruled out, our data do not support widespread nosocomial transmission as the source of infection in patients or health-care workers. Funding EU Horizon 2020 (RECoVer, VEO, and the European Joint Programme One Health METASTAVA), and the National Institute of Allergy and Infectious Diseases, National Institutes of Health.
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Affiliation(s)
| | - Suzan D Pas
- Microvida Laboratory for Microbiology, Bravis Hospital, Roosendaal, Netherlands; Microvida Laboratory for Microbiology, Amphia Hospital, Breda, Netherlands
| | | | | | - Jaco Verweij
- Laboratory for Medical Microbiology and Immunology, Elisabeth-TweeSteden Hospital, Tilburg, Netherlands
| | | | | | | | - Mark Pronk
- Viroscience, Erasmus MC, Rotterdam, Netherlands
| | | | | | | | | | | | - Robbert G Bentvelsen
- Microvida Laboratory for Microbiology, Amphia Hospital, Breda, Netherlands; Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Anton G M Buiting
- Laboratory for Medical Microbiology and Immunology, Elisabeth-TweeSteden Hospital, Tilburg, Netherlands; Department of Infection Control, Elisabeth-TweeSteden Hospital, Tilburg, Netherlands
| | | | - Bram M Diederen
- Microvida Laboratory for Microbiology, Bravis Hospital, Roosendaal, Netherlands
| | - Anneke M C Bergmans
- Microvida Laboratory for Microbiology, Bravis Hospital, Roosendaal, Netherlands
| | | | | | | | - Aura Timen
- Landelijke Coördinatie Infectieziektebestrijding, Rijksinstituut voor Volksgezondheid en Milieu, Bilthoven, Netherlands; VU University Amsterdam, Amsterdam, Netherlands
| | - Jan A J W Kluytmans
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands; Microvida Laboratory for Microbiology, Amphia Hospital, Breda, Netherlands; Department of Infection Control, Amphia Hospital, Breda, Netherlands
| | | | - Marjolein F Q Kluytmans van den Bergh
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands; Microvida Laboratory for Microbiology, Amphia Hospital, Breda, Netherlands; Department of Infection Control, Amphia Hospital, Breda, Netherlands
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Sprokholt JK, Kaptein TM, van Hamme JL, Overmars RJ, Gringhuis SI, Geijtenbeek TBH. RIG-I-like receptor activation by dengue virus drives follicular T helper cell formation and antibody production. PLoS Pathog 2017; 13:e1006738. [PMID: 29186193 PMCID: PMC5724900 DOI: 10.1371/journal.ppat.1006738] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [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: 02/03/2017] [Revised: 12/11/2017] [Accepted: 11/07/2017] [Indexed: 12/27/2022] Open
Abstract
Follicular T helper cells (TFH) are fundamental in orchestrating effective antibody-mediated responses critical for immunity against viral infections and effective vaccines. However, it is unclear how virus infection leads to TFH induction. We here show that dengue virus (DENV) infection of human dendritic cells (DCs) drives TFH formation via crosstalk of RIG-I-like receptor (RLR) RIG-I and MDA5 with type I Interferon (IFN) signaling. DENV infection leads to RLR-dependent IKKε activation, which phosphorylates IFNα/β receptor-induced STAT1 to drive IL-27 production via the transcriptional complex ISGF3. Inhibiting RLR activation as well as neutralizing antibodies against IL-27 prevented TFH formation. DENV-induced CXCR5+PD-1+Bcl-6+ TFH cells secreted IL-21 and activated B cells to produce IgM and IgG. Notably, RLR activation by synthetic ligands also induced IL-27 secretion and TFH polarization. These results identify an innate mechanism by which antibodies develop during viral disease and identify RLR ligands as potent adjuvants for TFH-promoting vaccination strategies.
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Affiliation(s)
- Joris K. Sprokholt
- Department of Experimental Immunology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Infection & Immunity Institute, Amsterdam, the Netherlands
| | - Tanja M. Kaptein
- Department of Experimental Immunology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Infection & Immunity Institute, Amsterdam, the Netherlands
| | - John L. van Hamme
- Department of Experimental Immunology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Infection & Immunity Institute, Amsterdam, the Netherlands
| | - Ronald J. Overmars
- Department of Experimental Immunology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Infection & Immunity Institute, Amsterdam, the Netherlands
| | - Sonja I. Gringhuis
- Department of Experimental Immunology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Infection & Immunity Institute, Amsterdam, the Netherlands
| | - Teunis B. H. Geijtenbeek
- Department of Experimental Immunology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Infection & Immunity Institute, Amsterdam, the Netherlands
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10
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Sprokholt JK, Kaptein TM, van Hamme JL, Overmars RJ, Gringhuis SI, Geijtenbeek TBH. RIG-I-like Receptor Triggering by Dengue Virus Drives Dendritic Cell Immune Activation and T H1 Differentiation. J Immunol 2017; 198:4764-4771. [PMID: 28507028 DOI: 10.4049/jimmunol.1602121] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 04/13/2017] [Indexed: 01/07/2023]
Abstract
Dengue virus (DENV) causes 400 million infections annually and is one of several viruses that can cause viral hemorrhagic fever, which is characterized by uncontrolled immune activation resulting in high fever and internal bleeding. Although the underlying mechanisms are unknown, massive cytokine secretion is thought to be involved. Dendritic cells (DCs) are the main target cells of DENV, and we investigated their role in DENV-induced cytokine production and adaptive immune responses. DENV infection induced DC maturation and secretion of IL-1β, IL-6, and TNF. Inhibition of DENV RNA replication abrogated these responses. Notably, silencing of RNA sensors RIG-I or MDA5 abrogated DC maturation, as well as cytokine responses by DENV-infected DCs. DC maturation was induced by type I IFN responses because inhibition of IFN-α/β receptor signaling abrogated DENV-induced DC maturation. Moreover, DENV infection of DCs resulted in CCL2, CCL3, and CCL4 expression, which was abrogated after RIG-I and MDA5 silencing. DCs play an essential role in TH cell differentiation, and we show that RIG-I and MDA5 triggering by DENV leads to TH1 polarization, which is characterized by high levels of IFN-γ. Notably, cytokines IL-6, TNF, and IFN-γ and chemokines CCL2, CCL3, and CCL4 have been associated with disease severity, endothelial dysfunction, and vasodilation. Therefore, we identified RIG-I and MDA5 as critical players in innate and adaptive immune responses against DENV, and targeting these receptors has the potential to decrease hemorrhagic fever in patients.
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Affiliation(s)
- Joris K Sprokholt
- Department of Experimental Immunology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands; and
- Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Tanja M Kaptein
- Department of Experimental Immunology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands; and
- Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - John L van Hamme
- Department of Experimental Immunology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands; and
- Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Ronald J Overmars
- Department of Experimental Immunology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands; and
- Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Sonja I Gringhuis
- Department of Experimental Immunology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands; and
- Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Teunis B H Geijtenbeek
- Department of Experimental Immunology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands; and
- Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
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